diff --git a/.Rbuildignore b/.Rbuildignore index 7cb7150..2937836 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -21,3 +21,4 @@ ^dev$ ^vignettes/adxx\.Rmd$ ^vignettes/pharmaversesdtm\.Rmd$ +^data-raw$ diff --git a/.lintr b/.lintr index e3e6a1e..6f19a35 100644 --- a/.lintr +++ b/.lintr @@ -9,5 +9,6 @@ linters: linters_with_defaults( exclusions: list( "R/data.R" = Inf, "inst" = list(undesirable_function_linter = Inf), - "vignettes" = list(undesirable_function_linter = Inf) + "vignettes" = list(undesirable_function_linter = Inf), + "data-raw" = list(undesirable_function_linter = Inf) ) diff --git a/R/data.R b/R/data.R index 659219e..08a2928 100644 --- a/R/data.R +++ b/R/data.R @@ -3,28 +3,21 @@ #' An updated SDTM AE dataset that uses the CDISC pilot project #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda} -"admiral_ae" - -#' Adverse Events Dataset-raw -#' -#' A SDTM AE dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true} # nolint -"raw_ae" +"ae" #' Concomitant Medication Dataset #' #' A SDTM CM dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true} # nolint -"admiral_cm" +"cm" #' Demography Dataset #' #' A SDTM DM dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true} # nolint -"admiral_dm" +"dm" #' Disposition Dataset-updated #' @@ -32,14 +25,7 @@ #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda} #' @author Gopi Vegesna -"admiral_ds" - -#' Disposition Dataset-raw -#' -#' A SDTM DS dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ds.xpt?raw=true} # nolint -"raw_ds" +"ds" #' Electrocardiogram Dataset #' @@ -52,7 +38,7 @@ #' A SDTM EX dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true} # nolint -"admiral_ex" +"ex" #' Ophthalmology Exposure Dataset #' @@ -67,14 +53,7 @@ #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_lb.rda} #' @author Annie Yang -"admiral_lb" - -#' Laboratory Measurements Dataset -#' -#' A SDTM LB dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/lb.xpt?raw=true} # nolint -"raw_lb" +"lb" #' Medical History Dataset-updated #' @@ -82,21 +61,14 @@ #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint #' @author Annie Yang -"admiral_mh" - -#' Medical History Dataset-raw -#' -#' A SDTM MH dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint -"raw_mh" +"mh" #' Ophthalmic Examinations Dataset #' #' A SDTM OE dataset simulated by Ophthalmology team #' #' @author Gordon Miller -"admiral_oe" +"oe_ophtha" #' Pharmacokinetics Concentrations Dataset #' @@ -104,7 +76,7 @@ #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pc.rda} #' @author Antonio Rodríguez Contestí -"admiral_pc" +"pc" #' Pharmacokinetic Parameters Dataset #' @@ -112,21 +84,14 @@ #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pp.rda} #' @author Antonio Rodríguez Contestí -"admiral_pp" - -#' Questionnaire Dataset -#' -#' A SDTM QS dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/qs.xpt?raw=true} # nolint -"raw_qs" +"pp" #' Questionnaire Dataset #' #' A SDTM QS dataset from the CDISC pilot project & Ophthalmology test data #' #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_qs.rda} # nolint -"admiral_qs" +"qs" #' Ophthalmology Questionnaire Dataset #' @@ -140,93 +105,86 @@ #' A SDTM SC dataset simulated by Ophthalmology team #' #' @author Gordon Miller -"admiral_sc" +"sc_ophtha" #' Tumor Identification Dataset #' #' A SDTM TU dataset simulated by Gopi Vegesna #' #' @author Gopi Vegesna -"admiral_tu" +"tu_onco" #' Tumor Results Dataset #' #' A SDTM TR dataset simulated by Gopi Vegesna #' #' @author Gopi Vegesna -"admiral_tr" +"tr_onco" #' Disease Response Dataset #' #' A SDTM RS dataset simulated by Gopi Vegesna #' #' @author Gopi Vegesna -"admiral_rs" +"rs_onco" #' Supplemental Adverse Events Dataset #' #' A SDTM SUPPAE dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true} # nolint -"admiral_suppae" +"suppae" #' Supplemental Disposition Dataset-updated #' #' A SDTM SUPPDS dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint -"admiral_suppds" - -#' Supplemental Disposition Dataset-raw -#' -#' A SDTM SUPPDS dataset from the CDISC pilot project -#' -#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint -"raw_suppds" +"suppds" #' Supplemental Demography Dataset #' #' A SDTM SUPPDM dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true} # nolint -"admiral_suppdm" +"suppdm" #' Supplemental Tumor Results Dataset #' #' A SDTM SUPPTR dataset simulated by Gopi Vegesna #' #' @author Gopi Vegesna -"admiral_supptr" +"supptr_onco" #' Trial Design Dataset #' #' A SDTM TS dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true} # nolint -"admiral_ts" +"ts" #' Vital Signs Dataset #' #' A SDTM VS dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true} # nolint -"admiral_vs" +"vs" #' SMQ Dataset #' #' An example SMQ dataset #' -"admiral_smq_db" +"smq_db" #' SDG Dataset #' #' An example SDG dataset #' -"admiral_sdg_db" +"sdg_db" #' Subject Visits Dataset #' #' A SDTM SV dataset from the CDISC pilot project #' #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true} # nolint -"admiral_sv" +"sv" diff --git a/dev/README.md b/data-raw/README.md similarity index 100% rename from dev/README.md rename to data-raw/README.md diff --git a/dev/update_ae.R b/data-raw/ae.R similarity index 53% rename from dev/update_ae.R rename to data-raw/ae.R index c8dfb1c..a098453 100644 --- a/dev/update_ae.R +++ b/data-raw/ae.R @@ -3,9 +3,12 @@ library(dplyr) library(admiral) library(metatools) +library(haven) -data("raw_ae") +raw_ae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true") # nolint +raw_suppae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true") # nolint ae <- convert_blanks_to_na(raw_ae) +suppae <- convert_blanks_to_na(raw_suppae) # create possible AELAT values - as collected on CRF ---- lat <- c("LEFT", "RIGHT", "BOTH") @@ -24,4 +27,6 @@ admiral_ae <- ae %>% attr(admiral_ae, "label") <- "Adverse Events" # Save dataset ---- -save(admiral_ae, file = "data/admiral_ae.rda", compress = "bzip2") +ae <- admiral_ae +save(ae, file = "data/ae.rda", compress = "bzip2") +usethis::use_data(suppae, overwrite = TRUE) diff --git a/data-raw/batch_run.sh b/data-raw/batch_run.sh new file mode 100644 index 0000000..049b95e --- /dev/null +++ b/data-raw/batch_run.sh @@ -0,0 +1,34 @@ +#!/bin/bash +# direct copy from CDISC pilot +Rscript data-raw/ex.R +Rscript data-raw/cm.R +Rscript data-raw/sv.R +Rscript data-raw/ts.R +Rscript data-raw/vs.R +Rscript data-raw/dm.R + +# Update from CDISC pilot +Rscript data-raw/ae.R +Rscript data-raw/ds.R +Rscript data-raw/lb.R +Rscript data-raw/mh.R +Rscript data-raw/qs.R + +# build from program +Rscript data-raw/pc.R +Rscript data-raw/pp.R +Rscript data-raw/query_databases.R # sdg_db, smq_db + + +# admiralophtha +Rscript data-raw/ex_ophtha.R +Rscript data-raw/qs_ophtha.R +# admiralophtha build from program +Rscript data-raw/oe_ophtha.R +Rscript data-raw/sc_ophtha.R + + +# admiralonco build from program +Rscript data-raw/tr_onco.R +Rscript data-raw/tu_onco.R +Rscript data-raw/rs_onco.R diff --git a/data-raw/cm.R b/data-raw/cm.R new file mode 100644 index 0000000..2657e4e --- /dev/null +++ b/data-raw/cm.R @@ -0,0 +1,7 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +raw_cm <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true") # nolint +cm <- convert_blanks_to_na(raw_cm) + +usethis::use_data(cm, overwrite = TRUE) diff --git a/data-raw/dm.R b/data-raw/dm.R new file mode 100644 index 0000000..e35f39f --- /dev/null +++ b/data-raw/dm.R @@ -0,0 +1,11 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint +raw_dm <- read_xpt(paste0(sdtm_path, "dm", ".xpt?raw=true")) +raw_suppdm <- read_xpt(paste0(sdtm_path, "suppdm", ".xpt?raw=true")) +dm <- convert_blanks_to_na(raw_dm) +suppdm <- convert_blanks_to_na(raw_suppdm) + +usethis::use_data(dm, overwrite = TRUE) +usethis::use_data(suppdm, overwrite = TRUE) diff --git a/dev/update_ds.R b/data-raw/ds.R similarity index 80% rename from dev/update_ds.R rename to data-raw/ds.R index 32816f0..1ba12ea 100644 --- a/dev/update_ds.R +++ b/data-raw/ds.R @@ -5,13 +5,15 @@ library(tidyselect) library(labelled) library(admiral) library(metatools) +library(haven) -data("admiral_dm") -data("raw_ds") -data("raw_suppds") +data("dm") +sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint +raw_ds <- read_xpt(paste0(sdtm_path, "ds", ".xpt?raw=true")) +raw_suppds <- read_xpt(paste0(sdtm_path, "suppds", ".xpt?raw=true")) # Converting blank to NA -dm <- convert_blanks_to_na(admiral_dm) +dm <- convert_blanks_to_na(dm) ds1a <- convert_blanks_to_na(raw_ds) suppds1a <- convert_blanks_to_na(raw_suppds) @@ -97,5 +99,7 @@ admiral_ds <- select(ds3, all_of(dsnames)) attr(admiral_ds, "label") <- "Disposition" -save(admiral_ds, file = "data/admiral_ds.rda", compress = "bzip2") -save(admiral_suppds, file = "data/admiral_suppds.rda", compress = "bzip2") +ds <- admiral_ds +suppds <- admiral_suppds +save(ds, file = "data/ds.rda", compress = "bzip2") +save(suppds, file = "data/suppds.rda", compress = "bzip2") diff --git a/data-raw/ex.R b/data-raw/ex.R new file mode 100644 index 0000000..20d31d1 --- /dev/null +++ b/data-raw/ex.R @@ -0,0 +1,7 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +raw_ex <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true") # nolint +ex <- convert_blanks_to_na(raw_ex) + +usethis::use_data(ex, overwrite = TRUE) diff --git a/dev/ex_ophtha.R b/data-raw/ex_ophtha.R similarity index 90% rename from dev/ex_ophtha.R rename to data-raw/ex_ophtha.R index f93e9c5..7aaeaa2 100644 --- a/dev/ex_ophtha.R +++ b/data-raw/ex_ophtha.R @@ -1,12 +1,13 @@ library(dplyr) library(tidyselect) -library(pharmaversesdtm) +data("dm") +data("ex") # Make ex_ophtha dataset -ex_ophtha <- admiral_dm %>% +ex_ophtha <- dm %>% # Start by merging on ophtha_dm to use the SUBJID variable select(USUBJID, SUBJID) %>% - right_join(admiral_ex, by = c("USUBJID"), multiple = "all") %>% + right_join(ex, by = c("USUBJID"), multiple = "all") %>% # Create EXLOC & EXLAT, change EXROUTE & EXDOSFRM to something eye-related mutate( EXLOC = "EYE", diff --git a/dev/update_lb.R b/data-raw/lb.R similarity index 84% rename from dev/update_lb.R rename to data-raw/lb.R index 1f381fa..5ceaa66 100644 --- a/dev/update_lb.R +++ b/data-raw/lb.R @@ -1,9 +1,13 @@ # Update LB by adding percentage differential lab test rows library(dplyr) +library(haven) +library(admiral) + +sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint +raw_lb <- read_xpt(paste0(sdtm_path, "lb", ".xpt?raw=true")) +lb <- raw_lb %>% convert_blanks_to_na() -data("raw_lb") -lb <- raw_lb # Subset on differential lab tests lb_diff_abs <- lb %>% @@ -76,4 +80,5 @@ admiral_lb <- lb %>% attr(admiral_lb, "label") <- "Laboratory Test Results" -save(admiral_lb, file = "data/admiral_lb.rda", compress = "bzip2") +lb <- admiral_lb +save(lb, file = "data/lb.rda", compress = "bzip2") diff --git a/dev/update_mh.R b/data-raw/mh.R similarity index 83% rename from dev/update_mh.R rename to data-raw/mh.R index f265bf4..456869f 100644 --- a/dev/update_mh.R +++ b/data-raw/mh.R @@ -1,11 +1,16 @@ # Add new variables to MH library(metatools) +library(lubridate) +library(haven) +library(admiral) +library(dplyr) -data("admiral_dm") -data("raw_mh") +data("dm") +sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint +raw_mh <- read_xpt(paste0(sdtm_path, "mh", ".xpt?raw=true")) # Convert blank to NA -dm <- convert_blanks_to_na(admiral_dm) %>% +dm <- convert_blanks_to_na(dm) %>% select(STUDYID, USUBJID, RFSTDTC, RFENDTC, RFXSTDTC, RFXENDTC) mh <- convert_blanks_to_na(raw_mh) # Set seed so that result stays the same for each run @@ -68,4 +73,5 @@ admiral_mh <- mh %>% ) attr(admiral_mh, "label") <- "Medical History" -save(admiral_mh, file = "data/admiral_mh.rda", compress = "bzip2") +mh <- admiral_mh +save(mh, file = "data/mh.rda", compress = "bzip2") diff --git a/dev/oe.R b/data-raw/oe_ophtha.R similarity index 94% rename from dev/oe.R rename to data-raw/oe_ophtha.R index 80db542..b7e23dd 100644 --- a/dev/oe.R +++ b/data-raw/oe_ophtha.R @@ -6,12 +6,12 @@ library(tidyselect) library(admiral) # Read in data -data("admiral_dm") -data("admiral_sv") +data("dm") +data("sv") # Convert blank to NA -dm <- convert_blanks_to_na(admiral_dm) -sv <- convert_blanks_to_na(admiral_sv) +dm <- convert_blanks_to_na(dm) +sv <- convert_blanks_to_na(sv) # set seed to get same results each run set.seed(999) @@ -108,7 +108,7 @@ oe4 <- bind_rows(oe31, oe32, oe33, oe34) %>% "OETPTNUM" = NA ) -oe <- oe4 %>% +oe_ophtha <- oe4 %>% select( STUDYID, DOMAIN, USUBJID, OESEQ, OECAT, OESCAT, OEDTC, VISIT, VISITNUM, VISITDY, OESTRESN, OESTRESC, OEORRES, OETEST, OETESTCD, OETSTDTL, OELAT, OELOC, OEDY, @@ -142,8 +142,7 @@ oe <- oe4 %>% OETPTNUM = "Planned Time Point Number" ) -attr(oe, "label") <- "Ophthalmic Examinations" +attr(oe_ophtha, "label") <- "Ophthalmic Examinations" -admiral_oe <- oe -save(admiral_oe, file = "data/admiral_oe.rda", compress = "bzip2") +save(oe_ophtha, file = "data/oe_ophtha.rda", compress = "bzip2") diff --git a/dev/pc.R b/data-raw/pc.R similarity index 96% rename from dev/pc.R rename to data-raw/pc.R index 5224171..5e43b0e 100644 --- a/dev/pc.R +++ b/data-raw/pc.R @@ -6,10 +6,11 @@ library(ggplot2) library(labelled) library(admiral) -data("admiral_ex") -data("admiral_dm") -ex <- admiral_ex -dm <- admiral_dm +data("ex") +data("dm") + +# set seed to get same results each run +set.seed(999) # Remove screen failures, they will not make it to drug infusion dm1 <- dm %>% @@ -158,5 +159,4 @@ plot <- ggplot(pc, aes(x = PCTPTNUM, y = PCSTRESN, group = USUBJID)) + # ---- Save output ---- -admiral_pc <- pc -save(admiral_pc, file = "data/admiral_pc.rda", compress = "bzip2") +save(pc, file = "data/pc.rda", compress = "bzip2") diff --git a/dev/pp.R b/data-raw/pp.R similarity index 98% rename from dev/pp.R rename to data-raw/pp.R index 42102b0..653a83f 100644 --- a/dev/pp.R +++ b/data-raw/pp.R @@ -198,5 +198,4 @@ pp <- pp %>% # ---- Save output ---- -admiral_pp <- pp -save(admiral_pp, file = "data/admiral_pp.rda", compress = "bzip2") +save(pp, file = "data/pp.rda", compress = "bzip2") diff --git a/dev/update_qs.R b/data-raw/qs.R similarity index 91% rename from dev/update_qs.R rename to data-raw/qs.R index a083959..bc8c4cc 100644 --- a/dev/update_qs.R +++ b/data-raw/qs.R @@ -2,11 +2,16 @@ library(metatools) library(dplyr) +library(haven) +library(admiral) -# take qs test data from previous ADMIRAL project ==== -data("raw_qs") -# create new QS data - keep standard variables from previous ADMIRAL project's QS ==== +# from