From 9059dd171f0b620b6fdc9d5f3d5162ce5247d33c Mon Sep 17 00:00:00 2001
From: Nils Kehrein <nils.kehrein@gmail.com>
Date: Fri, 22 Nov 2024 13:57:34 +0100
Subject: [PATCH] readme updated
---
NEWS.md | 2 +
R/plot.R | 1 +
README.Rmd | 31 ++++++------
README.md | 57 +++++++++++++----------
doc/figures/readme-unnamed-chunk-5-1.png | Bin 0 -> 6256 bytes
doc/figures/readme-unnamed-chunk-6-1.png | Bin 4334 -> 6480 bytes
man/plot.Rd | 3 ++
vignettes/cvasi-1-manual.Rmd | 2 +-
vignettes/cvasi-2-howto.Rmd | 2 +-
9 files changed, 59 insertions(+), 39 deletions(-)
create mode 100644 doc/figures/readme-unnamed-chunk-5-1.png
diff --git a/NEWS.md b/NEWS.md
index a349ecf..9bd2eee 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
# cvasi Development version
+# cvasi 1.3.1
+
* Improved `import_toxswa()`: now supports scaling of imported time series,
importing selected *TOXSWA* output variables, as well as importing selected
substance concentrations
diff --git a/R/plot.R b/R/plot.R
index 642889f..373f12e 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -7,6 +7,7 @@
#' @param x object to plot
#' @param y unused parameter
#' @param ... unused parameters
+#' @return *ggplot2* plot object
NULL
# S3 overload to plot dose response curves
diff --git a/README.Rmd b/README.Rmd
index d350ee1..691e498 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -9,6 +9,8 @@ knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "doc/figures/readme-",
+ fig.height=4,
+ fig.align='center',
out.width = "100%"
)
@@ -18,8 +20,8 @@ library(cvasi)
# cvasi: Calibration, Validation, and Simulation of TKTD models in R
<!-- badges: start -->
-<!--[](https://cran.r-project.org/package=cvasi)-->
-<!--[](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml)-->
+[](https://cran.r-project.org/package=cvasi)
+[](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml)
<!--[](https://app.codecov.io/gh/xy/cvasi?branch=main)-->
<!-- badges: end -->
@@ -38,7 +40,7 @@ The package provides facilities to
* import fitted parameters from *morse*
* and more
-A graphical user interface implemented in [Shiny](https://www.rstudio.com/products/shiny/)
+A graphical user interface implemented in [Shiny](https://posit.co/products/open-source/rstudio/)
is also available, see the *[cvasi.ui](https://github.com/cvasi-tktd/cvasi.ui/)*
package. Please have a look at the [Changelog](NEWS.md)
for an overview of user-facing updates and changes.
@@ -68,8 +70,8 @@ on your machine. *Rtools* are required to compile the package's C code.
The package contains the following vignettes
-* [User Manual](doc/cvasi-1-manual.md)
-* [Modeling Howto](doc/cvasi-2-howto.md)
+* [User Manual](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-1-manual.md)
+* [Modeling Howto](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-2-howto.md)
They can also be accessed locally by executing an *R* statement such as:
```{r, eval=FALSE}
@@ -80,23 +82,26 @@ vignette("cvasi-1-manual", package="cvasi")
## Usage
Basic usage:
-```{r,message=FALSE}
+```{r,message=FALSE,out.width="70%"}
library(cvasi)
# create and parameterize a GUTS-RED-IT scenario
GUTS_RED_IT() %>%
set_param(c(kd=0.0005, hb=0, alpha=0.4, beta=1.5)) %>%
set_exposure(data.frame(time=c(0, 100, 101, 200, 201, 400),
- conc=c(0, 0, 0.1, 0.1, 0, 0))) -> scenario
+ conc=c(0, 0, 0.1, 0.1, 0, 0))) %>%
+ set_times(1:400) -> scenario
# simulate scenario
-scenario %>%
- simulate(times=1:400) %>%
- tail()
+results <- scenario %>% simulate()
+tail(results)
+
+# ... and plot simulation results
+plot(results)
```
Calculation of effects:
-```{r out.width="50%",warning=FALSE}
+```{r out.width="60%",warning=FALSE}
# calculate effect level
scenario %>% effect()
@@ -105,8 +110,8 @@ scenario %>% dose_response() -> drc
head(drc)
# plot the dose-response curve
-library(ggplot2)
-ggplot(drc) + geom_point(aes(mf,effect)) + scale_x_log10()
+plot(drc)
+
# derive EPx values
scenario %>% epx()
```
diff --git a/README.md b/README.md
index 18dda65..0a49224 100644
--- a/README.md
+++ b/README.md
@@ -4,8 +4,10 @@
# cvasi: Calibration, Validation, and Simulation of TKTD models in R
<!-- badges: start -->
-<!--[](https://cran.r-project.org/package=cvasi)-->
-<!--[](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml)-->
+
+[](https://cran.r-project.org/package=cvasi)
+[](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml)
<!--[](https://app.codecov.io/gh/xy/cvasi?branch=main)-->
<!-- badges: end -->
@@ -26,10 +28,10 @@ The package provides facilities to
- and more
A graphical user interface implemented in
-[Shiny](https://www.rstudio.com/products/shiny/) is also available, see
-the *[cvasi.ui](https://github.com/cvasi-tktd/cvasi.ui/)* package.
