Package 'thekidsbiostats'

checkbox_labels

Description

Apply factor labels to categorical responses (checkboxes) per REDCap data dictionary

Apply factor labels to categorical responses (checkboxes) per REDCap data dictionary

Usage

checkbox_labels(x, dict)

checkbox_labels(x, dict)

Arguments

x	checkbox ⁠Variable / Field Name⁠ per data dictionary
dict	REDCap data dictionary

Value

Named list of character objects

Named list of character objects

Examples

## Not run: 

dat <- tibble(var___0 = c("0", "1"), var___1 = c("1", "0"))

dictionary <- tibble(`Variable / Field Name` = "var",
  `Choices, Calculations, OR Slider Labels` = "0, No | 1, Yes")

dat <- labelled::set_variable_labels(dat, .labels = checkbox_labels("var", dictionary))


## End(Not run)

## Not run: 

dat <- tibble(var___0 = c("0", "1"), var___1 = c("1", "0"))

dictionary <- tibble(`Variable / Field Name` = "var",
  `Choices, Calculations, OR Slider Labels` = "0, No | 1, Yes")

dat <- labelled::set_variable_labels(dat, .labels = checkbox_labels("var", dictionary))


## End(Not run)

---

clean_REDCap

Description

Clean a REDCap extract by applying factor levels and convert column classes per the REDCap data dictionary.

Usage

clean_REDCap(
  d,
  dict,
  numeric_date = FALSE,
  yesno_to_bool = FALSE,
  quiet = FALSE
)

Arguments

d	REDCap (data frame)
dict	REDCap data dictionary (data frame)
numeric_date	(default FALSE) set to TRUE if MS Excel has helpfully converted to a numeric date
yesno_to_bool	(default FALSE) convert factors with levels c("Yes", "No") to logical objects?
quiet	(default FALSE) pass quiet argument to lubridate functions

Value

cleaned data frame

Examples

## Not run: 

dat <- tibble(var = c("0", "1"))

dictionary <- tibble(`Variable / Field Name` = "var",
  `Field Type` = "radio",
  `Field Label` = "Label",
  `Choices, Calculations, OR Slider Labels` = "0, No | 1, Yes",
  `Text Validation Type OR Show Slider Number` = NA)

(dat_clean <- clean_REDCap(dat, dictionary))


## End(Not run)

---

Create a new project structure

Description

Creates a new project folder with subfolders, an RProj file, and optional Quarto report. Can optionally open the project in a new session and close the current one.

Usage

create_project(
  project_name,
  path = NULL,
  folders = c("data-raw", "data", "admin", "docs", "reports", "scripts"),
  ext_name = "html",
  create_report = FALSE,
  create_rproj = TRUE,
  open_project = TRUE,
  ...
)

Arguments

project_name	Name of the new project folder.
path	Parent directory for the project. If NULL, prompts the user.
folders	Character vector of subfolders to create.
ext_name	Name of the report extension for create_template().
create_report	Whether to create a report using create_template().
create_rproj	Whether to include a .Rproj file.
open_project	Whether to open the new project in a new RStudio session.
...	Additional arguments passed to create_template().

Value

Invisibly returns the project path.

---

Shiny Addin: Create New Project

Description

Launches a Shiny app to create a project with folders, report, and control over session state.

Usage

create_project_addin()

---

Create a Quarto report template

Description

Copies extension files into ⁠_extensions/⁠ and creates a .qmd report file. Optionally opens the created file. If the file already exists, no overwrite occurs and a warning is shown.

Usage

create_template(
  file_name = NULL,
  directory = "reports",
  ext_name = "html",
  title = NULL,
  subtitle = NULL,
  author = NULL,
  affiliation = NULL,
  include_reproducibility = TRUE,
  open_file = TRUE
)

Arguments

file_name	Name of the report file (without .qmd).
directory	Directory to save the report and extensions in.
ext_name	Name of the template extension (e.g. "html", "word").
title	Title of the report.
subtitle	Subtitle of the report.
author	Author name (defaults to Sys.info()[['user']]).
affiliation	Affiliation of the author.
include_reproducibility	Whether or not to include a 'Reproducibility Information' section, which outputs the R session information (default: TRUE).
open_file	Whether to open the file after creation (default: TRUE).

