From 0878e4972b70c037fc932235169488a2201a1840 Mon Sep 17 00:00:00 2001
From: biopsichas <svajunas.plunge@gmail.com>
Date: Tue, 21 May 2024 12:36:37 +0300
Subject: [PATCH] all water yield page added

---
 DESCRIPTION                                 |   2 +-
 NAMESPACE                                   |   1 -
 R/helper.R                                  |   1 -
 docs/404.html                               |   2 +-
 docs/LICENSE-text.html                      |   2 +-
 docs/articles/index.html                    |   2 +-
 docs/articles/sc-crops.html                 |   2 +-
 docs/articles/sc-wy.html                    | 113 +++++++++++++++++++-
 docs/authors.html                           |   6 +-
 docs/index.html                             |   2 +-
 docs/pkgdown.yml                            |   2 +-
 docs/reference/add_suffix_to_duplicate.html |   2 +-
 docs/reference/aggregate_aa.html            |   2 +-
 docs/reference/calculate_wyr.html           |   2 +-
 docs/reference/copy_file_version.html       |   2 +-
 docs/reference/dotty_fig.html               |   2 +-
 docs/reference/find_par_range.html          |   2 +-
 docs/reference/index.html                   |   2 +-
 docs/reference/plot_dotty.html              |   2 +-
 docs/reference/plot_dotty_yields.html       |   2 +-
 docs/reference/plot_esco_range.html         |   2 +-
 docs/reference/plot_phu_yld_bms.html        |   2 +-
 docs/reference/read_tbl.html                |   2 +-
 docs/reference/sample_lhs.html              |   8 +-
 docs/reference/update_par.html              |   2 +-
 docs/reference/write_tbl.html               |   2 +-
 docs/search.json                            |   2 +-
 vignettes/sc-wy.Rmd                         |  93 +++++++++++++++-
 28 files changed, 230 insertions(+), 36 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b134121..0bed1ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SWATtunR
 Type: Package
 Title: Soft & Hard Calibration, Validation Package for SWAT+ models
-Version: 0.0.1.9001
+Version: 0.0.1.9002
 Authors@R: c(
     person("Svajunas", "Plunge", , "svajunas.plunge@gmail.com", role = c("aut", "cre"),
         comment = c(ORCID = '0000-0001-8897-3349')),
diff --git a/NAMESPACE b/NAMESPACE
index 1f65c90..c1cd9a3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(calculate_wyr)
 export(copy_file_version)
 export(plot_dotty)
 export(plot_dotty_yields)
diff --git a/R/helper.R b/R/helper.R
index 6d59ea0..e04169a 100644
--- a/R/helper.R
+++ b/R/helper.R
@@ -165,7 +165,6 @@ find_par_range <- function(par, sim, obj, rel_rng) {
 #' # Calculate WYR
 #' wyr <- calculate_wyr(sim)
 #' }
-#' @export
 #' @keywords calculate
 
 calculate_wyr <- function(sim) {
diff --git a/docs/404.html b/docs/404.html
index 175ddbc..2ebf314 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 56014a0..53a2e3d 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 4bbc82c..12299a0 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/sc-crops.html b/docs/articles/sc-crops.html
index e283ffb..5f2e617 100644
--- a/docs/articles/sc-crops.html
+++ b/docs/articles/sc-crops.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/sc-wy.html b/docs/articles/sc-wy.html
index 9c7d532..42af389 100644
--- a/docs/articles/sc-wy.html
+++ b/docs/articles/sc-wy.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -167,12 +167,119 @@ <h2 id="scw_step4">4. Extracting and plotting water yield ratio vs esco paramete
 values<a class="anchor" aria-label="anchor" href="#scw_step4"></a>
 </h2>
 <p>The water yield ratio is calculated for each simulation. The range of
-esco values that produce water yield ratios within a specified range of
-the observed water yield ratio is identified using the <a href="../reference/plot_esco_range.html">plot_esco_range</a>
+<strong>esco</strong> values that produce water yield ratios within a
+specified range of the observed water yield ratio is identified using
+the <a href="../reference/plot_esco_range.html">plot_esco_range</a>
 function.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/plot_esco_range.html">plot_esco_range</a></span><span class="op">(</span><span class="va">sim_esco</span>, <span class="va">obs_wy_ratio</span><span class="op">)</span></span></code></pre></div>
 <p><img src="figs/sim_esco.png" width="100%" style="display: block; margin: auto;"></p>
+</div>
+<div class="section level2">
+<h2 id="scw_step5">5. (Optional) If only esco is not enough, use esco, epco parameters
+for calibration together<a class="anchor" aria-label="anchor" href="#scw_step5"></a>
+</h2>
+<p>In certain situations <strong>esco</strong> parameter might not be
+enough to reach observed water yield ratio. Addition of the plant uptake
+compensation factor (<strong>epco</strong>) might help in such cases.
+This parameter determines how water uptake is distributed across soil
+layers to meet plant transpiration needs. If the upper soil layers lack
+sufficient water, the model can draw more water from deeper layers, a
+process governed by the <strong>epco</strong> value. When
+<strong>epco</strong> is close to 1.0, there is greater flexibility,
+allowing significant compensation from lower soil layers. Conversely,
+when <strong>epc</strong> is near 0.0, the model restricts water uptake
+primarily to the original depth distribution, limiting compensation from
+deeper layers.</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># The esco and epco parameter range is defined .</span></span>
+<span><span class="va">par_bnd</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span><span class="st">'esco.hru | change = absval'</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.05</span>, <span class="fl">0.95</span><span class="op">)</span>,</span>
+<span>                  <span class="st">'epco.hru | change = absval'</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.05</span>, <span class="fl">0.95</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># And sampled with lhs </span></span>
+<span><span class="va">esco_epco</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/sample_lhs.html">sample_lhs</a></span><span class="op">(</span><span class="va">par_bnd</span>, <span class="fl">12</span><span class="op">)</span> </span>
+<span></span>
+<span><span class="co">##Run simulations for defined parameter sets</span></span>
+<span><span class="va">sim_esco_epco</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/run_swatplus.html" class="external-link">run_swatplus</a></span><span class="op">(</span>project_path <span class="op">=</span> <span class="va">model_path</span>,</span>
+<span>                         output <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>precip  <span class="op">=</span>  <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span><span class="st">'basin_wb_day'</span>, </span>
+<span>                                                                <span class="st">'precip'</span>, </span>
+<span>                                                                <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       surq_cha <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_wb_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'surq_cha'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       surq_res <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_wb_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'surq_res'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       latq_cha <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_wb_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'latq_cha'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       latq_res <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_wb_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'latq_res'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       qtile <span class="op">=</span>    <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_wb_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'qtile'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
+<span>                                       flo <span class="op">=</span>      <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'basin_aqu_day'</span>,</span>
+<span>                                                                variable <span class="op">=</span> <span class="st">'flo'</span>,</span>
+<span>                                                                unit <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span>                         <span class="op">)</span>,</span>
+<span>                         parameter <span class="op">=</span> <span class="va">esco_epco</span>,</span>
+<span>                         n_thread <span class="op">=</span> <span class="va">cores</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co">## Save the results to the file</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">sim_esco</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">sc_res</span>, <span class="st">"/sim_esco_epco.rds"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="scw_step6">6. Updating parameter values in the <code>hydrology.hyd</code> file
+with selected values<a class="anchor" aria-label="anchor" href="#scw_step6"></a>
+</h2>
+<p>After determining which model parameter values allow the simulated
+water yield ratio to match the observed values, these parameters need to
+be updated in the <code>hydrology.hyd</code> file. Following code
+snippet backs up existing file and updates values in it.</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co">## Initialize unmodified backup version of hydrology.hyd</span></span>
+<span><span class="kw">if</span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files.html" class="external-link">file.exists</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">model_path</span>, <span class="st">'/hydrology.hyd.bkp0'</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="fu"><a href="../reference/copy_file_version.html">copy_file_version</a></span><span class="op">(</span><span class="va">model_path</span>, <span class="st">'hydrology.hyd'</span>, file_version <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span>
+<span><span class="op">}</span></span>
+<span></span>
+<span><span class="co"># Read the hydrology.hyd input file</span></span>
+<span><span class="va">hydrology_hyd</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/read_tbl.html">read_tbl</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">model_path</span>, <span class="st">'/hydrology.hyd.bkp0'</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">hydrology_hyd</span><span class="op">$</span><span class="va">esco</span> <span class="op">&lt;-</span> <span class="fl">0.39</span></span>
+<span><span class="co">## If needed update epco as well</span></span>
+<span><span class="co">## hydrology_hyd$epco &lt;- some value</span></span>
+<span></span>
+<span><span class="co">## Update hydrology.hyd file</span></span>
+<span><span class="fu"><a href="../reference/write_tbl.html">write_tbl</a></span><span class="op">(</span><span class="va">hydrology_hyd</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">model_path</span>, <span class="st">'/hydrology.hyd'</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'%-16s'</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">'%12.5f'</span>, <span class="fl">14</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="final-recheck-for-yield-results">7. Final recheck for yield results<a class="anchor" aria-label="anchor" href="#final-recheck-for-yield-results"></a>
+</h2>
+<p>Updating parameters in the hydrology.hyd file might impact crop yield
+simulation. To ensure that the water yield soft calibration has not
+adversely affected the crop yield soft calibration, it is important to
+recheck it at the end. If the results match the observed yields, the
+soft calibration is complete, and you can celebrate. Otherwise, you
+should consider revisiting the <a href="../articles/sc-cy.html">crop
+yield soft calibration</a> steps.</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co">## Rerun model for crop yields results</span></span>
+<span><span class="va">phu_yld_recheck</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/run_swatplus.html" class="external-link">run_swatplus</a></span><span class="op">(</span>project_path <span class="op">=</span> <span class="va">model_path</span>,</span>
+<span>                          output <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>yld <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'mgtout'</span>,</span>
+<span>                                                            variable <span class="op">=</span> <span class="st">'yld'</span>,</span>
+<span>                                                            unit <span class="op">=</span> <span class="va">crops</span><span class="op">)</span>,</span>
+<span>                                        bms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'mgtout'</span>,</span>
+<span>                                                            variable <span class="op">=</span> <span class="st">'bioms'</span>,</span>
+<span>                                                            unit <span class="op">=</span> <span class="va">crops</span><span class="op">)</span>,</span>
+<span>                                        phu <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/SWATrunR/man/define_output.html" class="external-link">define_output</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">'mgtout'</span>,</span>
+<span>                                                            variable <span class="op">=</span> <span class="st">'phu'</span>,</span>
+<span>                                                            unit <span class="op">=</span> <span class="va">crops</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="co">## Save the results to the file</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">phu_yld_recheck</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">sc_res</span>, <span class="st">"/phu_yld_recheck.rds"</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co">## Plot yields </span></span>
+<span><span class="fu"><a href="../reference/plot_phu_yld_bms.html">plot_phu_yld_bms</a></span><span class="op">(</span><span class="va">phu_yld_recheck</span>, <span class="fl">0</span>, <span class="va">yield_mean</span>, <span class="va">yield_min</span>, <span class="va">yield_max</span><span class="op">)</span></span></code></pre></div>
 </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside>
diff --git a/docs/authors.html b/docs/authors.html
index 9e18e3f..f829270 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -74,13 +74,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Plunge S, Schuerz C, Strauch M, Piniewski M (2024).
 <em>SWATtunR: Soft &amp; Hard Calibration, Validation Package for SWAT+ models</em>.
-R package version 0.0.1.9001, <a href="https://github.com/biopsichas/SWATtunR" class="external-link">https://github.com/biopsichas/SWATtunR</a>. 
+R package version 0.0.1.9002, <a href="https://github.com/biopsichas/SWATtunR" class="external-link">https://github.com/biopsichas/SWATtunR</a>. 
