From 743507a7c84c2f56d10f87a479a15fc12d09bb9b Mon Sep 17 00:00:00 2001 From: andrewhooker Date: Thu, 16 Nov 2023 13:26:10 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20andrewho?= =?UTF-8?q?oker/PopED@10ce95514c4b419f88819b53ac4b293b46dd4c2d=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 | 52 +- articles/intro-poped.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 | 4 +- reference/a_line_search.html | 50 +- 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 | 2 +- reference/ed_mftot.html | 4 +- reference/evaluate.e.ofv.fim.html | 8 +- 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/getTruncatedNormal.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 | 202 ++--- reference/ofv_criterion.html | 2 +- reference/ofv_fim.html | 2 +- reference/optim_ARS.html | 818 +++++++++--------- reference/optim_LS.html | 96 +- reference/pargen.html | 2 +- reference/plot_efficiency_of_windows-1.png | Bin 340192 -> 349879 bytes reference/plot_efficiency_of_windows.html | 2 +- reference/plot_model_prediction.html | 2 +- reference/poped_optim.html | 64 +- reference/poped_optimize.html | 28 +- reference/rand.html | 18 +- reference/randn.html | 18 +- reference/shrinkage.html | 2 +- reference/summary.poped_optim.html | 24 +- reference/tic.html | 2 +- reference/toc.html | 6 +- search.json | 2 +- 60 files changed, 748 insertions(+), 744 deletions(-) diff --git a/articles/examples.html b/articles/examples.html index 5ba7739..acee157 100644 --- a/articles/examples.html +++ b/articles/examples.html @@ -786,9 +786,9 @@

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

 tic(); eval <- evaluate_design(poped.db); toc()
-#> Elapsed time: 2.812 seconds.
+#> Elapsed time: 2.759 seconds.
 tic(); eval <- evaluate_design(poped.db.Rcpp); toc()
-#> Elapsed time: 1.346 seconds.
+#> Elapsed time: 1.318 seconds.

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

@@ -1129,7 +1129,7 @@

Model with continuous covariates
 ev <- evaluate_design(poped_db_2) 
 round(ev$ofv,1)
-#> [1] 42
+#> [1] 42.3 
 round(ev$rse)
@@ -1148,11 +1148,11 @@

Model with continuous covariates

- + - + @@ -1214,51 +1214,51 @@

Model with continuous covariates0%

- - + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - +
WT_CL3128
WT_V2322
d_CL3.25 3.3223.0417.6822.5817.32 21.02 21.95 10.06
25%3.263.3327.3220.943.253.3227.1020.76 21.03 21.95 10.07
50%3.273.3429.6222.703.263.3329.0622.27 21.03 21.96 10.07
75%3.303.3731.5324.163.323.3931.4524.10 21.03 21.96 10.07
100%3.373.4538.6529.613.433.5040.5331.05 21.03 21.9610.0810.07
@@ -1935,7 +1935,7 @@

#> 5.030673 2.983917 14.014958 29.787587 36.758952 26.753311 31.645011 #> SIGMA[2,2] #> 25.341368 -#> Elapsed time: 0.14 seconds. +#> Elapsed time: 0.142 seconds.

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

@@ -1968,7 +1968,7 @@ 
#>   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: 0.135 seconds.

Design evaluation for a subset of model parameters of interest (Ds diff --git a/articles/intro-poped.html b/articles/intro-poped.html index c77c399..6bdb676 100644 --- a/articles/intro-poped.html +++ b/articles/intro-poped.html @@ -460,7 +460,7 @@

Design optimization#> d_CL 0.0625 28 26 #> sig_prop 0.04 14 15 #> -#> Total running time: 17.162 seconds +#> Total running time: 17.17 seconds plot_model_prediction(output$poped.db)

We see that there are four distinct sample times for this design. @@ -518,7 +518,7 @@

Optimize over a discrete design s #> d_CL 0.0625 28 27 #> sig_prop 0.04 14 15 #> -#> Total running time: 10.384 seconds +#> Total running time: 10.479 seconds plot_model_prediction(output_discrete$poped.db, model_num_points = 300)