Value

Invisibly returns path to created .qmd file, or NULL if skipped.

---

Shiny Addin: Create Report Template

Description

Launches a Shiny app to generate a report template in a user-selected folder.

Usage

create_template_addin()

---

Example of a (fictional) uncleaned data set for analysis

Description

Includes variables that represent common patient information, with column names that would generally be problematic in an analytical setting without some form of cleaning.

Usage

data_patient

Format

data.frame

---

factor_convert

Description

Apply factor labels to categorical responses per REDCap data dictionary.

Apply factor labels to categorical responses per REDCap data dictionary.

Usage

factor_convert(x, d, dict)

factor_convert(x, d, dict)

Arguments

x	character vector
d	REDCap import
dict	REDCap data dictionary

Examples

## Not run: 

dat <- tibble(var = c("0", "1"))

dictionary <- tibble(`Variable / Field Name` = "var",
  `Choices, Calculations, OR Slider Labels` = "0, No | 1, Yes")

mutate(dat, across("var", factor_convert, d = dat, dict = dictionary))


## End(Not run)

## Not run: 

dat <- tibble(var = c("0", "1"))

dictionary <- tibble(`Variable / Field Name` = "var",
  `Choices, Calculations, OR Slider Labels` = "0, No | 1, Yes")

mutate(dat, across("var", factor_convert, d = dat, dict = dictionary))


## End(Not run)

---

factor_table

Description

factor_table

factor_table

Usage

factor_table(x, rows = "\\|", cols = ",")

factor_table(x, rows = "\\|", cols = ",")

Arguments

x	character vector of REDCap options (e.g. 0, No | 1, Yes)
rows	(default "\|") Regex defining row separator
cols	(default ",") Regex defining column separator

Details

For a more thorough example, see the vignette.

Value

2 column tibble of factor levels ("key") and labels ("value")

2 column tibble of factor levels ("key") and labels ("value")

Examples

## Not run:  factor_table("0, No | 1, Yes") 

## Not run:  factor_table("0, No | 1, Yes")

---

fct_case_when

Description

Essentially the same as dplyr::case_when but the variable is of class factor, ordered based on the order entered into the case_when statement

Usage

fct_case_when(..., message = T)

Arguments

...

as per dplyr::case_when, essentially all input is passed through to dplyr::case_when A sequence of two-sided formulas. The left hand side (LHS) determines which values match this case. The right hand side (RHS) provides the replacement value. The LHS must evaluate to a logical vector. The RHS does not need to be logical, but all RHS must evaluate to the same type of vector. Both LHS and RHS may have the same length of either 1 or n. The value of n must be consistent across all cases. The case of n == 0 is treated as a variant of n != 1. NULL inputs are ignored.

message

prints the resulting factor levels. This is TRUE by default as output may often not be as expected

Details

For a more thorough example, see the vignette.

Value

A vector of length 1 or n, of class factor, matching the length of the logical input or output vectors. Inconsistent lengths or types will generate an error.

Examples

## Not run: 

  x <- 1:50
  case_when(
    x %% 35 == 0 ~ "fizz buzz",
    x %% 5 == 0 ~ "fizz",
    x %% 7 == 0 ~ "buzz",
    TRUE ~ "no fizz buzz"
  ) %>% table

  fct_case_when(
    message = F,
    x %% 35 == 0 ~ "fizz buzz",
    x %% 5 == 0 ~ "fizz",
    x %% 7 == 0 ~ "buzz",
    TRUE ~ "no fizz buzz"
  ) %>% table


## End(Not run)

---

Insert Callout via RStudio Addin

Description

Launches a Shiny app as an RStudio addin to insert a Quarto callout at the cursor position. The user selects a callout type from a dropdown, sees a preview colour, and inserts formatted callout text into the current script.

