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replace usage of scda and scda.2022 with random.cdisc.data #250

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May 15, 2024
Merged

replace usage of scda and scda.2022 with random.cdisc.data #250

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1fb2d9e
replace usage of `scda` and `scda.2022` with `random.cdisc.data`
ayogasekaram May 10, 2024
6253c11
[skip style] [skip vbump] Restyle files
github-actions[bot] May 13, 2024
53393af
revert changes to panel-tabset
ayogasekaram May 14, 2024
1d51d3f
reverse any layout changes
ayogasekaram May 14, 2024
91b664c
remove extra space from graphs and listings
ayogasekaram May 14, 2024
5b4e36e
remove extra space from tables
ayogasekaram May 14, 2024
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25 changes: 11 additions & 14 deletions book/graphs/efficacy/fstg01.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,14 @@ subtitle: Subgroup Analysis of Best Overall Response
```{r setup, message = FALSE}
#| code-fold: show

library(scda)
library(scda.2022)
library(dplyr)
library(tern)
library(nestcolor)

adsl_f <- synthetic_cdisc_dataset("latest", "adsl") %>%
adsl_f <- random.cdisc.data::cadsl %>%
select(STUDYID, USUBJID, ARMCD, ARM, SEX, BMRKR2, STRATA1, STRATA2)

adrs_f <- synthetic_cdisc_dataset("latest", "adrs") %>%
adrs_f <- random.cdisc.data::cadrs %>%
filter(PARAMCD == "INVET") %>%
select(STUDYID, USUBJID, PARAMCD, AVISIT, AVALC)

Expand Down Expand Up @@ -69,7 +67,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot1")`
`r webr_code_labels <- c("setup", "plot1")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -117,7 +115,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot2")`
`r webr_code_labels <- c("setup", "plot2")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -147,7 +145,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot3")`
`r webr_code_labels <- c("setup", "plot3")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -157,7 +155,9 @@ plot
## {{< fa regular file-lines sm fw >}} Preview

<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->

<!-- skip strict because of https://github.com/insightsengineering/tern/issues/1186 -->

```{r plot4, test = list(plot_v4 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
df <- extract_rsp_subgroups(
variables = list(
Expand All @@ -180,7 +180,7 @@ plot <- g_forest(
plot
```

`r webr_code_labels <- c("setup", "plot4")`
`r webr_code_labels <- c("setup", "plot4")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -227,7 +227,7 @@ width <- 20
height <- 5
```

`r webr_code_labels <- c("setup", "plot5")`
`r webr_code_labels <- c("setup", "plot5")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -244,11 +244,8 @@ library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(scda)
library(scda.2022)

ADSL <- synthetic_cdisc_dataset("latest", "adsl")
ADRS <- synthetic_cdisc_dataset("latest", "adrs")
ADSL <- random.cdisc.data::cadsl
ADRS <- random.cdisc.data::cadrs
})
datanames <- c("ADSL", "ADRS")
datanames(data) <- datanames
Expand Down
18 changes: 7 additions & 11 deletions book/graphs/efficacy/fstg02.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,6 @@ library(tern)
library(dplyr)
library(forcats)
library(nestcolor)
library(scda)
library(scda.2022)

preprocess_adtte <- function(adtte) {
# Save variable labels before data processing steps.
Expand Down Expand Up @@ -51,7 +49,7 @@ preprocess_adtte <- function(adtte) {
adtte
}

anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
anl <- random.cdisc.data::cadtte %>%
preprocess_adtte()
```

Expand Down Expand Up @@ -82,7 +80,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot1")`
`r webr_code_labels <- c("setup", "plot1")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -124,7 +122,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot2")`
`r webr_code_labels <- c("setup", "plot2")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -155,7 +153,7 @@ plot <- g_forest(tbl = result)
plot
```

