In ggPMXdevelopment/ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

PK uses cases

library(ggPMX)


svn_path <- "~/projects/ggPMX_doc/USER_EXAMPLES/MLX//"
options(xtable.comment = FALSE)
uc <- read.csv(text="case,work_dir,type,input,dv,dvid,occ,cats,conts
1_popPK_model,PK_WITH_COVARIATE_IOV/1_popPK_model,PK,PKdata_ggPMX.csv,DV,ytype,iss,SEX;RACE;DISE;ILOW,AGE0;WT0;HT0;TRT
PK_NO_COVARIATE,PK_NO_COVARIATE,PK,oral_data.txt,y,,,,
PK_NO_RE,PK_NO_RE,PK,warfarin_data2.csv,dv,dvid,,sex,wt
PK_WITH_COVARIATE,PK_WITH_COVARIATE,PK,warfarin_data3.csv,dv,dvid,,sex,wt
PK_WITH_COVARIATE_2,PK_WITH_COVARIATE_2,PK,warfarin_data4.csv,dv,dvid,,sex,wt
PK_WITH_COVARIATE_3,PK_WITH_COVARIATE_3,PK,PKdata_ggPMX.csv,DV,YTYPE,,SEX;RACE;ILOW,AGE0;WT0;TRT",
header=TRUE,
stringsAsFactors = FALSE)

uc1 <- uc
uc1$work_dir <- NULL

# knitr::opts_knit$get(kable.force.latex = TRUE)
print(xtable::xtable(uc1,caption="PK uses cases parameters"), scalebox='0.75')

PK_NO_COVARIATE

init the controller

work_dir <- "PK_NO_COVARIATE"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS_NO_FINEGRID"),
  input=file.path(work_dir,"oral_data.txt"),
  dv="y",
  dvid="dvid")

Residual plots

# ctr %>% pmx_plot_dv_pred
# ctr %>% pmx_plot_iwres_ipred
# ctr %>% pmx_plot_iwres_time
# ctr %>% pmx_plot_npde_pred
# ctr %>% pmx_plot_npde_time
# ctr %>% pmx_plot_dv_pred
# ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

# ctr %>% pmx_plot_individual(1)

QQ plots

# ctr %>% pmx_plot_iwres_qq
# ctr %>% pmx_plot_npde_qq

PK_NO_RE

init the controller

work_dir <- "PK_NO_RE"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS"),
  input=file.path(work_dir,"warfarin_data2.csv"),
  dv="dv",
  dvid="dvid",
  cats="sex",
  conts="wt")

Residual plots

ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_iwres_ipred
ctr %>% pmx_plot_iwres_time
ctr %>% pmx_plot_npde_pred
ctr %>% pmx_plot_npde_time
ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

ctr %>% pmx_plot_individual(1)

QQ plots

ctr %>% pmx_plot_iwres_qq
ctr %>% pmx_plot_npde_qq

Stratification

1_popPK_model

init the controller

work_dir <- "PK_WITH_COVARIATE_IOV/1_popPK_model"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS"),
  input=file.path(work_dir,"PKdata_ggPMX.csv"),
  dv="DV",
  dvid="YTYPE",
  cats=c("SEX","RACE","DISE","ILOW"),
  conts=c("AGE0","WT0","HT0","TRT"),
  occ="ISS")

Residual plots

ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_iwres_ipred
ctr %>% pmx_plot_iwres_time
ctr %>% pmx_plot_npde_pred
ctr %>% pmx_plot_npde_time
ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

ctr %>% pmx_plot_individual(1)