 </p>
       <pre>@Manual{,
   title = {SWATtunR: Soft &amp; Hard Calibration, Validation Package for SWAT+ models},
   author = {Svajunas Plunge and Christoph Schuerz and Michel Strauch and Mikołaj Piniewski},
   year = {2024},
-  note = {R package version 0.0.1.9001},
+  note = {R package version 0.0.1.9002},
   url = {https://github.com/biopsichas/SWATtunR},
 }</pre>
     </div>
diff --git a/docs/index.html b/docs/index.html
index f820144..17538e0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f7ad4fb..5c1a6df 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   sc-crops: sc-crops.html
   sc-wy: sc-wy.html
-last_built: 2024-05-20T15:08Z
+last_built: 2024-05-21T09:33Z
 
diff --git a/docs/reference/add_suffix_to_duplicate.html b/docs/reference/add_suffix_to_duplicate.html
index 2cfc78e..eeb0609 100644
--- a/docs/reference/add_suffix_to_duplicate.html
+++ b/docs/reference/add_suffix_to_duplicate.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/aggregate_aa.html b/docs/reference/aggregate_aa.html
index beb11a7..37169ca 100644
--- a/docs/reference/aggregate_aa.html
+++ b/docs/reference/aggregate_aa.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/calculate_wyr.html b/docs/reference/calculate_wyr.html
index f694dba..a5b4ebc 100644
--- a/docs/reference/calculate_wyr.html
+++ b/docs/reference/calculate_wyr.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/copy_file_version.html b/docs/reference/copy_file_version.html
index 5cecea1..d335e65 100644
--- a/docs/reference/copy_file_version.html
+++ b/docs/reference/copy_file_version.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dotty_fig.html b/docs/reference/dotty_fig.html
index fe08145..04dd084 100644
--- a/docs/reference/dotty_fig.html
+++ b/docs/reference/dotty_fig.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/find_par_range.html b/docs/reference/find_par_range.html
index 1506ad4..0004018 100644
--- a/docs/reference/find_par_range.html
+++ b/docs/reference/find_par_range.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 4119e6e..907cf9f 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/plot_dotty.html b/docs/reference/plot_dotty.html
index b6f60be..1d7a016 100644
--- a/docs/reference/plot_dotty.html
+++ b/docs/reference/plot_dotty.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/plot_dotty_yields.html b/docs/reference/plot_dotty_yields.html
index 34e3a55..6d95b5f 100644
--- a/docs/reference/plot_dotty_yields.html
+++ b/docs/reference/plot_dotty_yields.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/plot_esco_range.html b/docs/reference/plot_esco_range.html
index 603bdf0..458aabe 100644
--- a/docs/reference/plot_esco_range.html
+++ b/docs/reference/plot_esco_range.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/plot_phu_yld_bms.html b/docs/reference/plot_phu_yld_bms.html
index e8d671c..261b4b3 100644
--- a/docs/reference/plot_phu_yld_bms.html
+++ b/docs/reference/plot_phu_yld_bms.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_tbl.html b/docs/reference/read_tbl.html
index 72c37d0..7d1a7f4 100644
--- a/docs/reference/read_tbl.html
+++ b/docs/reference/read_tbl.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/sample_lhs.html b/docs/reference/sample_lhs.html
index 7b3a16d..1c97dc4 100644
--- a/docs/reference/sample_lhs.html
+++ b/docs/reference/sample_lhs.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -90,9 +90,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   param1 param2 param3</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span>  0.364  0.572   7.11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span>  0.743  1.46    1.69</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span>  0.300  0.737   5.82</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span>  0.549  0.536   3.28</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span>  0.143  0.788   5.72</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span>  0.824  1.93    7.55</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/update_par.html b/docs/reference/update_par.html
index d482c0d..5f6d520 100644
--- a/docs/reference/update_par.html
+++ b/docs/reference/update_par.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/write_tbl.html b/docs/reference/write_tbl.html
index 774f0e5..deb8f22 100644
--- a/docs/reference/write_tbl.html
+++ b/docs/reference/write_tbl.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">SWATtunR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9001</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1.9002</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/search.json b/docs/search.json
index d156e91..20df9a9 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Svajunas Plunge. Author, maintainer. Christoph Schuerz. Author. Michel Strauch. Author. Mikołaj Piniewski. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Plunge S, Schuerz C, Strauch M, Piniewski M (2024). SWATtunR: Soft & Hard Calibration, Validation Package SWAT+ models. R package version 0.0.1.9001, https://github.com/biopsichas/SWATtunR.","code":"@Manual{,   title = {SWATtunR: Soft & Hard Calibration, Validation Package for SWAT+ models},   author = {Svajunas Plunge and Christoph Schuerz and Michel Strauch and Mikołaj Piniewski},   year = {2024},   note = {R package version 0.0.1.9001},   url = {https://github.com/biopsichas/SWATtunR}, }"},{"path":[]},{"path":"/index.html","id":"swattunr","dir":"","previous_headings":"","what":"SWATtunR","title":"Soft & Hard Calibration, Validation Package for SWAT+ models","text":"Text text text","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Soft & Hard Calibration, Validation Package for SWAT+ models","text":"Text text text Text text text","code":"# If the package 'remotes' is not installed run first: install.packages(\"remotes\")  # The installation of `SWATprepR`. remotes::install_github(\"biopsichas/SWATtunR\")"},{"path":"/reference/hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello, World! — hello","title":"Hello, World! — hello","text":"Prints 'Hello, world!'.","code":""},{"path":"/reference/hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello, World! — hello","text":"","code":"hello()"},{"path":"/reference/hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello, World! — hello","text":"","code":"hello() #> Error in hello(): could not find function \"hello\""},{"path":"/reference/read_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a SWAT+ input file which has a tabular structure. — read_tbl","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"function reads SWAT+ input file tabular structure tibble.","code":""},{"path":"/reference/read_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"","code":"read_tbl(file_path, col_names = NULL, n_skip = 1)"},{"path":"/reference/read_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"file_path Path SWAT+ input file. col_names (optional) character vector specifying column names. provided, column names inferred file. Default col_names = NULL. n_skip (optional) Number header rows skip. Default n_skip = 1.","code":""},{"path":"/reference/read_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"tibble representing SWAT+ input file.","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a running ID to duplicated names — add_suffix_to_duplicate","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"Add running ID duplicated names","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"","code":"add_suffix_to_duplicate(col_name)"},{"path":"/reference/add_suffix_to_duplicate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"col_name Character vector column names","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"col_name character vector IDs duplicated names","code":""},{"path":"/reference/write_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Write SWAT+ input file, which has a tabular structure. — write_tbl","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"Write SWAT+ input file, tabular structure.","code":""},{"path":"/reference/write_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"","code":"write_tbl(tbl, file_path, fmt)"},{"path":"/reference/write_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"tbl SWAT input table tibble (data.frame) format. file_path Write path SWAT+ input file. fmt Character vector format strings define print format table column.","code":""},{"path":"/reference/write_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"Writes text file table file path.","code":""},{"path":[]},{"path":"/reference/write_tbl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"","code":"if (FALSE) { ## Read the hydrology.hyd input file hydrology_hyd <- read_tbl(paste0(model_path, '/hydrology.hyd')) hydrology_hyd$esco <- 1 ## Updating hydrology.hyd file hydr_hyd_fmt <- c('%-16s', rep('%12.5f', 14)) write_tbl(hydrology_hyd, paste0(model_path, '/hydrology.hyd'), hydr_hyd_fmt) }"},{"path":"/reference/copy_file_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a file with an optional version suffix. — copy_file_version","title":"Copy a file with an optional version suffix. — copy_file_version","text":"function copies file one location another, optional version suffix appended filename.","code":""},{"path":"/reference/copy_file_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a file with an optional version suffix. — copy_file_version","text":"","code":"copy_file_version(model_path, file_name, file_version = NULL)"},{"path":"/reference/copy_file_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a file with an optional version suffix. — copy_file_version","text":"model_path path directory containing file. file_name name file copied. file_version optional version suffix appended filename. Default file_version = NULL, adds '.bkp' filename.","code":""},{"path":"/reference/copy_file_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a file with an optional version suffix. — copy_file_version","text":"None","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"function generates boxplots visualize Plant Heat Units (PHU) fractions, yields, biomass changes days maturity.","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"","code":"plot_phu_yld_bms(   sim_result,   x_label,   yield = NULL,   yield_min = NULL,   yield_max = NULL )"},{"path":"/reference/plot_phu_yld_bms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"sim_result simulation results containing PHU, yield, biomass data. x_label Labels x-axis representing changes days maturity. yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL yield_max (optional) maximum observed yield values crop. Default yield_max = NULL","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"combined ggplot object showing boxplots PHU fractions, yields, biomass.","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"","code":"if (FALSE) { plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) }"},{"path":"/reference/sample_lhs.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample parameters space — sample_lhs","title":"Sample parameters space — sample_lhs","text":"function samples parameter space using Latin Hypercube Sampling (LHS).","code":""},{"path":"/reference/sample_lhs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample parameters space — sample_lhs","text":"","code":"sample_lhs(par, n)"},{"path":"/reference/sample_lhs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample parameters space — sample_lhs","text":"par matrix data frame specifying parameter ranges. n number samples generate.","code":""},{"path":"/reference/sample_lhs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample parameters space — sample_lhs","text":"tibble containing sampled parameter values.","code":""},{"path":"/reference/sample_lhs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample parameters space — sample_lhs","text":"","code":"# Define parameter ranges parameters <- data.frame(   param1 = c(0, 1),   param2 = c(0, 2),   param3 = c(0, 10) )  # Sample the parameter space sample_space <- sample_lhs(parameters, 3) sample_space #> # A tibble: 3 × 3 #>   param1 param2 param3 #>    <dbl>  <dbl>  <dbl> #> 1  0.364  0.572   7.11 #> 2  0.743  1.46    1.69 #> 3  0.300  0.737   5.82"},{"path":"/reference/plot_dotty_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Dotty Yields — plot_dotty_yields","title":"Plot Dotty Yields — plot_dotty_yields","text":"function creates dotty plots simulated yields, comparing observed yields (available).","code":""},{"path":"/reference/plot_dotty_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Dotty Yields — plot_dotty_yields","text":"","code":"plot_dotty_yields(sim_result, yield = NULL, yield_min = NULL, yield_max = NULL)"},{"path":"/reference/plot_dotty_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Dotty Yields — plot_dotty_yields","text":"sim_result simulation results containing yield data. yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL yield_max (optional) maximum observed yield values crop. Default yield_max = NULL","code":""},{"path":"/reference/plot_dotty_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Dotty Yields — plot_dotty_yields","text":"combined ggplot object showing dottty plots 4 parameters.","code":""},{"path":"/reference/plot_dotty_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Dotty Yields — plot_dotty_yields","text":"","code":"if (FALSE) { plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) }"},{"path":"/reference/dotty_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a dotty plot — dotty_fig","title":"Make a dotty plot — dotty_fig","text":"Make dotty plot","code":""},{"path":"/reference/dotty_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a dotty plot — dotty_fig","text":"","code":"dotty_fig(sim_yield, yield = NULL, yield_min = NULL, yield_max = NULL)"},{"path":"/reference/dotty_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a dotty plot — dotty_fig","text":"sim_yield dataframe yield data yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL. yield_max (optional) maximum observed yield values crop. Default yield_max = NULL.","code":""},{"path":"/reference/dotty_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a dotty plot — dotty_fig","text":"ggplot object dotty plot","code":""},{"path":"/reference/dotty_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make a dotty plot — dotty_fig","text":"","code":"if (FALSE) { dotty_fig(sim_yield) }"},{"path":"/reference/plot_dotty.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Dotty — plot_dotty","title":"Plot Dotty — plot_dotty","text":"function creates dotty plot visualize relationship parameter values performance results.","code":""},{"path":"/reference/plot_dotty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Dotty — plot_dotty","text":"","code":"plot_dotty(   par,   var,   y_label = \"y\",   n_col = 3,   y_lim = NULL,   y_inter = NULL,   trend = FALSE,   run_ids = NULL,   low_up = FALSE )"},{"path":"/reference/plot_dotty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Dotty — plot_dotty","text":"par data frame model parameter values simulation. var model performance result vector list vectors plotted parameter values. y_label (optional) Labels y-axis, either single label vector corresponding variable var list. Default y_label = 'y'. n_col (optional) Number columns facet grid. Default n_col = 3. y_lim (optional) Limits y-axis. Default y_lim = NULL. y_inter (optional) Y-axis intercept value. Default y_inter = NULL. trend (optional) Logical, indicating whether add trend line. Default trend = FALSE. run_ids (optional) numeric vector run IDs highlighted plot. Default run_ids = NULL. low_up (optional) Logical, TRUE whole possible parameter range used x axis. Default low_up = FALSE.","code":""},{"path":"/reference/plot_dotty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Dotty — plot_dotty","text":"ggplot object representing dotty plot.","code":""},{"path":"/reference/plot_dotty.