Closes #2498 update data("sdtm") in templates and vignettes (#2509)

* #2498 update data("sdtm") in templates and vignettes

* run styler

* #2498 update spacing to be consistent

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

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 %>%

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

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

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

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

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

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)) %>%

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 ----
 

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 ----

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

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

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

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

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)

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)

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}

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}

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}

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)
 ```

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))
 ```
 

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}

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}

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")