diff --git a/articles/examples.html b/articles/examples.html index 97162b9..e499b8a 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: 2.76 seconds.
+#> Elapsed time: 2.806 seconds.
 tic(); eval <- evaluate_design(poped.db.Rcpp); toc()
-#> Elapsed time: 1.187 seconds.
+#> Elapsed time: 1.197 seconds.

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

diff --git a/articles/handling_LOQ.html b/articles/handling_LOQ.html index 1577580..88b8264 100644 --- a/articles/handling_LOQ.html +++ b/articles/handling_LOQ.html @@ -283,8 +283,8 @@

LOQ handlingcat("D6 evaluation time: ",e_time_D6[1],"seconds \n" ) cat("D2 evaluation time: ",e_time_D2[1],"deconds \n" ) -#> D6 evaluation time: 0.047 seconds -#> D2 evaluation time: 0.008 deconds +#> D6 evaluation time: 0.045 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 a20b965..189e8b2 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: 16.882 seconds
+#> Total running time: 16.844 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: 10.329 seconds +#> Total running time: 10.314 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: 3.708 seconds +#> Total running time: 3.711 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 418d8d5..c3813a4 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: 2024-10-08T07:34Z +last_built: 2024-10-08T07:41Z 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 6f0bfb2..70dcc81 100644 --- a/reference/Doptim.html +++ b/reference/Doptim.html @@ -329,7 +329,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/Dtrace.html b/reference/Dtrace.html index ed9e1a6..f34f401 100644 --- a/reference/Dtrace.html +++ b/reference/Dtrace.html @@ -192,7 +192,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LEDoptim.html b/reference/LEDoptim.html index e547c3e..3630639 100644 --- a/reference/LEDoptim.html +++ b/reference/LEDoptim.html @@ -266,7 +266,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL.html b/reference/LinMatrixL.html index 71729bf..5a754f2 100644 --- a/reference/LinMatrixL.html +++ b/reference/LinMatrixL.html @@ -127,7 +127,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixLH.html b/reference/LinMatrixLH.html index 5d425d2..36de49f 100644 --- a/reference/LinMatrixLH.html +++ b/reference/LinMatrixLH.html @@ -154,7 +154,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/LinMatrixL_occ.html b/reference/LinMatrixL_occ.html index f8440d7..0242d17 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: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/RS_opt.html b/reference/RS_opt.html index 96f74aa..bf3a243 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: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function @@ -443,7 +443,7 @@

Examples#> SIGMA[1,1] 0.01 33 33 #> SIGMA[2,2] 0.25 26 26 #> -#> Total running time: 0.038 seconds +#> Total running time: 0.037 seconds if (FALSE) { # \dontrun{ diff --git a/reference/a_line_search.html b/reference/a_line_search.html index 32c042a..7a27693 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: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function @@ -274,7 +274,7 @@

Examples#> Group 1: 100 [0.01,100] #> #> -#> Line search run time: 0.329 seconds +#> Line search run time: 0.327 seconds #> *************************** #> diff --git a/reference/bfgsb_min.html b/reference/bfgsb_min.html index c9e5ffa..c00f224 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: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockexp.html b/reference/blockexp.html index 8a2961f..c3e6cd4 100644 --- a/reference/blockexp.html +++ b/reference/blockexp.html @@ -131,7 +131,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockfinal.html b/reference/blockfinal.html index 8c83b02..298555e 100644 --- a/reference/blockfinal.html +++ b/reference/blockfinal.html @@ -233,7 +233,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <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: 1.615 seconds +#> Total running time: 1.592 seconds diff --git a/reference/blockheader.html b/reference/blockheader.html index e01f732..e7d9559 100644 --- a/reference/blockheader.html +++ b/reference/blockheader.html @@ -217,7 +217,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/blockopt.html b/reference/blockopt.html index 26ca994..8acabaa 100644 --- a/reference/blockopt.html +++ b/reference/blockopt.html @@ -102,7 +102,7 @@

Examples#> return(list(y = y, poped.db = poped.db)) #> }) #> } -#> <bytecode: 0x55ccc1a1c8e8> +#> <bytecode: 0x55f4536f0b00> #> <environment: namespace:PopED> ## -- parameter definition function diff --git a/reference/build_sfg.html b/reference/build_sfg.html index eb00aaa..dbb0423 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: 0x55ccbc252358> +#> <environment: 0x55f4528194d0> 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: 0x55ccbc252358> +#> <environment: 0x55f4528194d0>