Here we see that the optimization ran somewhat quicker, but gave a @@ -583,7 +583,7 @@

Cost function to optimize dose#> d_CL 0.0625 28 28 #> sig_prop 0.04 14 14 #> -#> Total running time: 3.889 seconds +#> Total running time: 3.866 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/pkgdown.yml b/pkgdown.yml index d6f8d5b..c98124c 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: model_def_other_pkgs: model_def_other_pkgs.html examples: examples.html intro-poped: intro-poped.html -last_built: 2023-11-16T13:16Z +last_built: 2023-11-16T13:23Z 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 dd1b7a6..fd847d0 100644 --- a/reference/Doptim.html +++ b/reference/Doptim.html @@ -352,7 +352,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/Dtrace.html b/reference/Dtrace.html index ab5762b..00edd90 100644 --- a/reference/Dtrace.html +++ b/reference/Dtrace.html @@ -215,7 +215,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LEDoptim.html b/reference/LEDoptim.html index 122e5af..806448a 100644 --- a/reference/LEDoptim.html +++ b/reference/LEDoptim.html @@ -289,7 +289,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL.html b/reference/LinMatrixL.html index 9ea725b..d53557b 100644 --- a/reference/LinMatrixL.html +++ b/reference/LinMatrixL.html @@ -152,7 +152,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixLH.html b/reference/LinMatrixLH.html index b934903..b9ee760 100644 --- a/reference/LinMatrixLH.html +++ b/reference/LinMatrixLH.html @@ -179,7 +179,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL_occ.html b/reference/LinMatrixL_occ.html index 29d07ac..1041faf 100644 --- a/reference/LinMatrixL_occ.html +++ b/reference/LinMatrixL_occ.html @@ -176,7 +176,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/RS_opt.html b/reference/RS_opt.html index 25aac0c..87b44ba 100644 --- a/reference/RS_opt.html +++ b/reference/RS_opt.html @@ -346,7 +346,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function @@ -466,7 +466,7 @@

Examples#> SIGMA[1,1] 0.01 33 33 #> SIGMA[2,2] 0.25 26 26 #> -#> Total running time: 0.038 seconds +#> Total running time: 0.036 seconds if (FALSE) { diff --git a/reference/a_line_search.html b/reference/a_line_search.html index 82d8ce0..6d9bdd1 100644 --- a/reference/a_line_search.html +++ b/reference/a_line_search.html @@ -215,7 +215,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function @@ -256,52 +256,50 @@