Usage

insert_callout()

Value

A Shiny application that runs within RStudio.

Examples

## Not run: 
if (interactive()) {
  insert_callout()
}

## End(Not run)

---

Insert Callout via RStudio Addin

Description

Inserts a Quarto callout block with placeholder text directly at the cursor.

Usage

insert_callout_2()

Value

None. Inserts text into the active RStudio document.

Examples

## Not run: 
insert_callout()

## End(Not run)

---

Insert Margin Block at Cursor

Description

Inserts a Quarto column-margin block with placeholder text directly at the cursor.

Usage

insert_margin()

Value

None. Inserts text into the active RStudio document.

Examples

## Not run: 
if (interactive()) {
  insert_margin()
}

## End(Not run)

---

RStudio Addin: Insert child Quarto tabset for model output

Description

This Shiny gadget inserts a model_name <- "mod" line and a child chunk to include a preformatted tabset from an external Quarto file. It also optionally previews the output.

Usage

insert_model_tabset()

Value

Inserts code into the active RStudio document and copies a child QMD file.

---

Image Size Parameters for Save Function

Description

Size parameters (mm) for a standard A4 page with "quarter", "half portrait", "half landscape", #' "full portrait", "full landscape". Identifiers for "pdf" and "png" devices included.

Usage

layout_params

Format

data.frame

---

Create a copy-pasteable variable dictionary template

Description

Create a copy-pasteable variable dictionary template

Usage

make_column_dict(
  data,
  quiet = FALSE,
  auto_clean = TRUE,
  new_names = NULL,
  labels = NULL,
  file = NULL,
  ...
)

Arguments

data	A data.frame or tibble containing the original data with column names to be replaced.
quiet	Logical, default FALSE: suppress printing the generated R code string to the console.
auto_clean	Logical, default TRUE: generate suggested new names using janitor::clean_names()
new_names	Optional character string, If specified, fills the $new column with these labels. Length must match the number of columns in data.
labels	Optional character string. If specified, fills the $label column with these labels. Length must match the number of columns in data.
file	Optional character string. If specified, writes dictionary template to file path (available formats: .csv, .txt, .xlsx, .rds, .R)
...	Additional arguments passed to janitor::clean_names()

Details

The default behaviour is to print a tribble template to the console. Set quiet=TRUE to suppress this output. If the file path has the extension .R, this writes the R code in the format of a tribble to the file.

Value

A data.frame (invisibly returned) with one row per column name in data and three columns:

old

Original column names.

new

Suggested new column names (optionally cleaned using janitor::clean_names()).

label

Empty character field for user-supplied variable labels.

Examples

data("data_patient", package = "thekidsbiostats")

# Create a data dictionary and formulate some cleaned column names, assign to `dict` object
dict <- make_column_dict(data_patient, auto_clean = TRUE, quiet = FALSE)

---

Modify flextable Labels

Description

Apply formatting and styling specifically to the label cells of a flextable object. Label cells are automatically identified as the cells with the smallest left padding in the specified column, which typically correspond to row labels.

Usage

modify_labels(
  x,
  label_col = 1,
  j = NULL,
  hline = NULL,
  bold = NULL,
  italic = NULL,
  color = NULL,
  bg = NULL,
  highlight = NULL,
  fontsize = NULL,
  font = NULL,
  rotation = NULL,
  align = NULL,
  border = NULL,
  border.top = NULL,
  border.left = NULL,
  border.bottom = NULL,
  border.right = NULL,
  padding = NULL,
  padding.top = NULL,
  padding.left = NULL,
  padding.bottom = NULL,
  padding.right = NULL
)

