chore: replace scda with random.cdisc.data

insightsengineering · Apr 9, 2024 · 64d9e1f · 64d9e1f
1 parent 882639c
commit 64d9e1f
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Showing 14 changed files with 153 additions and 242 deletions.
diff --git a/RNA-seq/app.R b/RNA-seq/app.R
@@ -7,9 +7,11 @@ nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers
 ## Data reproducible code ----
 data <- teal_data()
 data <- within(data, {
-  library(scda.2022)
   library(nestcolor)
-  ADTTE <- scda::synthetic_cdisc_dataset("rcd_2022_06_27", "adtte") %>%
+  library(random.cdisc.data)
+
+  ADSL <- radsl(seed = 1)
+  ADTTE <- radtte(ADSL, seed = 1) %>%
     dplyr::mutate(is_event = CNSR == 0)
   MAE <- hermes::multi_assay_experiment
 })

diff --git a/RNA-seq/renv.lock b/RNA-seq/renv.lock
@@ -2660,37 +2660,25 @@
       ],
       "Hash": "c19df082ba346b0ffa6f833e92de34d1"
     },
-    "scda": {
-      "Package": "scda",
-      "Version": "0.1.6",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda",
-      "RemoteRef": "v0.1.6",
-      "RemoteSha": "665d4540a8f3c9e8d9271c33b5dd70296b49636c",
-      "Remotes": "insightsengineering/scda.2022@*release",
+    "random.cdisc.data": {
+      "Package": "random.cdisc.data",
+      "Version": "0.3.15",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
-        "utils"
-      ],
-      "Hash": "050ae235c739506fb50990d8e03518bb"
-    },
-    "scda.2022": {
-      "Package": "scda.2022",
-      "Version": "0.1.5",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda.2022",
-      "RemoteRef": "v0.1.5",
-      "RemoteSha": "5b08051312fababe15476f21323d17bcbb0543cf",
-      "Requirements": [
-        "R"
+        "checkmate",
+        "dplyr",
+        "lifecycle",
+        "lubridate",
+        "magrittr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyr",
+        "yaml"
       ],
-      "Hash": "0e04543b6e8a5f658699c9cdc50534c8"
+      "Hash": "c92edb70a24230a0b30f961c431c9fdf"
     },
     "shape": {
       "Package": "shape",

diff --git a/early-dev/app.R b/early-dev/app.R
@@ -8,14 +8,13 @@ nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers
 ## Data reproducible code ----
 data <- teal_data()
 data <- within(data, {
-  library(scda)
-  library(scda.2022)
+  library(random.cdisc.data)
   library(dplyr)
   library(nestcolor)
   # optional libraries
   library(sparkline)
 
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+  ADSL <- radsl(seed = 1)
 
   # derive ADSL treatment duration
   adsl_labels <- teal.data::col_labels(ADSL, fill = FALSE)
@@ -34,7 +33,7 @@ data <- within(data, {
     droplevels()
   teal.data::col_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels
 
-  ADAE <- synthetic_cdisc_dataset("latest", "adae")
+  ADAE <- radae(ADSL, seed = 1)
 
   # derive common flags for AEs
   adae_labels <- teal.data::col_labels(ADAE, fill = FALSE)
@@ -67,7 +66,7 @@ data <- within(data, {
       AELLT = "Lowest Level Term"
     )
 
-  ADCM <- synthetic_cdisc_dataset("latest", "adcm")
+  ADCM <- radcm(ADSL, seed = 1)
 
   # process ADCM
   ADCM <- ADCM %>%
@@ -80,7 +79,7 @@ data <- within(data, {
       AENDT = "Analysis End Date"
     )
 
-  ADEX <- synthetic_cdisc_dataset("latest", "adex")
+  ADEX <- radex(ADSL, seed = 1)
 
   # process ADEX
   ADEX <- ADEX %>%
@@ -93,7 +92,7 @@ data <- within(data, {
       AENDT = "Analysis End Date"
     )
 
-  ADTR <- synthetic_cdisc_dataset("latest", "adtr")
+  ADTR <- radtr(ADSL, seed = 1)
 
