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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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4 changes: 2 additions & 2 deletions book/_quarto.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ execute:
engine: knitr
webr:
channel-type: "post-message"
packages: ["tern", "scda", "scda.2022", "dplyr"]
packages: ["tern", "random.cdisc.data", "dplyr"]
show-startup-message: false
autoload-packages: false

Expand Down Expand Up @@ -118,4 +118,4 @@ website:
profile:
group:
- [stable, development]
default: stable
default: stable
39 changes: 19 additions & 20 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 All @@ -49,7 +47,9 @@ var_labels(anl_rsp_arms_ab) <- c(anl_labels, is_rsp = "Is Responder")
## {{< 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 plot1, test = list(plot_v1 = "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 @@ -69,8 +69,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
Expand All @@ -79,7 +78,9 @@ 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 plot2, test = list(plot_v2 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
anl_rsp_comb_arms_ac <- anl %>%
mutate(is_rsp = AVALC %in% c("CR", "PR")) %>%
Expand Down Expand Up @@ -117,8 +118,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot Selecting Columns and <br/> Changing the Alpha Level
Expand All @@ -127,7 +127,9 @@ 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 plot3, test = list(plot_v3 = "plot"), fig.width = 10, fig.height = 4, 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 @@ -147,8 +149,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot with Fixed <br/> Symbol Size
Expand All @@ -157,7 +158,9 @@ 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 @@ -180,8 +183,7 @@ plot <- g_forest(
plot
```

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

## Plot of CR Only, Setting <br/> Values Indicating Response
Expand All @@ -190,7 +192,9 @@ 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 plot5, test = list(plot_v5 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
anl_cr_arms_ab <- anl %>%
mutate(is_rsp = AVALC == "CR") %>%
Expand Down Expand Up @@ -227,8 +231,7 @@ width <- 20
height <- 5
```

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

{{< include ../../_utils/save_results.qmd >}}
Expand All @@ -244,11 +247,8 @@ 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 Expand Up @@ -306,5 +306,4 @@ shinyApp(app$ui, app$server)
:::

{{< include ../../repro.qmd >}}

::::
29 changes: 13 additions & 16 deletions book/graphs/efficacy/fstg02.qmd
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
---
title: FSTG02
subtitle: Subgroup Analysis of Survival Duration
editor_options:
chunk_output_type: console
ayogasekaram marked this conversation as resolved.
Show resolved Hide resolved
---

------------------------------------------------------------------------
Expand All @@ -17,8 +19,6 @@ 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 +51,7 @@ preprocess_adtte <- function(adtte) {
adtte
}

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

Expand All @@ -61,6 +61,7 @@ anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
## {{< fa regular file-lines sm fw >}} Preview

<!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->

```{r plot1, test = list(plot_v1 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
anl1 <- anl

Expand All @@ -82,8 +83,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
Expand All @@ -92,6 +92,7 @@ plot
## {{< fa regular file-lines sm fw >}} Preview

<!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->

```{r plot2, test = list(plot_v2 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
anl2 <- anl %>%
mutate(
Expand Down Expand Up @@ -124,8 +125,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot Selecting Columns and <br/> Changing the Alpha Level
Expand All @@ -134,6 +134,7 @@ plot
## {{< fa regular file-lines sm fw >}} Preview

<!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->

```{r plot3, test = list(plot_v3 = "plot"), fig.width = 8, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
anl3 <- anl

Expand All @@ -155,8 +156,7 @@ plot <- g_forest(tbl = result)
plot
```

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

## Plot with Fixed <br/> Symbol Size
Expand All @@ -165,6 +165,7 @@ plot
## {{< fa regular file-lines sm fw >}} Preview

<!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->

```{r plot4, test = list(plot_v4 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
anl4 <- anl

Expand Down Expand Up @@ -195,8 +196,7 @@ height <- 4
plot_v3.width <- 8 # nolint: object_name.
```

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

{{< include ../../_utils/save_results.qmd >}}
Expand All @@ -212,19 +212,17 @@ 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 Expand Up @@ -282,5 +280,4 @@ shinyApp(app$ui, app$server)
:::

{{< include ../../repro.qmd >}}

::::
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