From 543f81b6e4912c37a6a25196f56864032c2238a9 Mon Sep 17 00:00:00 2001 From: andrewhooker Date: Mon, 7 Oct 2024 07:14:46 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20andrewho?= =?UTF-8?q?oker/PopED@136c82f61f12f9e1ecf110bdbaf6c53307c4bfb4=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/examples.html | 8 ++++---- articles/handling_LOQ.html | 2 +- articles/intro-poped.html | 6 +++--- articles/model_def_other_pkgs.html | 6 +++--- pkgdown.yml | 2 +- reference/Doptim.html | 2 +- reference/Dtrace.html | 2 +- reference/LEDoptim.html | 2 +- reference/LinMatrixL.html | 2 +- reference/LinMatrixLH.html | 2 +- reference/LinMatrixL_occ.html | 2 +- reference/RS_opt.html | 2 +- reference/a_line_search.html | 4 ++-- reference/bfgsb_min.html | 2 +- reference/blockexp.html | 2 +- reference/blockfinal.html | 4 ++-- reference/blockheader.html | 2 +- reference/blockopt.html | 2 +- reference/build_sfg.html | 4 ++-- reference/calc_autofocus.html | 2 +- reference/calc_ofv_and_fim.html | 2 +- reference/calc_ofv_and_grad.html | 2 +- reference/create.poped.database.html | 2 +- reference/ed_laplace_ofv.html | 4 ++-- reference/ed_mftot.html | 2 +- reference/evaluate.e.ofv.fim.html | 4 ++-- reference/evaluate.fim.html | 2 +- reference/evaluate_design.html | 2 +- reference/evaluate_fim_map.html | 2 +- reference/feps.add.html | 2 +- reference/feps.add.prop.html | 2 +- reference/feps.prop.html | 2 +- reference/ff.PK.1.comp.oral.md.CL.html | 2 +- reference/ff.PK.1.comp.oral.md.KE.html | 2 +- reference/ff.PK.1.comp.oral.sd.CL.html | 2 +- reference/ff.PK.1.comp.oral.sd.KE.html | 2 +- reference/ff.PKPD.1.comp.oral.md.CL.imax.html | 4 ++-- reference/ff.PKPD.1.comp.sd.CL.emax.html | 2 +- reference/get_all_params.html | 2 +- reference/get_rse.html | 2 +- reference/gradf_eps.html | 2 +- reference/mfea.html | 2 +- reference/mftot.html | 2 +- reference/model_prediction.html | 2 +- reference/ofv_criterion.html | 2 +- reference/ofv_fim.html | 2 +- reference/optim_ARS.html | 10 +++++----- reference/optim_LS.html | 4 ++-- reference/pargen.html | 2 +- reference/plot_efficiency_of_windows.html | 2 +- reference/plot_model_prediction.html | 2 +- reference/poped_optim.html | 18 +++++++++--------- reference/poped_optimize.html | 10 +++++----- reference/shrinkage.html | 2 +- reference/summary.poped_optim.html | 10 +++++----- reference/tic.html | 2 +- reference/toc.html | 4 ++-- search.json | 2 +- 58 files changed, 93 insertions(+), 93 deletions(-) diff --git a/articles/examples.html b/articles/examples.html index 64e9a14..6ea527f 100644 --- a/articles/examples.html +++ b/articles/examples.html @@ -758,9 +758,9 @@

ODE solution of PK model, mult of describing the same model.

 tic(); eval <- evaluate_design(poped.db); toc()
-#> Elapsed time: 2.773 seconds.
+#> Elapsed time: 2.704 seconds.
 tic(); eval <- evaluate_design(poped.db.Rcpp); toc()
-#> Elapsed time: 1.179 seconds.
+#> Elapsed time: 1.18 seconds.

The difference is noticeable and gets larger for more complex ODE models.

@@ -1908,7 +1908,7 @@

#> 5.030673 2.983917 14.014958 29.787587 36.758952 26.753311 31.645011 #> SIGMA[2,2] #> 25.341368 -#> Elapsed time: 0.13 seconds. +#> Elapsed time: 0.128 seconds.

We can see that the result, based on MC sampling, is somewhat variable with so few samples.

