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Replace scda with random.cdisc.data #170

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merged 13 commits into from
Apr 10, 2024
Merged

Replace scda with random.cdisc.data #170

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64d9e1f
chore: replace `scda` with `random.cdisc.data`
vedhav Apr 9, 2024
2e92116
test: check main deployment
vedhav Apr 9, 2024
3350c6c
[skip deploy] Update renv.lock file for early-dev app
github-actions[bot] Apr 9, 2024
d48a0be
[skip deploy] Update renv.lock file for longitudinal app
github-actions[bot] Apr 9, 2024
532306d
[skip deploy] Update renv.lock file for RNA-seq app
github-actions[bot] Apr 9, 2024
b01eeb1
[skip deploy] Update renv.lock file for exploratory app
github-actions[bot] Apr 9, 2024
86db200
[skip deploy] Update renv.lock file for patient-profile app
github-actions[bot] Apr 9, 2024
2f4995d
[skip deploy] Update renv.lock file for safety app
github-actions[bot] Apr 9, 2024
b5a4c0e
[skip deploy] Update renv.lock file for efficacy app
github-actions[bot] Apr 9, 2024
ce57529
Merge branch 'main' into 154-use-rcd@main
kartikeyakirar Apr 10, 2024
0900320
chore: replace the docs with rda
vedhav Apr 10, 2024
273e0b9
chore: fix typo
vedhav Apr 10, 2024
cfa1950
Update .github/workflows/deploy.yml
vedhav Apr 10, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ jobs:
run: |
echo "BRANCH_NAME=dev" >> $GITHUB_ENV
if [ "${{ matrix.channel }}" == "stable" ]; then
echo "BRANCH_NAME=main" >> $GITHUB_ENV
echo "BRANCH_NAME=154-use-rcd@main" >> $GITHUB_ENV
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fi

- name: Setup job token 🔑
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6 changes: 4 additions & 2 deletions RNA-seq/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
})
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76 changes: 44 additions & 32 deletions RNA-seq/renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -2053,6 +2053,19 @@
],
"Hash": "c145edf05cc128e6ffcfa5d872c46329"
},
"lubridate": {
"Package": "lubridate",
"Version": "1.9.3",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"generics",
"methods",
"timechange"
],
"Hash": "680ad542fbcf801442c83a6ac5a2126c"
},
"magrittr": {
"Package": "magrittr",
"Version": "2.0.3",
Expand Down Expand Up @@ -2513,6 +2526,26 @@
],
"Hash": "082e1a198e3329d571f4448ef0ede4bc"
},
"random.cdisc.data": {
"Package": "random.cdisc.data",
"Version": "0.3.15",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"checkmate",
"dplyr",
"lifecycle",
"lubridate",
"magrittr",
"rlang",
"stringr",
"tibble",
"tidyr",
"yaml"
],
"Hash": "c92edb70a24230a0b30f961c431c9fdf"
},
"rappdirs": {
"Package": "rappdirs",
"Version": "0.3.3",
Expand Down Expand Up @@ -2660,38 +2693,6 @@
],
"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",
"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"
],
"Hash": "0e04543b6e8a5f658699c9cdc50534c8"
},
"shape": {
"Package": "shape",
"Version": "1.4.6.1",
Expand Down Expand Up @@ -3342,6 +3343,17 @@
],
"Hash": "829f27b9c4919c16b593794a6344d6c0"
},
"timechange": {
"Package": "timechange",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"cpp11"
],
"Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
},
"tinytex": {
"Package": "tinytex",
"Version": "0.50",
Expand Down
19 changes: 9 additions & 10 deletions early-dev/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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 %>%
Expand All @@ -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 %>%
Expand All @@ -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)
Expand All @@ -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 %>%
Expand Down
76 changes: 44 additions & 32 deletions early-dev/renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -1565,6 +1565,19 @@
],
"Hash": "c145edf05cc128e6ffcfa5d872c46329"
},
"lubridate": {
"Package": "lubridate",
"Version": "1.9.3",
"Source": "Repository",
"Repository": "RSPM",
"Requirements": [
"R",
"generics",
"methods",
"timechange"
],
"Hash": "680ad542fbcf801442c83a6ac5a2126c"
},
"magrittr": {
"Package": "magrittr",
"Version": "2.0.3",
Expand Down Expand Up @@ -2093,6 +2106,26 @@
],
"Hash": "082e1a198e3329d571f4448ef0ede4bc"
},
"random.cdisc.data": {
"Package": "random.cdisc.data",
"Version": "0.3.15",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"checkmate",
"dplyr",
"lifecycle",
"lubridate",
"magrittr",
"rlang",
"stringr",
"tibble",
"tidyr",
"yaml"
],
"Hash": "c92edb70a24230a0b30f961c431c9fdf"
},
"rappdirs": {
"Package": "rappdirs",
"Version": "0.3.3",
Expand Down Expand Up @@ -2312,38 +2345,6 @@
],
"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",
"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"
],
"Hash": "0e04543b6e8a5f658699c9cdc50534c8"
},
"shape": {
"Package": "shape",
"Version": "1.4.6.1",
Expand Down Expand Up @@ -3051,6 +3052,17 @@
],
"Hash": "829f27b9c4919c16b593794a6344d6c0"
},
"timechange": {
"Package": "timechange",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "RSPM",
"Requirements": [
"R",
"cpp11"
],
"Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
},
"tinytex": {
"Package": "tinytex",
"Version": "0.50",
Expand Down
11 changes: 5 additions & 6 deletions efficacy/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)))
Expand All @@ -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") %>%
Expand Down
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