Example 4

Example with all information in the yaml file (except from parameter name) and pre-filtered bootstrap results passed by user.

Setup environment

# ----- Load package -----
library(pmxpartabc)

# ----- Define directory and file names -----
run_dir    <- file.path(system.file(package = "pmxpartabc"), "examples")
run_prefix <- "run"
runno     <-  "6"
boot.object <-  read.csv(file.path(run_dir, "bootstrap_dir2", "raw_results_run5boot.csv"), header = TRUE, check.names = FALSE)
yaml.file.name <- file.path(system.file(package = "pmxpartabc"), "meta.yaml")

Parameter table 1 - using yaml file

output <- parframe2setup(run_dir, 
                         run_prefix, 
                         runno, 
                         bootstrap = TRUE, 
                         conf.level = 0.95, 
                         min_suc = TRUE, 
                         read.boot = TRUE, 
                         boot.obj = boot.object, 
                         yaml.file = TRUE, 
                         yaml.file.name = yaml.file.name)

tab <- parframe(out=output[[1]], meta=output[[2]], bootstrap=TRUE)  

tab1 <- pmxpartab(tab, output[[2]], columns=c(value="Estimate", rse="RSE%", ci95="95%CI", shrinkage="Shrinkage"))

print(tab1)
Parameter Estimate RSE% 95%CI Shrinkage
Typical Values
Central volume (L) 24.7 8.29 21.7 – 26.8
Clearance (L/h) 0.659 249 0.303 – 0.759
Peripheral volume (L) 76.5 195 68.4 – 115
Peripheral clearance (L/h) 1.83 34.7 1.83 – 1.95
Absorption rate constant (h-1) 0.653 52.7 0.559 – 0.790
Between Subject Variability
On Central volume 0.169 22.2 0.0999 – 0.219 0.300%
Correlation on Clearance, on Central Volume 0.140 199 0.0928 – 0.336
On Clearance 0.358 282 0.234 – 1.62 1.30%
Residual Error
Proportional Error (-) 0.102 147 0.0977 – 0.115 20.1%

Session information

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.1252 
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] pmxpartabc_0.2.0
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.1   xfun_0.29          bslib_0.3.1        purrr_0.3.4       
##  [5] colorspace_2.0-2   vctrs_0.3.8        generics_0.1.2     htmltools_0.5.2   
##  [9] yaml_2.2.2         utf8_1.2.2         rlang_1.0.0        pkgdown_1.6.1     
## [13] jquerylib_0.1.4    pillar_1.7.0       glue_1.6.1         DBI_1.1.1         
## [17] tweenr_1.0.2       bit64_4.0.5        lifecycle_1.0.1    stringr_1.4.0     
## [21] munsell_0.5.0      gtable_0.3.0       ragg_1.1.3         xpose_0.4.13      
## [25] memoise_2.0.0      evaluate_0.14      knitr_1.37         tzdb_0.1.2        
## [29] fastmap_1.1.0.9000 parallel_4.1.1     fansi_1.0.2        Rcpp_1.0.8        
## [33] readr_2.0.1        scales_1.1.1       cachem_1.0.6       desc_1.3.0        
## [37] vroom_1.5.4        jsonlite_1.7.3     bit_4.0.4          farver_2.1.0      
## [41] systemfonts_1.0.2  fs_1.5.2           textshaping_0.3.5  hms_1.1.1         
## [45] ggforce_0.3.3      ggplot2_3.3.5      digest_0.6.29      stringi_1.7.6     
## [49] dplyr_1.0.7        polyclip_1.10-0    grid_4.1.1         rprojroot_2.0.2   
## [53] cli_3.1.1          tools_4.1.1        magrittr_2.0.2     sass_0.4.0        
## [57] table1_1.4.2       tibble_3.1.6       Formula_1.2-4      tidyr_1.2.0       
## [61] crayon_1.4.2       pkgconfig_2.0.3    ellipsis_0.3.2     MASS_7.3-54       
## [65] assertthat_0.2.1   rmarkdown_2.11     rstudioapi_0.13    R6_2.5.1          
## [69] compiler_4.1.1