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Dotty — plot_dotty","text":"","code":"if (FALSE) { # plot_dotty(my_data, 'performance', y_label = 'y_label') }"},{"path":"/reference/update_par.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Parameters — update_par","title":"Update Parameters — update_par","text":"function updates parameters based different types changes.","code":""},{"path":"/reference/update_par.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Parameters — update_par","text":"","code":"update_par(par, par_up, change)"},{"path":"/reference/update_par.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Parameters — update_par","text":"par Numeric vector: Original parameter values. par_up Numeric vector: Values indicating update parameter. change Character scalar: Type change apply. Options \"relchg\" relative change, \"pctchg\" percentage change, \"abschg\" absolute change, \"absval\" setting absolute value change.","code":""},{"path":"/reference/update_par.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Parameters — update_par","text":"Numeric vector updated parameter values.","code":""},{"path":"/reference/update_par.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Parameters — update_par","text":"","code":"par <- c(10, 20, 30, 40) par_up <- c(0.1, 0.2, NA, 0.3) update_par(par, par_up, \"relchg\") # Returns updated parameters with relative change applied. #> [1] 11 24 30 52"},{"path":"/reference/aggregate_aa.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate and Average Annually — aggregate_aa","title":"Aggregate and Average Annually — aggregate_aa","text":"function takes data frame containing date column numerical columns, aggregates data annually, computes average annual sums.","code":""},{"path":"/reference/aggregate_aa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate and Average Annually — aggregate_aa","text":"","code":"aggregate_aa(tbl)"},{"path":"/reference/aggregate_aa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate and Average Annually — aggregate_aa","text":"tbl data frame contains 'date' column numerical columns.","code":""},{"path":"/reference/aggregate_aa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate and Average Annually — aggregate_aa","text":"numeric vector mean annual sums column input data frame.","code":""},{"path":"/reference/aggregate_aa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Aggregate and Average Annually — aggregate_aa","text":"","code":"if (FALSE) { flo <- aggregate_aa(sim$simulation$flo) }"},{"path":"/reference/calculate_wyr.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Water Yield Ratio (WYR) — calculate_wyr","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"function calculates Water Yield Ratio (WYR) based various components simulation, including precipitation, surface runoff, lateral flow, others. aggregates components computes ratio sum water yields precipitation.","code":""},{"path":"/reference/calculate_wyr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"","code":"calculate_wyr(sim)"},{"path":"/reference/calculate_wyr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"sim SWATrunR nested list containing simulation data. named element 'simulation' contains named elements: 'precip', 'surq_cha', 'surq_res', 'latq_cha', 'latq_res', 'qtile', 'flo'.","code":""},{"path":"/reference/calculate_wyr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"numeric value representing Water Yield Ratio (WYR).","code":""},{"path":"/reference/calculate_wyr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"","code":"if (FALSE) { # Calculate WYR wyr <- calculate_wyr(sim) }"},{"path":"/reference/find_par_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Find Parameter Range for Simulation — find_par_range","title":"Find Parameter Range for Simulation — find_par_range","text":"function identifies range parameter values produce simulation results within specified relative range target objective value. also returns parameter value minimizes absolute error relative objective.","code":""},{"path":"/reference/find_par_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find Parameter Range for Simulation — find_par_range","text":"","code":"find_par_range(par, sim, obj, rel_rng)"},{"path":"/reference/find_par_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find Parameter Range for Simulation — find_par_range","text":"par numeric vector parameter values. sim numeric vector simulation results corresponding parameter values. obj numeric value representing objective value compare . rel_rng numeric value specifying relative range acceptable error.","code":""},{"path":"/reference/find_par_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find Parameter Range for Simulation — find_par_range","text":"list following components: par_rng numeric vector length 2 containing minimum maximum parameter values within specified relative range objective. par_val numeric value parameter minimizes absolute error relative objective. x numeric vector interpolated parameter values. y numeric vector interpolated simulation results corresponding x.","code":""},{"path":"/reference/find_par_range.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Find Parameter Range for Simulation — find_par_range","text":"","code":"if (FALSE) { find_par_range(sim[[1]], calculate_wyr(sim), 0.27, 0.05) }"},{"path":"/reference/plot_esco_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot ESCO Range — plot_esco_range","title":"Plot ESCO Range — plot_esco_range","text":"function creates ggplot visualization ESCO range data, highlighting specific values limits horizontal vertical lines.","code":""},{"path":"/reference/plot_esco_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot ESCO Range — plot_esco_range","text":"","code":"plot_esco_range(sim, obs_wy_ratio, rel_wyr_lim = 0.05)"},{"path":"/reference/plot_esco_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot ESCO Range — plot_esco_range","text":"sim simulation results water balance data. Including: precip Variable 'basin_wb_day' output file. surq_cha Variable 'basin_wb_day' output file. surq_res Variable 'basin_wb_day' output file. latq_cha Variable 'basin_wb_day' output file. latq_res Variable 'basin_wb_day' output file. qtile Variable 'basin_wb_day' output file. flo Variable ''basin_aqu_day' output file. obs_wy_ratio numeric value representing observed water yield ratio. rel_wyr_lim numeric value specifying relative range acceptable error.","code":""},{"path":"/reference/plot_esco_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot ESCO Range — plot_esco_range","text":"ggplot object.","code":""},{"path":"/reference/plot_esco_range.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot ESCO Range — plot_esco_range","text":"","code":"if (FALSE) { plot_esco_range(sim_esco, obs_wy_ratio) }"},{"path":"/articles/soft-cal.html","id":"loading-required-packages","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Soft-Cal Crop Yields","text":"SWATtunR package essential soft calibration, provides necessary functions calibration process. Additional packages required data manipulation, visualization, SWAT+ model runs, etc.","code":"library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/soft-cal.html","id":"defining-settings","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Soft-Cal Crop Yields","text":"step requires defining SWAT+ model path, path crop data file, observed water yield precipitation ratio. crop yield soft calibration, ’s essential accurate data observed crop yields dry weight. data typically sourced '*.csv' file, columns specifying plant names corresponding mean yields. additional information accessible, minimum maximum ranges average annual observed yields, ’s advisable include '*.csv' file well, columns labeled yield_min yield_max respectively. ensures comprehensive dataset effective calibration analysis. Crops observed yield data example provided .","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Path to the crop data file crop_data_path <- '../inst/extdata/crop2.csv'  # Observed water yield to precipitation ratio obs_wy_ratio <- 0.27  # Set the path to save results of the soft calibration sc_res <- '../test/simulations' ## crops_obs <- read_csv(crop_data_path, show_col_types = FALSE) %>%    filter(!is.na(yield_mean))  head(crops_obs, 3) ## # A tibble: 3 × 4 ##   plant_name yield_min yield_max yield_mean ##   <chr>          <dbl>     <dbl>      <dbl> ## 1 akgs            8         12         10   ## 2 csil            7.34      13.5       11.2 ## 3 sgbt           11.0       16.9       14.0"},{"path":"/articles/soft-cal.html","id":"days-to-maturity-parameter-changes","dir":"Articles","previous_headings":"","what":"3. Days to maturity parameter changes","title":"Soft-Cal Crop Yields","text":"settings following step allows define, days maturity changes applied soft-calibration.","code":""},{"path":"/articles/soft-cal.html","id":"initialization","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.1. Initialization","title":"Soft-Cal Crop Yields","text":"Preparation step requires conversion observed yields information numeric vectors initialization 'plants.plt' file.","code":"# Convert observed yields to numeric vectors for(i in c(\"yield_mean\", \"yield_min\", \"yield_max\")){   if(i %in% colnames(crops_obs)){     assign(i, deframe(select(crops_obs, all_of(c(\"plant_name\", i)))))    } else {     assign(i, NULL)   } }  ## Initialize unmodified backup version of plants.plt if(!file.exists(paste0(model_path, '/plants.plt.bkp0'))) {   copy_file_version(model_path, 'plants.plt', file_version = 0) }"},{"path":"/articles/soft-cal.html","id":"days-to-maturity-changes","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.2. Days to maturity changes","title":"Soft-Cal Crop Yields","text":"following code generates parameter input table changes required SWAT+ model run. names converted SWATrunR syntax days maturity parameter. code snippet also samples changes days maturity, allowing users define crops used soft calibration initial values days maturity.","code":"# Reading the plants.plt input file from the initial unchanged backup file plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt.bkp0')) plants_plt <- select(plants_plt, - any_of('description'))  # Define all crops which should be calibrated # Alternatively define a name vector (if you also want to consider crops  # which are not given in the observation input file). crops <- crops_obs$plant_name # crops <- c('crop1', 'crop2', 'crop3')  # Get a vector with days_mat initial values for the selected crops dmat_init <- plants_plt %>%   filter(name %in% crops) %>%    select(name, days_mat) %>%   mutate(days_mat = ifelse(days_mat == 0, 110, days_mat)) %>%    ## if days_mat is 0, set it to 110 (as it is the default value)   deframe()  # Sample changes for days to maturity. Depending on the number of cores you have  # available choose a reasonable interval for the days to maturity which you want  # to test. With an interval of 10 e.g. you have to do 12 simulations (3 rounds  # on 4 cores), with an interval of 5 its 23 simulations. dmat_step <- 20 dmat_chg <- round(seq(-30, 100, dmat_step))  # Generate the parameter input table with the changes for all crops and convert  # the names into SWATrunR syntax par_dmat <- map_df(dmat_init, ~ .x + dmat_chg) %>%    set_names(., paste0('dmat_', names(.),                       '::days_mat.pdb | change = absval | name = ' , names(.)))"},{"path":"/articles/soft-cal.html","id":"run-simulations","dir":"Articles","previous_headings":"","what":"4. Run simulations","title":"Soft-Cal Crop Yields","text":"Days maturity parameter changes applied SWAT+ model, simulations run analyze PHU fractions, yields biomass selected crops. SWATrunR package used run simulations.","code":"# Set the number of cores. E.g. for 12 runs use 4 6, or 12 cores (if available) cores <- 3  ylds_phu_dmat <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)                               ),                               parameter = par_dmat,                               start_date = '2015-01-01',                               end_date = '2020-12-31',                               years_skip = 2,                               n_thread = cores)  # Optionally save the simulation runs. if(!dir.exists(sc_res)) dir.create(sc_res) saveRDS(ylds_phu_dmat, paste0(sc_res, \"/ylds_phu_mat3.rds\"))"},{"path":"/articles/soft-cal.html","id":"plot-phu-fractions-yields-and-biomass-for-days-to-maturity-changes","dir":"Articles","previous_headings":"","what":"5. Plot PHU fractions, yields, and biomass for days to maturity changes","title":"Soft-Cal Crop Yields","text":"figure, visualize PHU fractions, yields, biomass various days maturity settings. graphical representation serves reference adjust initial values days_mat crop simulation. grain crops, typically dry harvest, aim PHU fractions ranging approximately 1.2 1.5 optimize yield. Vegetables, hand, tend PHU fraction around 1, possibly slightly , considered optimal. Crops like basil broccoli harvested reaching full maturity. cases, PHU fractions can lower 1, ranging 0.5 0.9. Furthermore, ’s crucial ensure simulated yields fall within range locally observed yields maintain accuracy relevance.","code":"plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max)"},{"path":"/articles/soft-cal.html","id":"select-days-to-maturity-parameter-changes-to-apply","dir":"Articles","previous_headings":"","what":"6. Select days to maturity parameter changes to apply","title":"Soft-Cal Crop Yields","text":"Based figure provided, identify necessary adjustments days maturity parameter SWAT+ model. adjustments made ensure PHU fractions, yields, biomass values specified crops align observed data.","code":"# Add values based on figure to this line (please add all crops from the initial selection) # names(dmat_init) # Print all crop names chg_dmat_sel <- c(akgs = -30, csil = 10, sgbt =  70,                    wbar =   -10, wira = -10, wiry =  0, wwht =  -30)   # Adding defined changes to initial days_mat values of crops dmat_sel <- chg_dmat_sel[names(dmat_init)] + dmat_init dmat_sel <- enframe(dmat_sel, value = 'days_mat_upd')"},{"path":"/articles/soft-cal.html","id":"write-d_mat-modifications-into-file","dir":"Articles","previous_headings":"","what":"7. Write d_mat modifications into file","title":"Soft-Cal Crop Yields","text":"Write changes plants.plt file update days maturity values selected crops also backup updated file plants.plt.bkp1 file.","code":"## [1] TRUE"},{"path":"/articles/soft-cal.html","id":"check-initial-crop-lai_pot-harv_idx-tmp_base-bm_e-parameters","dir":"Articles","previous_headings":"","what":"8. Check initial crop lai_pot, harv_idx, tmp_base, bm_e parameters","title":"Soft-Cal Crop Yields","text":"fixing days maturity values, might needed address values lai_pot, harv_idx, tmp_base, bm_e parameters selected crops. parameters crucial simulation adjusted PHU fractions, yields, biomass values within expected range.","code":"plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt'))  par_ini <- plants_plt %>%   filter(name %in% crops) %>%   select(name, lai_pot, harv_idx, tmp_base, bm_e)#, days_mat) par_ini ## # A tibble: 7 × 5 ##   name  lai_pot harv_idx tmp_base  bm_e ##   <chr>   <dbl>    <dbl>    <dbl> <dbl> ## 1 csil      4       0.9         8  39   ## 2 sgbt      5       2           4  30   ## 3 wbar      4       0.54        0  30   ## 4 wwht      4       0.4         0  30   ## 5 wira      3.5     0.23        5  38   ## 6 wiry      4       0.4         0  30   ## 7 akgs      4       0.75        0  12.5"},{"path":"/articles/soft-cal.html","id":"step9","dir":"Articles","previous_headings":"","what":"9. Create sample of lai_pot, harv_idx, tmp_base, bm_e parameters with LHS","title":"Soft-Cal Crop Yields","text":"use lhs package create sample parameter values selected