Arguments

x	A flextable object.
label_col	Numeric or character; the column used to identify label rows. Label rows are automatically detected as those with the smallest left padding in this column. Default is 1.
j	Numeric or character; the column(s) to which the styling/formatting should be applied, which by default is label_col.
hline	specifies a horizontal line above label cells. Can be an fp_border object, a color string (e.g., "red"), or a logical value (TRUE for default border, FALSE for no line). Note that j is ignored for hline, use border to apply to specific columns only.
bold	Logical; make label text bold.
italic	Logical; make label text italic.
color	Character; text colour of the label cells.
bg	Character; background colour of the label cells.
highlight	Character; highlight colour for the label cells.
fontsize	Numeric; font size of the label cells.
font	Character; font family name of the label cells.
rotation	Numeric; rotation of label text, can be one of "lrtb", "tbrl", "btlr".
align	Character; text alignment of label ("left", "center", "right" or "justify").
border, border.top, border.left, border.bottom, border.right	Optional fp_border objects to set cell borders.
padding, padding.top, padding.left, padding.bottom, padding.right	Optional numeric values to set cell padding.

Details

This function identifies label cells by finding the rows in column label_col with the smallest left padding. It then applies any formatting options specified and leaving unchanged those options that were left unspecified.

Horizontal lines specified via hline are applied above the label cells and across the entire table. If hline is a logical value, TRUE applies a default border and FALSE makes it transparent.

Value

A flextable object with the specified modifications applied to the label cells.

Examples

library(flextable)
df <- data.frame(Group = c("A","B","C"), Value = 1:3)
ft <- thekids_table(df)  # or flextable(df)
ft <- modify_labels(ft, bold = TRUE, hline = "black", fontsize = 12)

---

Preprocess font changes to Quarto (.qmd) HTML reports

Description

This function "pre-processes" a .qmd file to use different (Google) fonts, without having to locally download and install the font files.

Usage

preprocess_qmd(
  file_path,
  base_family = getOption("thekidsbiostats.font", "Barlow"),
  update_global_option = T
)

Arguments

file_path	File path to the .qmd file to update.
base_family	Font base family to consider. Defaults to the global option when loading thekidsbiostats. Otherwise, any Google font family can be specified (must be in sysfonts::font_families_google()).
update_global_option	Update the global option for thekidsbiostats.font based on the new font family specified. Default TRUE.

Value

Updates the YAML header of the input .qmd file (formatted per thekidsbiostats template) with the specified font base_family.

Note

Works only for HTML report types that have mainfont and ⁠include-in-header⁠ arguments in the YAML header as specified in the thekidsbiostats HTML template. The template can be created using thekidsbiostats::create_template.

Examples

## Not run: 
preprocess_qmd(file_path = "path_to_qmd", base_family = "Monsieur La Doulaise")

## End(Not run)

---

round_df

Description

A function, for data frames or tibbles, to round all numeric columns in a data frame or tibble.

Usage

round_df(x, digits = 2, con_char = F)

Arguments

x	a data frame or tibble vector
digits	integer indicating the number of decimal places to be used
con_char	logical as to whether you want the rounded columns to be converted to character class (T) or not (F); default is F

Details

The option exists to keep these columns as numeric (simply rounding), or to convert them to characters keeping trailing zeroes in the process.

Value

object of class tibble"

Examples

## Not run: 
round_df(iris, 0)

round_df(iris, 0, con_char = T) %>% str

## End(Not run)

---

round_vec

Description

A function, for vectors, to keep trailing zeroes when rounding numbers.

Usage

round_vec(x, digits = 2)

Arguments

x	a numeric vector
digits	integer indicating the number of decimal places to be used.

Details

For a more thorough example, see the vignette.

Value

object of class character"

Examples

round_vec(mtcars$wt, 2)

---

The Kids Colour Scales for ggplot2

Description

Scale functions (fill and colour) for ggplot2.

