Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add missing table 36 screenshot #236

Merged
merged 4 commits into from
Aug 19, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,15 @@ Depends:
R (>= 3.6),
tern (>= 0.9.5)
Imports:
cards (>= 0.1.0),
cardx (>= 0.1.0),
cards (>= 0.2.0),
cardx (>= 0.2.0),
checkmate (>= 2.1.0),
cowplot (>= 1.0.0),
dplyr (>= 1.0.0),
formatters (>= 0.5.8),
ggplot2 (>= 3.5.0),
gt (>= 0.10.1),
gtsummary (>= 1.7.2),
gtsummary (>= 2.0.0),
lubridate (>= 1.7.10),
magrittr (>= 1.5),
purrr (>= 1.0.1),
Expand Down
Binary file modified quarto/assets/images/screenshots/table_17.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added quarto/assets/images/screenshots/table_36.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
4 changes: 2 additions & 2 deletions quarto/figure-templates/template-fig_01.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@ Required variables:

- **`df`**: The variables specified by `arm_var`, `id_var`, `saffl_var`, `trtsdtm_var`, and `trtedtm_var`.

| Argument | Description | Default |
|:--------------|:------------------------------------------|:--------------|
| **Argument** | **Description** | **Default** |
|:--------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `arm_var` | (`character`) Arm variable used to split table into columns. | `"ARM"` |
| `saffl_var` | (`character`) Flag variable used to indicate inclusion in safety population. | `"SAFFL"` |
Expand Down
4 changes: 2 additions & 2 deletions quarto/figure-templates/template-fig_02.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,8 @@ Required variables:

- **`df`**: The variables specified by `arm_var`, `id_var`, `saffl_var`, and `eosdy_var`.

| Argument | Description | Default |
|:--------------|:------------------------------------------|:--------------|
| **Argument** | **Description** | **Default** |
|:--------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `arm_var` | (`character`) Arm variable used to split table into columns. | `"ARM"` |
| `saffl_var` | (`character`) Flag variable used to indicate inclusion in safety population. | `"SAFFL"` |
Expand Down
6 changes: 3 additions & 3 deletions quarto/figure-templates/template-fig_14.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,8 @@ Required variables:

- **`df`**: The variables `AVAL` and `PARAMCD`, and the variables specified by `arm_var`, `saffl_var`, and `visit_var`.

| Argument | Description | Default |
|:--------------|:------------------------------------------|:--------------|
| **Argument** | **Description** | **Default** |
|:--------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADVS) required to build table. | *No default* |
| `arm_var` | (`character`) Arm variable used to split table into columns. | `"ARM"` |
| `saffl_var` | (`character`) Flag variable used to indicate inclusion in safety population. | `"SAFFL"` |
Expand All @@ -51,7 +51,7 @@ Required variables:
| `x_lab` | (`character`) x-axis label. | `paste0("Time from first dose (", u_trtdur, ")")` |
| `y_lab` | (`character`) y-axis label. | `"Percent of Patients (%)"` |
| `yticks` | (`vector` of `numeric`) y-axis tick positions. If `NA` (default), tick mark positions are automatically calculated. | `NA` |
| `ggtheme` | (`function`) Function from `ggplot2` to apply over the plot. | `NULL` |
| `ggtheme` | (`function`) Function from `ggplot2` to apply over the plot. | `NULL` |
| `add_table` | (`flag`) whether "Number of Patients" table should be printed under the plot. | `TRUE` |
| `annotations` | (named `list` of `character`) List of annotations to add to the table. Valid annotation types are `title`, `subtitles`, and `caption`. Each name-value pair should use the annotation type as name and the desired string as value. | `NULL` |

Expand Down
8 changes: 4 additions & 4 deletions quarto/table-templates/template-table_02.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ Required variables:
- **`df`**: The variables specified by `vars`, `arm_var`, and `saffl_var`.
- **`alt_counts_df`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var`.

| Argument | Description | Default |
| **Argument** | **Description** | **Default** |
|:-----------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` |
Expand Down Expand Up @@ -131,7 +131,7 @@ Required variables:
- **`df`**: `SAFFL` and the variables specified by `vars` and `arm_var`.
- **`alt_counts_df`** (if specified and `tplyr_raw = FALSE`): `SAFFL`, `USUBJID`, and the variable specified by `arm_var`.

| Argument | Description | Default |
| **Argument** | **Description** | **Default** |
|:-----------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` |
Expand Down Expand Up @@ -200,7 +200,7 @@ Required variables:
- **`df`**: `SAFFL` and the variables specified by `vars` and `arm_var`.
- **`alt_counts_df`** (if specified and `tplyr_raw = FALSE`): `SAFFL`, `USUBJID`, and the variable specified by `arm_var`.

| Argument | Description | Default |
| **Argument** | **Description** | **Default** |
|:-----------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|
| `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` |
Expand All @@ -211,5 +211,5 @@ Required variables:
| `lbl_vars` | (`character`) Labels corresponding to variables in `vars` to print in the table. Labels should be ordered according to the order of variables in `vars`. | `formatters::var_labels(df, fill = TRUE)[vars]` |
| `lbl_overall` | (`character`) If specified, an overall column will be added to the table with the given value as the column label. | `"Total Population"` |

Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_02.R#L257).
Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_02.R#L257).
:::
2 changes: 1 addition & 1 deletion quarto/table-templates/template-table_03.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ Required variables:
- **`adsl`**: `USUBJID`, `ENRLDT`, `RANDDT`, and the variables specified by `arm_var`, `scrnfl_var`, `scrnfailfl_var`, and `scrnfail_var`.
- **`alt_counts_df`** (if specified): `USUBJID`, and the variable specified by `arm_var`.

| Argument | Description | Default |
| **Argument** | **Description** | **Default** |
|:-----------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------|
| `adsl` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
| `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` |
Expand Down
Loading
Loading