crops. sample used run SWAT+ simulations evaluate impact parameter changes model output.","code":"## Make sure your updates will not produce unrealistic values (i.e. negative values)!!! par_bnd <- tibble('lai_pot.pdb | change = relchg' = c(-0.3, 0.3),                   'harv_idx.pdb | change = relchg' = c(-0.3, 0.3),                   'tmp_base.pdb | change = relchg' = c(-0.3, 0.3),                   'bm_e.pdb | change = relchg' = c(-0.3, 0.1))  par_crop <- sample_lhs(par_bnd, 10)"},{"path":"/articles/soft-cal.html","id":"step10","dir":"Articles","previous_headings":"","what":"10. Run SWATrunR for prepared parameter set","title":"Soft-Cal Crop Yields","text":"","code":"ylds_plnt_par <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops)),                               parameter = par_crop,                               n_thread = cores) saveRDS(ylds_plnt_par, paste0(sc_res, \"/ylds_plnt_par3.rds\"))"},{"path":"/articles/soft-cal.html","id":"step11","dir":"Articles","previous_headings":"","what":"11. Examine results in figures","title":"Soft-Cal Crop Yields","text":"Plotting simulation results dotty plots can help identify parameter sensitivities modify . examining patterns dotty plots, may consider adjusting certain parameter ranges (step 9) rerunning model (step 10) observe changes results. Subsequently, can reanalyze outcomes (step 11) gain insights refine understanding system modeled.","code":"## Plot dotty figures for the selected crops plot_dotty_yields(ylds_plnt_par, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step1","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Crop Yields","text":"SWATtunR package essential soft calibration, provides necessary functions calibration process. Additional packages required data manipulation, visualization, SWAT+ model runs, etc.","code":"## Required libraries to run workflow library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/sc-crops.html","id":"scc_step2","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Crop Yields","text":"step requires defining SWAT+ model path, path crop data file. crop yield soft calibration, ’s essential accurate data observed crop yields dry weight. data typically sourced '*.csv' file, columns specifying plant names corresponding mean yields. additional information accessible, minimum maximum ranges average annual observed yields, ’s advisable include '*.csv' file well, columns labeled yield_min yield_max respectively. ensures comprehensive dataset effective calibration analysis. Crops observed yields data example provided .","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Path to the crop data file crop_data_path <- '../inst/extdata/crop2.csv'  # Set the path to save results of the soft calibration sc_res <- '../test/simulations'  # Set the number of cores available for calculations.   # Number of cores for 12 runs use 3, 4, 6, or 12 cores (if available) cores <- 3 ## crops_obs <- read_csv(crop_data_path, show_col_types = FALSE) %>%    filter(!is.na(yield_mean))  head(crops_obs, 3) ## # A tibble: 3 × 4 ##   plant_name yield_min yield_max yield_mean ##   <chr>          <dbl>     <dbl>      <dbl> ## 1 akgs            8         12         10   ## 2 csil            7.34      13.5       11.2 ## 3 sgbt           11.0       16.9       14.0"},{"path":"/articles/sc-crops.html","id":"scc_step3","dir":"Articles","previous_headings":"","what":"3. Days to maturity parameter changes","title":"Crop Yields","text":"settings following step allows define, days maturity changes applied soft-calibration.","code":""},{"path":"/articles/sc-crops.html","id":"scc_step31","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.1. Initialization","title":"Crop Yields","text":"preparation step requires conversion observed yields information numeric vectors initialization 'plants.plt' file.","code":"# Convert observed yields to numeric vectors for(i in c(\"yield_mean\", \"yield_min\", \"yield_max\")){   if(i %in% colnames(crops_obs)){     assign(i, deframe(select(crops_obs, all_of(c(\"plant_name\", i)))))    } else {     assign(i, NULL)   } }  ## Initialize unmodified backup version of plants.plt if(!file.exists(paste0(model_path, '/plants.plt.bkp0'))) {   copy_file_version(model_path, 'plants.plt', file_version = 0) }"},{"path":"/articles/sc-crops.html","id":"scc_step32","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.2. Days to maturity changes","title":"Crop Yields","text":"following code generates parameter input table changes required SWAT+ model run. names converted SWATrunR syntax days maturity parameter. code snippet also samples changes days maturity, allowing users define crops used soft calibration initial values days maturity.","code":"# Reading the plants.plt input file from the initial unchanged backup file plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt.bkp0')) plants_plt <- select(plants_plt, - any_of('description'))  # Define all crops which should be calibrated # Alternatively define a name vector (if you also want to consider crops  # which are not given in the observation input file). crops <- crops_obs$plant_name # crops <- c('crop1', 'crop2', 'crop3')  # Get a vector with days_mat initial values for the selected crops dmat_init <- plants_plt %>%   filter(name %in% crops) %>%    select(name, days_mat) %>%   mutate(days_mat = ifelse(days_mat == 0, 110, days_mat)) %>%    ## if days_mat is 0, set it to 110 (as it is the default value)   deframe()  # Sample changes for days to maturity. Depending on the number of cores you have  # available choose a reasonable interval for the days to maturity which you want  # to test. With an interval of 10 e.g. you have to do 12 simulations (3 rounds  # on 4 cores), with an interval of 5 its 23 simulations. dmat_step <- 20 dmat_chg <- round(seq(-30, 100, dmat_step))  # Generate the parameter input table with the changes for all crops and convert  # the names into SWATrunR syntax par_dmat <- map_df(dmat_init, ~ .x + dmat_chg) %>%    set_names(., paste0('dmat_', names(.),                       '::days_mat.pdb | change = absval | name = ' , names(.)))"},{"path":"/articles/sc-crops.html","id":"scc_step4","dir":"Articles","previous_headings":"","what":"4. Run simulations","title":"Crop Yields","text":"Days maturity parameter changes applied SWAT+ model, simulations run analyze PHU fractions, yields biomass selected crops. SWATrunR package used run simulations.","code":"ylds_phu_dmat <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)                               ),                               parameter = par_dmat,                               start_date = '2015-01-01',                               end_date = '2020-12-31',                               years_skip = 2,                               n_thread = cores)  # Optionally save the simulation runs. if(!dir.exists(sc_res)) dir.create(sc_res) saveRDS(ylds_phu_dmat, paste0(sc_res, \"/ylds_phu_mat.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step5","dir":"Articles","previous_headings":"","what":"5. Plot PHU fractions, yields, and biomass for days to maturity changes","title":"Crop Yields","text":"figure, visualize PHU fractions, yields, biomass various days maturity settings. graphical representation serves reference adjust initial values days_mat crop simulation. grain crops, typically dry harvest, aim PHU fractions ranging approximately 1.2 1.5 optimize yield. Vegetables, hand, tend PHU fraction around 1, possibly slightly , considered optimal. Crops like basil broccoli harvested reaching full maturity. cases, PHU fractions can lower 1, ranging 0.5 0.9. Furthermore, ’s crucial ensure simulated yields fall within range locally observed yields maintain accuracy relevance.","code":"plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step6","dir":"Articles","previous_headings":"","what":"6. Select days to maturity parameter changes to apply","title":"Crop Yields","text":"Based figure provided, identify necessary adjustments days maturity parameter SWAT+ model. adjustments made ensure PHU fractions, yields, biomass values specified crops align observed data.","code":"# Add values based on figure to this line (please add all crops from the initial selection) # names(dmat_init) # Print all crop names chg_dmat_sel <- c(akgs = -30, csil = 10, sgbt =  70,                    wbar =   -10, wira = -10, wiry =  0, wwht =  -30)   # Adding defined changes to initial days_mat values of crops dmat_sel <- chg_dmat_sel[names(dmat_init)] + dmat_init dmat_sel <- enframe(dmat_sel, value = 'days_mat_upd')"},{"path":"/articles/sc-crops.html","id":"scc_step7","dir":"Articles","previous_headings":"","what":"7. Write d_mat modifications into file","title":"Crop Yields","text":"Write changes plants.plt file update days maturity values selected crops also backup updated file plants.plt.bkp1 file.","code":"# Update the days_mat values in plants.plt according to the changes defined above. plants_plt <- plants_plt %>%   left_join(., dmat_sel, by = 'name') %>%   mutate(days_mat = ifelse(!is.na(days_mat_upd), days_mat_upd, days_mat)) %>%   select(-days_mat_upd)  ## Overwriting original plants.plt with the updated days_mat values. plants_plt_fmt <- c('%-12s', '%-18s', '%-12s', rep('%12.5f', ncol(plants_plt) - 3)) write_tbl(plants_plt, paste0(model_path, '/plants.plt'), fmt = plants_plt_fmt)  # Create a backup file with the changed days_mat values copy_file_version(model_path, 'plants.plt', file_version = 1) ## [1] TRUE"},{"path":"/articles/sc-crops.html","id":"scc_step8","dir":"Articles","previous_headings":"","what":"8. Check initial crop lai_pot, harv_idx, tmp_base, bm_e parameters","title":"Crop Yields","text":"fixing days maturity values, might needed address values lai_pot, harv_idx, tmp_base, bm_e parameters selected crops. parameters crucial simulation adjusted PHU fractions, yields, biomass values within expected range.","code":"plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt'))  par_ini <- plants_plt %>%   filter(name %in% crops) %>%   select(name, lai_pot, harv_idx, tmp_base, bm_e)#, days_mat) par_ini ## # A tibble: 7 × 5 ##   name  lai_pot harv_idx tmp_base  bm_e ##   <chr>   <dbl>    <dbl>    <dbl> <dbl> ## 1 csil      4       0.9         8  39   ## 2 sgbt      5       2           4  30   ## 3 wbar      4       0.54        0  30   ## 4 wwht      4       0.4         0  30   ## 5 wira      3.5     0.23        5  38   ## 6 wiry      4       0.4         0  30   ## 7 akgs      4       0.75        0  12.5"},{"path":"/articles/sc-crops.html","id":"scc_step9","dir":"Articles","previous_headings":"","what":"9. Create sample of lai_pot, harv_idx, tmp_base, bm_e parameters with LHS","title":"Crop Yields","text":"use sample_lhs function create sample parameter values selected crops. sample used run SWAT+ simulations evaluate impact parameter changes model output. syntax parameter boundaries found SWATrunR page.","code":"## Define changes to be applied to the initial parameter values ## Make sure your updates will not produce unrealistic values (i.e. negative values)!!! par_bnd <- tibble('lai_pot.pdb | change = relchg' = c(-0.3, 0.3),                   'harv_idx.pdb | change = relchg' = c(-0.3, 0.3),                   'tmp_base.pdb | change = relchg' = c(-0.3, 0.3),                   # 'tmp_base.pdb | change = abschg' = c(-2, 2),                   'bm_e.pdb | change = relchg' = c(-0.3, 0.1))  par_crop <- sample_lhs(par_bnd, 10) ## 10 samples for each parameter will be generated.  ## The number of samples can be adjusted based on the available computational resources. ## Recommended number of samples is 50-100."},{"path":"/articles/sc-crops.html","id":"scc_step10","dir":"Articles","previous_headings":"","what":"10. Run SWATrunR for prepared parameter set","title":"Crop Yields","text":"Run SWAT+ model updated parameters selected crops rerun. simulation results used evaluate impact parameter changes model output.","code":"ylds_plnt_par <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops)),                               parameter = par_crop,                               n_thread = cores)  ## Save the results to the file saveRDS(ylds_plnt_par, paste0(sc_res, \"/ylds_plnt_par.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step11","dir":"Articles","previous_headings":"","what":"11. Examine results in figures","title":"Crop Yields","text":"Plotting simulation results dotty plots can help identify parameter sensitivities modify . examining patterns dotty plots, may consider adjusting certain parameter ranges (step 9) rerunning model (step 10) observe changes results. Subsequently, can reanalyze outcomes plot_dotty_yields function gain insights refine understanding system modeled.","code":"## Plot dotty figures for the selected crops plot_dotty_yields(ylds_plnt_par, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step12","dir":"Articles","previous_headings":"","what":"12. Update parameter values in plants.plt file","title":"Crop Yields","text":"examining results SWAT+ simulations, can adjust parameter values plants.plt file. parameters need changed, sensitive might help improve model performance. Different crops exhibit different sensitivities parameters, important select parameters crop. Following code sniplet shows update plants.plt file.","code":"## Fix changes you want to write in plants.plt file chg_par <- tibble(   name     = c(\"akgs\",\"barl\", \"csil\", \"sgbt\", \"wbar\", \"wira\", \"wiry\", \"wwht\"),   lai_pot  = c(    0,     0,      0,      0,      0,      0,      0,      0),   harv_idx = c(    0,     0,      0,      0,      0,      0,    0.3,    0.3),   tmp_base = c(    0,     0,      0,      0,      0,      0,   -0.2,   -0.2),   bm_e     = c(    0,     0,      0,      0,      0,      0,      0,      0)) %>%   left_join(select(plants_plt, name), ., by = 'name')  ## Update parameter values in plants.plt for (i in 1:ncol(par_bnd)) {   par_i <- names(chg_par)[i + 1]   chg_typ_i <- sub(\".*change = \", \"\", names(par_bnd)[i])   plants_plt[par_i] <- update_par(plants_plt[[par_i]], chg_par[[par_i]], chg_typ_i) }  ## Overwriting plants.plt with the updated parameter values. write_tbl(plants_plt, paste0(model_path, '/plants.plt'), fmt = plants_plt_fmt)"},{"path":"/articles/sc-crops.html","id":"scc_step13","dir":"Articles","previous_headings":"","what":"13. Rerun final plants.plt parameter selection","title":"Crop Yields","text":"updating plants.plt file new parameter values, can rerun SWAT+ model evaluate impact parameter changes model output. simulation results provide model, soft calibrated selected crops.","code":"phu_yld_final <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)))  ## Save the results to the file saveRDS(phu_yld_final, paste0(sc_res, \"/phu_yld_final.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step14","dir":"Articles","previous_headings":"","what":"14. Examine the final results","title":"Crop Yields","text":"Egamine final results SWAT+ simulations. simulation results provide model, soft calibrated selected crops. -depth analysis, users can employ additional SWATdoctR functions, like plot_hru_pw_day(). function enables visualization daily time series variables output file hru_pw_day.txt related hydrological response units , providing valuable insights model’s performance behavior. might help understanding model’s outputs decide crop yield soft calibration results acceptable. completing soft calibration process crops proceed soft calibration water yield presented another page.","code":"plot_phu_yld_bms(phu_yld_final, 0, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-wy.html","id":"scw_step1","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Water Yield","text":"yet loaded crop yields soft calibration, please load following libraries.","code":"## Required libraries to run workflow library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/sc-wy.html","id":"scw_step2","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Water Yield","text":"step requires defining SWAT+ model path observed water yield precipitation ratio.","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Set the path to save results of the soft calibration sc_res <- '../test/simulations'  # Observed water yield to precipitation ratio obs_wy_ratio <- 0.27  # Set the number of cores available for calculations.   # Number of cores for 12 runs use 3, 4, 6, or 12 cores (if available) cores <- 3"},{"path":"/articles/sc-wy.html","id":"scw_step3","dir":"Articles","previous_headings":"","what":"3. Defining esco parameter range and running model","title":"Water Yield","text":"soil evaporation compensation factor (esco) important coefficient modeling soil moisture dynamics. allows users adjust depth distribution used satisfy soil evaporative demand, accounting factors capillary action, crusting, cracks. increasing esco value, model can draw evaporative demand deeper soil layers. means model reduced amount water available water yield. esco values range 0.01 1.","code":"# The esco parameter range is sampled. esco <- tibble('esco.hru | change = absval' = seq(0.05,0.95, length.out = max(cores, 4)))  sim_esco <- run_swatplus(project_path = model_path,                          output = list(precip  =  define_output('basin_wb_day',                                                                  'precip',                                                                  1),                                        surq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_cha',                                                                 unit = 1),                                        surq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_res',                                                                 unit = 1),                                        latq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_cha',                                                                 unit = 1),                                        latq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_res',                                                                 unit = 1),                                        qtile =    define_output(file = 'basin_wb_day',                                                                 variable = 'qtile',                                                                 unit = 1),                                        flo =      define_output(file = 'basin_aqu_day',                                                                 variable = 'flo',                                                                 unit = 1)                          ),                          parameter = esco,                          n_thread = cores) ## Save the results to the file saveRDS(sim_esco, paste0(sc_res, \"/sim_esco.rds\"))"},{"path":"/articles/sc-wy.html","id":"scw_step4","dir":"Articles","previous_headings":"","what":"4. Extracting and plotting water yield ratio vs esco parameter values","title":"Water Yield","text":"water yield ratio calculated simulation. range esco values produce water yield ratios within specified range observed water yield ratio identified using plot_esco_range function.","code":"plot_esco_range(sim_esco, obs_wy_ratio)"}]
+[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Svajunas Plunge. Author, maintainer. Christoph Schuerz. Author. Michel Strauch. Author. Mikołaj Piniewski. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Plunge S, Schuerz C, Strauch M, Piniewski M (2024). SWATtunR: Soft & Hard Calibration, Validation Package SWAT+ models. R package version 0.0.1.9002, https://github.com/biopsichas/SWATtunR.","code":"@Manual{,   title = {SWATtunR: Soft & Hard Calibration, Validation Package for SWAT+ models},   author = {Svajunas Plunge and Christoph Schuerz and Michel Strauch and Mikołaj Piniewski},   year = {2024},   note = {R package version 0.0.1.9002},   url = {https://github.com/biopsichas/SWATtunR}, }"},{"path":[]},{"path":"/index.html","id":"swattunr","dir":"","previous_headings":"","what":"SWATtunR","title":"Soft & Hard Calibration, Validation Package for SWAT+ models","text":"Text text text","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Soft & Hard Calibration, Validation Package for SWAT+ models","text":"Text text text Text text text","code":"# If the package 'remotes' is not installed run first: install.packages(\"remotes\")  # The installation of `SWATprepR`. remotes::install_github(\"biopsichas/SWATtunR\")"},{"path":"/reference/hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello, World! — hello","title":"Hello, World! — hello","text":"Prints 'Hello, world!'.","code":""},{"path":"/reference/hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello, World! — hello","text":"","code":"hello()"},{"path":"/reference/hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello, World! — hello","text":"","code":"hello() #> Error in hello(): could not find function \"hello\""},{"path":"/reference/read_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Read a SWAT+ input file which has a tabular structure. — read_tbl","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"function reads SWAT+ input file tabular structure tibble.","code":""},{"path":"/reference/read_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"","code":"read_tbl(file_path, col_names = NULL, n_skip = 1)"},{"path":"/reference/read_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"file_path Path SWAT+ input file. col_names (optional) character vector specifying column names. provided, column names inferred file. Default col_names = NULL. n_skip (optional) Number header rows skip. Default n_skip = 1.","code":""},{"path":"/reference/read_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read a SWAT+ input file which has a tabular structure. — read_tbl","text":"tibble representing SWAT+ input file.","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a running ID to duplicated names — add_suffix_to_duplicate","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"Add running ID duplicated names","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"","code":"add_suffix_to_duplicate(col_name)"},{"path":"/reference/add_suffix_to_duplicate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"col_name Character vector column names","code":""},{"path":"/reference/add_suffix_to_duplicate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a running ID to duplicated names — add_suffix_to_duplicate","text":"col_name character vector IDs duplicated names","code":""},{"path":"/reference/write_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Write SWAT+ input file, which has a tabular structure. — write_tbl","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"Write SWAT+ input file, tabular structure.","code":""},{"path":"/reference/write_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"","code":"write_tbl(tbl, file_path, fmt)"},{"path":"/reference/write_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"tbl SWAT input table tibble (data.frame) format. file_path Write path SWAT+ input file. fmt Character vector format strings define print format table column.","code":""},{"path":"/reference/write_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"Writes text file table file path.","code":""},{"path":[]},{"path":"/reference/write_tbl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Write SWAT+ input file, which has a tabular structure. — write_tbl","text":"","code":"if (FALSE) { ## Read the hydrology.hyd input file hydrology_hyd <- read_tbl(paste0(model_path, '/hydrology.hyd')) hydrology_hyd$esco <- 1 ## Updating hydrology.hyd file hydr_hyd_fmt <- c('%-16s', rep('%12.5f', 14)) write_tbl(hydrology_hyd, paste0(model_path, '/hydrology.hyd'), hydr_hyd_fmt) }"},{"path":"/reference/copy_file_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy a file with an optional version suffix. — copy_file_version","title":"Copy a file with an optional version suffix. — copy_file_version","text":"function copies file one location another, optional version suffix appended filename.","code":""},{"path":"/reference/copy_file_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy a file with an optional version suffix. — copy_file_version","text":"","code":"copy_file_version(model_path, file_name, file_version = NULL)"},{"path":"/reference/copy_file_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy a file with an optional version suffix. — copy_file_version","text":"model_path path directory containing file. file_name name file copied. file_version optional version suffix appended filename. Default file_version = NULL, adds '.bkp' filename.","code":""},{"path":"/reference/copy_file_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy a file with an optional version suffix. — copy_file_version","text":"None","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"function generates boxplots visualize Plant Heat Units (PHU) fractions, yields, biomass changes days maturity.","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"","code":"plot_phu_yld_bms(   sim_result,   x_label,   yield = NULL,   yield_min = NULL,   yield_max = NULL )"},{"path":"/reference/plot_phu_yld_bms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"sim_result simulation results containing PHU, yield, biomass data. x_label Labels x-axis representing changes days maturity. yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL yield_max (optional) maximum observed yield values crop. Default yield_max = NULL","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"combined ggplot object showing boxplots PHU fractions, yields, biomass.","code":""},{"path":"/reference/plot_phu_yld_bms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot PHU, yield, and biomass over days to maturity — plot_phu_yld_bms","text":"","code":"if (FALSE) { plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) }"},{"path":"/reference/sample_lhs.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample parameters space — sample_lhs","title":"Sample parameters space — sample_lhs","text":"function samples parameter space using Latin Hypercube Sampling (LHS).","code":""},{"path":"/reference/sample_lhs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample parameters space — sample_lhs","text":"","code":"sample_lhs(par, n)"},{"path":"/reference/sample_lhs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample parameters space — sample_lhs","text":"par matrix data frame specifying parameter ranges. n number samples generate.","code":""},{"path":"/reference/sample_lhs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample parameters space — sample_lhs","text":"tibble containing sampled parameter values.","code":""},{"path":"/reference/sample_lhs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample parameters space — sample_lhs","text":"","code":"# Define parameter ranges parameters <- data.frame(   param1 = c(0, 1),   param2 = c(0, 2),   param3 = c(0, 10) )  # Sample the parameter space sample_space <- sample_lhs(parameters, 3) sample_space #> # A tibble: 3 × 3 #>   param1 param2 param3 #>    <dbl>  <dbl>  <dbl> #> 1  0.549  0.536   3.28 #> 2  0.143  0.788   5.72 #> 3  0.824  1.93    7.55"},{"path":"/reference/plot_dotty_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Dotty Yields — plot_dotty_yields","title":"Plot Dotty Yields — plot_dotty_yields","text":"function creates dotty plots simulated yields, comparing observed yields (available).","code":""},{"path":"/reference/plot_dotty_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Dotty Yields — plot_dotty_yields","text":"","code":"plot_dotty_yields(sim_result, yield = NULL, yield_min = NULL, yield_max = NULL)"},{"path":"/reference/plot_dotty_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Dotty Yields — plot_dotty_yields","text":"sim_result simulation results containing yield data. yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL yield_max (optional) maximum observed yield values crop. Default yield_max = NULL","code":""},{"path":"/reference/plot_dotty_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Dotty Yields — plot_dotty_yields","text":"combined ggplot object showing dottty plots 4 parameters.","code":""},{"path":"/reference/plot_dotty_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Dotty Yields — plot_dotty_yields","text":"","code":"if (FALSE) { plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) }"},{"path":"/reference/dotty_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a dotty plot — dotty_fig","title":"Make a dotty plot — dotty_fig","text":"Make dotty plot","code":""},{"path":"/reference/dotty_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a dotty plot — dotty_fig","text":"","code":"dotty_fig(sim_yield, yield = NULL, yield_min = NULL, yield_max = NULL)"},{"path":"/reference/dotty_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a dotty plot — dotty_fig","text":"sim_yield dataframe yield data yield (optional) mean yield values crop. Default yield = NULL. yield_min (optional) minimum observed yield values crop. Default yield_min = NULL. yield_max (optional) maximum observed yield values crop. Default yield_max = NULL.","code":""},{"path":"/reference/dotty_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a dotty plot — dotty_fig","text":"ggplot object dotty plot","code":""},{"path":"/reference/dotty_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make a dotty plot — dotty_fig","text":"","code":"if (FALSE) { dotty_fig(sim_yield) }"},{"path":"/reference/plot_dotty.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Dotty — plot_dotty","title":"Plot Dotty — plot_dotty","text":"function creates dotty plot visualize relationship parameter values performance results.","code":""},{"path":"/reference/plot_dotty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Dotty — plot_dotty","text":"","code":"plot_dotty(   par,   var,   y_label = \"y\",   n_col = 3,   y_lim = NULL,   y_inter = NULL,   trend = FALSE,   run_ids = NULL,   low_up = FALSE )"},{"path":"/reference/plot_dotty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Dotty — plot_dotty","text":"par data frame model parameter values simulation. var model performance result vector list vectors plotted parameter values. y_label (optional) Labels y-axis, either single label vector corresponding variable var list. Default y_label = 'y'. n_col (optional) Number columns facet grid. Default n_col = 3. y_lim (optional) Limits y-axis. Default y_lim = NULL. y_inter (optional) Y-axis intercept value. Default y_inter = NULL. trend (optional) Logical, indicating whether add trend line. Default trend = FALSE. run_ids (optional) numeric vector run IDs highlighted plot. Default run_ids = NULL. low_up (optional) Logical, TRUE whole possible parameter range used x axis. Default low_up = FALSE.","code":""},{"path":"/reference/plot_dotty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Dotty — plot_dotty","text":"ggplot object representing dotty plot.","code":""},{"path":"/reference/plot_dotty.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Dotty — plot_dotty","text":"","code":"if (FALSE) { # plot_dotty(my_data, 'performance', y_label = 'y_label') }"},{"path":"/reference/update_par.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Parameters — update_par","title":"Update Parameters — update_par","text":"function updates parameters based different types changes.","code":""},{"path":"/reference/update_par.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Parameters — update_par","text":"","code":"update_par(par, par_up, change)"},{"path":"/reference/update_par.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Parameters — update_par","text":"par Numeric vector: Original parameter values. par_up Numeric vector: Values indicating update parameter. change Character scalar: Type change apply. Options \"relchg\" relative change, \"pctchg\" percentage change, \"abschg\" absolute change, \"absval\" setting absolute value change.","code":""},{"path":"/reference/update_par.