diff --git a/docs/articles/a_posteriori_dosing.html b/docs/articles/a_posteriori_dosing.html index f0d7824..ddd8c3a 100644 --- a/docs/articles/a_posteriori_dosing.html +++ b/docs/articles/a_posteriori_dosing.html @@ -150,8 +150,7 @@

Introduction0.01 , 0.02 , 0.2 , -0.06 , 0.004, 0.003, 0.08)}), covariates = c("CLCREAT4H","TBW","PoverF"), - sigma = c(additive_a = 0.2, proportional_b = 0.1)) -#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ + sigma = c(additive_a = 0.2, proportional_b = 0.1))

A posteriori dose selection diff --git a/docs/articles/auc_based_dosing.html b/docs/articles/auc_based_dosing.html index d63f897..bec4ea3 100644 --- a/docs/articles/auc_based_dosing.html +++ b/docs/articles/auc_based_dosing.html @@ -150,8 +150,7 @@

Introduction0 , 0, 0.282, 0 , 0, 0, 0)}), covariates = c("CLCREAT","WT","DIAL"), - sigma = c(additive_a = 3.4, proportional_b = 0.227)) -#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

+ sigma = c(additive_a = 3.4, proportional_b = 0.227))

Discontinuous intravenous infusion diff --git a/docs/articles/multiple_endpoints.html b/docs/articles/multiple_endpoints.html index 1d50d04..fe6d409 100644 --- a/docs/articles/multiple_endpoints.html +++ b/docs/articles/multiple_endpoints.html @@ -193,8 +193,7 @@

warfarin PKPD model=c(additive_a = 0.144, proportional_b = 0.15), pca=c(additive_a = 3.91, proportional_b = 0.0) ) - ) -#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

+ )

data: first subject from the warfarin dataset @@ -237,19 +236,19 @@

data: first subject from t map_warf_01 #> $eta #> ETA_ktr ETA_ka ETA_cl ETA_v ETA_emax ETA_ec50 -#> -0.43461299 -0.69405538 0.82338134 -0.02303193 0.06846897 0.14181369 +#> -0.43629043 -0.69246533 0.82338031 -0.02295265 0.06901167 0.14181589 #> ETA_kout ETA_e0 -#> -0.19868748 -0.12379062 +#> -0.19873712 -0.12377532 #> #> $model #> ── Solved rxode2 object ── #> ── Parameters ($params): ── #> THETA_ktr ETA_ktr THETA_ka ETA_ka THETA_cl ETA_cl -#> 0.10600000 -0.43461299 -0.08700000 -0.69405538 -2.03000000 0.82338134 +#> 0.10600000 -0.43629043 -0.08700000 -0.69246533 -2.03000000 0.82338031 #> THETA_v ETA_v THETA_emax ETA_emax THETA_ec50 ETA_ec50 -#> 2.07000000 -0.02303193 3.40000000 0.06846897 0.00724000 0.14181369 +#> 2.07000000 -0.02295265 3.40000000 0.06901167 0.00724000 0.14181589 #> THETA_kout ETA_kout THETA_e0 ETA_e0 -#> -2.90000000 -0.19868748 4.57000000 -0.12379062 +#> -2.90000000 -0.19873712 4.57000000 -0.12377532 #> ── Initial Conditions ($inits): ── #> depot gut center effect #> 0 0 0 0 @@ -257,12 +256,12 @@

data: first subject from t #> # A tibble: 1,451 × 18 #> time ktr ka cl v emax ec50 kout e0 DCP PD kin #> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 0 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0 1 3.85 -#> 2 0.1 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0.0204 0.983 3.85 -#> 3 0.2 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0.0785 0.939 3.85 -#> 4 0.3 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0.170 0.876 3.85 -#> 5 0.4 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0.290 0.806 3.85 -#> 6 0.5 0.720 0.458 0.299 7.74 0.970 1.16 0.0451 85.3 0.436 0.735 3.85 +#> 1 0 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0 1 3.85 +#> 2 0.1 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0.0204 0.983 3.85 +#> 3 0.2 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0.0785 0.939 3.85 +#> 4 0.3 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0.170 0.876 3.85 +#> 5 0.4 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0.290 0.806 3.85 +#> 6 0.5 0.719 0.459 0.299 7.74 0.970 1.16 0.0451 85.3 0.435 0.735 3.85 #> # ℹ 1,445 more rows #> # ℹ 6 more variables: cp <dbl>, pca <dbl>, depot <dbl>, gut <dbl>, #> # center <dbl>, effect <dbl> diff --git a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png index 00b61f7..6d5622a 100644 Binary files a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png index 4e79fd5..78c8f09 100644 Binary files a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/posologyr_user_defined_models.html b/docs/articles/posologyr_user_defined_models.html index 158466a..face26c 100644 --- a/docs/articles/posologyr_user_defined_models.html +++ b/docs/articles/posologyr_user_defined_models.html @@ -368,15 +368,14 @@

Full model0 , 0 , 0.282, 0 , 0 , 0 , 0)}), sigma = c(additive_a = 3.4, proportional_b = 0.227), - covariates = c("CLCREAT","WT","DIAL")) -#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

+ covariates = c("CLCREAT","WT","DIAL"))

Resulting R object 

 mod_vancomyin_Goti2018
 #> $ppk_model
-#> rxode2 NA model named rx_7bbe45c9bd81b7f28b1e0f7c8463811c model (✔ ready). 
+#> rxode2 NA model named rx_bea2f6b6b859e434ba4a129a70799409 model (✔ ready). 
 #> $state: centr, periph, AUC
 #> $params: THETA_Cl, CLCREAT, DIAL, THETA_Vc, WT, THETA_Vp, THETA_Q, ETA_Cl, ETA_Vc, ETA_Vp
 #> $lhs: TVCl, TVVc, TVVp, TVQ, Cl, Vc, Vp, Q, ke, k12, k21, Cc
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index ab0db48..47bf413 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -8,5 +8,5 @@ articles:
   multiple_endpoints: multiple_endpoints.html
   patient_data_input: patient_data_input.html
   posologyr_user_defined_models: posologyr_user_defined_models.html
-last_built: 2023-12-07T21:04Z
+last_built: 2023-12-10T17:47Z
 
diff --git a/docs/reference/poso_dose_auc.html b/docs/reference/poso_dose_auc.html
index 9432c6d..e5f451c 100644
--- a/docs/reference/poso_dose_auc.html
+++ b/docs/reference/poso_dose_auc.html
@@ -268,7 +268,6 @@ 
Examples

 sigma = lotri::lotri({prop + add ~ c(0.05,0.0,0.00)}))
 #>  
 #>  
-#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
 # df_patient01: event table for Patient01, following a 30 minutes intravenous
 # infusion
 df_patient01 <- data.frame(ID=1,
@@ -281,7 +280,7 @@ 
Examples

 poso_dose_auc(dat=df_patient01,prior_model=mod_run001,
 time_auc=12,target_auc=45)
 #> $dose
-#> [1] 396.0041
+#> [1] 396.0047
 #> 
 #> $type_of_estimate
 #> [1] "point estimate"
@@ -290,8 +289,8 @@ 
Examples

 #> [1] 45
 #> 
 #> $indiv_param
-#>   THETA_Cl THETA_Vc THETA_Ka    ETA_Cl     ETA_Vc    ETA_Ka
-#> 1        4       70        1 0.6019036 -0.4291744 0.1278464
+#>   THETA_Cl THETA_Vc THETA_Ka   ETA_Cl     ETA_Vc    ETA_Ka
+#> 1        4       70        1 0.601905 -0.4291724 0.1278486
 #>
diff --git a/docs/reference/poso_dose_conc.html b/docs/reference/poso_dose_conc.html index 2c284e2..b39f6a9 100644 --- a/docs/reference/poso_dose_conc.html +++ b/docs/reference/poso_dose_conc.html @@ -263,7 +263,6 @@

