From 3b9f5566ed1c6df85aba5c339f65d0cbb631123f Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Thu, 25 Jul 2024 00:53:43 +0200 Subject: [PATCH 1/4] Update snapshot after upgrade the admiraldev --- tests/testthat/_snaps/derive_blfl.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/testthat/_snaps/derive_blfl.md b/tests/testthat/_snaps/derive_blfl.md index 606a22b..49bbb4b 100644 --- a/tests/testthat/_snaps/derive_blfl.md +++ b/tests/testthat/_snaps/derive_blfl.md @@ -80,33 +80,33 @@ # derive_blfl sdmt_in validations work - Required variable `DOMAIN` is missing + Required variable `DOMAIN` is missing in `sdtm_in` --- - Required variables `oak_id`, `raw_source` and `patient_number` are missing + Required variables `oak_id`, `raw_source`, and `patient_number` are missing in `sdtm_in` --- - Required variables `VSORRES`, `VSSTAT`, `VSTESTCD` and `VSDTC` are missing + Required variables `VSORRES`, `VSSTAT`, `VSTESTCD`, and `VSDTC` are missing in `sdtm_in` # derive_blfl dm_domain validations work - Required variables `USUBJID` and `RFXSTDTC` are missing + Required variables `USUBJID` and `RFXSTDTC` are missing in `dm_domain` # derive_blfl tgt_var and ref_var validations work - `tgt_var` must be a character scalar but is a list + Argument `tgt_var` must be a scalar of class , but is a list. --- - `ref_var` must be a character scalar but is a data frame + Argument `ref_var` must be a scalar of class , but is a tibble. --- - `tgt_var` must be one of 'VSBLFL' or 'VSLOBXFL' but is 'DMLOBXFL' + Argument `tgt_var` must be equal to one of "VSBLFL" or "VSLOBXFL". # derive_blfl DOMAIN validation works - `domain` must be a character scalar but is `4` + Argument `domain` must be a scalar of class , but is an integer. From 89100280df02726028b5816017a61e4f4f856bf4 Mon Sep 17 00:00:00 2001 From: Ramiro Magno Date: Sun, 28 Jul 2024 19:17:53 +0100 Subject: [PATCH 2/4] Closes #58 - Update `domain_example()` documentation --- R/domain_example.R | 27 ++++----------------------- man/domain_example.Rd | 28 +++++----------------------- 2 files changed, 9 insertions(+), 46 deletions(-) diff --git a/R/domain_example.R b/R/domain_example.R index 58aae4e..54b43b6 100644 --- a/R/domain_example.R +++ b/R/domain_example.R @@ -18,29 +18,10 @@ #' #' ### Example SDTM domains #' -#' \describe{ -#' \item{`"ae_ophtha"`}{Ophthalmology Adverse Events Dataset.} -#' \item{`"ae"`}{Adverse Events Dataset-updated.} -#' \item{`"ce_vaccine"`}{Clinical Events Dataset for Vaccine Studies.} -#' \item{`"cm"`}{Concomitant Medication Dataset.} -#' \item{`"dm_vaccine"`}{Demographics Dataset for Vaccine Studies.} -#' \item{`"dm"`}{Demography Dataset.} -#' \item{`"ds"`}{Disposition Dataset-updated.} -#' \item{`"eg"`}{ Electrocardiogram Dataset.} -#' \item{`"ex_ophtha"`}{Ophthalmology Exposure Dataset.} -#' \item{`"ex_vaccine"`}{Exposures Dataset for Vaccine Studies.} -#' \item{`"ex"`}{Exposure Dataset.} -#' \item{`"face_vaccine"`}{Findings About Clinical Events Dataset for Vaccine Studies.} -#' \item{`"is_vaccine"`}{Immunogenicity Specimen Assessments Dataset for Vaccine Studies.} -#' \item{`"lb"`}{Laboratory Measurements Dataset.} -#' \item{`"mh"`}{Medical History Dataset-updated.} -#' \item{`"oe_ophtha"`}{Ophthalmology Adverse Events Dataset.} -#' \item{`"pc"`}{Pharmacokinetics Concentrations Dataset.} -#' \item{`"pp"`}{Pharmacokinetics Parameters Dataset.} -#' \item{`"qs_ophtha"`}{Ophthalmology Questionnaire Dataset.} -#' \item{`"rs_onco_irecist"`}{Disease Response Dataset (iRECIST).} -#' \item{`"rs_onco"`}{Disease Response Dataset.