CDISC pilot study ---- +sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint +raw_qs <- read_xpt(paste0(sdtm_path, "qs", ".xpt?raw=true")) %>% + convert_blanks_to_na() + +# create new QS data - keep standard variables from previous ADMIRAL project's QS ---- qs1 <- raw_qs %>% # select standard variables select(STUDYID, DOMAIN, USUBJID, QSBLFL, VISITNUM, VISIT, VISITDY, QSDTC, QSDY) %>% @@ -98,4 +103,5 @@ admiral_qs <- raw_qs %>% QSDY = "Study Day of Finding" ) -save(admiral_qs, file = "data/admiral_qs.rda", compress = "bzip2") +qs <- admiral_qs +save(qs, file = "data/qs.rda", compress = "bzip2") diff --git a/dev/qs_ophtha.R b/data-raw/qs_ophtha.R similarity index 95% rename from dev/qs_ophtha.R rename to data-raw/qs_ophtha.R index f9be6cb..59dc6ad 100644 --- a/dev/qs_ophtha.R +++ b/data-raw/qs_ophtha.R @@ -1,9 +1,11 @@ -library(pharmaversesdtm) library(dplyr) library(stringr) +data("qs") +# set seed to get same results each run +set.seed(999) # create new QS data - keep standard variables from previous ADMIRAL project's QS ==== -qs1 <- admiral_qs %>% +qs1 <- qs %>% # select standard variables select(STUDYID, DOMAIN, USUBJID, QSBLFL, VISITNUM, VISIT, VISITDY, QSDTC, QSDY) %>% # keep unique subjects and visits per subject @@ -119,10 +121,10 @@ qs3 <- qs2 %>% ) %>% ungroup() -# NOTE: the QS2 dataset made above should be stacked below the admiral_qs dataset. +# NOTE: the QS2 dataset made above should be stacked below the qs dataset. # output qs_ophtha.RDS # remove the original vfq part from admiral_qs -admiral_qs_novfq <- admiral_qs %>% filter(QSCAT != "NEI VFQ-25") +admiral_qs_novfq <- qs %>% filter(QSCAT != "NEI VFQ-25") qs_ophtha <- rbind(admiral_qs_novfq, qs3) diff --git a/dev/query_databases.R b/data-raw/query_databases.R similarity index 93% rename from dev/query_databases.R rename to data-raw/query_databases.R index e07b869..8b99388 100644 --- a/dev/query_databases.R +++ b/data-raw/query_databases.R @@ -65,8 +65,8 @@ smq_db <- bind_rows(pregsmq, bilismq) %>% termvar = "AEDECOD" ) -admiral_smq_db <- smq_db -save(admiral_smq_db, file = "data/admiral_smq_db.rda", compress = "bzip2") +# admiral_smq_db <- smq_db +save(smq_db, file = "data/smq_db.rda", compress = "bzip2") sdg_db <- tribble( ~termname, @@ -94,5 +94,4 @@ sdg_db <- tribble( version = "2019-09" ) -admiral_sdg_db <- sdg_db -save(admiral_sdg_db, file = "data/admiral_sdg_db.rda", compress = "bzip2") +save(sdg_db, file = "data/sdg_db.rda", compress = "bzip2") diff --git a/dev/rs.R b/data-raw/rs_onco.R similarity index 96% rename from dev/rs.R rename to data-raw/rs_onco.R index a744003..dae7c64 100644 --- a/dev/rs.R +++ b/data-raw/rs_onco.R @@ -7,10 +7,10 @@ library(admiral) library(metatools) # Reading input data -data("admiral_tr") +data("tr_onco") # Converting blank to NA -tr <- convert_blanks_to_na(admiral_tr) +tr <- convert_blanks_to_na(tr_onco) keyvar <- c( "STUDYID", "USUBJID", "TREVAL", "TREVALID", @@ -188,7 +188,7 @@ rs <- select(rs6, c( VISITNUM, VISIT, RSDTC, RSDY )) -rs <- rs %>% add_labels( +rs_onco <- rs %>% add_labels( STUDYID = "Study Identifier", DOMAIN = "Domain Abbreviation", USUBJID = "Unique Subject Identifier", @@ -210,7 +210,6 @@ rs <- rs %>% add_labels( RSDY = "Study Day of Response Assessment" ) -attr(rs, "label") <- "Disease Response" +attr(rs_onco, "label") <- "Disease Response" -admiral_rs <- rs -save(admiral_rs, file = "data/admiral_rs.rda", compress = "bzip2") +save(rs_onco, file = "data/rs_onco.rda", compress = "bzip2") diff --git a/dev/sc.R b/data-raw/sc_ophtha.R similarity index 88% rename from dev/sc.R rename to data-raw/sc_ophtha.R index 2ef33d6..5c11f9c 100644 --- a/dev/sc.R +++ b/data-raw/sc_ophtha.R @@ -3,11 +3,9 @@ library(dplyr) library(metatools) -data("admiral_dm") -data("admiral_sv") +data("dm") +data("sv") -dm <- admiral_dm -sv <- admiral_sv # Remove screen failures, they will not make it to drug infusion dm1 <- dm %>% @@ -42,7 +40,7 @@ sc_seq <- sc %>% "SCCAT", "SCORRES", "SCSTRESC", "EPOCH", "SCDTC", "SCDY" ) -sc <- sc_seq %>% +sc_ophtha <- sc_seq %>% ungroup() %>% # Sort data arrange(STUDYID, USUBJID, SCSEQ) %>% @@ -62,10 +60,9 @@ sc <- sc_seq %>% SCDY = "Study Day of Examination" ) -admiral_sc <- sc # assign dataset label -attr(admiral_sc, "label") <- "Subject Characteristic" +attr(sc_ophtha, "label") <- "Subject Characteristic" # Save output -save(admiral_sc, file = "data/admiral_sc.rda", compress = "bzip2") +save(sc_ophtha, file = "data/sc_ophtha.rda", compress = "bzip2") diff --git a/data-raw/sv.R b/data-raw/sv.R new file mode 100644 index 0000000..8313e0c --- /dev/null +++ b/data-raw/sv.R @@ -0,0 +1,7 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +raw_sv <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true") # nolint +sv <- convert_blanks_to_na(raw_sv) + +usethis::use_data(sv, overwrite = TRUE) diff --git a/dev/tr.R