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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')
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")
# 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
# ctr %>% pmx_plot_individual(1)
# ctr %>% pmx_plot_iwres_qq # ctr %>% pmx_plot_npde_qq
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")
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
ctr %>% pmx_plot_individual(1)
ctr %>% pmx_plot_iwres_qq ctr %>% pmx_plot_npde_qq
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")
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
ctr %>% pmx_plot_individual(1)
ctr %>% pmx_plot_eta_box ctr %>% pmx_plot_eta_hist
ctr %>% pmx_plot_eta_cats ctr %>% pmx_plot_eta_conts
ctr %>% pmx_plot_iwres_qq ctr %>% pmx_plot_npde_qq
ctr %>% pmx_plot_eta_matrix
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"))
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
ctr %>% pmx_plot_individual(1)
ctr %>% pmx_plot_eta_box ctr %>% pmx_plot_eta_hist
ctr %>% pmx_plot_iwres_qq ctr %>% pmx_plot_npde_qq
ctr %>% pmx_plot_eta_matrix
ctr %>% pmx_plot_eta_cats ctr %>% pmx_plot_eta_conts
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")
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
ctr %>% pmx_plot_individual(1,strat.facet=~DAY)
ctr %>% pmx_plot_eta_box ctr %>% pmx_plot_eta_hist
ctr %>% pmx_plot_iwres_qq ctr %>% pmx_plot_npde_qq
ctr %>% pmx_plot_eta_matrix
ctr %>% pmx_plot_eta_cats ctr %>% pmx_plot_eta_conts
#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")
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
ctr %>% pmx_plot_individual(1,strat.facet=~DAY)
ctr %>% pmx_plot_eta_box(has.jitter=TRUE) ctr %>% pmx_plot_eta_hist
ctr %>% pmx_plot_iwres_qq ctr %>% pmx_plot_npde_qq
ctr %>% pmx_plot_eta_matrix
ctr %>% pmx_plot_eta_cats ctr %>% pmx_plot_eta_conts
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