Examples

sigma = lotri::lotri({prop + add ~ c(0.05,0.0,0.00)})) #> #> -#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ # df_patient01: event table for Patient01, following a 30 minutes intravenous # infusion df_patient01 <- data.frame(ID=1, @@ -277,7 +276,7 @@

Examples

poso_dose_conc(dat=df_patient01,prior_model=mod_run001, time_c=1,duration=0.5,target_conc=80) #> $dose -#> [1] 6886.021 +#> [1] 6886.019 #> #> $type_of_estimate #> [1] "point estimate" @@ -287,7 +286,7 @@

Examples

#> #> $indiv_param #> THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> 1 4 70 1 0.6019038 -0.4291742 0.1278461 +#> 1 4 70 1 0.6019037 -0.4291733 0.1278479 #>
diff --git a/docs/reference/poso_estim_map.html b/docs/reference/poso_estim_map.html index 66e6840..f8486f5 100644 --- a/docs/reference/poso_estim_map.html +++ b/docs/reference/poso_estim_map.html @@ -179,13 +179,13 @@

Examples

poso_estim_map(dat=df_patient01,prior_model=mod_run001) #> $eta #> ETA_Cl ETA_Vc ETA_Ka -#> 0.6019037 -0.4291725 0.1278482 +#> 0.6019036 -0.4291731 0.1278485 #> #> $model #> ── Solved rxode2 object ── #> ── Parameters ($params): ── #> THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> 4.0000000 70.0000000 1.0000000 0.6019037 -0.4291725 0.1278482 +#> 4.0000000 70.0000000 1.0000000 0.6019036 -0.4291731 0.1278485 #> ── Initial Conditions ($inits): ── #> depot centr AUC #> 0 0 0 diff --git a/docs/reference/poso_estim_mcmc.html b/docs/reference/poso_estim_mcmc.html index 077be2f..bf089c1 100644 --- a/docs/reference/poso_estim_mcmc.html +++ b/docs/reference/poso_estim_mcmc.html @@ -206,123 +206,123 @@