@@ -1941,7 +1941,7 @@ 
#>   5.021700   2.980981  14.068646  29.765030  36.691675  26.754137  31.469425 
 #> SIGMA[2,2] 
 #>  25.311870
-#> Elapsed time: 0.13 seconds.
+#> Elapsed time: 0.127 seconds.

Design evaluation for a subset of model parameters of interest (Ds diff --git a/articles/handling_LOQ.html b/articles/handling_LOQ.html index c60bc45..64d14a6 100644 --- a/articles/handling_LOQ.html +++ b/articles/handling_LOQ.html @@ -283,7 +283,7 @@

LOQ handlingcat("D6 evaluation time: ",e_time_D6[1],"seconds \n" ) cat("D2 evaluation time: ",e_time_D2[1],"deconds \n" ) -#> D6 evaluation time: 0.045 seconds +#> D6 evaluation time: 0.047 seconds #> D2 evaluation time: 0.007 deconds

The D2 method is the same as removing the last design point, as you can se below.

diff --git a/articles/intro-poped.html b/articles/intro-poped.html index 897fb2b..4db39fd 100644 --- a/articles/intro-poped.html +++ b/articles/intro-poped.html @@ -432,7 +432,7 @@

Design optimization#> d_CL 0.0625 28 26 #> sig_prop 0.04 14 15 #> -#> Total running time: 16.684 seconds +#> Total running time: 16.663 seconds plot_model_prediction(output$poped.db)

We see that there are four distinct sample times for this design. @@ -493,7 +493,7 @@

Optimize over a discrete design s #> d_CL 0.0625 28 27 #> sig_prop 0.04 14 15 #> -#> Total running time: 10.179 seconds +#> Total running time: 10.195 seconds plot_model_prediction(output_discrete$poped.db, model_num_points = 300)

Here we see that the optimization ran somewhat quicker, but gave a @@ -558,7 +558,7 @@

Cost function to optimize dose#> d_CL 0.0625 28 28 #> sig_prop 0.04 14 14 #> -#> Total running time: 3.701 seconds +#> Total running time: 3.661 seconds

We see that the optimal doses are 31.6 and 55.2 for the two groups. This leads to population trough concentrations of 0.2 and 0.35 for the two groups of patients at 240 hours:

diff --git a/articles/model_def_other_pkgs.html b/articles/model_def_other_pkgs.html index b9ccf7f..00386b6 100644 --- a/articles/model_def_other_pkgs.html +++ b/articles/model_def_other_pkgs.html @@ -781,7 +781,7 @@

Version information#> collate C.UTF-8 #> ctype C.UTF-8 #> tz UTC -#> date 2024-10-04 +#> date 2024-10-07 #> pandoc 3.1.11 @ /opt/hostedtoolcache/pandoc/3.1.11/x64/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -838,7 +838,7 @@

Version information#> pkgdown 2.1.1 2024-09-17 [1] RSPM #> pkgload 1.4.0 2024-06-28 [1] RSPM #> PKPDsim * 1.4.0 2024-08-19 [1] RSPM -#> PopED * 0.6.0.9005 2024-10-04 [1] local +#> PopED * 0.6.0.9005 2024-10-07 [1] local #> PreciseSums 0.7 2024-09-17 [1] RSPM #> profvis 0.4.0 2024-09-20 [1] RSPM #> promises 1.3.0 2024-04-05 [1] RSPM @@ -863,7 +863,7 @@