Distribution plots

ctr %>% pmx_plot_eta_box
ctr %>% pmx_plot_eta_hist

Relationships between estimated inter-individual random effects (ETA) and covariates

ctr %>% pmx_plot_eta_cats
ctr %>% pmx_plot_eta_conts

QQ plots

ctr %>% pmx_plot_iwres_qq
ctr %>% pmx_plot_npde_qq

Distribution and correlation structure of estimated inter-individual random effects (ETA)

ctr %>% pmx_plot_eta_matrix

Stratification

PK_WITH_COVARIATE

init the controller

work_dir <- "PK_WITH_COVARIATE"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS"),
  input=file.path(work_dir,"warfarin_data3.csv"),
  dv="dv",
  dvid="dvid",
  cats=c("sex"),
  conts=c("wt"))

Residual plots

ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_iwres_ipred
ctr %>% pmx_plot_iwres_time
ctr %>% pmx_plot_npde_pred
ctr %>% pmx_plot_npde_time
ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

ctr %>% pmx_plot_individual(1)

Distribution plots

ctr %>% pmx_plot_eta_box
ctr %>% pmx_plot_eta_hist

QQ plots

ctr %>% pmx_plot_iwres_qq
ctr %>% pmx_plot_npde_qq

Distribution and correlation structure of estimated inter-individual random effects (ETA)

ctr %>% pmx_plot_eta_matrix

Relationships between estimated inter-individual random effects (ETA) and covariates

ctr %>% pmx_plot_eta_cats
ctr %>% pmx_plot_eta_conts

Stratification

PK_WITH_COVARIATE_2

init the controller

work_dir <- "PK_WITH_COVARIATE_2"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS"),
  input=file.path(work_dir,"warfarin_data4.csv"),
  dv="dv",
  dvid="dvid",
  cats=c("sex"),
  conts=c("wt"),
  strats="day")

Residual plots

ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_iwres_ipred
ctr %>% pmx_plot_iwres_time
ctr %>% pmx_plot_npde_pred
ctr %>% pmx_plot_npde_time
ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

ctr %>% pmx_plot_individual(1,strat.facet=~DAY)

Distribution plots

ctr %>% pmx_plot_eta_box
ctr %>% pmx_plot_eta_hist

QQ plots

ctr %>% pmx_plot_iwres_qq
ctr %>% pmx_plot_npde_qq

Distribution and correlation structure of estimated inter-individual random effects (ETA)

ctr %>% pmx_plot_eta_matrix

Relationships between estimated inter-individual random effects (ETA) and covariates

ctr %>% pmx_plot_eta_cats
ctr %>% pmx_plot_eta_conts

Stratification

PK_WITH_COVARIATE_3

init the controller

#svn_path = "~/ggPMX/trunk/USER_EXAMPLES/MLX"
work_dir <- "PK_WITH_COVARIATE_3"
work_dir <- file.path(svn_path,work_dir)
ctr <- pmx_mlx(
  "standing",
  directory=file.path(work_dir,"RESULTS"),
  input=file.path(work_dir,"PKdata_ggPMX.csv"),
  dv="DV",
  dvid="DVID",
  cats=c("SEX", "RACE", "ILOW"),
  conts=c("AGE0", "WT0","TRT"),
  strats="DOSE")

Residual plots

ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_iwres_ipred
ctr %>% pmx_plot_iwres_time
ctr %>% pmx_plot_npde_pred
ctr %>% pmx_plot_npde_time
ctr %>% pmx_plot_dv_pred
ctr %>% pmx_plot_abs_iwres_ipred

Individual plots

ctr %>% pmx_plot_individual(1,strat.facet=~DAY)

Distribution plots

ctr %>% pmx_plot_eta_box(has.jitter=TRUE)
ctr %>% pmx_plot_eta_hist

QQ plots

ctr %>% pmx_plot_iwres_qq
ctr %>% pmx_plot_npde_qq

Distribution and correlation structure of estimated inter-individual random effects (ETA)

ctr %>% pmx_plot_eta_matrix

Relationships between estimated inter-individual random effects (ETA) and covariates

ctr %>% pmx_plot_eta_cats
ctr %>% pmx_plot_eta_conts

Stratification

ggPMXdevelopment/ggPMX documentation built on Dec. 11, 2023, 5:24 a.m.