Examples

n_iter=50,n_chains=2) #> $eta #> ETA_Cl ETA_Vc ETA_Ka -#> 1 0.40724811 -0.563030161 0.024021160 -#> 2 0.81114568 -0.110337316 0.056504832 -#> 3 0.12305559 -0.798025341 0.214300318 -#> 4 0.51633018 -0.151828205 0.307573339 -#> 5 0.77447898 -0.108730610 0.551635983 -#> 6 0.49079173 -0.354675200 0.003646606 -#> 7 0.71255279 -0.459976731 0.130391402 -#> 8 0.64376520 -0.465368428 0.357712480 -#> 9 0.67891164 -0.369511650 0.464462086 -#> 10 0.50999711 0.006100256 0.501523061 -#> 11 0.60211068 -0.506164720 0.161508835 -#> 12 0.53467781 -0.290158899 0.653308924 -#> 13 0.30551284 -0.646386356 0.310843478 -#> 14 0.48252547 -0.612463109 -0.359678265 -#> 15 0.60616342 -0.188623774 0.650670197 -#> 16 0.41325485 -0.269308778 0.215313102 -#> 17 0.80534116 -0.509250930 -0.134419998 -#> 18 0.29525589 -0.870778188 -0.266469345 -#> 19 0.30843774 -0.774518817 -0.092544206 -#> 20 0.44341975 -0.456903155 0.044147116 -#> 21 0.45556449 -0.368768240 -0.181832064 -#> 22 0.49986244 -0.372678275 0.281556420 -#> 23 0.68558958 -0.466350022 -0.007472740 -#> 24 0.62021839 -0.663196418 -0.338663195 -#> 25 0.54346411 -0.736113314 -0.154516098 -#> 26 0.46810716 -0.562021559 0.050963946 -#> 27 0.42819893 -0.648301575 -0.257027130 -#> 28 0.57031956 -0.374778034 -0.040288335 -#> 29 0.61054638 -0.077630968 0.534770044 -#> 30 0.51449289 -0.259913093 0.750363813 -#> 31 0.74930802 -0.164666311 0.167144258 -#> 32 0.76727874 -0.391483870 0.294896119 -#> 33 0.69212535 -0.079457901 0.313828707 -#> 34 0.62488375 -0.354105032 0.421647317 -#> 35 0.56914053 0.007012069 0.791853732 -#> 36 0.64130561 -0.377613884 -0.012506102 -#> 37 0.36059214 -0.129325952 0.356552754 -#> 38 0.55722775 -0.276262116 0.044992769 -#> 39 0.50017650 -0.649341860 -0.463561650 -#> 40 0.61704468 -0.663278730 -0.271667859 -#> 41 0.35985516 -0.492073132 -0.196825367 -#> 42 0.30906490 -0.602324893 -0.342556745 -#> 43 0.55790578 -0.457062133 0.420471747 -#> 44 0.35764039 -0.428515713 0.059715457 -#> 45 0.12293162 -0.608056645 0.438637670 -#> 46 0.65159622 -0.230761434 -0.102654171 -#> 47 0.57516879 -0.230715910 0.911452424 -#> 48 0.49877334 -0.079345798 0.424548880 -#> 49 0.86132480 -0.239350275 0.718566397 -#> 50 0.74385923 0.072715489 0.836524138 +#> 1 0.49736166 -0.262121438 1.012791880 +#> 2 0.54867885 -0.313105643 0.700858819 +#> 3 0.35618499 -0.428159537 0.312859730 +#> 4 0.68348235 -0.725390484 -0.355357424 +#> 5 0.53854472 -0.725390484 0.052456140 +#> 6 0.76378421 -0.207208125 0.118263957 +#> 7 0.34178653 -0.606758120 -0.009326937 +#> 8 0.71300224 0.073971130 0.965766216 +#> 9 0.56473442 -0.442291495 0.187630445 +#> 10 0.75335923 -0.007895713 0.612019539 +#> 11 0.61808333 0.098674909 0.844866760 +#> 12 0.85168297 0.081762586 0.328986718 +#> 13 0.54928142 -0.099485832 0.739588632 +#> 14 0.53339934 -0.245302394 0.462482036 +#> 15 -0.03385513 -0.499919754 -0.067405380 +#> 16 0.16336486 -0.073058695 0.458429533 +#> 17 0.68364663 -0.161355561 0.913277515 +#> 18 0.52989970 -0.092357651 0.486759238 +#> 19 0.52204473 0.120074745 0.771758754 +#> 20 0.50494570 -0.412120495 -0.022826847 +#> 21 0.60283779 -0.174731915 0.734969825 +#> 22 0.21846006 -0.948046174 -0.443361940 +#> 23 0.36434913 -0.820263597 0.246778461 +#> 24 0.25858386 -0.345394639 0.371309690 +#> 25 0.55594589 -0.427938369 0.278366240 +#> 26 0.83529453 0.049160104 0.550076922 +#> 27 0.60677631 -0.088650526 0.418853980 +#> 28 0.74920862 -0.038164327 0.679137405 +#> 29 0.59444010 -0.415678065 0.162725448 +#> 30 0.47286379 -0.563601975 0.162725448 +#> 31 0.25385690 -0.239083530 0.335122495 +#> 32 0.67400948 -0.269812832 0.339485713 +#> 33 0.57709621 -0.132746082 0.693889638 +#> 34 0.57709621 -0.440217754 0.693889638 +#> 35 0.54314647 -0.497463421 0.067216964 +#> 36 0.42395755 -0.580508660 -0.201718524 +#> 37 0.49189322 0.216248595 0.928388159 +#> 38 0.72275366 0.100873423 0.735143212 +#> 39 0.76643086 -0.007212241 0.939468417 +#> 40 0.72911004 0.019521980 0.480476616 +#> 41 0.62720098 -0.371735990 0.111745310 +#> 42 0.64644424 -0.175250875 0.886925363 +#> 43 0.65646514 -0.278625493 0.412340584 +#> 44 0.63514102 -0.146320876 0.647829405 +#> 45 0.50500610 -0.431836723 0.510020600 +#> 46 0.16194699 -1.003972434 -0.239243585 +#> 47 0.47637019 -0.814945833 -0.542386231 +#> 48 0.04990222 -1.237399504 -0.792847300 +#> 49 0.16252571 -0.110445392 0.907665005 +#> 50 0.76267378 0.055284486 0.517292001 #> 51 0.00000000 0.000000000 0.000000000 -#> 52 0.45746971 -0.897543636 0.568924579 -#> 53 0.25706727 -0.488742654 -0.126433915 -#> 54 0.77709488 -0.038371275 0.416589300 -#> 55 0.50230392 -0.282611828 0.386640710 -#> 56 0.54861797 -0.620359156 0.109686401 -#> 57 0.75013086 -0.307488976 0.038291109 -#> 58 0.51554245 -0.002879128 0.780816140 -#> 59 0.42249259 -0.033981756 0.446226653 -#> 60 0.69115757 -0.034362509 0.741642418 -#> 61 0.33264648 -0.173253981 0.496776974 -#> 62 0.40911373 -0.495052869 -0.362851153 -#> 63 0.51458281 -0.526967721 -0.094508739 -#> 64 0.54648326 -0.488712420 -0.187693787 -#> 65 0.62519583 -0.175074775 0.807044469 -#> 66 0.47492816 -0.331933105 0.387466961 -#> 67 0.65235268 -0.413473484 0.510944182 -#> 68 0.54857774 -0.324282272 0.650774667 -#> 69 0.70025067 -0.137400166 0.489193284 -#> 70 0.64082333 -0.281925642 0.091037845 -#> 71 0.01065260 -0.404277767 0.259191020 -#> 72 0.52900391 -0.221640608 0.104667645 -#> 73 0.72398979 -0.688791705 -0.071975868 -#> 74 0.38182074 -0.813560664 -0.214194461 -#> 75 0.18317080 -0.644669717 0.054994854 -#> 76 0.81953866 -0.129080906 0.705106121 -#> 77 0.41834539 -0.719796557 0.082003237 -#> 78 0.53704078 -0.414576656 -0.100080012 -#> 79 0.57609252 -0.580794185 -0.234245184 -#> 80 0.48264993 -0.840443977 -0.122120935 -#> 81 0.68066536 -0.280088969 0.274558701 -#> 82 0.20082927 -0.795288416 0.127442150 -#> 83 0.66103074 -0.222148406 0.239650188 -#> 84 0.70714278 -0.219377644 0.789180126 -#> 85 0.32535128 -0.831682608 -0.182062192 -#> 86 0.57269176 -0.382498665 0.570136217 -#> 87 0.38256449 -0.670831758 0.423190048 -#> 88 0.53889312 -0.514421231 -0.208715285 -#> 89 0.72907564 -0.364021492 0.542533185 -#> 90 0.71364531 -0.178311121 0.671033998 -#> 91 0.55489160 -0.292349780 0.442871675 -#> 92 0.13813960 -0.877512133 0.110538811 -#> 93 0.73298678 -0.022147763 0.348447964 -#> 94 -0.44378584 -0.478718355 0.989763748 -#> 95 0.09672523 0.029995441 0.586702566 -#> 96 0.34230907 -0.337439274 0.359174943 -#> 97 0.74623185 -0.364881750 0.057345358 -#> 98 0.53219919 -0.732652539 -0.400099299 -#> 99 0.35553164 -0.634254439 -0.461993056 -#> 100 0.71376140 -0.568168626 -0.118299509 +#> 52 -0.32510845 -0.247505533 0.203168958 +#> 53 0.41565543 -0.971672357 -0.373031810 +#> 54 0.54520690 -0.430499756 0.399877250 +#> 55 0.34777650 -0.102875040 0.934708353 +#> 56 0.62483321 -0.472529432 0.041681308 +#> 57 0.67252155 -0.190584947 0.216975990 +#> 58 0.60080782 -0.467557073 0.055296919 +#> 59 0.36321747 -0.587474319 0.380827704 +#> 60 0.64741941 -0.481480329 0.779594815 +#> 61 0.63160323 -0.673916617 0.163354881 +#> 62 0.50393097 -0.477923184 0.111312936 +#> 63 0.58119086 -0.345136198 0.207976659 +#> 64 0.32537071 -0.645524365 0.773049372 +#> 65 0.34209301 -0.190589916 0.503819926 +#> 66 0.45089573 -0.448928390 0.320597640 +#> 67 0.39165903 -0.187480975 0.655541929 +#> 68 0.29384770 -0.737768703 0.101634813 +#> 69 0.45991758 -0.604094043 0.019797880 +#> 70 0.35161437 -0.821770632 -0.302467002 +#> 71 0.65951226 -0.606347919 -0.110533359 +#> 72 0.64332975 -0.581616255 0.008811059 +#> 73 0.59524686 -0.722079523 -0.473902807 +#> 74 0.46116937 -0.637414125 0.259448880 +#> 75 0.35255296 -0.736687702 -0.286711440 +#> 76 0.58420542 -0.638167580 -0.054221560 +#> 77 0.03675916 -0.949568514 0.110610862 +#> 78 0.72860194 -0.164145530 0.451100331 +#> 79 0.72423340 -0.231529186 0.280245634 +#> 80 0.41967496 -0.357759456 0.049850726 +#> 81 0.70890501 -0.390941524 0.359375875 +#> 82 0.47072632 -0.398318466 0.721909252 +#> 83 0.58288271 -0.475525140 0.159237297 +#> 84 0.58094183 -0.451730153 0.458914153 +#> 85 0.73445793 -0.422510113 0.282273638 +#> 86 0.47088580 -0.257518422 0.413667028 +#> 87 0.41767648 -0.425489607 0.063308776 +#> 88 0.54899227 -0.720928960 -0.344959777 +#> 89 0.54576298 -0.189540066 0.015207382 +#> 90 0.69256150 -0.234299049 0.526472741 +#> 91 0.31618207 -0.424795896 0.429293273 +#> 92 0.49028868 -0.279826340 0.044334433 +#> 93 0.51648170 -0.362280053 0.243448317 +#> 94 0.36094833 -0.529721548 0.446227081 +#> 95 0.22528867 -0.188420404 0.380832433 +#> 96 0.50372692 -0.548128256 0.621383745 +#> 97 0.57413960 -0.332209792 0.409978711 +#> 98 0.58110199 -0.527798199 -0.108794061 +#> 99 0.74944672 -0.342941324 0.825504385 +#> 100 0.67503782 -0.278951230 0.080529833 #> #> $model #> ── Solved rxode2 object ── #> ── Parameters ($params): ── #> # A tibble: 100 × 7 -#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 4 70 1 0.407 -0.563 0.0240 -#> 2 2 4 70 1 0.811 -0.110 0.0565 -#> 3 3 4 70 1 0.123 -0.798 0.214 -#> 4 4 4 70 1 0.516 -0.152 0.308 -#> 5 5 4 70 1 0.774 -0.109 0.552 -#> 6 6 4 70 1 0.491 -0.355 0.00365 -#> 7 7 4 70 1 0.713 -0.460 0.130 -#> 8 8 4 70 1 0.644 -0.465 0.358 -#> 9 9 4 70 1 0.679 -0.370 0.464 -#> 10 10 4 70 1 0.510 0.00610 0.502 +#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 4 70 1 0.497 -0.262 1.01 +#> 2 2 4 70 1 0.549 -0.313 0.701 +#> 3 3 4 70 1 0.356 -0.428 0.313 +#> 4 4 4 70 1 0.683 -0.725 -0.355 +#> 5 5 4 70 1 0.539 -0.725 0.0525 +#> 6 6 4 70 1 0.764 -0.207 0.118 +#> 7 7 4 70 1 0.342 -0.607 -0.00933 +#> 8 8 4 70 1 0.713 0.0740 0.966 +#> 9 9 4 70 1 0.565 -0.442 0.188 +#> 10 10 4 70 1 0.753 -0.00790 0.612 #> # ℹ 90 more rows #> ── Initial Conditions ($inits): ── #> depot centr AUC @@ -332,14 +332,14 @@