Version information#> stringi 1.8.4 2024-05-06 [1] RSPM #> stringr 1.5.1 2023-11-14 [1] RSPM #> svglite 2.1.3 2023-12-08 [1] RSPM -#> sys 3.4.2 2023-05-23 [1] RSPM +#> sys 3.4.3 2024-10-04 [1] RSPM #> systemfonts 1.1.0 2024-05-15 [1] RSPM #> textshaping 0.4.0 2024-05-24 [1] RSPM #> tibble 3.2.1 2023-03-20 [1] RSPM diff --git a/pkgdown.yml b/pkgdown.yml index cc77573..2377301 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: articles/handling_LOQ: handling_LOQ.html intro-poped: intro-poped.html articles/model_def_other_pkgs: model_def_other_pkgs.html -last_built: 2024-10-04T15:19Z +last_built: 2024-10-07T07:11Z urls: reference: https://andrewhooker.github.io/PopED/reference article: https://andrewhooker.github.io/PopED/articles diff --git a/reference/Doptim.html b/reference/Doptim.html index db2a75f..11c8e6f 100644 --- a/reference/Doptim.html +++ b/reference/Doptim.html @@ -329,7 +329,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/Dtrace.html b/reference/Dtrace.html index 54d4fff..308766b 100644 --- a/reference/Dtrace.html +++ b/reference/Dtrace.html @@ -192,7 +192,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LEDoptim.html b/reference/LEDoptim.html index 6d226b9..2f71d84 100644 --- a/reference/LEDoptim.html +++ b/reference/LEDoptim.html @@ -266,7 +266,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL.html b/reference/LinMatrixL.html index bcaf8e5..5799362 100644 --- a/reference/LinMatrixL.html +++ b/reference/LinMatrixL.html @@ -127,7 +127,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixLH.html b/reference/LinMatrixLH.html index bef3a51..c078eb1 100644 --- a/reference/LinMatrixLH.html +++ b/reference/LinMatrixLH.html @@ -154,7 +154,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL_occ.html b/reference/LinMatrixL_occ.html index 42877d1..14eb5dc 100644 --- a/reference/LinMatrixL_occ.html +++ b/reference/LinMatrixL_occ.html @@ -151,7 +151,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/RS_opt.html b/reference/RS_opt.html index d701cb8..013823b 100644 --- a/reference/RS_opt.html +++ b/reference/RS_opt.html @@ -323,7 +323,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/a_line_search.html b/reference/a_line_search.html index ee9d610..0b667bf 100644 --- a/reference/a_line_search.html +++ b/reference/a_line_search.html @@ -190,7 +190,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function @@ -274,7 +274,7 @@

Examples#> Group 1: 100 [0.01,100] #> #> -#> Line search run time: 0.319 seconds +#> Line search run time: 0.322 seconds #> *************************** #> diff --git a/reference/bfgsb_min.html b/reference/bfgsb_min.html index 51ef21a..d77f624 100644 --- a/reference/bfgsb_min.html +++ b/reference/bfgsb_min.html @@ -139,7 +139,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockexp.html b/reference/blockexp.html index 28d6b30..ac5cb89 100644 --- a/reference/blockexp.html +++ b/reference/blockexp.html @@ -131,7 +131,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockfinal.html b/reference/blockfinal.html index f3978e3..f88b9be 100644 --- a/reference/blockfinal.html +++ b/reference/blockfinal.html @@ -233,7 +233,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function @@ -311,7 +311,7 @@

Examples#> sig_prop 0.01 32 32 #> sig_add 0.25 26 26 #> -#> Total running time: 1.583 seconds +#> Total running time: 1.585 seconds diff --git a/reference/blockheader.html b/reference/blockheader.html index 2ed6920..fa6642d 100644 --- a/reference/blockheader.html +++ b/reference/blockheader.html @@ -217,7 +217,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockopt.html b/reference/blockopt.html index afa9517..fd3daa3 100644 --- a/reference/blockopt.html +++ b/reference/blockopt.html @@ -102,7 +102,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x560c76c80270> +#> <bytecode: 0x55c05a078048> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/build_sfg.html b/reference/build_sfg.html index 746722b..5992bde 100644 --- a/reference/build_sfg.html +++ b/reference/build_sfg.html @@ -96,7 +96,7 @@

Examples#> function (x, a, bpop, b, bocc) #> parameters = c(CL = bpop[1] * exp(b[1]), Favail = bpop[2], KA = bpop[3] * #> exp(b[2]), V = bpop[4] * exp(b[3]), DOSE = a[1], TAU = a[2]) -#> <environment: 0x560c75dd01c0> +#> <environment: 0x55c0591a3620> etas <- c(Favail="exp",KA="exp",V="add",CL="exp") build_sfg(model="ff.PK.1.comp.oral.md.CL",etas = etas) @@ -104,7 +104,7 @@

Examples#> parameters = c(CL = bpop[1] * exp(b[1]), Favail = bpop[2] * exp(b[2]), #> KA = bpop[3] * exp(b[3]), V = bpop[4] + b[4], DOSE = a[1], #> TAU = a[2]) -#> <environment: 0x560c75dd01c0> +#> <environment: 0x55c0591a3620>