In tsahota/NMproject: Script Based 'NONMEM' Model Development

## DO NOT MODIFY THIS BLOCK (unless you know what you're doing)
library(knitr)
library(rprojroot)
opts_knit$set(root.dir = find_root(
  has_file(".Rprofile") | 
    is_rstudio_project | 
    is_r_package | 
    is_git_root
))
opts_chunk$set(echo = FALSE)
opts_chunk$set(message = FALSE)
if(!is.null(knitr::opts_knit$get('rmarkdown.pandoc.to'))){
  .m <- params$m  
}

## LOAD PACKAGES HERE

library(dplyr)
library(ggplot2)

devtools::load_all()

model object

wait_finish(.m)
.m

idEXPstat <- function(d, ...){ ## example statistic function
  ## arg = nonmem dataset data.frame
  ## return data.frame with statistic column
  d %>% group_by(ID, ...) %>% filter(is.na(AMT)) %>%
    summarise(
      AUC = AUC(time = TIME, conc = DV),
      CMAX = max(DV, na.rm = TRUE),
      TMAX = TIME[which.max(DV)]
    ) %>%
    tidyr::gather(key = "exposure", value = "statistic", AUC:TMAX) %>%
    ungroup()
}

EXPstat <- function(d, ...){ ## example statistic function
  ## arg = nonmem dataset data.frame
  ## return data.frame with statistic column
  d %>% idEXPstat(...) %>%  ## reuse idEXPstat for individual stats
    ## summarise over study and any other variables (...)
    group_by(exposure, ...) %>%
    summarise(
      median = median(statistic, na.rm = TRUE),
      cv = 100*sd(statistic, na.rm = TRUE)/mean(statistic, na.rm = TRUE)
    ) %>%
    tidyr::gather(key = "type", value = "statistic", median:cv)
}

plot profile of this subset

d <- .m %>%
  input_data(filter = TRUE)

d %>% mutate(id_period = paste(ID, TIME)) %>%
  ggplot(aes(x = TIME, y = DV, group = ID)) + theme_bw() +
  geom_line()

ppc_data0 <- .m %>% ppc_data(EXPstat)

ppc_data0 %>%
  filter(type %in% "median") %>%
  ## redefine exposure to include the type of summary
  mutate(exposure = paste(type, exposure, sep = "_")) %>%
  ppc_histogram_plot(exposure)

ppc_data0 %>%
  filter(type %in% "cv") %>%
  ## redefine exposure to include the type of summary
  mutate(exposure = paste(type, exposure, sep = "_")) %>%
  ppc_histogram_plot(exposure)

addWT_c <- . %>% mutate(
  WT_c = Hmisc::cut2(WT, g = 2)
)

ppc_data0 <- .m %>% ppc_data(EXPstat, WT_c, pre_proc = addWT_c)

ppc_data0 %>%
  filter(type %in% "median") %>%
  ## redefine exposure to include the type of summary
  mutate(exposure = paste(type, exposure, sep = "_")) %>%
  ppc_histogram_plot(WT_c, exposure)

ppc_data0 %>%
  filter(type %in% "cv") %>%
  ## redefine exposure to include the type of summary
  mutate(exposure = paste(type, exposure, sep = "_")) %>%
  ppc_histogram_plot(WT_c, exposure)

ppc_data0 %>%
  filter(type %in% "median") %>%
  ## redefine exposure to include the type of summary
  mutate(exposure = paste(type, exposure, sep = "_")) %>%
  ppc_whisker_plot(WT_c, exposure)

ppc_data0 %>%
  ppc_whisker_plot(WT_c, type) + 
  facet_wrap(~type+exposure, scales = "free")

ppc_data0 <- .m %>% ppc_data(idEXPstat)

ppc_data0 %>%
  ppc_whisker_plot(factor(ID), exposure)

tsahota/NMproject documentation built on Oct. 1, 2022, 11:51 a.m.