Examples

#> #> ── First part of data (object): ── #> # A tibble: 200 × 13 -#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 1 4 70 1 6.01 39.9 1.02 0.151 25.0 938. 995. -#> 2 1 14 4 70 1 6.01 39.9 1.02 0.151 7.40 0.00155 295. -#> 3 2 1 4 70 1 9.00 62.7 1.06 0.144 16.3 915. 1020. -#> 4 2 14 4 70 1 9.00 62.7 1.06 0.144 5.13 0.000971 321. -#> 5 3 1 4 70 1 4.52 31.5 1.24 0.144 35.7 802. 1124. -#> 6 3 14 4 70 1 4.52 31.5 1.24 0.144 9.97 0.0000811 314. +#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 1 4 70 1 6.58 53.9 2.75 0.122 30.1 2.74e+ 2 1623. +#> 2 1 14 4 70 1 6.58 53.9 2.75 0.122 7.25 9.82e-10 390. +#> 3 2 1 4 70 1 6.92 51.2 2.02 0.135 28.2 4.60e+ 2 1444. +#> 4 2 14 4 70 1 6.92 51.2 2.02 0.135 6.52 1.83e- 9 334. +#> 5 3 1 4 70 1 5.71 45.6 1.37 0.125 26.3 7.31e+ 2 1200. +#> 6 3 14 4 70 1 5.71 45.6 1.37 0.125 8.63 1.39e- 5 394. #> # ℹ 194 more rows #> # ℹ 1 more variable: AUC <dbl> #> diff --git a/docs/reference/poso_estim_sir.html b/docs/reference/poso_estim_sir.html index e399b5a..bde7e22 100644 --- a/docs/reference/poso_estim_sir.html +++ b/docs/reference/poso_estim_sir.html @@ -182,124 +182,124 @@

