#26: update program name/rerun

pharmaverse · Jul 18, 2023 · fd772f3 · fd772f3
1 parent efcce34
commit fd772f3
Show file tree

Hide file tree

Showing 50 changed files with 47 additions and 49 deletions.
diff --git a/data-raw/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/data-raw/mh.R b/data-raw/mh.R
@@ -3,6 +3,7 @@ library(metatools)
 library(lubridate)
 library(haven)
 library(admiral)
+library(dplyr)
 
 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

diff --git a/data-raw/oe.R → data-raw/oe_ophtha.R b/data-raw/oe.R → 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,
@@ -142,7 +142,7 @@ oe <- oe4 %>%
     OETPTNUM = "Planned Time Point Number"
   )
 
-attr(oe, "label") <- "Ophthalmic Examinations"
+attr(oe_ophtha, "label") <- "Ophthalmic Examinations"
 
 
-save(oe, file = "data/oe.rda", compress = "bzip2")
+save(oe_ophtha, file = "data/oe_ophtha.rda", compress = "bzip2")
diff --git a/data-raw/pc.R b/data-raw/pc.R
@@ -6,10 +6,8 @@ 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)

diff --git a/data-raw/qs_ophtha.R b/data-raw/qs_ophtha.R
@@ -1,9 +1,9 @@
-library(pharmaversesdtm)
 library(dplyr)
 library(stringr)
+data("qs")
 
 # 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 +119,10 @@ 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/data-raw/rs.R → data-raw/rs_onco.R b/data-raw/rs.R → data-raw/rs_onco.R
@@ -7,10 +7,10 @@ library(admiral)
 library(metatools)
 
 # Reading input data
-data("admiral_tr")
+data("tr")
 
 # Converting blank to NA
-tr <- convert_blanks_to_na(admiral_tr)
+tr <- convert_blanks_to_na(tr)
 
 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",
@@ -210,6 +210,6 @@ rs <- rs %>% add_labels(
   RSDY = "Study Day of Response Assessment"
 )
 
-attr(rs, "label") <- "Disease Response"
+attr(rs_onco, "label") <- "Disease Response"
 
-save(rs, file = "data/rs.rda", compress = "bzip2")
+save(rs_onco, file = "data/rs_onco.rda", compress = "bzip2")
diff --git a/data-raw/sc.R → data-raw/sc_ophtha.R b/data-raw/sc.R → 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) %>%
@@ -64,7 +62,7 @@ sc <- sc_seq %>%
 
 
 # assign dataset label
-attr(sc, "label") <- "Subject Characteristic"
+attr(sc_ophtha, "label") <- "Subject Characteristic"
 
 # Save output
-save(sc, file = "data/sc.rda", compress = "bzip2")
+save(sc_ophtha, file = "data/sc_ophtha.rda", compress = "bzip2")
diff --git a/data-raw/tr.R → data-raw/tr_onco.R b/data-raw/tr.R → 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",
@@ -391,8 +391,8 @@ tr <- tr %>% add_labels(
   TRDY = "Study Day of Tumor Measurement"
 )
 
-attr(tr, "label") <- "Tumor Results"
+attr(tr_onco, "label") <- "Tumor Results"
 
 
-save(tr, file = "data/tr.rda", compress = "bzip2")
-save(supptr, file = "data/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/tu.R → data-raw/tu_onco.R b/data-raw/tu.R → 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")
+data("supptr")
 
-tr <- convert_blanks_to_na(admiral_tr)
-supptr <- convert_blanks_to_na(admiral_supptr)
+tr <- convert_blanks_to_na(tr)
+supptr <- convert_blanks_to_na(supptr)
 
 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",
@@ -79,6 +79,6 @@ tu <- tu %>% add_labels(
   TUDY = "Study Day of Tumor Identification"
 )
 
-attr(tu, "label") <- "Tumor Identification"
+attr(tu_onco, "label") <- "Tumor Identification"
 
-save(tu, file = "data/tu.rda", compress = "bzip2")
+save(tu_onco, file = "data/tu_onco.rda", compress = "bzip2")
diff --git a/data/admiral_ae.rda b/data/admiral_ae.rda
diff --git a/data/admiral_ds.rda b/data/admiral_ds.rda
diff --git a/data/admiral_lb.rda b/data/admiral_lb.rda
diff --git a/data/admiral_mh.rda b/data/admiral_mh.rda
diff --git a/data/admiral_pc.rda b/data/admiral_pc.rda
diff --git a/data/admiral_pp.rda b/data/admiral_pp.rda
diff --git a/data/admiral_qs.rda b/data/admiral_qs.rda
diff --git a/data/admiral_rs.rda b/data/admiral_rs.rda
diff --git a/data/admiral_sc.rda b/data/admiral_sc.rda
diff --git a/data/admiral_sdg_db.rda b/data/admiral_sdg_db.rda
diff --git a/data/admiral_smq_db.rda b/data/admiral_smq_db.rda
diff --git a/data/admiral_suppds.rda b/data/admiral_suppds.rda
diff --git a/data/admiral_supptr.rda b/data/admiral_supptr.rda
diff --git a/data/admiral_tr.rda b/data/admiral_tr.rda
diff --git a/data/admiral_tu.rda b/data/admiral_tu.rda
diff --git a/data/ae.rda b/data/ae.rda
diff --git a/data/cm.rda b/data/cm.rda
diff --git a/data/dm.rda b/data/dm.rda
diff --git a/data/ds.rda b/data/ds.rda
diff --git a/data/ex.rda b/data/ex.rda
diff --git a/data/ex_ophtha.rda b/data/ex_ophtha.rda
diff --git a/data/lb.rda b/data/lb.rda
diff --git a/data/mh.rda b/data/mh.rda
diff --git a/data/admiral_oe.rda → data/oe_ophtha.rda b/data/admiral_oe.rda → data/oe_ophtha.rda
diff --git a/data/pc.rda b/data/pc.rda
diff --git a/data/pp.rda b/data/pp.rda
diff --git a/data/qs.rda b/data/qs.rda
diff --git a/data/qs_ophtha.rda b/data/qs_ophtha.rda
diff --git a/data/rs_onco.rda b/data/rs_onco.rda
diff --git a/data/sc_ophtha.rda b/data/sc_ophtha.rda
diff --git a/data/sdg_db.rda b/data/sdg_db.rda
diff --git a/data/smq_db.rda b/data/smq_db.rda
diff --git a/data/suppae.rda b/data/suppae.rda
diff --git a/data/suppdm.rda b/data/suppdm.rda
diff --git a/data/suppds.rda b/data/suppds.rda
diff --git a/data/supptr_onco.rda b/data/supptr_onco.rda
diff --git a/data/sv.rda b/data/sv.rda
diff --git a/data/tr_onco.rda b/data/tr_onco.rda
diff --git a/data/ts.rda b/data/ts.rda
diff --git a/data/tu_onco.rda b/data/tu_onco.rda
diff --git a/data/vs.rda b/data/vs.rda