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Parameters — update_par","text":"Numeric vector updated parameter values.","code":""},{"path":"/reference/update_par.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Parameters — update_par","text":"","code":"par <- c(10, 20, 30, 40) par_up <- c(0.1, 0.2, NA, 0.3) update_par(par, par_up, \"relchg\") # Returns updated parameters with relative change applied. #> [1] 11 24 30 52"},{"path":"/reference/aggregate_aa.html","id":null,"dir":"Reference","previous_headings":"","what":"Aggregate and Average Annually — aggregate_aa","title":"Aggregate and Average Annually — aggregate_aa","text":"function takes data frame containing date column numerical columns, aggregates data annually, computes average annual sums.","code":""},{"path":"/reference/aggregate_aa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aggregate and Average Annually — aggregate_aa","text":"","code":"aggregate_aa(tbl)"},{"path":"/reference/aggregate_aa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Aggregate and Average Annually — aggregate_aa","text":"tbl data frame contains 'date' column numerical columns.","code":""},{"path":"/reference/aggregate_aa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Aggregate and Average Annually — aggregate_aa","text":"numeric vector mean annual sums column input data frame.","code":""},{"path":"/reference/aggregate_aa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Aggregate and Average Annually — aggregate_aa","text":"","code":"if (FALSE) { flo <- aggregate_aa(sim$simulation$flo) }"},{"path":"/reference/calculate_wyr.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Water Yield Ratio (WYR) — calculate_wyr","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"function calculates Water Yield Ratio (WYR) based various components simulation, including precipitation, surface runoff, lateral flow, others. aggregates components computes ratio sum water yields precipitation.","code":""},{"path":"/reference/calculate_wyr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"","code":"calculate_wyr(sim)"},{"path":"/reference/calculate_wyr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"sim SWATrunR nested list containing simulation data. named element 'simulation' contains named elements: 'precip', 'surq_cha', 'surq_res', 'latq_cha', 'latq_res', 'qtile', 'flo'.","code":""},{"path":"/reference/calculate_wyr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"numeric value representing Water Yield Ratio (WYR).","code":""},{"path":"/reference/calculate_wyr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Water Yield Ratio (WYR) — calculate_wyr","text":"","code":"if (FALSE) { # Calculate WYR wyr <- calculate_wyr(sim) }"},{"path":"/reference/find_par_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Find Parameter Range for Simulation — find_par_range","title":"Find Parameter Range for Simulation — find_par_range","text":"function identifies range parameter values produce simulation results within specified relative range target objective value. also returns parameter value minimizes absolute error relative objective.","code":""},{"path":"/reference/find_par_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find Parameter Range for Simulation — find_par_range","text":"","code":"find_par_range(par, sim, obj, rel_rng)"},{"path":"/reference/find_par_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find Parameter Range for Simulation — find_par_range","text":"par numeric vector parameter values. sim numeric vector simulation results corresponding parameter values. obj numeric value representing objective value compare . rel_rng numeric value specifying relative range acceptable error.","code":""},{"path":"/reference/find_par_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find Parameter Range for Simulation — find_par_range","text":"list following components: par_rng numeric vector length 2 containing minimum maximum parameter values within specified relative range objective. par_val numeric value parameter minimizes absolute error relative objective. x numeric vector interpolated parameter values. y numeric vector interpolated simulation results corresponding x.","code":""},{"path":"/reference/find_par_range.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Find Parameter Range for Simulation — find_par_range","text":"","code":"if (FALSE) { find_par_range(sim[[1]], calculate_wyr(sim), 0.27, 0.05) }"},{"path":"/reference/plot_esco_range.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot ESCO Range — plot_esco_range","title":"Plot ESCO Range — plot_esco_range","text":"function creates ggplot visualization ESCO range data, highlighting specific values limits horizontal vertical lines.","code":""},{"path":"/reference/plot_esco_range.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot ESCO Range — plot_esco_range","text":"","code":"plot_esco_range(sim, obs_wy_ratio, rel_wyr_lim = 0.05)"},{"path":"/reference/plot_esco_range.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot ESCO Range — plot_esco_range","text":"sim simulation results water balance data. Including: precip Variable 'basin_wb_day' output file. surq_cha Variable 'basin_wb_day' output file. surq_res Variable 'basin_wb_day' output file. latq_cha Variable 'basin_wb_day' output file. latq_res Variable 'basin_wb_day' output file. qtile Variable 'basin_wb_day' output file. flo Variable ''basin_aqu_day' output file. obs_wy_ratio numeric value representing observed water yield ratio. rel_wyr_lim numeric value specifying relative range acceptable error.","code":""},{"path":"/reference/plot_esco_range.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot ESCO Range — plot_esco_range","text":"ggplot object.","code":""},{"path":"/reference/plot_esco_range.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot ESCO Range — plot_esco_range","text":"","code":"if (FALSE) { plot_esco_range(sim_esco, obs_wy_ratio) }"},{"path":"/articles/soft-cal.html","id":"loading-required-packages","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Soft-Cal Crop Yields","text":"SWATtunR package essential soft calibration, provides necessary functions calibration process. Additional packages required data manipulation, visualization, SWAT+ model runs, etc.","code":"library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/soft-cal.html","id":"defining-settings","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Soft-Cal Crop Yields","text":"step requires defining SWAT+ model path, path crop data file, observed water yield precipitation ratio. crop yield soft calibration, ’s essential accurate data observed crop yields dry weight. data typically sourced '*.csv' file, columns specifying plant names corresponding mean yields. additional information accessible, minimum maximum ranges average annual observed yields, ’s advisable include '*.csv' file well, columns labeled yield_min yield_max respectively. ensures comprehensive dataset effective calibration analysis. Crops observed yield data example provided .","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Path to the crop data file crop_data_path <- '../inst/extdata/crop2.csv'  # Observed water yield to precipitation ratio obs_wy_ratio <- 0.27  # Set the path to save results of the soft calibration sc_res <- '../test/simulations' ## crops_obs <- read_csv(crop_data_path, show_col_types = FALSE) %>%    filter(!is.na(yield_mean))  head(crops_obs, 3) ## # A tibble: 3 × 4 ##   plant_name yield_min yield_max yield_mean ##   <chr>          <dbl>     <dbl>      <dbl> ## 1 akgs            8         12         10   ## 2 csil            7.34      13.5       11.2 ## 3 sgbt           11.0       16.9       14.0"},{"path":"/articles/soft-cal.html","id":"days-to-maturity-parameter-changes","dir":"Articles","previous_headings":"","what":"3. Days to maturity parameter changes","title":"Soft-Cal Crop Yields","text":"settings following step allows define, days maturity changes applied soft-calibration.","code":""},{"path":"/articles/soft-cal.html","id":"initialization","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.1. Initialization","title":"Soft-Cal Crop Yields","text":"Preparation step requires conversion observed yields information numeric vectors initialization 'plants.plt' file.","code":"# Convert observed yields to numeric vectors for(i in c(\"yield_mean\", \"yield_min\", \"yield_max\")){   if(i %in% colnames(crops_obs)){     assign(i, deframe(select(crops_obs, all_of(c(\"plant_name\", i)))))    } else {     assign(i, NULL)   } }  ## Initialize unmodified backup version of plants.plt if(!file.exists(paste0(model_path, '/plants.plt.bkp0'))) {   copy_file_version(model_path, 'plants.plt', file_version = 0) }"},{"path":"/articles/soft-cal.html","id":"days-to-maturity-changes","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.2. Days to maturity changes","title":"Soft-Cal Crop Yields","text":"following code generates parameter input table changes required SWAT+ model run. names converted SWATrunR syntax days maturity parameter. code snippet also samples changes days maturity, allowing users define crops used soft calibration initial values days maturity.","code":"# Reading the plants.plt input file from the initial unchanged backup file plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt.bkp0')) plants_plt <- select(plants_plt, - any_of('description'))  # Define all crops which should be calibrated # Alternatively define a name vector (if you also want to consider crops  # which are not given in the observation input file). crops <- crops_obs$plant_name # crops <- c('crop1', 'crop2', 'crop3')  # Get a vector with days_mat initial values for the selected crops dmat_init <- plants_plt %>%   filter(name %in% crops) %>%    select(name, days_mat) %>%   mutate(days_mat = ifelse(days_mat == 0, 110, days_mat)) %>%    ## if days_mat is 0, set it to 110 (as it is the default value)   deframe()  # Sample changes for days to maturity. Depending on the number of cores you have  # available choose a reasonable interval for the days to maturity which you want  # to test. With an interval of 10 e.g. you have to do 12 simulations (3 rounds  # on 4 cores), with an interval of 5 its 23 simulations. dmat_step <- 20 dmat_chg <- round(seq(-30, 100, dmat_step))  # Generate the parameter input table with the changes for all crops and convert  # the names into SWATrunR syntax par_dmat <- map_df(dmat_init, ~ .x + dmat_chg) %>%    set_names(., paste0('dmat_', names(.),                       '::days_mat.pdb | change = absval | name = ' , names(.)))"},{"path":"/articles/soft-cal.html","id":"run-simulations","dir":"Articles","previous_headings":"","what":"4. Run simulations","title":"Soft-Cal Crop Yields","text":"Days maturity parameter changes applied SWAT+ model, simulations run analyze PHU fractions, yields biomass selected crops. SWATrunR package used run simulations.","code":"# Set the number of cores. E.g. for 12 runs use 4 6, or 12 cores (if available) cores <- 3  ylds_phu_dmat <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)                               ),                               parameter = par_dmat,                               start_date = '2015-01-01',                               end_date = '2020-12-31',                               years_skip = 2,                               n_thread = cores)  # Optionally save the simulation runs. if(!dir.exists(sc_res)) dir.create(sc_res) saveRDS(ylds_phu_dmat, paste0(sc_res, \"/ylds_phu_mat3.rds\"))"},{"path":"/articles/soft-cal.html","id":"plot-phu-fractions-yields-and-biomass-for-days-to-maturity-changes","dir":"Articles","previous_headings":"","what":"5. Plot PHU fractions, yields, and biomass for days to maturity changes","title":"Soft-Cal Crop Yields","text":"figure, visualize PHU fractions, yields, biomass various days maturity settings. graphical representation serves reference adjust initial values days_mat crop simulation. grain crops, typically dry harvest, aim PHU fractions ranging approximately 1.2 1.5 optimize yield. Vegetables, hand, tend PHU fraction around 1, possibly slightly , considered optimal. Crops like basil broccoli harvested reaching full maturity. cases, PHU fractions can lower 1, ranging 0.5 0.9. Furthermore, ’s crucial ensure simulated yields fall within range locally observed yields maintain accuracy relevance.","code":"plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max) plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max)"},{"path":"/articles/soft-cal.html","id":"select-days-to-maturity-parameter-changes-to-apply","dir":"Articles","previous_headings":"","what":"6. Select days to maturity parameter changes to apply","title":"Soft-Cal Crop Yields","text":"Based figure provided, identify necessary adjustments days maturity parameter SWAT+ model. adjustments made ensure PHU fractions, yields, biomass values specified crops align observed data.","code":"# Add values based on figure to this line (please add all crops from the initial selection) # names(dmat_init) # Print all crop names chg_dmat_sel <- c(akgs = -30, csil = 10, sgbt =  70,                    wbar =   -10, wira = -10, wiry =  0, wwht =  -30)   # Adding defined changes to initial days_mat values of crops dmat_sel <- chg_dmat_sel[names(dmat_init)] + dmat_init dmat_sel <- enframe(dmat_sel, value = 'days_mat_upd')"},{"path":"/articles/soft-cal.html","id":"write-d_mat-modifications-into-file","dir":"Articles","previous_headings":"","what":"7. Write d_mat modifications into file","title":"Soft-Cal Crop Yields","text":"Write changes plants.plt file update days maturity values selected crops also backup updated file plants.plt.bkp1 file.","code":"## [1] TRUE"},{"path":"/articles/soft-cal.html","id":"check-initial-crop-lai_pot-harv_idx-tmp_base-bm_e-parameters","dir":"Articles","previous_headings":"","what":"8. Check initial crop lai_pot, harv_idx, tmp_base, bm_e parameters","title":"Soft-Cal Crop Yields","text":"fixing days maturity values, might needed address values lai_pot, harv_idx, tmp_base, bm_e parameters selected crops. parameters crucial simulation adjusted PHU fractions, yields, biomass values within expected range.","code":"plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt'))  par_ini <- plants_plt %>%   filter(name %in% crops) %>%   select(name, lai_pot, harv_idx, tmp_base, bm_e)#, days_mat) par_ini ## # A tibble: 7 × 5 ##   name  lai_pot harv_idx tmp_base  bm_e ##   <chr>   <dbl>    <dbl>    <dbl> <dbl> ## 1 csil      4       0.9         8  39   ## 2 sgbt      5       2           4  30   ## 3 wbar      4       0.54        0  30   ## 4 wwht      4       0.4         0  30   ## 5 wira      3.5     0.23        5  38   ## 6 wiry      4       0.4         0  30   ## 7 akgs      4       0.75        0  12.5"},{"path":"/articles/soft-cal.html","id":"step9","dir":"Articles","previous_headings":"","what":"9. Create sample of lai_pot, harv_idx, tmp_base, bm_e parameters with LHS","title":"Soft-Cal Crop Yields","text":"use lhs package create sample parameter values selected crops. sample used run SWAT+ simulations evaluate impact parameter changes model output.","code":"## Make sure your updates will not produce unrealistic values (i.e. negative values)!!! par_bnd <- tibble('lai_pot.pdb | change = relchg' = c(-0.3, 0.3),                   'harv_idx.pdb | change = relchg' = c(-0.3, 0.3),                   'tmp_base.pdb | change = relchg' = c(-0.3, 0.3),                   'bm_e.pdb | change = relchg' = c(-0.3, 0.1))  par_crop <- sample_lhs(par_bnd, 10)"},{"path":"/articles/soft-cal.html","id":"step10","dir":"Articles","previous_headings":"","what":"10. Run SWATrunR for prepared parameter set","title":"Soft-Cal Crop Yields","text":"","code":"ylds_plnt_par <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops)),                               parameter = par_crop,                               n_thread = cores) saveRDS(ylds_plnt_par, paste0(sc_res, \"/ylds_plnt_par3.rds\"))"},{"path":"/articles/soft-cal.html","id":"step11","dir":"Articles","previous_headings":"","what":"11. Examine results in figures","title":"Soft-Cal Crop Yields","text":"Plotting simulation results dotty plots can help identify parameter sensitivities modify . examining patterns dotty plots, may consider adjusting certain parameter ranges (step 9) rerunning model (step 10) observe changes results. Subsequently, can reanalyze outcomes (step 11) gain insights refine understanding system modeled.","code":"## Plot dotty figures for the selected crops plot_dotty_yields(ylds_plnt_par, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step1","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Crop Yields","text":"SWATtunR package essential soft calibration, provides necessary functions calibration process. Additional packages required data manipulation, visualization, SWAT+ model runs, etc.","code":"## Required libraries to run workflow library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/sc-crops.html","id":"scc_step2","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Crop Yields","text":"step requires defining SWAT+ model path, path crop data file. crop yield soft calibration, ’s essential accurate data observed crop yields dry weight. data typically sourced '*.csv' file, columns specifying plant names corresponding mean yields. additional information accessible, minimum maximum ranges average annual observed yields, ’s advisable include '*.csv' file well, columns labeled yield_min yield_max respectively. ensures comprehensive dataset effective calibration analysis. Crops observed yields data example provided .","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Path to the crop data file crop_data_path <- '../inst/extdata/crop2.csv'  # Set the path to save results of the soft calibration sc_res <- '../test/simulations'  # Set the number of cores available for calculations.   # Number of cores for 12 runs use 3, 4, 6, or 12 cores (if available) cores <- 3 ## crops_obs <- read_csv(crop_data_path, show_col_types = FALSE) %>%    filter(!is.na(yield_mean))  head(crops_obs, 3) ## # A tibble: 3 × 4 ##   plant_name yield_min yield_max yield_mean ##   <chr>          <dbl>     <dbl>      <dbl> ## 1 akgs            8         12         10   ## 2 csil            7.34      13.5       11.2 ## 3 sgbt           11.0       16.9       14.0"},{"path":"/articles/sc-crops.html","id":"scc_step3","dir":"Articles","previous_headings":"","what":"3. Days to maturity parameter changes","title":"Crop Yields","text":"settings following step allows define, days maturity changes applied soft-calibration.","code":""},{"path":"/articles/sc-crops.html","id":"scc_step31","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.1. Initialization","title":"Crop Yields","text":"preparation step requires conversion observed yields information numeric vectors initialization 'plants.plt' file.","code":"# Convert observed yields to numeric vectors for(i in c(\"yield_mean\", \"yield_min\", \"yield_max\")){   if(i %in% colnames(crops_obs)){     assign(i, deframe(select(crops_obs, all_of(c(\"plant_name\", i)))))    } else {     assign(i, NULL)   } }  ## Initialize unmodified backup version of plants.plt if(!file.exists(paste0(model_path, '/plants.plt.bkp0'))) {   copy_file_version(model_path, 'plants.plt', file_version = 0) }"},{"path":"/articles/sc-crops.html","id":"scc_step32","dir":"Articles","previous_headings":"3. Days to maturity parameter changes","what":"3.2. Days to maturity changes","title":"Crop Yields","text":"following code generates parameter input table changes required SWAT+ model run. names converted SWATrunR syntax days maturity parameter. code snippet also samples changes days maturity, allowing users define crops used soft calibration initial values days maturity.","code":"# Reading the plants.plt input file from the initial unchanged backup file plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt.bkp0')) plants_plt <- select(plants_plt, - any_of('description'))  # Define all crops which should be calibrated # Alternatively define a name vector (if you also want to consider crops  # which are not given in the observation input file). crops <- crops_obs$plant_name # crops <- c('crop1', 'crop2', 'crop3')  # Get a vector with days_mat initial values for the selected crops dmat_init <- plants_plt %>%   filter(name %in% crops) %>%    select(name, days_mat) %>%   mutate(days_mat = ifelse(days_mat == 0, 110, days_mat)) %>%    ## if days_mat is 0, set it to 110 (as it is the default value)   deframe()  # Sample changes for days to maturity. Depending on the number of cores you have  # available choose a reasonable interval for the days to maturity which you want  # to test. With an interval of 10 e.g. you have to do 12 simulations (3 rounds  # on 4 cores), with an interval of 5 its 23 simulations. dmat_step <- 20 dmat_chg <- round(seq(-30, 100, dmat_step))  # Generate the parameter input table with the changes for all crops and convert  # the names into SWATrunR syntax par_dmat <- map_df(dmat_init, ~ .x + dmat_chg) %>%    set_names(., paste0('dmat_', names(.),                       '::days_mat.pdb | change = absval | name = ' , names(.)))"},{"path":"/articles/sc-crops.html","id":"scc_step4","dir":"Articles","previous_headings":"","what":"4. Run simulations","title":"Crop Yields","text":"Days maturity parameter changes applied SWAT+ model, simulations run analyze PHU fractions, yields biomass selected crops. SWATrunR package used run simulations.","code":"ylds_phu_dmat <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)                               ),                               parameter = par_dmat,                               start_date = '2015-01-01',                               end_date = '2020-12-31',                               years_skip = 2,                               n_thread = cores)  # Optionally save the simulation runs. if(!dir.exists(sc_res)) dir.create(sc_res) saveRDS(ylds_phu_dmat, paste0(sc_res, \"/ylds_phu_mat.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step5","dir":"Articles","previous_headings":"","what":"5. Plot PHU fractions, yields, and biomass for days to maturity changes","title":"Crop Yields","text":"figure, visualize PHU fractions, yields, biomass various days maturity settings. graphical representation serves reference adjust initial values days_mat crop simulation. grain crops, typically dry harvest, aim PHU fractions ranging approximately 1.2 1.5 optimize yield. Vegetables, hand, tend PHU fraction around 1, possibly slightly , considered optimal. Crops like basil broccoli harvested reaching full maturity. cases, PHU fractions can lower 1, ranging 0.5 0.9. Furthermore, ’s crucial ensure simulated yields fall within range locally observed yields maintain accuracy relevance.","code":"plot_phu_yld_bms(ylds_phu_dmat, dmat_chg, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step6","dir":"Articles","previous_headings":"","what":"6. Select days to maturity parameter changes to apply","title":"Crop Yields","text":"Based figure provided, identify necessary adjustments days maturity parameter SWAT+ model. adjustments made ensure PHU fractions, yields, biomass values specified crops align observed data.","code":"# Add values based on figure to this line (please add all crops from the initial selection) # names(dmat_init) # Print all crop names chg_dmat_sel <- c(akgs = -30, csil = 10, sgbt =  70,                    wbar =   -10, wira = -10, wiry =  0, wwht =  -30)   # Adding defined changes to initial days_mat values of crops dmat_sel <- chg_dmat_sel[names(dmat_init)] + dmat_init dmat_sel <- enframe(dmat_sel, value = 'days_mat_upd')"},{"path":"/articles/sc-crops.html","id":"scc_step7","dir":"Articles","previous_headings":"","what":"7. Write d_mat modifications into file","title":"Crop Yields","text":"Write changes plants.plt file update days maturity values selected crops also backup updated file plants.plt.bkp1 file.","code":"# Update the days_mat values in plants.plt according to the changes defined above. plants_plt <- plants_plt %>%   left_join(., dmat_sel, by = 'name') %>%   mutate(days_mat = ifelse(!is.na(days_mat_upd), days_mat_upd, days_mat)) %>%   select(-days_mat_upd)  ## Overwriting original plants.plt with the updated days_mat values. plants_plt_fmt <- c('%-12s', '%-18s', '%-12s', rep('%12.5f', ncol(plants_plt) - 3)) write_tbl(plants_plt, paste0(model_path, '/plants.plt'), fmt = plants_plt_fmt)  # Create a backup file with the changed days_mat values copy_file_version(model_path, 'plants.plt', file_version = 1) ## [1] TRUE"},{"path":"/articles/sc-crops.html","id":"scc_step8","dir":"Articles","previous_headings":"","what":"8. Check initial crop lai_pot, harv_idx, tmp_base, bm_e parameters","title":"Crop Yields","text":"fixing days maturity values, might needed address values lai_pot, harv_idx, tmp_base, bm_e parameters selected crops. parameters crucial simulation adjusted PHU fractions, yields, biomass values within expected range.","code":"plants_plt <- read_tbl(file_path = paste0(model_path, '/plants.plt'))  par_ini <- plants_plt %>%   filter(name %in% crops) %>%   select(name, lai_pot, harv_idx, tmp_base, bm_e)#, days_mat) par_ini ## # A tibble: 7 × 5 ##   name  lai_pot harv_idx tmp_base  bm_e ##   <chr>   <dbl>    <dbl>    <dbl> <dbl> ## 1 csil      4       0.9         8  39   ## 2 sgbt      5       2           4  30   ## 3 wbar      4       0.54        0  30   ## 4 wwht      4       0.4         0  30   ## 5 wira      3.5     0.23        5  38   ## 6 wiry      4       0.4         0  30   ## 7 akgs      4       0.75        0  12.5"},{"path":"/articles/sc-crops.html","id":"scc_step9","dir":"Articles","previous_headings":"","what":"9. Create sample of lai_pot, harv_idx, tmp_base, bm_e parameters with LHS","title":"Crop Yields","text":"use sample_lhs function create sample parameter values selected crops. sample used run SWAT+ simulations evaluate impact parameter changes model output. syntax parameter boundaries found SWATrunR page.","code":"## Define changes to be applied to the initial parameter values ## Make sure your updates will not produce unrealistic values (i.e. negative values)!!! par_bnd <- tibble('lai_pot.pdb | change = relchg' = c(-0.3, 0.3),                   'harv_idx.pdb | change = relchg' = c(-0.3, 0.3),                   'tmp_base.pdb | change = relchg' = c(-0.3, 0.3),                   # 'tmp_base.pdb | change = abschg' = c(-2, 2),                   'bm_e.pdb | change = relchg' = c(-0.3, 0.1))  par_crop <- sample_lhs(par_bnd, 10) ## 10 samples for each parameter will be generated.  ## The number of samples can be adjusted based on the available computational resources. ## Recommended number of samples is 50-100."},{"path":"/articles/sc-crops.html","id":"scc_step10","dir":"Articles","previous_headings":"","what":"10. Run SWATrunR for prepared parameter set","title":"Crop Yields","text":"Run SWAT+ model updated parameters selected crops rerun. simulation results used evaluate impact parameter changes model output.","code":"ylds_plnt_par <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops)),                               parameter = par_crop,                               n_thread = cores)  ## Save the results to the file saveRDS(ylds_plnt_par, paste0(sc_res, \"/ylds_plnt_par.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step11","dir":"Articles","previous_headings":"","what":"11. Examine results in figures","title":"Crop Yields","text":"Plotting simulation results dotty plots can help identify parameter sensitivities modify . examining patterns dotty plots, may consider adjusting certain parameter ranges (step 9) rerunning model (step 10) observe changes results. Subsequently, can reanalyze outcomes plot_dotty_yields function gain insights refine understanding system modeled.","code":"## Plot dotty figures for the selected crops plot_dotty_yields(ylds_plnt_par, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-crops.html","id":"scc_step12","dir":"Articles","previous_headings":"","what":"12. Update parameter values in plants.plt file","title":"Crop Yields","text":"examining results SWAT+ simulations, can adjust parameter values plants.plt file. parameters need changed, sensitive might help improve model performance. Different crops exhibit different sensitivities parameters, important select parameters crop. Following code sniplet shows update plants.plt file.","code":"## Fix changes you want to write in plants.plt file chg_par <- tibble(   name     = c(\"akgs\",\"barl\", \"csil\", \"sgbt\", \"wbar\", \"wira\", \"wiry\", \"wwht\"),   lai_pot  = c(    0,     0,      0,      0,      0,      0,      0,      0),   harv_idx = c(    0,     0,      0,      0,      0,      0,    0.3,    0.3),   tmp_base = c(    0,     0,      0,      0,      0,      0,   -0.2,   -0.2),   bm_e     = c(    0,     0,      0,      0,      0,      0,      0,      0)) %>%   left_join(select(plants_plt, name), ., by = 'name')  ## Update parameter values in plants.plt for (i in 1:ncol(par_bnd)) {   par_i <- names(chg_par)[i + 1]   chg_typ_i <- sub(\".*change = \", \"\", names(par_bnd)[i])   plants_plt[par_i] <- update_par(plants_plt[[par_i]], chg_par[[par_i]], chg_typ_i) }  ## Overwriting plants.plt with the updated parameter values. write_tbl(plants_plt, paste0(model_path, '/plants.plt'), fmt = plants_plt_fmt)"},{"path":"/articles/sc-crops.html","id":"scc_step13","dir":"Articles","previous_headings":"","what":"13. Rerun final plants.plt parameter selection","title":"Crop Yields","text":"updating plants.plt file new parameter values, can rerun SWAT+ model evaluate impact parameter changes model output. simulation results provide model, soft calibrated selected crops.","code":"phu_yld_final <- run_swatplus(project_path = model_path,                               output = list(yld = define_output(file = 'mgtout',                                                                 variable = 'yld',                                                                 unit = crops),                                             bms = define_output(file = 'mgtout',                                                                 variable = 'bioms',                                                                 unit = crops),                                             phu = define_output(file = 'mgtout',                                                                 variable = 'phu',                                                                 unit = crops)))  ## Save the results to the file saveRDS(phu_yld_final, paste0(sc_res, \"/phu_yld_final.rds\"))"},{"path":"/articles/sc-crops.html","id":"scc_step14","dir":"Articles","previous_headings":"","what":"14. Examine the final results","title":"Crop Yields","text":"Egamine final results SWAT+ simulations. simulation results provide model, soft calibrated selected crops. -depth analysis, users can employ additional SWATdoctR functions, like plot_hru_pw_day(). function enables visualization daily time series variables output file hru_pw_day.txt related hydrological response units , providing valuable insights model’s performance behavior. might help understanding model’s outputs decide crop yield soft calibration results acceptable. completing soft calibration process crops proceed soft calibration water yield presented another page.","code":"plot_phu_yld_bms(phu_yld_final, 0, yield_mean, yield_min, yield_max)"},{"path":"/articles/sc-wy.html","id":"scw_step1","dir":"Articles","previous_headings":"","what":"1. Loading required packages","title":"Water Yield","text":"yet loaded crop yields soft calibration, please load following libraries.","code":"## Required libraries to run workflow library(SWATtunR) library(SWATrunR) library(tidyverse) library(tibble) library(purrr)"},{"path":"/articles/sc-wy.html","id":"scw_step2","dir":"Articles","previous_headings":"","what":"2. Defining settings","title":"Water Yield","text":"step requires defining SWAT+ model path observed water yield precipitation ratio.","code":"# Path to the SWAT+ model model_path <- '../test/my_dearest_model'  # Set the path to save results of the soft calibration sc_res <- '../test/simulations'  # Observed water yield to precipitation ratio obs_wy_ratio <- 0.27  # Set the number of cores available for calculations.   # Number of cores for 12 runs use 3, 4, 6, or 12 cores (if available) cores <- 3"},{"path":"/articles/sc-wy.html","id":"scw_step3","dir":"Articles","previous_headings":"","what":"3. Defining esco parameter range and running model","title":"Water Yield","text":"soil evaporation compensation factor (esco) important coefficient modeling soil moisture dynamics. allows users adjust depth distribution used satisfy soil evaporative demand, accounting factors capillary action, crusting, cracks. increasing esco value, model can draw evaporative demand deeper soil layers. means model reduced amount water available water yield. esco values range 0.01 1.","code":"# The esco parameter range is sampled. esco <- tibble('esco.hru | change = absval' = seq(0.05,0.95, length.out = max(cores, 4)))  sim_esco <- run_swatplus(project_path = model_path,                          output = list(precip  =  define_output('basin_wb_day',                                                                  'precip',                                                                  1),                                        surq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_cha',                                                                 unit = 1),                                        surq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_res',                                                                 unit = 1),                                        latq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_cha',                                                                 unit = 1),                                        latq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_res',                                                                 unit = 1),                                        qtile =    define_output(file = 'basin_wb_day',                                                                 variable = 'qtile',                                                                 unit = 1),                                        flo =      define_output(file = 'basin_aqu_day',                                                                 variable = 'flo',                                                                 unit = 1)                          ),                          parameter = esco,                          n_thread = cores) ## Save the results to the file saveRDS(sim_esco, paste0(sc_res, \"/sim_esco.rds\"))"},{"path":"/articles/sc-wy.html","id":"scw_step4","dir":"Articles","previous_headings":"","what":"4. Extracting and plotting water yield ratio vs esco parameter values","title":"Water Yield","text":"water yield ratio calculated simulation. range esco values produce water yield ratios within specified range observed water yield ratio identified using plot_esco_range function.","code":"plot_esco_range(sim_esco, obs_wy_ratio)"},{"path":"/articles/sc-wy.html","id":"scw_step5","dir":"Articles","previous_headings":"","what":"5. (Optional) If only esco is not enough, use esco, epco parameters for calibration together","title":"Water Yield","text":"certain situations esco parameter might enough reach observed water yield ratio. Addition plant uptake compensation factor (epco) might help cases. parameter determines water uptake distributed across soil layers meet plant transpiration needs. upper soil layers lack sufficient water, model can draw water deeper layers, process governed epco value. epco close 1.0, greater flexibility, allowing significant compensation lower soil layers. Conversely, epc near 0.0, model restricts water uptake primarily original depth distribution, limiting compensation deeper layers.","code":"# The esco and epco parameter range is defined . par_bnd <- tibble('esco.hru | change = absval' = c(0.05, 0.95),                   'epco.hru | change = absval' = c(0.05, 0.95))  # And sampled with lhs  esco_epco <- sample_lhs(par_bnd, 12)   ##Run simulations for defined parameter sets sim_esco_epco <- run_swatplus(project_path = model_path,                          output = list(precip  =  define_output('basin_wb_day',                                                                  'precip',                                                                  1),                                        surq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_cha',                                                                 unit = 1),                                        surq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'surq_res',                                                                 unit = 1),                                        latq_cha = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_cha',                                                                 unit = 1),                                        latq_res = define_output(file = 'basin_wb_day',                                                                 variable = 'latq_res',                                                                 unit = 1),                                        qtile =    define_output(file = 'basin_wb_day',                                                                 variable = 'qtile',                                                                 unit = 1),                                        flo =      define_output(file = 'basin_aqu_day',                                                                 variable = 'flo',                                                                 unit = 1)                          ),                          parameter = esco_epco,                          n_thread = cores)  ## Save the results to the file saveRDS(sim_esco, paste0(sc_res, \"/sim_esco_epco.rds\"))"},{"path":"/articles/sc-wy.html","id":"scw_step6","dir":"Articles","previous_headings":"","what":"6. Updating parameter values in the hydrology.hyd file with selected values","title":"Water Yield","text":"determining model parameter values allow simulated water yield ratio match observed values, parameters need updated hydrology.hyd file. Following code snippet backs existing file updates values .","code":"## Initialize unmodified backup version of hydrology.hyd if(!file.exists(paste0(model_path, '/hydrology.hyd.bkp0'))) {   copy_file_version(model_path, 'hydrology.hyd', file_version = 0) }  # Read the hydrology.hyd input file hydrology_hyd <- read_tbl(paste0(model_path, '/hydrology.hyd.bkp0'))  hydrology_hyd$esco <- 0.39 ## If needed update epco as well ## hydrology_hyd$epco <- some value  ## Update hydrology.hyd file write_tbl(hydrology_hyd, paste0(model_path, '/hydrology.hyd'), c('%-16s', rep('%12.5f', 14)))"},{"path":"/articles/sc-wy.html","id":"final-recheck-for-yield-results","dir":"Articles","previous_headings":"","what":"7. Final recheck for yield results","title":"Water Yield","text":"Updating parameters hydrology.hyd file might impact crop yield simulation. ensure water yield soft calibration adversely affected crop yield soft calibration, important recheck end. results match observed yields, soft calibration complete, can celebrate. Otherwise, consider revisiting crop yield soft calibration steps.","code":"## Rerun model for crop yields results phu_yld_recheck <- run_swatplus(project_path = model_path,                           output = list(yld = define_output(file = 'mgtout',                                                             variable = 'yld',                                                             unit = crops),                                         bms = define_output(file = 'mgtout',                                                             variable = 'bioms',                                                             unit = crops),                                         phu = define_output(file = 'mgtout',                                                             variable = 'phu',                                                             unit = crops))) ## Save the results to the file saveRDS(phu_yld_recheck, paste0(sc_res, \"/phu_yld_recheck.rds\"))  ## Plot yields  plot_phu_yld_bms(phu_yld_recheck, 0, yield_mean, yield_min, yield_max)"}]
diff --git a/vignettes/sc-wy.Rmd b/vignettes/sc-wy.Rmd
index a4a44c2..d0e5fee 100644
--- a/vignettes/sc-wy.Rmd
+++ b/vignettes/sc-wy.Rmd
@@ -45,7 +45,7 @@ The soil evaporation compensation factor (**esco**) is an important coefficient
 
 
 
-```{r run_dmat, message = FALSE, warning = FALSE, eval = FALSE}
+```{r run_esco, message = FALSE, warning = FALSE, eval = FALSE}
 # The esco parameter range is sampled.
 esco <- tibble('esco.hru | change = absval' = seq(0.05,0.95, length.out = max(cores, 4)))
 
@@ -79,7 +79,7 @@ saveRDS(sim_esco, paste0(sc_res, "/sim_esco.rds"))
 ```
 ## 4. Extracting and plotting water yield ratio vs esco parameter values {#scw_step4}
 
-The water yield ratio is calculated for each simulation. The range of esco values that produce water yield ratios within a specified range of the observed water yield ratio is identified using the [plot_esco_range](../reference/plot_esco_range.html) function. 
+The water yield ratio is calculated for each simulation. The range of **esco** values that produce water yield ratios within a specified range of the observed water yield ratio is identified using the [plot_esco_range](../reference/plot_esco_range.html) function. 
 
 ```{r wy_ratio_f, message = FALSE,  warning = FALSE, eval = FALSE}
 plot_esco_range(sim_esco, obs_wy_ratio)
@@ -93,3 +93,92 @@ plot_esco_range(sim_esco, obs_wy_ratio)
 knitr::include_graphics('figs/sim_esco.png')
 ```
 
+## 5. (Optional) If only esco is not enough, use esco, epco parameters for calibration together {#scw_step5}
+
+In certain situations **esco** parameter might not be enough to reach observed water yield ratio. Addition of the plant uptake compensation factor (**epco**) might help in such cases. This parameter determines how water uptake is distributed across soil layers to meet plant transpiration needs. If the upper soil layers lack sufficient water, the model can draw more water from deeper layers, a process governed by the **epco** value. When **epco** is close to 1.0, there is greater flexibility, allowing significant compensation from lower soil layers. Conversely, when **epc** is near 0.0, the model restricts water uptake primarily to the original depth distribution, limiting compensation from deeper layers.
+
+```{r run_esco_epco, message = FALSE, warning = FALSE, eval = FALSE}
+# The esco and epco parameter range is defined .
+par_bnd <- tibble('esco.hru | change = absval' = c(0.05, 0.95),
+                  'epco.hru | change = absval' = c(0.05, 0.95))
+
+# And sampled with lhs 
+esco_epco <- sample_lhs(par_bnd, 12) 
+
+##Run simulations for defined parameter sets
+sim_esco_epco <- run_swatplus(project_path = model_path,
+                         output = list(precip  =  define_output('basin_wb_day', 
+                                                                'precip', 
+                                                                1),
+                                       surq_cha = define_output(file = 'basin_wb_day',
+                                                                variable = 'surq_cha',
+                                                                unit = 1),
+                                       surq_res = define_output(file = 'basin_wb_day',
+                                                                variable = 'surq_res',
+                                                                unit = 1),
+                                       latq_cha = define_output(file = 'basin_wb_day',
+                                                                variable = 'latq_cha',
+                                                                unit = 1),
+                                       latq_res = define_output(file = 'basin_wb_day',
+                                                                variable = 'latq_res',
+                                                                unit = 1),
+                                       qtile =    define_output(file = 'basin_wb_day',
+                                                                variable = 'qtile',
+                                                                unit = 1),
+                                       flo =      define_output(file = 'basin_aqu_day',
+                                                                variable = 'flo',
+                                                                unit = 1)
+                         ),
+                         parameter = esco_epco,
+                         n_thread = cores)
+
+## Save the results to the file
+saveRDS(sim_esco, paste0(sc_res, "/sim_esco_epco.rds"))
+```
+
+## 6. Updating parameter values in the `hydrology.hyd` file with selected values {#scw_step6}
+
+After determining which model parameter values allow the simulated water yield ratio to match the observed values, these parameters need to be updated in the `hydrology.hyd` file. Following code snippet backs up existing file and updates values in it. 
+
+```{r update_p, message = FALSE, warning = FALSE, eval = FALSE}
+
+## Initialize unmodified backup version of hydrology.hyd
+if(!file.exists(paste0(model_path, '/hydrology.hyd.bkp0'))) {
+  copy_file_version(model_path, 'hydrology.hyd', file_version = 0)
+}
+
+# Read the hydrology.hyd input file
+hydrology_hyd <- read_tbl(paste0(model_path, '/hydrology.hyd.bkp0'))
+
+hydrology_hyd$esco <- 0.39
+## If needed update epco as well
+## hydrology_hyd$epco <- some value
+
+## Update hydrology.hyd file
+write_tbl(hydrology_hyd, paste0(model_path, '/hydrology.hyd'), c('%-16s', rep('%12.5f', 14)))
+
+```
+
+## 7. Final recheck for yield results
+
+Updating parameters in the hydrology.hyd file might impact crop yield simulation. To ensure that the water yield soft calibration has not adversely affected the crop yield soft calibration, it is important to recheck it at the end. If the results match the observed yields, the soft calibration is complete, and you can celebrate. Otherwise, you should consider revisiting the [crop yield soft calibration](../articles/sc-cy.html) steps.
+
+```{r recheck, message = FALSE, warning = FALSE, eval = FALSE}
+## Rerun model for crop yields results
+phu_yld_recheck <- run_swatplus(project_path = model_path,
+                          output = list(yld = define_output(file = 'mgtout',
+                                                            variable = 'yld',
+                                                            unit = crops),
+                                        bms = define_output(file = 'mgtout',
+                                                            variable = 'bioms',
+                                                            unit = crops),
+                                        phu = define_output(file = 'mgtout',
+                                                            variable = 'phu',
+                                                            unit = crops)))
+## Save the results to the file
+saveRDS(phu_yld_recheck, paste0(sc_res, "/phu_yld_recheck.rds"))
+
+## Plot yields 
+plot_phu_yld_bms(phu_yld_recheck, 0, yield_mean, yield_min, yield_max)
+```
+