Usage

scale_fill_thekids(
  palette = "primary",
  discrete = TRUE,
  reverse = FALSE,
  begin = 0,
  end = 1,
  na.value = thekids_colours$coolgrey_50,
  ...
)

scale_colour_thekids(
  palette = "primary",
  discrete = TRUE,
  reverse = FALSE,
  begin = 0,
  end = 1,
  na.value = thekids_colours$coolgrey_50,
  ...
)

scale_color_thekids(
  palette = "primary",
  discrete = TRUE,
  reverse = FALSE,
  begin = 0,
  end = 1,
  na.value = thekids_colours$coolgrey_50,
  ...
)

Arguments

palette	Name of the palette in thekids_palettes.
discrete	A boolean indicating whether fill aesthetic is discrete or not.
reverse	A boolean indicating whether the palette should be reversed.
begin	A numeric value between 0 and 1 at which the colour palette should begin.
end	A numeric value between 0 and 1 at which the colour palette should end.
na.value	A colour to use for missing values (Default='coolgrey_50').
...	Additional arguments passed to discrete_scale() and scale_colour_gradientn()/scale_fill_gradientn(), used respectively when discrete is TRUE or FALSE

---

The Kids Research Institute Australia Colours

Description

Colour names and HEX codes consistent with Institute guidelines.

Usage

thekids_colours

Format

A named character string. The following colours can be accessed with three variants (main colours and their 50% or 10% tint variations):

• Saffron: saffron, saffron_50, saffron_10

• Pumpkin: pumpkin, pumpkin_50, pumpkin_10

• Teal: teal, teal_50, teal_10

• Dark teal: darkteal, darkteal_50, darkteal_10

• Celestial blue: celestialblue, celestialblue_50, celestialblue_10

• Azure blue: azureblue, azureblue_50, azureblue_10

• Midnight blue: midnightblue, midnightblue_50, midnightblue_10

• Cool grey: coolgrey, coolgrey_50, coolgrey_10

Source

The Kids Research Institute Australia style guide.

Examples

names(thekids_colours)
thekids_colours$teal
thekids_colours$saffron_50

---

Fit a Statistical Model and Pass to Output Handler

Description

This function fits a statistical model to the given dataset using a specified formula based on the dependent (y) and independent (x and formula) variables. After fitting, the model is passed to a dedicated output handler (thekids_model_output) for further processing or customization. Supported model types include linear regression, negative binomial regression, and quantile regression.

Usage

thekids_model(data, y, x, formula = "", model = "linear", ...)

Arguments

data	A data frame containing the variables to be used in the model.
y	Character string specifying the name of the dependent variable.
x	Character string specifying the name of the primary independent variable.
formula	Optional character string specifying additional terms to include in the formula. If not provided, the formula will be auto-generated as y ~ x.
model	Character string specifying the type of model to fit. Currently supported are "linear", "negbin", or "quantile".
...	Additional arguments passed to the underlying modeling functions.

Details

This function validates the specified model type and constructs a formula based on the supplied arguments. The data is reduced to complete cases for the variables included in the formula before fitting the model. The fitted model is passed to thekids_model_output for further handling, allowing for streamlined customization of model outputs.

For a more thorough example, see the vignette.

Value

Model output relating to the appropriate modeling function (e.g., lm, glm.nb, or rq). This is the same object returned by thekids_model_output if the latter is called directly.

See Also

thekids_model_output

Examples

# Example 1: Linear model
## Not run: 
data(mtcars)
thekids_model(mtcars, y = "mpg", x = "wt", model = "linear")

## End(Not run)

# Example 2: Linear model with factor
## Not run: 
thekids_model(mtcars %>% mutate(cyl = as.factor(cyl)), y = "mpg", x = "cyl", model = "linear")

## End(Not run)

# Example 3: Quantile regression
## Not run: 
library(quantreg)
data(engel)
thekids_model(engel, y = "foodexp", x = "income", model = "quantile", tau = 0.5)

## End(Not run)

---

Generate Model Output for Specified Model Type

Description

This function identifies the type of the fitted model and chooses the appropriate method to produce model output.

Usage

thekids_model_output(model, by = NULL, data = NULL, ...)

Arguments

model	A fitted model object produced by thekids_model or another modeling function.
by	The main predictor of interest.
data	A data frame containing the variables to be used in the model.
...	Additional arguments passed to the output method for the specific model type.

Details

This function acts as a wrapper, delegating the call to the appropriate output method based on the class of the model object. The actual behaviour is determined by the specific method implementation for the model type.

