diff --git a/NEWS.md b/NEWS.md index 52632e3bef..07b2f5c5ef 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,6 +5,8 @@ - New function `derive_vars_crit_flag()` for deriving criterion flag variables (`CRITy`, `CRITyFL`, `CRITyFLN`). (#2468) +- Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498) + ## Updates of Existing Functions ## Breaking Changes diff --git a/inst/example_scripts/derive_single_dose.R b/inst/example_scripts/derive_single_dose.R index 17900e05bc..d840653bdf 100644 --- a/inst/example_scripts/derive_single_dose.R +++ b/inst/example_scripts/derive_single_dose.R @@ -1,7 +1,7 @@ library(pharmaversesdtm) library(admiral) library(dplyr) -data(ex) +ex <- pharmaversesdtm::ex # check that there is only one start/end date of exposure per subject and visit check_cond <- ex %>% diff --git a/inst/templates/ad_adae.R b/inst/templates/ad_adae.R index e68fcd1d4d..f4db91f1cb 100644 --- a/inst/templates/ad_adae.R +++ b/inst/templates/ad_adae.R @@ -14,12 +14,10 @@ library(lubridate) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("ae") -data("admiral_adsl") -data("ex_single") -data("suppae") - -adsl <- admiral_adsl +ae <- pharmaversesdtm::ae +suppae <- pharmaversesdtm::suppae +adsl <- admiral::admiral_adsl +ex_single <- admiral::ex_single # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adcm.R b/inst/templates/ad_adcm.R index 0cf4dc1c21..41b0541f8c 100644 --- a/inst/templates/ad_adcm.R +++ b/inst/templates/ad_adcm.R @@ -14,10 +14,8 @@ library(lubridate) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("cm") -data("admiral_adsl") - -adsl <- admiral_adsl +cm <- pharmaversesdtm::cm +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adeg.R b/inst/templates/ad_adeg.R index 7c1bbff4e9..ea0983e9e2 100644 --- a/inst/templates/ad_adeg.R +++ b/inst/templates/ad_adeg.R @@ -17,11 +17,8 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("admiral_adsl") -data("eg") - -adsl <- admiral_adsl -eg <- eg +eg <- pharmaversesdtm::eg +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adex.R b/inst/templates/ad_adex.R index 822386ac00..ca7bb17e34 100644 --- a/inst/templates/ad_adex.R +++ b/inst/templates/ad_adex.R @@ -15,10 +15,9 @@ library(stringr) # Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions # as needed and assign to the variables below. # The CDISC pilot datasets are used for demonstration purpose. -data("admiral_adsl") -data("ex") -adsl <- admiral_adsl +ex <- pharmaversesdtm::ex +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adlb.R b/inst/templates/ad_adlb.R index f5a55b706a..b04807ec83 100644 --- a/inst/templates/ad_adlb.R +++ b/inst/templates/ad_adlb.R @@ -15,10 +15,8 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("lb") -data("admiral_adsl") - -adsl <- admiral_adsl +lb <- pharmaversesdtm::lb +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adlbhy.R b/inst/templates/ad_adlbhy.R index 6a84ef3aa8..5060443fa1 100644 --- a/inst/templates/ad_adlbhy.R +++ b/inst/templates/ad_adlbhy.R @@ -16,9 +16,7 @@ library(lubridate) # ADLBHY is a special dataset specifically used to check for potential drug induced liver injuries # Please see "Hy's Law Implementation Guide" on the admiral website