From 6b66b152ec5577f47d246691227707d2539ef039 Mon Sep 17 00:00:00 2001 From: Pooja Kumari Date: Mon, 12 Feb 2024 13:17:05 +0530 Subject: [PATCH 1/7] #82 Resolve Bug: Duplicate observation for group USUBJID and VISIT --- R/data.R | 3 ++- data-raw/sv.R | 12 ++++++++++++ data/sv.rda | Bin 10100 -> 10062 bytes man/sv.Rd | 3 ++- 4 files changed, 16 insertions(+), 2 deletions(-) diff --git a/R/data.R b/R/data.R index adf6077..4ed3459 100644 --- a/R/data.R +++ b/R/data.R @@ -218,7 +218,8 @@ #' Subject Visits Dataset #' -#' A SDTM SV dataset from the CDISC pilot project +#' A SDTM SV dataset from the CDISC pilot project. Duplicate observation for group +#' variable USUBJID and VISIT is corrected. #' #' @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 "sv" diff --git a/data-raw/sv.R b/data-raw/sv.R index 3a40165..178173a 100644 --- a/data-raw/sv.R +++ b/data-raw/sv.R @@ -4,9 +4,21 @@ # Load libraries ----- library(haven) library(admiral) +library(dplyr) 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) +sv <- sv %>% + group_by(USUBJID, VISITNUM) %>% + mutate( + ASEQ = row_number(), + n=n()) %>% + mutate( + VISIT = ifelse(n > 1, paste0("UNSCHEDULED ", floor(VISITNUM), ".", ASEQ), VISIT), + VISITNUM = ifelse(n > 1, as.numeric(paste0(floor(VISITNUM), ".", ASEQ)), VISITNUM)) %>% + ungroup() %>% + select(-ASEQ,-n) + # Label dataset ---- attr(sv, "label") <- "Subject Visits" diff --git a/data/sv.rda b/data/sv.rda index c24f1cc06961abb8a4577fe25668b3edd06c91cb..ff082ed96ba1036df4a2cf08e602b85047b783a4 100644 GIT binary patch delta 9813 zcmY*;vto663v9fLbHiE@m8c@f^rZQ z$Vmk}Wu+pT(=?TMsEru;fBp8guf4CmuC@2`to1zmzVH34 z{f0h97sO`dVUaQEu%vY1VcWZpKdk=n-wz+2A5HoC!{ZMhJ~)4g`sLg;H@65+H#fIy zE8PC`UCeI`Tvi}q*)q3>uBQKQ!;%wMr3G|fcH6XKzbF{6N{EjIc#1a1t!s#|$EW;X zS1-4nZYypyu-ra|C%gRz;N~gV^s)QLZbtJ?f2QY(+X>5j_pg$`9Fgnom<(Lbv5w6->AxB85~_( z%H~cIC86n`@>NNp`P~Fd`)9lq1e3G+e(Q;k&$W^S8>W=SxO=NV-E9MmemCng{u4{| z%p+7_`{=c?ZpH?WS)OM{uIioD<-cR?zvzVt$n2x)Z>0YD&4#9*NG<3-@+yyjy~c~D z7z5Y)jp?R42lh)>^adXi9$e+ra82*`PDgcjbHce*5^B4W5?Q`Eh30RonZ7qFdDfi^ zS6^yZo>#CsYST~N-l%+&vTJ8k2Y52(nf_aWek-S8=rS!UcXNMa>iu-W=xW{hi9^B6 z&%o%>CDXcp{5cHML?^B6wt*AAJa>2FpC;~)SEsivSX)Vje_^V(DHN(n^tIcUTh!en zfu}ql|IGOVJ#hR1Ys$K1&Dx>9i@Y$>7CJ_n0Q#F;b$H;~kqa1U?syOB$R5wj+{ky+ zg44IsZx?M-wzMA%V5rA+EzC`Ie{C40-Z~NtVK+twZPb(H?e#`V4sK>7SG)4t+gDmn 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zZ!*UH^&{cy2cbhzLHFj~H2o2u@D=Mp!qLxJ`WD4e=HIiw9&32xxpqDw7Lj1qmP~l^ zuT>`e^UBRLobUledvrGLd+APcrN@I%NvqYp{p0_aycys^i{eP{vGV8f zKR&;}iZ6NN{VvYzdGsSk`uF+J7m90NU0(j--i^5UZf4;1=fC|h;c5Dt5WM;JC1 z+66Vl%@9bTagK_A6B6=*?X=#GbG(?*$owe`SYLbvt#x33?(rqb zB8J~h2wwzS*{p_r@wtXG9E=VVg*1Mj;q&r{n?pd~>#?7?(~VYL`T129Uq^&2_^eYM z*f`{zz8-P&1BuTo;&vQtuH}c5tTRrEMwR z&uDe1(LeeWl3%A?vwvhfc)j-^&9}DlVQo?Kv9b-Tm~%~FsN@(}!u%*B(zVz8*bDBORIkqvLg4{8a^M`#mH1!{z<+ nUnAeEpShnS9IHt<iWu diff --git a/man/sv.Rd b/man/sv.Rd index cc9f846..c314008 100644 --- a/man/sv.Rd +++ b/man/sv.Rd @@ -14,6 +14,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w sv } \description{ -A SDTM SV dataset from the CDISC pilot project +A SDTM SV dataset from the CDISC pilot project. Duplicate observation for group +variable USUBJID and VISIT is corrected. } \keyword{datasets} From 0b2d1a0b047864e13aa99cda5fd0d3f55e0de17b Mon Sep 17 00:00:00 2001 From: Pooja Kumari Date: Mon, 12 Feb 2024 13:28:03 +0530 Subject: [PATCH 2/7] 85 Resolve Bug: addressed failed checks --- data-raw/sv.R | 8 +++++--- inst/WORDLIST | 1 + 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/data-raw/sv.R b/data-raw/sv.R index 178173a..ea3f4c9 100644 --- a/data-raw/sv.R +++ b/data-raw/sv.R @@ -12,12 +12,14 @@ sv <- sv %>% group_by(USUBJID, VISITNUM) %>% mutate( ASEQ = row_number(), - n=n()) %>% + n = n() + ) %>% mutate( VISIT = ifelse(n > 1, paste0("UNSCHEDULED ", floor(VISITNUM), ".", ASEQ), VISIT), - VISITNUM = ifelse(n > 1, as.numeric(paste0(floor(VISITNUM), ".", ASEQ)), VISITNUM)) %>% + VISITNUM = ifelse(n > 1, as.numeric(paste0(floor(VISITNUM), ".", ASEQ)), VISITNUM) + ) %>% ungroup() %>% - select(-ASEQ,-n) + select(-ASEQ, -n) # Label dataset ---- attr(sv, "label") <- "Subject Visits" diff --git a/inst/WORDLIST b/inst/WORDLIST index 0f85756..54c63e9 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -35,6 +35,7 @@ SUPPTR SV TAs Thampi +USUBJID VFQ Vegesna ae From 65ea580bccc863158642a296f7005e29d4b1eda5 Mon Sep 17 00:00:00 2001 From: Pooja Kumari Date: Mon, 12 Feb 2024 15:29:56 +0530 Subject: [PATCH 3/7] 85 Resolve Bug: Updates to add labels --- data-raw/sv.R | 8 +++++++- data/sv.rda | Bin 10062 -> 10081 bytes 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/data-raw/sv.R b/data-raw/sv.R index ea3f4c9..67268c4 100644 --- a/data-raw/sv.R +++ b/data-raw/sv.R @@ -5,6 +5,7 @@ library(haven) library(admiral) library(dplyr) +library(metatools) 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) @@ -19,7 +20,12 @@ sv <- sv %>% VISITNUM = ifelse(n > 1, as.numeric(paste0(floor(VISITNUM), ".", ASEQ)), VISITNUM) ) %>% ungroup() %>% - select(-ASEQ, -n) + select(-ASEQ, -n) %>% + add_labels( + VISIT = "Visit Name", + VISITNUM = "Visit Number" + ) + # Label dataset ---- attr(sv, "label") <- "Subject Visits" diff --git a/data/sv.rda b/data/sv.rda index ff082ed96ba1036df4a2cf08e602b85047b783a4..9c170afe831ad6226ae6202c985ea103a15f16f6 100644 GIT binary patch literal 10081 zcmY*c8ke7)q5to}k&^l0pB^WC;DRgl>N20!1>k{nwf&Yge9bUiXi*LhFo*yQE%gXh4&-pe0|AA}pHBXlhmUn&eaan!p z_~4nk#(}rK>%VXrUGs&D`#IgWE-t?450HFG0O|`D-~9jU*yV$3&cegRmwC-)z{SNG z%Xj&p+GW!wmkkP8lm0t(+FSIfub=MQF+NDK#^2f5{q=F4s0f!0G=F|7)vdnZ%$e#p z(D5_napPlZC_({FjT=96RiL}L6r@lniOVeXhHK~a+P%q}{%=5&uZv5B%ldQGE-st@ z7yh&0$0TiiwM@~peS#b+p;?jtp8wE$5FD0bIG*@8ot$AWH5O>fDoBl+=f2-UZgO-t zZHx2$c=xI-!*XhD-P8_HzvS$T%|!)+fxy-E*L#Wt7+^?U+8$aKL8GiN0roWX1G~+}EwPHwD5VG!QvU;I#`tz@i$A;<~J(522 zx_s%9xOSR&^uYM=ezTwCKJEnlu6*iXWNo1#gx^>DZp+JcF6>t^Y}4&G-We~qt$aII 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from the CDISC pilot project. Duplicate observation for group -#' variable USUBJID and VISIT is corrected. +#' variable `USUBJID` and `VISIT` is corrected. #' #' @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 "sv" diff --git a/inst/WORDLIST b/inst/WORDLIST index 54c63e9..0f85756 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -35,7 +35,6 @@ SUPPTR SV TAs Thampi -USUBJID VFQ Vegesna ae diff --git a/man/sv.Rd b/man/sv.Rd index c314008..7899cdb 100644 --- a/man/sv.Rd +++ b/man/sv.Rd @@ -15,6 +15,6 @@ sv } \description{ A SDTM SV dataset from the CDISC pilot project. Duplicate observation for group -variable USUBJID and VISIT is corrected. +variable `USUBJID` and `VISIT` is corrected. } \keyword{datasets} From 83ccc7a643d642ff6706ff27ac9436076e5c5ff3 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Mon, 12 Feb 2024 10:40:42 +0000 Subject: [PATCH 5/7] #85: turn on markdown --- DESCRIPTION | 1 + man/ae_ophtha.Rd | 4 ++-- man/ex_ophtha.Rd | 4 ++-- man/get_terms.Rd | 10 +++++----- man/qs_ophtha.Rd | 2 +- man/sv.Rd | 2 +- 6 files changed, 12 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 99d8cb3..675ae39 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,6 +21,7 @@ URL: https://pharmaverse.github.io/pharmaversesdtm/main/, https://github.com/pha Depends: R (>= 3.5.0) Encoding: UTF-8 LazyData: true +Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 Suggests: devtools, diff --git a/man/ae_ophtha.Rd b/man/ae_ophtha.Rd index 28d8050..be4c86a 