Examples#> ***************************** #> Line Search #> +#> Searching xt8 on group 1 +#> Searching xt6 on group 1 +#> group 1 -- xt[6] changed from 36 to 0.01 +#> OFV(MF) changed from 55.3964 to 55.7162 +#> group 1 -- xt[6] changed from 0.01 to 90.0025 +#> OFV(MF) changed from 55.7162 to 55.7556 +#> group 1 -- xt[6] changed from 90.0025 to 120 +#> OFV(MF) changed from 55.7556 to 55.7972 +#> Searching xt5 on group 1 +#> Searching xt3 on group 1 #> Searching xt4 on group 1 #> Searching xt7 on group 1 #> group 1 -- xt[7] changed from 72 to 90.0025 -#> OFV(MF) changed from 55.3964 to 55.512 -#> group 1 -- xt[7] changed from 90.0025 to 120 -#> OFV(MF) changed from 55.512 to 55.5449 -#> Searching xt3 on group 1 -#> group 1 -- xt[3] changed from 2 to 90.0025 -#> OFV(MF) changed from 55.5449 to 55.6117 -#> group 1 -- xt[3] changed from 90.0025 to 120 -#> OFV(MF) changed from 55.6117 to 55.6399 -#> Searching xt8 on group 1 -#> Searching xt6 on group 1 -#> group 1 -- xt[6] changed from 36 to 30.0075 -#> OFV(MF) changed from 55.6399 to 55.7221 +#> OFV(MF) changed from 55.7972 to 55.8529 #> Searching xt2 on group 1 #> group 1 -- xt[2] changed from 1 to 0.01 -#> OFV(MF) changed from 55.7221 to 55.7325 +#> OFV(MF) changed from 55.8529 to 55.89 #> group 1 -- xt[2] changed from 0.01 to 30.0075 -#> OFV(MF) changed from 55.7325 to 55.8112 +#> OFV(MF) changed from 55.89 to 55.9369 #> group 1 -- xt[2] changed from 30.0075 to 90.0025 -#> OFV(MF) changed from 55.8112 to 55.8255 +#> OFV(MF) changed from 55.9369 to 55.9441 #> group 1 -- xt[2] changed from 90.0025 to 120 -#> OFV(MF) changed from 55.8255 to 55.84 +#> OFV(MF) changed from 55.9441 to 55.9617 #> Searching xt1 on group 1 -#> Searching xt5 on group 1 -#> OFV(MF): 55.84 +#> OFV(MF): 55.9617 #> -#> Best value for OFV(MF) = 55.84 +#> Best value for OFV(MF) = 55.9617 #> #> Best value for xt: -#> Group 1: 0.5 6 24 30.01 120 120 120 120 +#> Group 1: 0.5 2 6 24 90 120 120 120 #> #> Searching a1 on individual/group 1 #> group 1 -- a[1] changed from 70 to 75.0025 -#> OFV(MF) changed from 55.84 to 56.0555 +#> OFV(MF) changed from 55.9617 to 56.1549 #> group 1 -- a[1] changed from 75.0025 to 100 -#> OFV(MF) changed from 56.0555 to 56.7349 -#> OFV(MF): 56.7349 -#> Best value for OFV(MF) = 56.7349 +#> OFV(MF) changed from 56.1549 to 56.7447 +#> OFV(MF): 56.7447 +#> Best value for OFV(MF) = 56.7447 #> #> Best value for a: #> Group 1: 100 [0.01,100] #> #> -#> Line search run time: 0.322 seconds +#> Line search run time: 0.314 seconds #> *************************** #> diff --git a/reference/bfgsb_min.html b/reference/bfgsb_min.html index 76c8a6e..7c1a7f9 100644 --- a/reference/bfgsb_min.html +++ b/reference/bfgsb_min.html @@ -164,7 +164,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockexp.html b/reference/blockexp.html index 7b69a88..d6d3b62 100644 --- a/reference/blockexp.html +++ b/reference/blockexp.html @@ -154,7 +154,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockfinal.html b/reference/blockfinal.html index 8dee4a7..e7d10bc 100644 --- a/reference/blockfinal.html +++ b/reference/blockfinal.html @@ -254,7 +254,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function @@ -332,7 +332,7 @@

Examples#> sig_prop 0.01 32 32 #> sig_add 0.25 26 26 #> -#> Total running time: 1.588 seconds +#> Total running time: 1.531 seconds diff --git a/reference/blockheader.html b/reference/blockheader.html index 99a4ce8..33637d7 100644 --- a/reference/blockheader.html +++ b/reference/blockheader.html @@ -240,7 +240,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockopt.html b/reference/blockopt.html index e64102c..140673f 100644 --- a/reference/blockopt.html +++ b/reference/blockopt.html @@ -125,7 +125,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x555ad756a4b8> +#> <bytecode: 0x55eddf040570> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/build_sfg.html b/reference/build_sfg.html index 48ea0e1..702f7cc 100644 --- a/reference/build_sfg.html +++ b/reference/build_sfg.html @@ -121,7 +121,7 @@

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: 0x555ad555c1b0> +#> <environment: 0x55eddd17c190> etas <- c(Favail="exp",KA="exp",V="add",CL="exp") build_sfg(model="ff.PK.1.comp.oral.md.CL",etas = etas) @@ -129,7 +129,7 @@

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: 0x555ad555c1b0> +#> <environment: 0x55eddd17c190>