for additional information - -data("admiral_adlb") -adlb <- admiral_adlb +adlb <- admiral::admiral_adlb adlb_annotated <- adlb %>% filter(PARAMCD %in% c("AST", "ALT", "BILI") & is.na(DTYPE)) %>% diff --git a/inst/templates/ad_admh.R b/inst/templates/ad_admh.R index 7bf9c66bd4..6130271a7b 100644 --- a/inst/templates/ad_admh.R +++ b/inst/templates/ad_admh.R @@ -13,14 +13,17 @@ library(lubridate) # Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("mh") -data("admiral_adsl") -data("queries_mh") -adsl <- admiral_adsl +mh <- pharmaversesdtm::mh +queries_mh <- admiral::queries_mh +adsl <- admiral::admiral_adsl -mh <- convert_blanks_to_na(mh) +# When SAS datasets are imported into R using haven::read_sas(), missing +# character values from SAS appear as "" characters in R, instead of appearing +# as NA values. Further details can be obtained via the following link: +# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +mh <- convert_blanks_to_na(mh) # Look-up tables ---- diff --git a/inst/templates/ad_adpc.R b/inst/templates/ad_adpc.R index 1b932fb934..850bf98082 100644 --- a/inst/templates/ad_adpc.R +++ b/inst/templates/ad_adpc.R @@ -19,31 +19,19 @@ library(pharmaversesdtm) # Contains example datasets from the CDISC pilot projec # as needed and assign to the variables below. # For illustration purposes read in admiral test data - # Load PC, EX, VS and ADSL -data("pc") -data("ex") -data("vs") - -data("admiral_adsl") - -adsl <- admiral_adsl +pc <- pharmaversesdtm::pc +ex <- pharmaversesdtm::ex +vs <- pharmaversesdtm::vs +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: # https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint -# Load EX - ex <- convert_blanks_to_na(ex) - -# Load PC - pc <- convert_blanks_to_na(pc) - -# Load VS for baseline height and weight - vs <- convert_blanks_to_na(vs) # ---- Lookup tables ---- diff --git a/inst/templates/ad_adpp.R b/inst/templates/ad_adpp.R index 4e84385de5..544c976ae1 100644 --- a/inst/templates/ad_adpp.R +++ b/inst/templates/ad_adpp.R @@ -19,8 +19,8 @@ library(stringr) # For illustration purposes read in admiral test data # Load PP and Adsl -data("pp") -data("admiral_adsl") +pp <- pharmaversesdtm::pp +admiral_adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adppk.R b/inst/templates/ad_adppk.R index 6c621b0428..9db9c4457a 100644 --- a/inst/templates/ad_adppk.R +++ b/inst/templates/ad_adppk.R @@ -18,14 +18,11 @@ library(pharmaversesdtm) # Contains example datasets from the CDISC pilot projec # For illustration purposes read in admiral test data # Load PC, EX, VS, LB and ADSL -data("pc") -data("ex") -data("vs") -data("lb") - -data("admiral_adsl") - -adsl <- admiral_adsl +pc <- pharmaversesdtm::pc +ex <- pharmaversesdtm::ex +vs <- pharmaversesdtm::vs +lb <- pharmaversesdtm::lb +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_adsl.R b/inst/templates/ad_adsl.R index 29ff33283b..98dd7bac52 100644 --- a/inst/templates/ad_adsl.R +++ b/inst/templates/ad_adsl.R @@ -15,11 +15,11 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("dm") -data("ds") -data("ex") -data("ae") -data("lb") +dm <- pharmaversesdtm::dm +ds <- pharmaversesdtm::ds +ex <- pharmaversesdtm::ex +ae <- pharmaversesdtm::ae +lb <- pharmaversesdtm::lb # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/inst/templates/ad_advs.R b/inst/templates/ad_advs.R index fd199c2382..b68ddcc399 100644 --- a/inst/templates/ad_advs.R +++ b/inst/templates/ad_advs.R @@ -15,10 +15,8 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("vs") -data("admiral_adsl") - -adsl <- admiral_adsl +vs <- pharmaversesdtm::vs +adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing diff --git a/vignettes/admiral.Rmd b/vignettes/admiral.Rmd index cdb3b9ce4a..7e3d56f51d 100644 --- a/vignettes/admiral.Rmd +++ b/vignettes/admiral.Rmd @@ -47,11 +47,11 @@ library(pharmaversesdtm) library(admiral) # Read in SDTM datasets -data("dm") -data("ds") -data("ex") -data("vs") -data("admiral_adsl") +dm <- pharmaversesdtm::dm +ds <- pharmaversesdtm::ds +ex <- pharmaversesdtm::ex +vs <- pharmaversesdtm::vs +admiral_adsl <- admiral::admiral_adsl ``` The `adsl` and `advs` objects will now be prepared to showcase [addition of variables](#addvars) diff --git a/vignettes/adsl.Rmd b/vignettes/adsl.Rmd index b952dd75b6..0fd9648968 100644 --- a/vignettes/adsl.Rmd +++ b/vignettes/adsl.Rmd @@ -65,11 +65,11 @@ library(pharmaversesdtm) library(lubridate) library(stringr) -data("dm") -data("ds") -data("ex") -data("ae") -data("lb") +dm <- pharmaversesdtm::dm +ds <- pharmaversesdtm::ds +ex <- pharmaversesdtm::ex +ae <- pharmaversesdtm::ae +lb <- pharmaversesdtm::lb dm <- convert_blanks_to_na(dm) ds <- convert_blanks_to_na(ds) diff --git a/vignettes/bds_exposure.Rmd b/vignettes/bds_exposure.Rmd index 4debbc39d2..8e9314741e 100644 --- a/vignettes/bds_exposure.Rmd +++ b/vignettes/bds_exposure.Rmd @@ -62,10 +62,9 @@ library(lubridate) library(stringr) library(tibble) -data("admiral_adsl") -data("ex") +ex <- pharmaversesdtm::ex +adsl <- admiral::admiral_adsl -adsl <- admiral_adsl ex <- convert_blanks_to_na(ex) ``` ```{r echo=FALSE} diff --git a/vignettes/bds_finding.Rmd b/vignettes/bds_finding.Rmd index 0eb8a3d5fe..59c2868475 100644 --- a/vignettes/bds_finding.Rmd +++ b/vignettes/bds_finding.Rmd @@ -66,10 +66,9 @@ library(lubridate) library(stringr) library(tibble) -data("admiral_adsl") -data("vs") +vs <- pharmaversesdtm::vs +adsl <- admiral::admiral_adsl -adsl <- admiral_adsl vs <- convert_blanks_to_na(vs) ``` ```{r echo=FALSE} diff --git a/vignettes/bds_tte.Rmd b/vignettes/bds_tte.Rmd index 4c48659608..75e115c20f 100644 --- a/vignettes/bds_tte.Rmd +++ b/vignettes/bds_tte.Rmd @@ -61,11 +61,10 @@ For example purpose, the ADSL dataset---which is included in `{admiral}`---and the SDTM datasets from `{pharmaversesdtm}` are used. ```{r} -data("ae") -data("admiral_adsl") +ae <- pharmaversesdtm::ae +adsl <- admiral::admiral_adsl ae <- convert_blanks_to_na(ae) -adsl <- admiral_adsl ``` ```{r echo=FALSE} diff --git a/vignettes/higher_order.Rmd b/vignettes/higher_order.Rmd index db73719473..01b3155a45 100644 --- a/vignettes/higher_order.Rmd +++ b/vignettes/higher_order.Rmd @@ -46,10 +46,10 @@ library(admiral) library(pharmaversesdtm) library(dplyr, warn.conflicts = FALSE) -data("admiral_adsl") -data("ae") -data("vs") -adsl <- admiral_adsl +ae <- pharmaversesdtm::ae +vs <- pharmaversesdtm::vs +adsl <- admiral::admiral_adsl + ae <- convert_blanks_to_na(ae) vs <- convert_blanks_to_na(vs) ``` diff --git a/vignettes/hys_law.Rmd b/vignettes/hys_law.Rmd index 95df56e868..2f6bdea729 100644 --- a/vignettes/hys_law.Rmd +++ b/vignettes/hys_law.Rmd @@ -52,8 +52,7 @@ We assume that an `ADLB` dataset is available [^1]. First we read in the `ADLB` parameters required for the Hy's Law parameters: ```{r, eval = TRUE} -data(admiral_adlb) -adlb <- admiral_adlb %>% +adlb <- admiral::admiral_adlb %>% filter(PARAMCD %in% c("AST", "ALT", "BILI") & is.na(DTYPE)) ``` diff --git a/vignettes/lab_grading.Rmd b/vignettes/lab_grading.Rmd index 0307ad4fa5..9ed7fdf668 100644 --- a/vignettes/lab_grading.Rmd +++ b/vignettes/lab_grading.Rmd @@ -101,9 +101,9 @@ library(dplyr, warn.conflicts = FALSE) library(stringr) library(tibble) -data("lb") +lb <- pharmaversesdtm::lb +adsl <- admiral::admiral_adsl -adsl <- admiral_adsl lb <- convert_blanks_to_na(lb) ``` ```{r echo=FALSE} diff --git a/vignettes/occds.Rmd b/vignettes/occds.Rmd index 0ae5fb0000..f481bae96b 100644 --- a/vignettes/occds.Rmd +++ b/vignettes/occds.Rmd @@ -58,11 +58,11 @@ library(dplyr, warn.conflicts = FALSE) library(pharmaversesdtm) library(lubridate) -data("ae") -data("admiral_adsl") +ae <- pharmaversesdtm::ae +adsl <- admiral::admiral_adsl +ex_single <- admiral::ex_single ae <- convert_blanks_to_na(ae) -adsl <- admiral_adsl ``` ```{r echo = FALSE} ae <- filter(ae, USUBJID %in% c("01-701-1015", "01-701-1023", "01-703-1086", "01-703-1096", "01-707-1037", "01-716-1024")) @@ -228,7 +228,6 @@ vignette](visits_periods.html#treatment_bds). The function `derive_vars_joined()` can be used to derive the last dose date before the start of the event. ```{r eval=TRUE} -data(ex_single) ex_single <- derive_vars_dtm( ex_single, dtc = EXSTDTC, @@ -424,7 +423,7 @@ The following example shows how to derive query variables for Standardized MedDR Queries (SMQs) in ADAE. ```{r, eval=TRUE} -data("queries") +queries <- admiral::queries ``` ```{r, eval=TRUE, echo=FALSE} diff --git a/vignettes/pk_adnca.Rmd b/vignettes/pk_adnca.Rmd index c354b3f644..7f0f7d8b3e 100644 --- a/vignettes/pk_adnca.Rmd +++ b/vignettes/pk_adnca.Rmd @@ -111,25 +111,15 @@ library(lubridate) library(stringr) library(tibble) -data("admiral_adsl") -data("ex") -data("pc") -data("vs") -data("lb") +ex <- pharmaversesdtm::ex +pc <- pharmaversesdtm::pc +vs <- pharmaversesdtm::vs +lb <- pharmaversesdtm::lb +adsl <- admiral::admiral_adsl -adsl <- admiral_adsl ex <- convert_blanks_to_na(ex) - -# Load PC - pc <- convert_blanks_to_na(pc) - -# Load VS for baseline height and weight - vs <- convert_blanks_to_na(vs) - -# Load LB for baseline lab values - lb <- convert_blanks_to_na(lb) %>% filter(LBBLFL == "Y") diff --git a/vignettes/questionnaires.Rmd b/vignettes/questionnaires.Rmd index 1982bc1285..18edb6fc4e 100644 --- a/vignettes/questionnaires.Rmd +++ b/vignettes/questionnaires.Rmd @@ -58,8 +58,7 @@ In this vignette we use the example data from the CDISC ADaM Supplements [^1]: The example `QS` data (`example_qs`) is included in the admiral package. ```{r} -data("example_qs") -qs <- example_qs +qs <- admiral::example_qs ``` ```{r echo=FALSE}