Examples

poso_estim_sir(dat=df_patient01,prior_model=mod_run001, n_sample=1e3,n_resample=1e2) #> $eta -#> ETA_Cl ETA_Vc ETA_Ka -#> 1 0.2679994 -0.13112123 5.967401e-01 -#> 2 0.4611585 -0.41091511 4.165087e-02 -#> 3 0.7111648 -0.25208914 2.856139e-01 -#> 4 0.4682708 -0.73882245 -3.124134e-01 -#> 5 0.3937168 -0.64124249 9.705775e-02 -#> 6 0.3937168 -0.64124249 9.705775e-02 -#> 7 0.2725197 -0.05999858 6.499541e-01 -#> 8 0.3937168 -0.64124249 9.705775e-02 -#> 9 0.8156592 -0.18909842 9.992836e-02 -#> 10 0.5995893 -0.60269376 -5.743076e-01 -#> 11 0.6691375 -0.59079497 4.271345e-01 -#> 12 0.5766533 -0.65742620 -1.647240e-01 -#> 13 0.8594692 0.06125631 4.171537e-01 -#> 14 0.3518958 -0.82409806 -2.902659e-01 -#> 15 0.5936046 -0.65734376 -2.499049e-01 -#> 16 0.5496519 -0.45696681 3.700461e-03 -#> 17 0.4682708 -0.73882245 -3.124134e-01 -#> 18 0.4032793 -0.42624606 4.532158e-02 -#> 19 0.9167175 -0.05896651 1.417114e-01 -#> 20 0.4519942 -0.80640277 -1.886841e-01 -#> 21 0.4032793 -0.42624606 4.532158e-02 -#> 22 0.4652994 -0.26727955 2.626289e-01 -#> 23 0.5452217 -0.17237583 4.468084e-01 -#> 24 0.4453857 -0.37948184 -5.103432e-02 -#> 25 0.5210469 -0.22149257 4.702114e-01 -#> 26 0.7446348 -0.23615738 -9.303725e-02 -#> 27 0.4519942 -0.80640277 -1.886841e-01 -#> 28 0.3518958 -0.82409806 -2.902659e-01 -#> 29 0.7489848 -0.29036293 1.232090e-01 -#> 30 0.6773654 -0.23087861 8.419649e-01 -#> 31 0.4196083 -0.49975075 2.290292e-01 -#> 32 0.2679994 -0.13112123 5.967401e-01 -#> 33 0.1080232 -0.71959270 -1.345680e-01 -#> 34 0.2437701 -0.65438519 2.772438e-01 -#> 35 0.5344965 -0.70674608 -5.314845e-01 -#> 36 0.5648737 -0.53074719 -7.768911e-02 -#> 37 0.5398181 -0.90618020 -4.369519e-01 -#> 38 0.5766533 -0.65742620 -1.647240e-01 -#> 39 0.5146523 -0.47545167 -3.661290e-03 -#> 40 0.5146523 -0.47545167 -3.661290e-03 -#> 41 0.5146523 -0.47545167 -3.661290e-03 -#> 42 0.6716634 -0.37950288 1.149491e-01 -#> 43 0.4502671 -0.79074224 4.627639e-01 -#> 44 0.4601762 -0.64703527 3.208253e-01 -#> 45 0.5344965 -0.70674608 -5.314845e-01 -#> 46 0.5671956 -0.37418593 2.945781e-01 -#> 47 0.7111648 -0.25208914 2.856139e-01 -#> 48 0.6165432 -0.54224186 2.248402e-01 -#> 49 0.5146523 -0.47545167 -3.661290e-03 -#> 50 0.5344965 -0.70674608 -5.314845e-01 -#> 51 0.6773654 -0.23087861 8.419649e-01 -#> 52 0.5766533 -0.65742620 -1.647240e-01 -#> 53 0.5648737 -0.53074719 -7.768911e-02 -#> 54 0.3937168 -0.64124249 9.705775e-02 -#> 55 0.4519942 -0.80640277 -1.886841e-01 -#> 56 0.5496519 -0.45696681 3.700461e-03 -#> 57 0.6174819 -0.06857429 6.233681e-01 -#> 58 0.7489848 -0.29036293 1.232090e-01 -#> 59 0.5766533 -0.65742620 -1.647240e-01 -#> 60 0.3439026 -0.35373879 6.817992e-01 -#> 61 0.5648737 -0.53074719 -7.768911e-02 -#> 62 0.5496519 -0.45696681 3.700461e-03 -#> 63 0.5671956 -0.37418593 2.945781e-01 -#> 64 0.7111648 -0.25208914 2.856139e-01 -#> 65 0.5676750 -0.35110421 1.421802e-01 -#> 66 0.5425279 -0.21511041 4.128249e-01 -#> 67 0.9652298 0.07906872 5.650511e-01 -#> 68 0.5496519 -0.45696681 3.700461e-03 -#> 69 0.5648737 -0.53074719 -7.768911e-02 -#> 70 0.8594692 0.06125631 4.171537e-01 -#> 71 0.2844637 -0.52664027 -7.479763e-02 -#> 72 0.4682708 -0.73882245 -3.124134e-01 -#> 73 0.5452217 -0.17237583 4.468084e-01 -#> 74 0.4910282 -0.04503763 5.934957e-01 -#> 75 0.3672503 -0.18246860 -1.035631e-06 -#> 76 0.2136315 -0.90686326 -3.987184e-01 -#> 77 0.4519942 -0.80640277 -1.886841e-01 -#> 78 0.3518958 -0.82409806 -2.902659e-01 -#> 79 0.5766533 -0.65742620 -1.647240e-01 -#> 80 0.4733822 -0.39712517 1.575903e-01 -#> 81 0.6716634 -0.37950288 1.149491e-01 -#> 82 0.3241315 -0.77792334 -1.097274e-01 -#> 83 0.3197599 -0.10474425 2.612698e-01 -#> 84 0.5146523 -0.47545167 -3.661290e-03 -#> 85 0.5676750 -0.35110421 1.421802e-01 -#> 86 0.4601762 -0.64703527 3.208253e-01 -#> 87 0.5676750 -0.35110421 1.421802e-01 -#> 88 0.5146523 -0.47545167 -3.661290e-03 -#> 89 0.7111648 -0.25208914 2.856139e-01 -#> 90 0.5425279 -0.21511041 4.128249e-01 -#> 91 0.6716634 -0.37950288 1.149491e-01 -#> 92 0.5936046 -0.65734376 -2.499049e-01 -#> 93 0.5344965 -0.70674608 -5.314845e-01 -#> 94 0.3518958 -0.82409806 -2.902659e-01 -#> 95 0.4453857 -0.37948184 -5.103432e-02 -#> 96 0.4601762 -0.64703527 3.208253e-01 -#> 97 0.4682708 -0.73882245 -3.124134e-01 -#> 98 0.7111648 -0.25208914 2.856139e-01 -#> 99 0.7489848 -0.29036293 1.232090e-01 -#> 100 0.7800076 -0.33988351 6.324268e-01 +#> ETA_Cl ETA_Vc ETA_Ka +#> 1 0.44852256 -0.29386695 0.25508142 +#> 2 0.62575211 -0.12598185 0.39581785 +#> 3 0.59394319 -0.61283467 0.44309473 +#> 4 0.40840374 -0.11424231 0.88523822 +#> 5 0.39724995 -0.81841411 0.03467140 +#> 6 0.39724995 -0.81841411 0.03467140 +#> 7 0.63383635 -0.09208788 0.75313256 +#> 8 0.56503241 -0.38163429 0.57870438 +#> 9 0.39724995 -0.81841411 0.03467140 +#> 10 0.63383635 -0.09208788 0.75313256 +#> 11 0.68819786 -0.43456690 0.60967953 +#> 12 0.70134619 -0.25923790 0.36886223 +#> 13 0.57930142 -0.19223329 0.36675144 +#> 14 0.48137467 -0.64077946 0.37626331 +#> 15 0.62575211 -0.12598185 0.39581785 +#> 16 0.70134619 -0.25923790 0.36886223 +#> 17 0.48137467 -0.64077946 0.37626331 +#> 18 0.56600985 -0.62603555 0.27337490 +#> 19 0.53665236 -0.51802076 0.20000937 +#> 20 0.45547826 -0.17371863 0.17395510 +#> 21 0.66424372 -0.24149717 0.47234145 +#> 22 0.57040379 -0.01801166 0.57500526 +#> 23 0.55291123 -0.28819509 0.20794277 +#> 24 0.67968027 -0.21978421 -0.09310346 +#> 25 0.52795909 -0.54265204 0.44086921 +#> 26 0.70134619 -0.25923790 0.36886223 +#> 27 0.47328909 -0.58699755 -0.04404405 +#> 28 0.52795909 -0.54265204 0.44086921 +#> 29 0.45793620 -0.19267881 0.41387686 +#> 30 0.25327703 0.03343085 0.50612767 +#> 31 0.52674334 -0.85568939 -0.49246147 +#> 32 0.50199137 -0.62194414 -0.24232686 +#> 33 0.59394319 -0.61283467 0.44309473 +#> 34 0.31373832 -0.09809849 0.57244114 +#> 35 0.18632569 -0.89355390 0.19705018 +#> 36 0.63383635 -0.09208788 0.75313256 +#> 37 0.53665236 -0.51802076 0.20000937 +#> 38 0.45722782 -0.71688383 0.07553748 +#> 39 -0.05336188 -0.69167479 0.14448127 +#> 40 0.45793620 -0.19267881 0.41387686 +#> 41 0.51192193 -0.27347692 0.10202829 +#> 42 0.63493108 -0.37178185 0.16556913 +#> 43 0.30917621 -0.14303649 0.80466715 +#> 44 0.38975992 -0.57378467 0.13013143 +#> 45 0.82675130 -0.28968964 0.69288199 +#> 46 0.47328909 -0.58699755 -0.04404405 +#> 47 0.63383635 -0.09208788 0.75313256 +#> 48 0.47328909 -0.58699755 -0.04404405 +#> 49 0.63844449 -0.62540066 -0.51541830 +#> 50 0.68819786 -0.43456690 0.60967953 +#> 51 0.55291123 -0.28819509 0.20794277 +#> 52 0.51192193 -0.27347692 0.10202829 +#> 53 0.39724995 -0.81841411 0.03467140 +#> 54 0.63493108 -0.37178185 0.16556913 +#> 55 0.44992593 -0.32358339 0.03937631 +#> 56 0.48137467 -0.64077946 0.37626331 +#> 57 0.53665236 -0.51802076 0.20000937 +#> 58 0.52795909 -0.54265204 0.44086921 +#> 59 0.11813435 -0.18505916 0.93527226 +#> 60 0.25020257 -0.74575927 0.09959267 +#> 61 0.52842062 -0.15474910 0.34863771 +#> 62 0.69634207 -0.07639143 0.66612093 +#> 63 0.52674334 -0.85568939 -0.49246147 +#> 64 0.49828543 -0.31856056 0.27567836 +#> 65 0.42622606 -0.54409046 0.44775164 +#> 66 0.15901163 -1.18927775 -0.57918034 +#> 67 0.17490942 -1.10956435 -0.45372110 +#> 68 0.69634207 -0.07639143 0.66612093 +#> 69 0.14302569 -1.10172538 -0.52271669 +#> 70 0.52674334 -0.85568939 -0.49246147 +#> 71 0.48033027 -0.64682978 -0.02260275 +#> 72 0.15901163 -1.18927775 -0.57918034 +#> 73 0.62575211 -0.12598185 0.39581785 +#> 74 0.49828543 -0.31856056 0.27567836 +#> 75 0.36795919 -0.75276468 -0.06179420 +#> 76 0.69634207 -0.07639143 0.66612093 +#> 77 0.54905702 -0.14764846 0.04712659 +#> 78 0.44852256 -0.29386695 0.25508142 +#> 79 0.32465620 -0.39749854 -0.07578372 +#> 80 0.63493108 -0.37178185 0.16556913 +#> 81 0.16422777 -0.25200611 0.13971027 +#> 82 0.45722782 -0.71688383 0.07553748 +#> 83 0.57040379 -0.01801166 0.57500526 +#> 84 0.47328909 -0.58699755 -0.04404405 +#> 85 0.67968027 -0.21978421 -0.09310346 +#> 86 0.45722782 -0.71688383 0.07553748 +#> 87 0.42474687 0.14418013 0.59865979 +#> 88 0.69634207 -0.07639143 0.66612093 +#> 89 0.52674334 -0.85568939 -0.49246147 +#> 90 0.42607558 -0.89032711 0.86664143 +#> 91 0.45793620 -0.19267881 0.41387686 +#> 92 0.51192193 -0.27347692 0.10202829 +#> 93 0.69634207 -0.07639143 0.66612093 +#> 94 0.68819786 -0.43456690 0.60967953 +#> 95 0.63493108 -0.37178185 0.16556913 +#> 96 0.63493108 -0.37178185 0.16556913 +#> 97 0.47874096 -0.35202249 -0.06691333 +#> 98 0.47874096 -0.35202249 -0.06691333 +#> 99 0.36795919 -0.75276468 -0.06179420 +#> 100 0.69634207 -0.07639143 0.66612093 #> #> $model #> ── Solved rxode2 object ── #> ── Parameters ($params): ── #> # A tibble: 100 × 7 -#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 4 70 1 0.268 -0.131 0.597 -#> 2 2 4 70 1 0.461 -0.411 0.0417 -#> 3 3 4 70 1 0.711 -0.252 0.286 -#> 4 4 4 70 1 0.468 -0.739 -0.312 -#> 5 5 4 70 1 0.394 -0.641 0.0971 -#> 6 6 4 70 1 0.394 -0.641 0.0971 -#> 7 7 4 70 1 0.273 -0.0600 0.650 -#> 8 8 4 70 1 0.394 -0.641 0.0971 -#> 9 9 4 70 1 0.816 -0.189 0.0999 -#> 10 10 4 70 1 0.600 -0.603 -0.574 +#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 4 70 1 0.449 -0.294 0.255 +#> 2 2 4 70 1 0.626 -0.126 0.396 +#> 3 3 4 70 1 0.594 -0.613 0.443 +#> 4 4 4 70 1 0.408 -0.114 0.885 +#> 5 5 4 70 1 0.397 -0.818 0.0347 +#> 6 6 4 70 1 0.397 -0.818 0.0347 +#> 7 7 4 70 1 0.634 -0.0921 0.753 +#> 8 8 4 70 1 0.565 -0.382 0.579 +#> 9 9 4 70 1 0.397 -0.818 0.0347 +#> 10 10 4 70 1 0.634 -0.0921 0.753 #> # ℹ 90 more rows #> ── Initial Conditions ($inits): ── #> depot centr AUC @@ -309,14 +309,14 @@