b/data-raw/tr_onco.R similarity index 95% rename from dev/tr.R rename to data-raw/tr_onco.R index 2e8243e..1028fb4 100644 --- a/dev/tr.R +++ b/data-raw/tr_onco.R @@ -9,14 +9,14 @@ library(metatools) set.seed(1) # Reading input data ---- -data("admiral_dm") -data("admiral_suppdm") -data("admiral_sv") +data("dm") +data("suppdm") +data("sv") # Converting blank to NA -dm <- convert_blanks_to_na(admiral_dm) -suppdm <- convert_blanks_to_na(admiral_suppdm) -sv <- convert_blanks_to_na(admiral_sv) +dm <- convert_blanks_to_na(dm) +suppdm <- convert_blanks_to_na(suppdm) +sv <- convert_blanks_to_na(sv) # Creating data frame with visits ---- dm1 <- dm %>% @@ -342,7 +342,7 @@ supptr <- select( ) ) -supptr <- supptr %>% add_labels( +supptr_onco <- supptr %>% add_labels( STUDYID = "Study Identifier", RDOMAIN = "Related Domain Abbreviation", USUBJID = "Unique Subject Identifier", @@ -354,7 +354,7 @@ supptr <- supptr %>% add_labels( QORIG = "Origin" ) -attr(supptr, "label") <- "Supplemental Tumor Results" +attr(supptr_onco, "label") <- "Supplemental Tumor Results" # Creating TR ---- tr <- select(tr, c( @@ -364,7 +364,7 @@ tr <- select(tr, c( TREVAL, TREVALID, TRACPTFL, VISITNUM, VISIT, TRDTC, TRDY )) -tr <- tr %>% add_labels( +tr_onco <- tr %>% add_labels( STUDYID = "Study Identifier", DOMAIN = "Domain Abbreviation", USUBJID = "Unique Subject Identifier", @@ -391,10 +391,8 @@ tr <- tr %>% add_labels( TRDY = "Study Day of Tumor Measurement" ) -attr(tr, "label") <- "Tumor Results" +attr(tr_onco, "label") <- "Tumor Results" -admiral_tr <- tr -admiral_supptr <- supptr -save(admiral_tr, file = "data/admiral_tr.rda", compress = "bzip2") -save(admiral_supptr, file = "data/admiral_supptr.rda", compress = "bzip2") +save(tr_onco, file = "data/tr_onco.rda", compress = "bzip2") +save(supptr_onco, file = "data/supptr_onco.rda", compress = "bzip2") diff --git a/data-raw/ts.R b/data-raw/ts.R new file mode 100644 index 0000000..284414e --- /dev/null +++ b/data-raw/ts.R @@ -0,0 +1,7 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +raw_ts <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true") # nolint +ts <- convert_blanks_to_na(raw_ts) + +usethis::use_data(ts, overwrite = TRUE) diff --git a/dev/tu.R b/data-raw/tu_onco.R similarity index 87% rename from dev/tu.R rename to data-raw/tu_onco.R index 57a8600..6eaeb4e 100644 --- a/dev/tu.R +++ b/data-raw/tu_onco.R @@ -7,11 +7,11 @@ library(admiral) library(metatools) # Reading input data -- DUMMY DATA CREATED FROM TR data created from TR -data("admiral_tr") -data("admiral_supptr") +data("tr_onco") +data("supptr_onco") -tr <- convert_blanks_to_na(admiral_tr) -supptr <- convert_blanks_to_na(admiral_supptr) +tr <- convert_blanks_to_na(tr_onco) +supptr <- convert_blanks_to_na(supptr_onco) supptr1 <- supptr %>% mutate("DOMAIN" = RDOMAIN, TRSEQ = as.numeric(IDVARVAL), "TRLOC" = QVAL) %>% @@ -58,7 +58,7 @@ tu <- select(tu2, c( VISITNUM, VISIT, TUDTC, TUDY )) -tu <- tu %>% add_labels( +tu_onco <- tu %>% add_labels( STUDYID = "Study Identifier", DOMAIN = "Domain Abbreviation", USUBJID = "Unique Subject Identifier", @@ -79,7 +79,6 @@ tu <- tu %>% add_labels( TUDY = "Study Day of Tumor Identification" ) -attr(tu, "label") <- "Tumor Identification" +attr(tu_onco, "label") <- "Tumor Identification" -admiral_tu <- tu -save(admiral_tu, file = "data/admiral_tu.rda", compress = "bzip2") +save(tu_onco, file = "data/tu_onco.rda", compress = "bzip2") diff --git a/data-raw/vs.R b/data-raw/vs.R new file mode 100644 index 0000000..748cd25 --- /dev/null +++ b/data-raw/vs.R @@ -0,0 +1,7 @@ +# from CDISC pilot study ---- +library(haven) +library(admiral) +raw_vs <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true") # nolint +vs <- convert_blanks_to_na(raw_vs) + +usethis::use_data(vs, overwrite = TRUE) diff --git a/data/admiral_ae.rda 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\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda} } \usage{ -admiral_ae +ae } \description{ An updated SDTM AE dataset that uses the CDISC pilot project diff --git a/man/admiral_cm.Rd b/man/cm.Rd similarity index 91% rename from man/admiral_cm.Rd rename to man/cm.Rd index 12053da..2a29a81 100644 --- a/man/admiral_cm.Rd +++ b/man/cm.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_cm} -\alias{admiral_cm} +\name{cm} +\alias{cm} \title{Concomitant Medication Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 7510 rows and 21 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true} # nolint } \usage{ -admiral_cm +cm } \description{ A SDTM CM dataset from the CDISC pilot project diff --git a/man/admiral_dm.Rd b/man/dm.Rd similarity index 91% rename from man/admiral_dm.Rd rename to man/dm.Rd index 5ceba3f..e647445 100644 --- a/man/admiral_dm.Rd +++ b/man/dm.