library(dplyr)\nlibrary(tidyverse)\n\nlibrary(linpk)\nlibrary(haven)\n\nrm(list = ls())\n\n# basic structure\nstdy <- c(1, 2, 3)\nsex <- c(0, 1)\nrace <- c(1, 2, 3)\nntad <- c(0, 0.5, 1, 2, 4, 8, 12, 16, 24, 48, 72)\n# end basic structure\n\n# create dummy foundation with random wt, ht, bmi, age\nfoundation <- data.frame(stdy) %>% \n full_join(data.frame(sex), by = character()) %>%\n full_join(data.frame(race), by = character()) %>%\n mutate(\n c = NA,\n id = row_number(),\n wt = runif(row_number(), 70, 100),\n ht = runif(row_number(), 150, 200),\n bmi = wt \/ ((ht \/ 100) ^ 2),\n age = runif(row_number(), 30, 60)\n ) %>% \n mutate_at(\n vars(wt, ht, bmi), list(~ round(., 2))\n ) %>%\n mutate_at(\n vars(age), list(~ trunc(.))\n ) %>%\n full_join(data.frame(ntad), by = character())\n\n# prepare pc\nfoundation.pc <- foundation %>%\n mutate(\n evid = 0L,\n cmt = 2L,\n mdv = 0, \n amt = NA\n )\n\n# prepare ex\nfoundation.ex <- foundation %>%\n filter(ntad == 0) %>%\n mutate(\n evid = 1L,\n cmt = 1L,\n addl = NA,\n ii = NA, \n mdv = 1,\n amt = case_when(\n stdy == 1 ~ 100L,\n stdy == 2 ~ 200L,\n stdy == 3 ~ 300L,\n TRUE ~ -99L\n )\n )\n\n# set pc and ex and locf amt as dose\nfoundation.nonmem <- bind_rows(foundation.pc, foundation.ex) %>%\n arrange(stdy, id, ntad, evid) %>%\n mutate(\n dose = amt,\n tad = case_when(\n ntad == 0 & evid == 0 ~ -0.05,\n TRUE ~ ntad\n ),\n ) %>%\n group_by(stdy, id) %>%\n tidyr::fill(dose, .direction = c(\"downup\")) %>%\n ungroup() \n\n# populate dummy concs with pklin::pkprofile\nfoundation.nonmem$dv = pkprofile(foundation.nonmem$tad, cl=0.5, vc=11, ka=1.3, dose = list(amt = foundation.nonmem$dose))\n\n#introduce some randomness to pk concs\nfoundation.nonmem <- foundation.nonmem %>%\n mutate(\n dv = as.numeric(dv) * runif(row_number(), 1.1, 1.25) * (dose \/ 100),\n dv = ifelse(evid == 0, dv, NA), \n lndv = case_when(\n dv == 0 ~ 0,\n TRUE ~ log(dv)\n )\n ) %>%\n mutate_at(vars(dv, lndv), list(~ round(., digits = 2)))\n\n# housekeeping, replace NAs, column names to uppercase, etc.\nfoundation.nonmem.final <- foundation.nonmem %>% \n mutate(\n across(everything(), ~replace_na(.x, \".\"))\n ) %>%\n select(c, stdy, id, tad, ntad, dose, amt, addl, ii, evid, cmt, dv, lndv, mdv, sex, race, age, wt, ht, bmi)\n\nnames(foundation.nonmem.final) <- stringr::str_to_upper(names(foundation.nonmem.final))\n\n# export to csv and xpt\nsetwd(\"~\/R\")\nwrite_csv(foundation.nonmem.final, file = \"dummy_nonmem.csv\")\nwrite_xpt(foundation.nonmem.final, path = \"dummy_nonmem.xpt\", name = \"NM\", version = 5)<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"I’m making available here a basic NONMEM dataset example, along with the R code used to create it. Hopefully it will be helpful to someone in future! CSV download: http:\/\/jvdl.me\/downloads\/nonmem\/dummy_nonmem.csv XPT download: http:\/\/jvdl.me\/downloads\/nonmem\/dummy_nonmem.xpt<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[67,53,61],"tags":[70,72,71,69,68,64],"class_list":["post-395","post","type-post","status-publish","format-standard","hentry","category-pharma","category-programming","category-r","tag-dataset","tag-example","tag-free","tag-nonmem","tag-pharma","tag-r"],"_links":{"self":[{"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/posts\/395","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=395"}],"version-history":[{"count":7,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/posts\/395\/revisions"}],"predecessor-version":[{"id":404,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=\/wp\/v2\/posts\/395\/revisions\/404"}],"wp:attachment":[{"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=395"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=395"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/jvdl.me\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
![\"\"](\"http:\/\/jvdl.me\/wordpress\/wp-content\/uploads\/2021\/09\/nonmem_dummy.png\")
<\/figure>\n\n\n\n