Examples

#> #> ── First part of data (object): ── #> # A tibble: 200 × 13 -#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 1 4 70 1 5.23 61.4 1.82 0.0852 23.0 5.30e+2 1413. -#> 2 1 14 4 70 1 5.23 61.4 1.82 0.0852 10.6 2.95e-8 651. -#> 3 2 1 4 70 1 6.34 46.4 1.04 0.137 21.8 9.25e+2 1013. -#> 4 2 14 4 70 1 6.34 46.4 1.04 0.137 7.57 1.20e-3 352. -#> 5 3 1 4 70 1 8.15 54.4 1.33 0.150 21.5 7.51e+2 1169. -#> 6 3 14 4 70 1 8.15 54.4 1.33 0.150 5.29 2.31e-5 288. +#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 1 4 70 1 6.26 52.2 1.29 0.120 22.3 7.73e+2 1163. +#> 2 1 14 4 70 1 6.26 52.2 1.29 0.120 8.11 4.00e-5 423. +#> 3 2 1 4 70 1 7.48 61.7 1.49 0.121 20.4 6.72e+2 1258. +#> 4 2 14 4 70 1 7.48 61.7 1.49 0.121 6.67 2.75e-6 412. +#> 5 3 1 4 70 1 7.24 37.9 1.56 0.191 32.9 6.38e+2 1249. +#> 6 3 14 4 70 1 7.24 37.9 1.56 0.191 4.35 1.03e-6 165. #> # ℹ 194 more rows #> # ℹ 1 more variable: AUC <dbl> #> diff --git a/docs/reference/poso_inter_cmin.html b/docs/reference/poso_inter_cmin.html index 7622549..e8631a3 100644 --- a/docs/reference/poso_inter_cmin.html +++ b/docs/reference/poso_inter_cmin.html @@ -251,7 +251,7 @@

Examples

poso_inter_cmin(dat=df_patient01,prior_model=mod_run001, dose=1500,duration=0.5,target_cmin=2.5) #> $interval -#> [1] 17.76029 +#> [1] 17.76031 #> #> $type_of_estimate #> [1] "point estimate" @@ -261,7 +261,7 @@

Examples

#> #> $indiv_param #> THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> 1 4 70 1 0.6019035 -0.4291734 0.1278478 +#> 1 4 70 1 0.6019036 -0.4291701 0.1278592 #> diff --git a/docs/reference/poso_simu_pop.html b/docs/reference/poso_simu_pop.html index 9cc03b0..feb5d91 100644 --- a/docs/reference/poso_simu_pop.html +++ b/docs/reference/poso_simu_pop.html @@ -166,124 +166,124 @@

