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create _utils subdir; source from there
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@pawelru
pawelru committed Apr 29, 2024
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0 book/test-utils/envir_hook.qmd → book/_utils/envir_hook.qmd
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0 book/test-utils/save_results.qmd → book/_utils/save_results.qmd
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0 book/webr-utils/shinylive.qmd → book/_utils/shinylive.qmd
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0 book/webr-utils/webr.qmd → book/_utils/webr.qmd
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2 changes: 1 addition & 1 deletion book/appendix/reproducibility.qmd
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Expand Up @@ -4,7 +4,7 @@ title: Reproducibility

------------------------------------------------------------------------

{{< include ../test-utils/envir_hook.qmd >}}
{{< include ../_utils/envir_hook.qmd >}}

## Session Info

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16 changes: 8 additions & 8 deletions book/graphs/efficacy/fstg01.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Subgroup Analysis of Best Overall Response

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

:::: {.panel-tabset}
## Data Setup
Expand Down Expand Up @@ -70,7 +70,7 @@ plot
```

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

## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
Expand Down Expand Up @@ -118,7 +118,7 @@ plot
```

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

## Plot Selecting Columns and <br/> Changing the Alpha Level
Expand Down Expand Up @@ -148,7 +148,7 @@ plot
```

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

## Plot with Fixed <br/> Symbol Size
Expand Down Expand Up @@ -181,7 +181,7 @@ plot
```

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

## Plot of CR Only, Setting <br/> Values Indicating Response
Expand Down Expand Up @@ -228,10 +228,10 @@ height <- 5
```

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

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

## `teal` App

Expand Down Expand Up @@ -302,7 +302,7 @@ app <- init(
shinyApp(app$ui, app$server)
```

{{< include ../../webr-utils/shinylive.qmd >}}
{{< include ../../_utils/shinylive.qmd >}}
:::

{{< include ../../repro.qmd >}}
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14 changes: 7 additions & 7 deletions book/graphs/efficacy/fstg02.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Subgroup Analysis of Survival Duration

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

:::: {.panel-tabset}
## Data Setup
Expand Down Expand Up @@ -83,7 +83,7 @@ plot
```

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

## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
Expand Down Expand Up @@ -125,7 +125,7 @@ plot
```

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

## Plot Selecting Columns and <br/> Changing the Alpha Level
Expand Down Expand Up @@ -156,7 +156,7 @@ plot
```

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

## Plot with Fixed <br/> Symbol Size
Expand Down Expand Up @@ -196,10 +196,10 @@ plot_v3.width <- 8 # nolint: object_name.
```

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

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

## `teal` App

Expand Down Expand Up @@ -278,7 +278,7 @@ app <- init(
shinyApp(app$ui, app$server)
```

{{< include ../../webr-utils/shinylive.qmd >}}
{{< include ../../_utils/shinylive.qmd >}}
:::

{{< include ../../repro.qmd >}}
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18 changes: 9 additions & 9 deletions book/graphs/efficacy/kmg01.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Kaplan-Meier Plot

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

:::: {.panel-tabset}
## Data Setup
Expand Down Expand Up @@ -44,7 +44,7 @@ plot
```

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

## Plot of Failures
Expand All @@ -67,7 +67,7 @@ plot
```

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

## Plot Without <br/> Comparative Statistics
Expand All @@ -87,7 +87,7 @@ plot
```

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

## Plot Without <br/> Censoring Marks
Expand All @@ -109,7 +109,7 @@ plot
```

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

## Plot Modifying <br/> Censoring Marks
Expand All @@ -132,7 +132,7 @@ plot
```

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

## Plot Modifying Options for Statistics, <br/> Tie Handling, Stratification, etc.
Expand Down Expand Up @@ -160,7 +160,7 @@ plot
```

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

::: {.content-visible when-profile="development"}
Expand All @@ -170,7 +170,7 @@ height <- 6
```
:::

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

## `teal` App

Expand Down Expand Up @@ -240,7 +240,7 @@ app <- init(
shinyApp(app$ui, app$server)
```

{{< include ../../webr-utils/shinylive.qmd >}}
{{< include ../../_utils/shinylive.qmd >}}
:::

{{< include ../../repro.qmd >}}
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4 changes: 2 additions & 2 deletions book/graphs/efficacy/mmrmg01.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Plots for Mixed-Effect Model Repeated Measures Analysis

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

Given an MMRM fitted with `s_mmrm`, `g_mmrm_lsmeans` displays for each visit the adjusted means within group and/or difference in adjusted means between groups.
`g_mmrm_diagnostic` displays marginal residual plots for evaluating model fit.
Expand Down Expand Up @@ -114,7 +114,7 @@ plot <- g_mmrm_diagnostic(mmrm_results, type = "q-q-residual")
plot
```

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

## `teal` App

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4 changes: 2 additions & 2 deletions book/graphs/efficacy/mmrmg02.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Forest Plot for Mixed-Effect Model Repeated Measures

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

:::: {.panel-tabset}
## Data Setup
Expand Down Expand Up @@ -136,7 +136,7 @@ width <- 15
height <- 4
```

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

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

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22 changes: 11 additions & 11 deletions book/graphs/other/brg01.qmd
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Expand Up @@ -5,7 +5,7 @@ subtitle: Bar Chart

------------------------------------------------------------------------

{{< include ../../test-utils/envir_hook.qmd >}}
{{< include ../../_utils/envir_hook.qmd >}}

:::: {.panel-tabset}
## Data Setup
Expand Down Expand Up @@ -61,7 +61,7 @@ plot
```

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

## Plot of Percentage
Expand Down Expand Up @@ -92,7 +92,7 @@ plot
```

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

## Plot of Frequency with <br/> Total Number of Subjects
Expand Down Expand Up @@ -120,7 +120,7 @@ plot
```

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

## Plot of Frequency <br/> with Horizontal Bars
Expand All @@ -144,7 +144,7 @@ plot
```

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

## Plot of Percentage <br/> and Confidence Intervals
Expand Down Expand Up @@ -196,7 +196,7 @@ plot
```

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

## Plot of Percentage by <br/> Treatment and Covariate
Expand Down Expand Up @@ -229,7 +229,7 @@ plot
```

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

## Plot of Percentage by <br/> Covariate and Treatment
Expand Down Expand Up @@ -261,7 +261,7 @@ plot
```

`r webr_code_labels <- c("setup", "plot7")`
{{< include ../../webr-utils/webr.qmd >}}
{{< include ../../_utils/webr.qmd >}}
:::

## Plot of Percentage <br/> with Mean and Median
Expand Down Expand Up @@ -331,7 +331,7 @@ plot
```

`r webr_code_labels <- c("setup", "plot8")`
{{< include ../../webr-utils/webr.qmd >}}
{{< include ../../_utils/webr.qmd >}}
:::

## Plot of Categorical <br/> Variable
Expand Down Expand Up @@ -368,10 +368,10 @@ plot
```

`r webr_code_labels <- c("setup", "plot9")`
{{< include ../../webr-utils/webr.qmd >}}
{{< include ../../_utils/webr.qmd >}}
:::

{{< include ../../test-utils/save_results.qmd >}}
{{< include ../../_utils/save_results.qmd >}}

## `teal` App

Expand Down
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