   # process ADTR
   adtr_labels <- teal.data::col_labels(ADTR, fill = FALSE)
@@ -113,19 +112,19 @@ data <- within(data, {
 
 
   # process ADRS
-  ADRSSWIM <- synthetic_cdisc_dataset("latest", "adrs") %>%
+  ADRSSWIM <- radrs(ADSL, seed = 1) %>%
     filter(PARAMCD == "OVRINV") %>%
     arrange(USUBJID)
 
-  ADRS <- synthetic_cdisc_dataset("latest", "adrs")
+  ADRS <- radrs(ADSL, seed = 1)
   adrs_labels <- teal.data::col_labels(ADRS, fill = FALSE)
   ADRS <- ADRS %>%
     filter(PARAMCD %in% c("BESRSPI", "INVET")) %>%
     mutate(ADT = as.Date(ADTM)) %>%
     droplevels()
   teal.data::col_labels(ADRS)["ADT"] <- "Analysis Date"
 
-  ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+  ADLB <- radlb(ADSL, seed = 1)
 
   # process ADLB
   ADLB <- ADLB %>%

diff --git a/early-dev/renv.lock b/early-dev/renv.lock
@@ -2312,37 +2312,25 @@
       ],
       "Hash": "c19df082ba346b0ffa6f833e92de34d1"
     },
-    "scda": {
-      "Package": "scda",
-      "Version": "0.1.6",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda",
-      "RemoteRef": "v0.1.6",
-      "RemoteSha": "665d4540a8f3c9e8d9271c33b5dd70296b49636c",
-      "Remotes": "insightsengineering/scda.2022@*release",
+    "random.cdisc.data": {
+      "Package": "random.cdisc.data",
+      "Version": "0.3.15",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
-        "utils"
-      ],
-      "Hash": "050ae235c739506fb50990d8e03518bb"
-    },
-    "scda.2022": {
-      "Package": "scda.2022",
-      "Version": "0.1.5",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda.2022",
-      "RemoteRef": "v0.1.5",
-      "RemoteSha": "5b08051312fababe15476f21323d17bcbb0543cf",
-      "Requirements": [
-        "R"
+        "checkmate",
+        "dplyr",
+        "lifecycle",
+        "lubridate",
+        "magrittr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyr",
+        "yaml"
       ],
-      "Hash": "0e04543b6e8a5f658699c9cdc50534c8"
+      "Hash": "c92edb70a24230a0b30f961c431c9fdf"
     },
     "shape": {
       "Package": "shape",

diff --git a/efficacy/app.R b/efficacy/app.R
@@ -8,13 +8,12 @@ nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers
 data <- teal_data()
 data <- within(data, {
   library(dplyr)
-  library(scda)
-  library(scda.2022)
+  library(random.cdisc.data)
   library(nestcolor)
   # optional libraries
   library(sparkline)
 
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+  ADSL <- radsl(seed = 1)
   adsl_labels <- teal.data::col_labels(ADSL, fill = FALSE)
 
   char_vars_asl <- names(Filter(isTRUE, sapply(ADSL, is.character)))
@@ -34,14 +33,14 @@ data <- within(data, {
 
   teal.data::col_labels(ADSL) <- adsl_labels
 
-  ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
+  ADTTE <- radtte(ADSL, seed = 1)
 
-  ADRS <- synthetic_cdisc_dataset("latest", "adrs")
+  ADRS <- radrs(ADSL, seed = 1)
   adrs_labels <- teal.data::col_labels(ADRS, fill = FALSE)
   ADRS <- filter(ADRS, PARAMCD == "BESRSPI" | AVISIT == "FOLLOW UP")
   teal.data::col_labels(ADRS) <- adrs_labels
 
-  ADQS <- synthetic_cdisc_dataset("latest", "adqs")
+  ADQS <- radqs(ADSL, seed = 1)
   adqs_labels <- teal.data::col_labels(ADQS, fill = FALSE)
   ADQS <- ADQS %>%
     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%