`r webr_code_labels <- c("setup", "plot3")`
`r webr_code_labels <- c("setup", "plot3")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -195,7 +193,7 @@ height <- 4
plot_v3.width <- 8 # nolint: object_name.
```

`r webr_code_labels <- c("setup", "plot4")`
`r webr_code_labels <- c("setup", "plot4")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -212,19 +210,17 @@ library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(scda)
library(scda.2022)
library(dplyr)
library(forcats)

ADSL <- synthetic_cdisc_dataset("latest", "adsl")
ADSL <- random.cdisc.data::cadsl
ADSL <- ADSL %>%
filter(ARM %in% c("B: Placebo", "A: Drug X")) %>%
mutate(ARM = droplevels(fct_relevel(ARM, "B: Placebo"))) %>%
mutate(ARMCD = droplevels(fct_relevel(ARMCD, "ARM B")))
ADSL$RACE <- droplevels(ADSL$RACE)

ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
ADTTE <- random.cdisc.data::cadtte
adtte_labels <- col_labels(ADTTE)

ADTTE <- ADTTE %>%
Expand Down
23 changes: 9 additions & 14 deletions book/graphs/efficacy/kmg01.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,10 @@ subtitle: Kaplan-Meier Plot
#| code-fold: show

library(tern)
library(scda)
library(scda.2022)
library(dplyr)
library(nestcolor)

adtte <- synthetic_cdisc_dataset("latest", "adtte")
adtte <- random.cdisc.data::cadtte
anl <- adtte %>%
dplyr::filter(PARAMCD == "OS") %>%
dplyr::mutate(is_event = CNSR == 0)
Expand All @@ -43,7 +41,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot1")`
`r webr_code_labels <- c("setup", "plot1")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -66,7 +64,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot2")`
`r webr_code_labels <- c("setup", "plot2")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -86,7 +84,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot3")`
`r webr_code_labels <- c("setup", "plot3")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -108,7 +106,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot4")`
`r webr_code_labels <- c("setup", "plot4")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -131,7 +129,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot5")`
`r webr_code_labels <- c("setup", "plot5")`
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{{< include ../../_utils/webr.qmd >}}
:::

Expand Down Expand Up @@ -159,7 +157,7 @@ plot <- g_km(
plot
```

`r webr_code_labels <- c("setup", "plot6")`
`r webr_code_labels <- c("setup", "plot6")`
{{< include ../../_utils/webr.qmd >}}
:::

Expand All @@ -183,11 +181,8 @@ library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(scda)
library(scda.2022)

ADSL <- synthetic_cdisc_dataset("latest", "adsl")
ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
ADSL <- random.cdisc.data::cadsl
ADTTE <- random.cdisc.data::cadtte
})
datanames <- c("ADSL", "ADTTE")
datanames(data) <- datanames
Expand Down
12 changes: 4 additions & 8 deletions book/graphs/efficacy/mmrmg01.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,10 @@ Given an MMRM fitted with `s_mmrm`, `g_mmrm_lsmeans` displays for each visit the

library(dplyr)
library(tern.mmrm)
library(scda)
library(scda.2022)
library(nestcolor)

adsl <- synthetic_cdisc_dataset("latest", "adsl")
adqs <- synthetic_cdisc_dataset("latest", "adqs")
adsl <- random.cdisc.data::cadsl
adqs <- random.cdisc.data::cadqs

adqs_f <- adqs %>%
dplyr::filter(PARAMCD == "FKSI-FWB" & !AVISIT %in% c("BASELINE")) %>%
Expand Down Expand Up @@ -124,12 +122,10 @@ library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(scda)
library(scda.2022)
library(dplyr)

ADSL <- synthetic_cdisc_dataset("latest", "adsl")
ADQS <- synthetic_cdisc_dataset("latest", "adqs") %>%
ADSL <- random.cdisc.data::cadsl
ADQS <- random.cdisc.data::cadqs %>%
filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
mutate(
Expand Down
6 changes: 2 additions & 4 deletions book/graphs/efficacy/mmrmg02.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,12 @@ subtitle: Forest Plot for Mixed-Effect Model Repeated Measures
```{r setup, message = FALSE}
#| code-fold: show

library(scda)
library(scda.2022)
library(dplyr)
library(tern.mmrm)
library(nestcolor)

adsl <- synthetic_cdisc_dataset("latest", "adsl")
adqs <- synthetic_cdisc_dataset("latest", "adqs")
adsl <- random.cdisc.data::cadsl
adqs <- random.cdisc.data::cadqs

adqs_f <- adqs %>%
dplyr::filter(PARAMCD == "FKSI-FWB" & !AVISIT %in% c("BASELINE")) %>%
Expand Down
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