-Please have a look at the [Changelog](NEWS.md) for an overview of
-user-facing updates and changes.
+[Shiny](https://posit.co/products/open-source/rstudio/) is also
+available, see the *[cvasi.ui](https://github.com/cvasi-tktd/cvasi.ui/)*
+package. Please have a look at the [Changelog](NEWS.md) for an overview
+of user-facing updates and changes.
## Installation
@@ -55,8 +57,10 @@ your machine. *Rtools* are required to compile the package’s C code.
The package contains the following vignettes
-- [User Manual](doc/cvasi-1-manual.md)
-- [Modeling Howto](doc/cvasi-2-howto.md)
+- [User
+ Manual](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-1-manual.md)
+- [Modeling
+ Howto](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-2-howto.md)
They can also be accessed locally by executing an *R* statement such as:
@@ -75,12 +79,12 @@ library(cvasi)
GUTS_RED_IT() %>%
set_param(c(kd=0.0005, hb=0, alpha=0.4, beta=1.5)) %>%
set_exposure(data.frame(time=c(0, 100, 101, 200, 201, 400),
- conc=c(0, 0, 0.1, 0.1, 0, 0))) -> scenario
+ conc=c(0, 0, 0.1, 0.1, 0, 0))) %>%
+ set_times(1:400) -> scenario
# simulate scenario
-scenario %>%
- simulate(times=1:400) %>%
- tail()
+results <- scenario %>% simulate()
+tail(results)
#> time D H S
#> 395 395 0.004429420 0 0.998655
#> 396 396 0.004427206 0 0.998655
@@ -88,40 +92,45 @@ scenario %>%
#> 398 398 0.004422781 0 0.998655
#> 399 399 0.004420570 0 0.998655
#> 400 400 0.004418360 0 0.998655
+
+# ... and plot simulation results
+plot(results)
```
+<img src="doc/figures/readme-unnamed-chunk-5-1.png" width="70%" style="display: block; margin: auto;" />
+
Calculation of effects:
``` r
# calculate effect level
scenario %>% effect()
-#> # A tibble: 1 × 4
+#> # A tibble: 1 x 4
#> scenario L L.dat.start L.dat.end
#> <list> <dbl> <dbl> <dbl>
-#> 1 <GutsRdIt> 0.00135 0 400
+#> 1 <GutsRdIt> 0.00135 1 400
# create a dose-response curve
scenario %>% dose_response() -> drc
head(drc)
#> endpoint mf effect
-#> 1 L 3.812500 0.009920108
-#> 2 L 4.799653 0.013948570
-#> 3 L 6.042405 0.019601514
-#> 4 L 7.606938 0.027459506
-#> 5 L 9.576567 0.038355140
-#> 6 L 12.056184 0.053336114
+#> 1 L 3.812500 0.009915394
+#> 2 L 4.799653 0.013954569
+#> 3 L 6.042405 0.019597765
+#> 4 L 7.606938 0.027459877
+#> 5 L 9.576567 0.038357524
+#> 6 L 12.056184 0.053336214
# plot the dose-response curve
-library(ggplot2)
-ggplot(drc) + geom_point(aes(mf,effect)) + scale_x_log10()
+plot(drc)
```
-<img src="doc/figures/readme-unnamed-chunk-6-1.png" width="50%" />
+<img src="doc/figures/readme-unnamed-chunk-6-1.png" width="60%" style="display: block; margin: auto;" />
``` r
+
# derive EPx values
scenario %>% epx()
-#> # A tibble: 1 × 3
+#> # A tibble: 1 x 3
#> scenario L.EP10 L.EP50
#> <list> <dbl> <dbl>
#> 1 <GutsRdIt> 19.0 82.1
diff --git a/doc/figures/readme-unnamed-chunk-5-1.png b/doc/figures/readme-unnamed-chunk-5-1.png
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diff --git a/man/plot.Rd b/man/plot.Rd
index 959e748..8e9a7a3 100644
--- a/man/plot.Rd
+++ b/man/plot.Rd
@@ -20,6 +20,9 @@ a log10-scaled axis, \code{none} for no scaling, and \code{auto} for automatic s
\item{...}{unused parameters}
}
+\value{
+\emph{ggplot2} plot object
+}
\description{
These functions overload \code{\link[base:plot]{base::plot()}} to provide simple plotting
routines to display various time-series and scenario objects.
diff --git a/vignettes/cvasi-1-manual.Rmd b/vignettes/cvasi-1-manual.Rmd
index e2e7590..42edc7e 100644
--- a/vignettes/cvasi-1-manual.Rmd
+++ b/vignettes/cvasi-1-manual.Rmd
@@ -1,7 +1,7 @@
---
title: "User Manual"
author: "N. Kehrein"
-date: "24 Octobre, 2024"
+date: "24 October, 2024"
output:
rmarkdown::html_vignette:
toc: true
diff --git a/vignettes/cvasi-2-howto.Rmd b/vignettes/cvasi-2-howto.Rmd
index 98adff4..430d65e 100644
--- a/vignettes/cvasi-2-howto.Rmd
+++ b/vignettes/cvasi-2-howto.Rmd
@@ -1,7 +1,7 @@
---
title: "Modeling Howto"
author: "N. Kehrein and contributors"
-date: "24 Octobre, 2024"
+date: "24 October, 2024"
output:
rmarkdown::html_vignette:
toc: true