diff --git a/efficacy/renv.lock b/efficacy/renv.lock
@@ -2108,37 +2108,25 @@
       ],
       "Hash": "c19df082ba346b0ffa6f833e92de34d1"
     },
-    "scda": {
-      "Package": "scda",
-      "Version": "0.1.6",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda",
-      "RemoteRef": "v0.1.6",
-      "RemoteSha": "665d4540a8f3c9e8d9271c33b5dd70296b49636c",
-      "Remotes": "insightsengineering/scda.2022@*release",
+    "random.cdisc.data": {
+      "Package": "random.cdisc.data",
+      "Version": "0.3.15",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
-        "utils"
-      ],
-      "Hash": "050ae235c739506fb50990d8e03518bb"
-    },
-    "scda.2022": {
-      "Package": "scda.2022",
-      "Version": "0.1.5",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda.2022",
-      "RemoteRef": "v0.1.5",
-      "RemoteSha": "5b08051312fababe15476f21323d17bcbb0543cf",
-      "Requirements": [
-        "R"
+        "checkmate",
+        "dplyr",
+        "lifecycle",
+        "lubridate",
+        "magrittr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyr",
+        "yaml"
       ],
-      "Hash": "0e04543b6e8a5f658699c9cdc50534c8"
+      "Hash": "c92edb70a24230a0b30f961c431c9fdf"
     },
     "shape": {
       "Package": "shape",

diff --git a/exploratory/app.R b/exploratory/app.R
@@ -9,8 +9,7 @@ nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers
 ## Data reproducible code ----
 data <- teal_data()
 data <- within(data, {
-  library(scda)
-  library(scda.2022)
+  library(random.cdisc.data)
   library(dplyr)
   library(tidyr)
   library(ggExtra)
@@ -30,9 +29,9 @@ data <- within(data, {
   library(sparkline)
 
 
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-  ADRS <- synthetic_cdisc_dataset("latest", "adrs")
-  ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+  ADSL <- radsl(seed = 1)
+  ADRS <- radrs(ADSL, seed = 1)
+  ADLB <- radlb(ADSL, seed = 1)
   ADLBPCA <- ADLB %>%
     dplyr::select(USUBJID, STUDYID, SEX, ARMCD, AVAL, AVISIT, PARAMCD) %>%
     tidyr::pivot_wider(

diff --git a/exploratory/renv.lock b/exploratory/renv.lock
@@ -1912,37 +1912,25 @@
       ],
       "Hash": "c19df082ba346b0ffa6f833e92de34d1"
     },
-    "scda": {
-      "Package": "scda",
-      "Version": "0.1.6",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda",
-      "RemoteRef": "v0.1.6",
-      "RemoteSha": "665d4540a8f3c9e8d9271c33b5dd70296b49636c",
-      "Remotes": "insightsengineering/scda.2022@*release",
+    "random.cdisc.data": {
+      "Package": "random.cdisc.data",
+      "Version": "0.3.15",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
-        "utils"
-      ],
-      "Hash": "050ae235c739506fb50990d8e03518bb"
-    },
-    "scda.2022": {
-      "Package": "scda.2022",
-      "Version": "0.1.5",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "scda.2022",
-      "RemoteRef": "v0.1.5",
-      "RemoteSha": "5b08051312fababe15476f21323d17bcbb0543cf",
-      "Requirements": [
-        "R"
+        "checkmate",
+        "dplyr",
+        "lifecycle",
+        "lubridate",
+        "magrittr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyr",
+        "yaml"
       ],
-      "Hash": "0e04543b6e8a5f658699c9cdc50534c8"
+      "Hash": "c92edb70a24230a0b30f961c431c9fdf"
     },
     "shiny": {
       "Package": "shiny",

diff --git a/longitudinal/app.R b/longitudinal/app.R
@@ -12,8 +12,7 @@ data <- within(data, {
   library(DescTools)
   library(magrittr)
   library(dplyr)
-  library(scda)
-  library(scda.2022)
+  library(random.cdisc.data)
   library(stringr)
   # optional libraries
   library(sparkline)
@@ -23,8 +22,8 @@ data <- within(data, {
   # depending on if the data are SUBJECT LEVEL ANALYSIS DATASET or BASIC DATA STRUCTURE
   # if for example outcome variables are added to ADSL then do also add them as columns to ADLB
   # this is needed to be able to use plot splitting by outcome functionality
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-  ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+  ADSL <- radsl(seed = 1)
+  ADLB <- radlb(ADSL, seed = 1)
 
   ################################################################################
   # BEGIN: Analyst Input Required To Modify Values Below To Reflect Study Specifics