100644 --- a/man/ae_ophtha.Rd +++ b/man/ae_ophtha.Rd @@ -8,12 +8,12 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 36 columns. } \source{ -Constructed using `ae` from the `{pharmaversesdtm}` package # nolint +Constructed using \code{ae} from the \code{{pharmaversesdtm}} package # nolint } \usage{ ae_ophtha } \description{ -An example Adverse Events SDTM dataset with ophthalmology-specific variable `AELAT` +An example Adverse Events SDTM dataset with ophthalmology-specific variable \code{AELAT} } \keyword{datasets} diff --git a/man/ex_ophtha.Rd b/man/ex_ophtha.Rd index 5f6cb5e..18c26ae 100644 --- a/man/ex_ophtha.Rd +++ b/man/ex_ophtha.Rd @@ -8,12 +8,12 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 591 rows and 19 columns. } \source{ -Constructed using `ex` from the `{pharmaversesdtm}` package # nolint +Constructed using \code{ex} from the \code{{pharmaversesdtm}} package # nolint } \usage{ ex_ophtha } \description{ -An example Exposure SDTM dataset with ophthalmology-specific variables such as `EXLOC` and `EXLAT` +An example Exposure SDTM dataset with ophthalmology-specific variables such as \code{EXLOC} and \code{EXLAT} } \keyword{datasets} diff --git a/man/get_terms.Rd b/man/get_terms.Rd index d940320..d89bb97 100644 --- a/man/get_terms.Rd +++ b/man/get_terms.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/get_terms.R \name{get_terms} \alias{get_terms} -\title{An example function as expected by the `get_terms_fun` parameter of -`admiral::create_query_data()`} +\title{An example function as expected by the \code{get_terms_fun} parameter of +\code{admiral::create_query_data()}} \usage{ get_terms(basket_select, version, keep_id, temp_env) } @@ -12,11 +12,11 @@ get_terms(basket_select, version, keep_id, temp_env) \item{version}{MedDRA version} -\item{keep_id}{Should `GRPID` be included in the output?} +\item{keep_id}{Should \code{GRPID} be included in the output?} \item{temp_env}{Temporary environment} } \description{ -An example function as expected by the `get_terms_fun` parameter of -`admiral::create_query_data()` +An example function as expected by the \code{get_terms_fun} parameter of +\code{admiral::create_query_data()} } diff --git a/man/qs_ophtha.Rd b/man/qs_ophtha.Rd index d3e6006..ce993e7 100644 --- a/man/qs_ophtha.Rd +++ b/man/qs_ophtha.Rd @@ -8,7 +8,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 75922 rows and 20 columns. } \source{ -Constructed using `qs` from the `{pharmaversesdtm}` package # nolint +Constructed using \code{qs} from the \code{{pharmaversesdtm}} package # nolint } \usage{ qs_ophtha diff --git a/man/sv.Rd b/man/sv.Rd index 7899cdb..b2ae011 100644 --- a/man/sv.Rd +++ b/man/sv.Rd @@ -15,6 +15,6 @@ sv } \description{ A SDTM SV dataset from the CDISC pilot project. Duplicate observation for group -variable `USUBJID` and `VISIT` is corrected. +variable \code{USUBJID} and \code{VISIT} is corrected. } \keyword{datasets} From e3b96fac69e585ffdb1f97bc9e4e0c89cffca812 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Mon, 12 Feb 2024 10:58:34 +0000 Subject: [PATCH 6/7] #85: update roxygen version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 675ae39..b15ef93 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,7 +22,7 @@ Depends: R (>= 3.5.0) Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Suggests: devtools, lintr, From 97ecbc52d80c86dc589192051b023a25ae5c5ae5 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Mon, 12 Feb 2024 11:21:03 +0000 Subject: [PATCH 7/7] #85: update sv.rda --- data/sv.rda | Bin 10081 -> 10052 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/data/sv.rda b/data/sv.rda index 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