Examples

# estimate the prior distribution of population parameters poso_simu_pop(dat=df_patient01,prior_model=mod_run001,n_simul=100) #> $eta -#> ETA_Cl ETA_Vc ETA_Ka -#> 1 -0.405685873 0.255727046 -0.19994987 -#> 2 0.168863232 0.362470457 0.36978196 -#> 3 -0.397274612 -0.025681302 0.38382423 -#> 4 0.300818507 0.838894622 0.51024836 -#> 5 -0.593018012 0.322290611 0.12563880 -#> 6 -0.094713710 0.193955707 -0.23453661 -#> 7 -0.307652180 -0.413525151 -0.25415091 -#> 8 0.225731088 -0.381095872 0.47093112 -#> 9 -0.116372383 0.160926553 0.10695373 -#> 10 0.089726221 0.053581916 0.53553320 -#> 11 0.261037582 0.105805281 -0.10772076 -#> 12 -0.451417238 0.091871003 -0.22624305 -#> 13 -0.529238757 -0.068759016 0.14064092 -#> 14 -0.473099562 -0.336727386 0.20104400 -#> 15 0.401830945 0.071903819 -0.40063230 -#> 16 -0.353078928 -0.358343735 0.52607602 -#> 17 0.285518170 0.469113124 -1.00410888 -#> 18 -0.004799354 0.098936377 -0.14999348 -#> 19 -0.139963889 0.341711624 -0.70195938 -#> 20 0.756648984 0.166537053 -0.76328425 -#> 21 -0.646615298 0.320843667 0.86904169 -#> 22 0.305218188 -0.069892099 -0.19948560 -#> 23 0.040831534 -0.028159882 0.75580429 -#> 24 0.301294673 -0.502043299 -0.40771127 -#> 25 0.278066119 0.001336468 0.11578399 -#> 26 -0.131118458 -0.083852708 0.03019897 -#> 27 0.669627884 -0.229700953 0.05497179 -#> 28 -0.120985201 -0.277572997 0.13633472 -#> 29 -0.047814106 -0.210900395 -0.03367084 -#> 30 0.038222927 -0.079867392 0.31473728 -#> 31 -0.838271343 -0.086193967 -0.32549485 -#> 32 -0.229816655 -0.551278828 0.42453581 -#> 33 0.262472280 -0.314042381 -0.23578973 -#> 34 -0.480036824 -0.019650865 0.32182896 -#> 35 -0.211150040 0.013837432 -0.25612592 -#> 36 0.248828516 0.126327979 -0.38885632 -#> 37 -0.373563389 0.089796875 -0.43369736 -#> 38 0.322363643 0.511216606 -0.02644541 -#> 39 -0.643179708 -0.064446830 0.04386968 -#> 40 -0.044162963 0.862266584 -0.74980888 -#> 41 0.289650436 0.092206489 0.52547264 -#> 42 0.966601613 -0.365461121 0.03297253 -#> 43 0.264271990 0.302167657 -0.64038830 -#> 44 -0.043747700 0.040431782 -0.01957620 -#> 45 -0.127791961 -0.261948063 -0.39546700 -#> 46 0.029649086 -0.342314641 0.24409704 -#> 47 0.275299027 -0.091149872 -0.29137703 -#> 48 -0.238015074 0.156354784 0.43957466 -#> 49 0.203048017 -0.717635153 -0.77542924 -#> 50 0.285532177 -0.869346814 -0.29224191 -#> 51 0.202781671 0.187541692 0.11178506 -#> 52 0.216243902 0.222473391 -0.67473809 -#> 53 0.506165217 -0.034542599 -0.03055766 -#> 54 -0.219306520 0.110051707 0.09309839 -#> 55 -0.046686266 0.137879259 -0.28200030 -#> 56 -0.006276491 0.182935981 0.37301158 -#> 57 0.605869628 -0.184665609 0.38401660 -#> 58 -0.069895369 0.234078584 -0.19646084 -#> 59 -0.694746813 0.198764143 -0.13836866 -#> 60 -0.237380814 -0.978029888 0.32981412 -#> 61 0.017306712 -0.500146243 0.56021582 -#> 62 0.027218891 -0.270374998 0.01604977 -#> 63 0.630428858 -0.683705763 -0.78858996 -#> 64 -0.225972160 -1.281142858 -0.49715821 -#> 65 -0.603456747 0.947598042 -0.38490606 -#> 66 0.060522260 -0.372518557 0.56220804 -#> 67 0.194349803 -0.414470444 0.51841969 -#> 68 0.356872010 0.413791584 -0.04697531 -#> 69 -0.263396625 -0.044948193 0.62095434 -#> 70 0.155155536 0.567951941 0.13047124 -#> 71 -0.085047125 0.151981605 0.09265632 -#> 72 0.042892431 0.122012727 -0.05298408 -#> 73 -0.514237959 0.129619659 -1.22214162 -#> 74 0.558987418 0.480893210 -0.14276880 -#> 75 0.209894366 0.426497688 -0.37816601 -#> 76 -0.067459369 -0.574746547 -0.49992508 -#> 77 -0.194199400 0.143188463 -0.60799019 -#> 78 -0.323650512 0.105670465 0.17196343 -#> 79 0.767931892 0.676420488 0.02158285 -#> 80 -0.223061147 -0.162688216 -0.88181021 -#> 81 0.310689610 -0.595051248 0.06945858 -#> 82 0.773209170 0.059206792 0.41502296 -#> 83 -0.170130618 -0.090561497 -0.01888843 -#> 84 0.301699965 0.166102897 -0.16159094 -#> 85 0.146137057 -0.355585943 0.28340259 -#> 86 -0.481017347 -0.013319583 -0.14784661 -#> 87 0.165211246 0.502416410 -0.22257059 -#> 88 0.242502764 -0.108216504 -0.17939949 -#> 89 -0.605324417 -0.547328146 -0.42436153 -#> 90 -0.180478592 -0.353612222 0.27601742 -#> 91 -0.453667929 -0.775820891 0.35124463 -#> 92 -0.335635693 0.358789784 -0.12666541 -#> 93 0.684363813 0.075004843 0.37758052 -#> 94 -0.210610255 -0.016802484 0.57048132 -#> 95 0.076725310 0.636690142 0.53890615 -#> 96 -0.023863121 -0.132823865 -0.60013555 -#> 97 -0.506439688 0.126798566 0.82510155 -#> 98 0.003155287 -0.258136441 -0.48321102 -#> 99 0.060681301 0.171496959 0.30772064 -#> 100 0.571632214 0.085845212 -0.30852275 +#> ETA_Cl ETA_Vc ETA_Ka +#> 1 -0.088713429 0.657778814 0.482539929 +#> 2 0.024779356 0.698031088 -0.561559905 +#> 3 -0.304029379 -0.499987189 0.016071504 +#> 4 0.451357827 -0.846511350 -0.704708476 +#> 5 0.543587732 0.251604918 0.316886613 +#> 6 -0.330443435 -0.107931104 -0.393796622 +#> 7 -0.136087817 -0.483145924 0.139740759 +#> 8 -0.689545759 -0.862492706 0.103687178 +#> 9 0.420246256 -0.549074178 0.047185767 +#> 10 0.425258603 0.862404356 -0.167390190 +#> 11 -0.227509156 0.490325163 0.176819358 +#> 12 -0.239046457 -0.113336591 0.357634726 +#> 13 0.611836325 -0.007100804 -0.087267629 +#> 14 -0.359398492 -0.813314450 0.233305397 +#> 15 0.795502466 0.199594328 0.562177110 +#> 16 0.054789244 -0.389553037 0.482093493 +#> 17 -0.962858199 0.467670321 -0.455429897 +#> 18 0.657466098 0.099285889 0.308068118 +#> 19 0.184699317 0.280267768 0.041000396 +#> 20 -0.584463968 -0.029128631 -0.493139413 +#> 21 -1.055908743 -0.196718060 -0.403538741 +#> 22 -0.489590553 0.127412217 -0.011038822 +#> 23 0.159909243 -0.096954495 -0.004201785 +#> 24 -0.474577951 -0.140669221 -0.538539754 +#> 25 0.183522904 0.022811374 0.313685457 +#> 26 -0.367552647 -0.033672415 -0.061232256 +#> 27 -0.189274828 0.533978446 -0.469404763 +#> 28 -0.657634274 0.128731772 0.847483033 +#> 29 1.051023817 -0.435081054 0.202482521 +#> 30 0.856535556 -0.680246237 -0.007453003 +#> 31 -0.194833273 -0.675718041 -0.728366580 +#> 32 -0.910815595 -0.234757413 -0.195455592 +#> 33 0.028085043 0.497306684 0.241112751 +#> 34 -0.267231270 0.027329298 -1.054405756 +#> 35 -0.060056485 0.615777949 -0.586502007 +#> 36 0.225776754 0.555060904 0.311025225 +#> 37 0.222120429 -0.193915454 0.202972937 +#> 38 0.404186490 -0.151245337 -0.342301520 +#> 39 0.364625781 0.567361622 0.151514594 +#> 40 -1.025132129 0.448902967 0.026359040 +#> 41 0.289285640 -0.246130026 -0.473581338 +#> 42 -0.154038533 0.927733919 0.181588188 +#> 43 -0.022025325 0.872619302 0.134119925 +#> 44 -0.489804904 0.253779648 0.277949613 +#> 45 0.462010225 -0.311165299 -0.127382476 +#> 46 0.260468366 0.368789886 -0.311692292 +#> 47 0.257120952 -0.283153065 0.686607586 +#> 48 0.108468325 -1.001809097 0.476099240 +#> 49 -0.302927339 0.057778694 0.148540853 +#> 50 -0.188303023 0.590328845 -1.392815286 +#> 51 -0.867989622 -0.031555704 -0.130444325 +#> 52 -0.108838058 -0.463916571 0.215364862 +#> 53 -0.269351149 0.525022161 -0.808047559 +#> 54 -0.479084981 0.604059651 -0.288989776 +#> 55 -0.690879045 0.666040888 -0.327805402 +#> 56 0.019824115 -0.581495193 -0.034490510 +#> 57 0.100676719 0.351308076 0.057216712 +#> 58 -0.353533119 0.013805637 0.363635507 +#> 59 -0.531403314 -0.172698824 0.225684048 +#> 60 -0.127281637 -0.921468066 0.365019656 +#> 61 0.282144592 -0.593071630 0.345984144 +#> 62 0.926555192 -0.629831396 0.184001929 +#> 63 -0.158215134 -0.787065510 1.338552988 +#> 64 0.495007072 -1.073195859 -0.706941213 +#> 65 -0.536996930 -0.184222258 -0.625729577 +#> 66 0.497247849 -0.991201755 0.128326509 +#> 67 -0.363989123 -0.571189872 0.174799835 +#> 68 0.279521913 0.427851248 -0.225328712 +#> 69 0.089714046 0.281764087 0.117748885 +#> 70 -0.311261757 0.382812185 0.137124681 +#> 71 0.581333200 0.270634546 0.253852640 +#> 72 -0.544889684 -0.355512812 0.186011634 +#> 73 -0.869792795 0.163932335 -0.223194866 +#> 74 0.140964820 0.551690769 -0.038489024 +#> 75 1.115526759 0.337677529 -0.494461345 +#> 76 0.275930487 0.429192004 -0.055415346 +#> 77 -0.530956256 -0.271757881 -0.019338360 +#> 78 0.021425997 1.208914818 0.161434293 +#> 79 0.278166139 0.150441467 0.743808277 +#> 80 0.151298485 -0.888936251 -0.259950783 +#> 81 0.103944767 -0.107277416 0.464530432 +#> 82 0.566073487 -0.057631857 -0.094237606 +#> 83 -0.118308179 0.700750884 -0.664477413 +#> 84 -0.420754231 0.063564301 -0.048467328 +#> 85 -0.009610177 0.186680771 0.024464290 +#> 86 0.044863656 0.237561169 0.289888628 +#> 87 -0.416610518 -0.143699649 0.341219857 +#> 88 -1.181518399 0.899520309 0.265760067 +#> 89 -0.063059367 0.066039348 -0.605469917 +#> 90 0.208931133 -0.123476949 -0.665562659 +#> 91 0.288140477 0.250935100 -0.080051566 +#> 92 0.101704856 -0.055483309 1.352698049 +#> 93 0.517078953 1.104117086 -0.752468252 +#> 94 -0.291951481 -0.080034155 -0.151091387 +#> 95 -0.206103903 0.426983923 -0.153528703 +#> 96 0.611757708 0.194217066 -0.194746053 +#> 97 -0.653219723 -0.290014889 -0.036819270 +#> 98 -0.666456522 0.181437121 0.753227158 +#> 99 0.054177406 0.738175261 0.702728105 +#> 100 0.576569459 0.386006889 0.438725816 #> #> $model #> ── Solved rxode2 object ── #> ── Parameters ($params): ── #> # A tibble: 100 × 7 -#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 4 70 1 -0.406 0.256 -0.200 -#> 2 2 4 70 1 0.169 0.362 0.370 -#> 3 3 4 70 1 -0.397 -0.0257 0.384 -#> 4 4 4 70 1 0.301 0.839 0.510 -#> 5 5 4 70 1 -0.593 0.322 0.126 -#> 6 6 4 70 1 -0.0947 0.194 -0.235 -#> 7 7 4 70 1 -0.308 -0.414 -0.254 -#> 8 8 4 70 1 0.226 -0.381 0.471 -#> 9 9 4 70 1 -0.116 0.161 0.107 -#> 10 10 4 70 1 0.0897 0.0536 0.536 +#> sim.id THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 4 70 1 -0.0887 0.658 0.483 +#> 2 2 4 70 1 0.0248 0.698 -0.562 +#> 3 3 4 70 1 -0.304 -0.500 0.0161 +#> 4 4 4 70 1 0.451 -0.847 -0.705 +#> 5 5 4 70 1 0.544 0.252 0.317 +#> 6 6 4 70 1 -0.330 -0.108 -0.394 +#> 7 7 4 70 1 -0.136 -0.483 0.140 +#> 8 8 4 70 1 -0.690 -0.862 0.104 +#> 9 9 4 70 1 0.420 -0.549 0.0472 +#> 10 10 4 70 1 0.425 0.862 -0.167 #> # ℹ 90 more rows #> ── Initial Conditions ($inits): ── #> depot centr AUC @@ -293,14 +293,14 @@