} -#' } +#' - `"ae"`: Adverse Events (AE) data set. +#' - `"apsc"`: Associated Persons Subject Characteristics (APSC) data set. +#' - `"cm"`: Concomitant Medications (CM) data set. +#' - `"vs"`: Vital Signs (VS) data set. #' #' @param example A string with either the basename, file name, or relative path #' to a SDTM domain example file bundled with `{stdm.oak}`, e.g. `"cm"` diff --git a/man/domain_example.Rd b/man/domain_example.Rd index c5e214a..04b6206 100644 --- a/man/domain_example.Rd +++ b/man/domain_example.Rd @@ -33,29 +33,11 @@ constructed ad-hoc by the are bundled with \code{{sdtm.oak}}, thus obviating a dependence on \code{{pharmaversesdtm}}. \subsection{Example SDTM domains}{ - -\describe{ -\item{\code{"ae_ophtha"}}{Ophthalmology Adverse Events Dataset.} -\item{\code{"ae"}}{Adverse Events Dataset-updated.} -\item{\code{"ce_vaccine"}}{Clinical Events Dataset for Vaccine Studies.} -\item{\code{"cm"}}{Concomitant Medication Dataset.} -\item{\code{"dm_vaccine"}}{Demographics Dataset for Vaccine Studies.} -\item{\code{"dm"}}{Demography Dataset.} -\item{\code{"ds"}}{Disposition Dataset-updated.} -\item{\code{"eg"}}{ Electrocardiogram Dataset.} -\item{\code{"ex_ophtha"}}{Ophthalmology Exposure Dataset.} -\item{\code{"ex_vaccine"}}{Exposures Dataset for Vaccine Studies.} -\item{\code{"ex"}}{Exposure Dataset.} -\item{\code{"face_vaccine"}}{Findings About Clinical Events Dataset for Vaccine Studies.} -\item{\code{"is_vaccine"}}{Immunogenicity Specimen Assessments Dataset for Vaccine Studies.} -\item{\code{"lb"}}{Laboratory Measurements Dataset.} -\item{\code{"mh"}}{Medical History Dataset-updated.} -\item{\code{"oe_ophtha"}}{Ophthalmology Adverse Events Dataset.} -\item{\code{"pc"}}{Pharmacokinetics Concentrations Dataset.} -\item{\code{"pp"}}{Pharmacokinetics Parameters Dataset.} -\item{\code{"qs_ophtha"}}{Ophthalmology Questionnaire Dataset.} -\item{\code{"rs_onco_irecist"}}{Disease Response Dataset (iRECIST).} -\item{\code{"rs_onco"}}{Disease Response Dataset.} +\itemize{ +\item \code{"ae"}: Adverse Events (AE) data set. +\item \code{"apsc"}: Associated Persons Subject Characteristics (APSC) data set. +\item \code{"cm"}: Concomitant Medications (CM) data set. +\item \code{"vs"}: Vital Signs (VS) data set. } } } From c1d88a4e01bf91642ff12ba8616df3d3eb244c1f Mon Sep 17 00:00:00 2001 From: Ramiro Magno Date: Sun, 28 Jul 2024 19:22:30 +0100 Subject: [PATCH 3/4] Update word list --- inst/WORDLIST | 1 + 1 file changed, 1 insertion(+) diff --git a/inst/WORDLIST b/inst/WORDLIST index 3f90a5e..bd48eb6 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -64,3 +64,4 @@ RFSTDTC RFXSTDTC TPT xxTPT +APSC From d76831e55d1267d84e900d965a2d10e59ee40739 Mon Sep 17 00:00:00 2001 From: Ramiro Magno Date: Sun, 28 Jul 2024 19:29:45 +0100 Subject: [PATCH 4/4] Update `mutate.cnd_df()` docs --- _pkgdown.yml | 1 + man/mutate.cnd_df.Rd | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index e280f58..3c6b239 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -27,6 +27,7 @@ reference: - condition_add - ctl_new_rowid_pillar.cnd_df - tbl_sum.cnd_df + - mutate.cnd_df - title: SDTM examples desc: SDTM domain file examples diff --git a/man/mutate.cnd_df.Rd b/man/mutate.cnd_df.Rd index df68900..de6ec25 100644 --- a/man/mutate.cnd_df.Rd +++ b/man/mutate.cnd_df.Rd @@ -55,4 +55,3 @@ generic on conditioned data frames. This function implements a conditional mutate by only changing rows for which the condition stored in the conditioned data frame is \code{TRUE}. } -\keyword{internal} \ No newline at end of file