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_dm} -\alias{admiral_dm} +\name{dm} +\alias{dm} \title{Demography Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 306 rows and 25 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true} # nolint } \usage{ -admiral_dm +dm } \description{ A SDTM DM dataset from the CDISC pilot project diff --git a/man/admiral_ds.Rd b/man/ds.Rd similarity index 90% rename from man/admiral_ds.Rd rename to man/ds.Rd index 5428fc1..8aacb87 100644 --- a/man/admiral_ds.Rd +++ b/man/ds.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_ds} -\alias{admiral_ds} +\name{ds} +\alias{ds} \title{Disposition Dataset-updated} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 850 rows and 13 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda} } \usage{ -admiral_ds +ds } \description{ An updated SDTM DS dataset that uses the CDISC pilot project diff --git a/man/admiral_ex.Rd b/man/ex.Rd similarity index 91% rename from man/admiral_ex.Rd rename to man/ex.Rd index abc9d94..d28e838 100644 --- a/man/admiral_ex.Rd +++ b/man/ex.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_ex} -\alias{admiral_ex} +\name{ex} +\alias{ex} \title{Exposure Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 591 rows and 17 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true} # nolint } \usage{ -admiral_ex +ex } \description{ A SDTM EX dataset from the CDISC pilot project diff --git a/man/admiral_lb.Rd b/man/lb.Rd similarity index 91% rename from man/admiral_lb.Rd rename to man/lb.Rd index 1ec689c..bf43851 100644 --- a/man/admiral_lb.Rd +++ b/man/lb.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_lb} -\alias{admiral_lb} +\name{lb} +\alias{lb} \title{Laboratory Measurements Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 59580 rows and 23 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_lb.rda} } \usage{ -admiral_lb +lb } \description{ An updated SDTM LB dataset that uses data from the CDISC pilot project diff --git a/man/admiral_mh.Rd b/man/mh.Rd similarity index 92% rename from man/admiral_mh.Rd rename to man/mh.Rd index e3a9a3d..5df82e7 100644 --- a/man/admiral_mh.Rd +++ b/man/mh.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_mh} -\alias{admiral_mh} +\name{mh} +\alias{mh} \title{Medical History Dataset-updated} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1818 rows and 28 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint } \usage{ -admiral_mh +mh } \description{ An updated SDTM MH dataset that uses data from the CDISC pilot project diff --git a/man/admiral_oe.Rd b/man/oe_ophtha.Rd similarity index 89% rename from man/admiral_oe.Rd rename to man/oe_ophtha.Rd index 65778d3..82e04f6 100644 --- a/man/admiral_oe.Rd +++ b/man/oe_ophtha.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_oe} -\alias{admiral_oe} +\name{oe_ophtha} +\alias{oe_ophtha} \title{Ophthalmic Examinations Dataset} \format{ An object of class \code{grouped_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 15344 rows and 25 columns. } \usage{ -admiral_oe +oe_ophtha } \description{ A SDTM OE dataset simulated by Ophthalmology team diff --git a/man/admiral_pc.Rd b/man/pc.Rd similarity index 91% rename from man/admiral_pc.Rd rename to man/pc.Rd index c8db9e5..dec1aa0 100644 --- a/man/admiral_pc.Rd +++ b/man/pc.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_pc} -\alias{admiral_pc} +\name{pc} +\alias{pc} \title{Pharmacokinetics Concentrations Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3556 rows and 20 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pc.rda} } \usage{ -admiral_pc +pc } \description{ A SDTM PC dataset simulated by Antonio Rodríguez Contestí diff --git a/man/admiral_pp.Rd b/man/pp.Rd similarity index 77% rename from man/admiral_pp.Rd rename to man/pp.Rd index c75d89d..a8a514b 100644 --- a/man/admiral_pp.Rd +++ b/man/pp.Rd @@ -1,17 +1,17 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_pp} -\alias{admiral_pp} +\name{pp} +\alias{pp} \title{Pharmacokinetic Parameters Dataset} \format{ -An object of class \code{data.frame} with 2346 rows and 14 columns. +An object of class \code{data.frame} with 2352 rows and 14 columns. } \source{ \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pp.rda} } \usage{ -admiral_pp +pp } \description{ A SDTM PP dataset simulated by Antonio Rodríguez Contestí diff --git a/man/admiral_qs.Rd b/man/qs.Rd similarity index 90% rename from man/admiral_qs.Rd rename to man/qs.Rd index f182c9d..b9f5eab 100644 --- a/man/admiral_qs.Rd +++ b/man/qs.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_qs} -\alias{admiral_qs} +\name{qs} +\alias{qs} \title{Questionnaire Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 202907 rows and 20 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_qs.rda} # nolint } \usage{ -admiral_qs +qs } \description{ A SDTM QS dataset from the CDISC pilot project & Ophthalmology test data diff --git a/man/raw_ae.Rd b/man/raw_ae.Rd deleted file mode 100644 index f27d4dd..0000000 --- a/man/raw_ae.