Examples

#> #> ── First part of data (object): ── #> # A tibble: 200 × 13 -#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr -#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> -#> 1 1 1 4 70 1 2.67 90.4 0.819 0.0295 9.94 1.09e+3 899. -#> 2 1 14 4 70 1 2.67 90.4 0.819 0.0295 15.3 2.60e-2 1383. -#> 3 2 1 4 70 1 4.74 101. 1.45 0.0471 12.7 6.90e+2 1282. -#> 4 2 14 4 70 1 4.74 101. 1.45 0.0471 10.8 4.65e-6 1082. -#> 5 3 1 4 70 1 2.69 68.2 1.47 0.0394 19.0 6.80e+2 1296. -#> 6 3 14 4 70 1 2.69 68.2 1.47 0.0394 17.5 3.51e-6 1195. +#> sim.id time TVCl TVVc TVKa Cl Vc Ka K20 Cc depot centr +#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> +#> 1 1 1 4 70 1 3.66 135. 1.62 0.0271 10.2 6.10e+2 1373. +#> 2 1 14 4 70 1 3.66 135. 1.62 0.0271 10.4 4.35e-7 1402. +#> 3 2 1 4 70 1 4.10 141. 0.570 0.0291 4.86 1.31e+3 683. +#> 4 2 14 4 70 1 4.10 141. 0.570 0.0291 10.0 7.89e-1 1411. +#> 5 3 1 4 70 1 2.95 42.5 1.02 0.0695 24.1 9.43e+2 1025. +#> 6 3 14 4 70 1 2.95 42.5 1.02 0.0695 19.4 1.73e-3 826. #> # ℹ 194 more rows #> # ℹ 1 more variable: AUC <dbl> #> diff --git a/docs/reference/poso_time_cmin.html b/docs/reference/poso_time_cmin.html index 9aeb22e..698442d 100644 --- a/docs/reference/poso_time_cmin.html +++ b/docs/reference/poso_time_cmin.html @@ -289,11 +289,11 @@

Examples

#> [1] "point estimate" #> #> $cmin_estimate -#> [1] 2.489931 +#> [1] 2.489933 #> #> $indiv_param #> THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> 1 4 70 1 0.6019037 -0.4291738 0.1278474 +#> 1 4 70 1 0.6019036 -0.4291734 0.1278479 #> diff --git a/tests/testthat.R b/tests/testthat.R index 5a60cdc..78971b5 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ -data.table::setDTthreads(2) #throttle data.table for CRAN +rxode2::setRxThreads(2) # limit the number of threads library(testthat) library(posologyr) diff --git a/vignettes/a_posteriori_dosing.Rmd b/vignettes/a_posteriori_dosing.Rmd index 9d30d6f..ccf706e 100644 --- a/vignettes/a_posteriori_dosing.Rmd +++ b/vignettes/a_posteriori_dosing.Rmd @@ -13,10 +13,7 @@ knitr::opts_chunk$set( comment = "#>" ) set.seed(1) -``` - -```{r chunkname, echo=-1} -data.table::setDTthreads(2) +rxode2::setRxThreads(2) # limit the number of threads ``` ```{r setup} diff --git a/vignettes/a_priori_dosing.Rmd b/vignettes/a_priori_dosing.Rmd index fcd8c7f..91f0574 100644 --- a/vignettes/a_priori_dosing.Rmd +++ b/vignettes/a_priori_dosing.Rmd @@ -13,10 +13,7 @@ knitr::opts_chunk$set( comment = "#>" ) set.seed(1) -``` - -```{r chunkname, echo=-1} -data.table::setDTthreads(2) +rxode2::setRxThreads(2) # limit the number of threads ``` ```{r setup} diff --git a/vignettes/auc_based_dosing.Rmd b/vignettes/auc_based_dosing.Rmd index dfdf87d..778a6d5 100644 --- a/vignettes/auc_based_dosing.Rmd +++ b/vignettes/auc_based_dosing.Rmd @@ -13,10 +13,7 @@ knitr::opts_chunk$set( comment="#>" ) set.seed(1) -``` - -```{r chunkname, echo=-1} -data.table::setDTthreads(2) +rxode2::setRxThreads(2) # limit the number of threads ``` ```{r setup} diff --git a/vignettes/multiple_endpoints.Rmd b/vignettes/multiple_endpoints.Rmd index 4d5978c..8147e00 100644 --- a/vignettes/multiple_endpoints.Rmd +++ b/vignettes/multiple_endpoints.Rmd @@ -12,10 +12,8 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) -``` - -```{r chunkname, echo=-1} -data.table::setDTthreads(2) +set.seed(1) +rxode2::setRxThreads(2) # limit the number of threads ``` ```{r setup}