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_ae} -\alias{raw_ae} -\title{Adverse Events Dataset-raw} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 35 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true} # nolint -} -\usage{ -raw_ae -} -\description{ -A SDTM AE dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/raw_ds.Rd b/man/raw_ds.Rd deleted file mode 100644 index dc077f8..0000000 --- a/man/raw_ds.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_ds} -\alias{raw_ds} -\title{Disposition Dataset-raw} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 596 rows and 13 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ds.xpt?raw=true} # nolint -} -\usage{ -raw_ds -} -\description{ -A SDTM DS dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/raw_lb.Rd b/man/raw_lb.Rd deleted file mode 100644 index 916f441..0000000 --- a/man/raw_lb.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_lb} -\alias{raw_lb} -\title{Laboratory Measurements Dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 59580 rows and 23 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/lb.xpt?raw=true} # nolint -} -\usage{ -raw_lb -} -\description{ -A SDTM LB dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/raw_mh.Rd b/man/raw_mh.Rd deleted file mode 100644 index 5f0c55e..0000000 --- a/man/raw_mh.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_mh} -\alias{raw_mh} -\title{Medical History Dataset-raw} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1818 rows and 19 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint -} -\usage{ -raw_mh -} -\description{ -A SDTM MH dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/raw_qs.Rd b/man/raw_qs.Rd deleted file mode 100644 index 50b247c..0000000 --- a/man/raw_qs.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_qs} -\alias{raw_qs} -\title{Questionnaire Dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 121749 rows and 20 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/qs.xpt?raw=true} # nolint -} -\usage{ -raw_qs -} -\description{ -A SDTM QS dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/raw_suppds.Rd b/man/raw_suppds.Rd deleted file mode 100644 index da6608a..0000000 --- a/man/raw_suppds.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{raw_suppds} -\alias{raw_suppds} -\title{Supplemental Disposition Dataset-raw} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3 rows and 10 columns. -} -\source{ -\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint -} -\usage{ -raw_suppds -} -\description{ -A SDTM SUPPDS dataset from the CDISC pilot project -} -\keyword{datasets} diff --git a/man/admiral_rs.Rd b/man/rs_onco.Rd similarity index 88% rename from man/admiral_rs.Rd rename to man/rs_onco.Rd index 9a8b57f..fc7a7b5 100644 --- a/man/admiral_rs.Rd +++ b/man/rs_onco.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_rs} -\alias{admiral_rs} +\name{rs_onco} +\alias{rs_onco} \title{Disease Response Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 5808 rows and 19 columns. } \usage{ -admiral_rs +rs_onco } \description{ A SDTM RS dataset simulated by Gopi Vegesna diff --git a/man/admiral_sc.Rd b/man/sc_ophtha.Rd similarity index 88% rename from man/admiral_sc.Rd rename to man/sc_ophtha.Rd index e5cdd32..4203d62 100644 --- a/man/admiral_sc.Rd +++ b/man/sc_ophtha.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_sc} -\alias{admiral_sc} +\name{sc_ophtha} +\alias{sc_ophtha} \title{Subject Characteristic Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 254 rows and 12 columns. } \usage{ -admiral_sc +sc_ophtha } \description{ A SDTM SC dataset simulated by Ophthalmology team diff --git a/man/admiral_sdg_db.Rd b/man/sdg_db.Rd similarity index 83% rename from man/admiral_sdg_db.Rd rename to man/sdg_db.Rd index 237ebb7..bc13881 100644 --- a/man/admiral_sdg_db.Rd +++ b/man/sdg_db.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_sdg_db} -\alias{admiral_sdg_db} +\name{sdg_db} +\alias{sdg_db} \title{SDG Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16 rows and 5 columns. } \usage{ -admiral_sdg_db +sdg_db } \description{ An example SDG dataset diff --git a/man/admiral_smq_db.Rd b/man/smq_db.Rd similarity index 83% rename from man/admiral_smq_db.Rd rename to man/smq_db.Rd index d847e2e..b3395d7 100644 --- a/man/admiral_smq_db.Rd +++ b/man/smq_db.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_smq_db} -\alias{admiral_smq_db} +\name{smq_db} +\alias{smq_db} \title{SMQ Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 44 rows and 6 columns. } \usage{ -admiral_smq_db +smq_db } \description{ An example SMQ dataset diff --git a/man/admiral_suppae.Rd b/man/suppae.Rd similarity index 90% rename from man/admiral_suppae.Rd rename to man/suppae.Rd index 425a780..906c515 100644 --- a/man/admiral_suppae.Rd +++ b/man/suppae.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_suppae} -\alias{admiral_suppae} +\name{suppae} +\alias{suppae} \title{Supplemental Adverse Events Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 10 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true} # nolint } \usage{ -admiral_suppae +suppae } \description{ A SDTM SUPPAE dataset from the CDISC pilot project diff --git a/man/admiral_suppdm.Rd b/man/suppdm.Rd similarity index 90% rename from man/admiral_suppdm.Rd rename to man/suppdm.Rd index 9408e02..cb41f68 100644 --- a/man/admiral_suppdm.Rd +++ b/man/suppdm.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_suppdm} -\alias{admiral_suppdm} +\name{suppdm} +\alias{suppdm} \title{Supplemental Demography Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1197 rows and 10 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true} # nolint } \usage{ -admiral_suppdm +suppdm } \description{ A SDTM SUPPDM dataset from the CDISC pilot project diff --git a/man/admiral_suppds.Rd b/man/suppds.Rd similarity index 90% rename from man/admiral_suppds.Rd rename to man/suppds.Rd index e59b50e..b3e7308 100644 --- a/man/admiral_suppds.Rd +++ b/man/suppds.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_suppds} -\alias{admiral_suppds} +\name{suppds} +\alias{suppds} \title{Supplemental Disposition Dataset-updated} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3 rows and 9 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint } \usage{ -admiral_suppds +suppds } \description{ A SDTM SUPPDS dataset from the CDISC pilot project diff --git a/man/admiral_supptr.Rd b/man/supptr_onco.Rd similarity index 86% rename from man/admiral_supptr.Rd rename to man/supptr_onco.Rd index 97c3751..f54adb7 100644 --- a/man/admiral_supptr.Rd +++ b/man/supptr_onco.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_supptr} -\alias{admiral_supptr} +\name{supptr_onco} +\alias{supptr_onco} \title{Supplemental Tumor Results Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 55995 rows and 9 columns. } \usage{ -admiral_supptr +supptr_onco } \description{ A SDTM SUPPTR dataset simulated by Gopi Vegesna diff --git a/man/admiral_sv.Rd b/man/sv.Rd similarity index 91% rename from man/admiral_sv.Rd rename to man/sv.Rd index 00751ac..cc9f846 100644 --- a/man/admiral_sv.Rd +++ b/man/sv.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_sv} -\alias{admiral_sv} +\name{sv} +\alias{sv} \title{Subject Visits Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3559 rows and 8 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true} # nolint } \usage{ -admiral_sv +sv } \description{ A SDTM SV dataset from the CDISC pilot project diff --git a/man/admiral_tr.Rd b/man/tr_onco.Rd similarity index 88% rename from man/admiral_tr.Rd rename to man/tr_onco.Rd index 7a2e9be..caa8faf 100644 --- a/man/admiral_tr.Rd +++ b/man/tr_onco.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_tr} -\alias{admiral_tr} +\name{tr_onco} +\alias{tr_onco} \title{Tumor Results Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 55995 rows and 24 columns. } \usage{ -admiral_tr +tr_onco } \description{ A SDTM TR dataset simulated by Gopi Vegesna diff --git a/man/admiral_ts.Rd b/man/ts.Rd similarity index 91% rename from man/admiral_ts.Rd rename to man/ts.Rd index d5d488f..e61b4aa 100644 --- a/man/admiral_ts.Rd +++ b/man/ts.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_ts} -\alias{admiral_ts} +\name{ts} +\alias{ts} \title{Trial Design Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 33 rows and 6 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true} # nolint } \usage{ -admiral_ts +ts } \description{ A SDTM TS dataset from the CDISC pilot project diff --git a/man/admiral_tu.Rd b/man/tu_onco.Rd similarity index 88% rename from man/admiral_tu.Rd rename to man/tu_onco.Rd index 1edc5f5..928179f 100644 --- a/man/admiral_tu.Rd +++ b/man/tu_onco.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_tu} -\alias{admiral_tu} +\name{tu_onco} +\alias{tu_onco} \title{Tumor Identification Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 7734 rows and 18 columns. } \usage{ -admiral_tu +tu_onco } \description{ A SDTM TU dataset simulated by Gopi Vegesna diff --git a/man/admiral_vs.Rd b/man/vs.Rd similarity index 91% rename from man/admiral_vs.Rd rename to man/vs.Rd index 6b9f277..91cc1db 100644 --- a/man/admiral_vs.Rd +++ b/man/vs.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{admiral_vs} -\alias{admiral_vs} +\name{vs} +\alias{vs} \title{Vital Signs Dataset} \format{ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 29643 rows and 24 columns. @@ -11,7 +11,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true} # nolint } \usage{ -admiral_vs +vs } \description{ A SDTM VS dataset from the CDISC pilot project