Value

Output specific to the fitted model type, as determined by the appropriate output method (e.g., summary or custom output).

Examples

# Assuming `model` is a fitted model object
# thekids_model_output(model)

---

Generates a function, which when supplied to ggplot2 will return the appropriate colour palette, depending on the number of levels.

Description

Generates a function, which when supplied to ggplot2 will return the appropriate colour palette, depending on the number of levels.

Usage

thekids_pal(palette, discrete = FALSE, reverse = FALSE)

Arguments

palette	Character name of palette in thekids_palettes
discrete	Boolean Indicating whether the palette is discrete or not (i.e. sequential or diverging)
reverse	Boolean indicating whether the palette should be reversed

Value

A palette function based off the thekids_palettes. When called with an integer n, it returns a character vector of n hex colour values. Designed for use with scale_colour_thekids(), scale_fill_thekids() and other ggplot2 scale functions.

---

The Kids Research Institute Australia Colour Palettes

Description

Colour palettes using colours from The Kids Research Institute Australia.

Usage

thekids_palettes

Format

A nested list of colourmaps Palettes are stored in a nested list of palette variants, which can be accessed by: ⁠thekids_palettes$<variant>$<name>⁠

• Sequential palettes: Continuous colour gradients for ordered data values

  • thekids_palettes$sequential$primary

  • thekids_palettes$sequential$tint50

  • thekids_palettes$sequential$tint10

  • mono-colour sequential ramps, accessed by thekids_palettes$sequential$... saffron, pumpkin, teal, celestialblue, azureblue, midnightblue, coolgrey

  These return palette functions of the form ⁠function(n)⁠ for continuous scales.

• Diverging palettes: Two-ended colour gradients deviating about a central white reference point.

  • thekids_palettes$diverging$pumpkin2celestial

  • thekids_palettes$diverging$saffron2teal

  • thekids_palettes$diverging$saffron2midnight

  These return palette functions of the form ⁠function(n)⁠ for diverging scales.

• Qualitative palettes: Sets of visually distinct colours for nominal (unordered) categories.

  • thekids_palettes$qualitative$primary - NOT YET IMPLEMENTED

  • thekids_palettes$qualitative$tint50 - NOT YET IMPLEMENTED

  • thekids_palettes$qualitative$tint10 - NOT YET IMPLEMENTED

  These return a named list of colours.

Details

In addition to the nested lists (sequential, diverging and qualitative), there are also three separate lists at the base level, namely: ⁠$primary⁠, ⁠$tint50⁠, ⁠$tint10⁠. These historically contained the list of The Kids colours (which have now been moved to thekids_colours) but have been left here for backwards compatibility. Future updates of thekidsbiostats package will remove these lists from thekids_palettes object.

Source

The Kids Research Institute Australia style guide.

Examples

thekids_palettes$sequential$primary
thekids_palettes$sequential$midnightblue
thekids_palettes$diverging$saffron2teal

---

Save a ggplot with common practical defaults

Description

This function saves ggplot2 plots to common pre-specified sizes and ratios.

Usage

thekids_save(
  plot = ggplot2::last_plot(),
  filename,
  path = ".",
  layout = "full landscape",
  device = "pdf",
  dpi = 300,
  ...
)

Arguments

plot	Plot to save; defaults to last plot displayed.
filename	File name to create on disk.
path	Path of the directory to save plot to. Defaults to current working directory.
layout	Size to save plot to. Can be a vector of strings. Default "full landscape". See details.
device	Device to use. Can be a vector of strings. Default "pdf".
dpi	Plot resolution. Default 300.
...	Other defaults passed to ggsave.

Details

Plot layouts can take the values "quarter", "half portrait", "half landscape, "full portrait", "full landscape". Each of these are based on the dimensions of a standard A4 page.

Examples

## Not run: 
gg <- ggplot(mtcars, aes(hp, mpg, color = as.factor(cyl))) +
geom_point() +
theme_thekids()

thekids_save("example", layout = "half landscape", device = "png")
thekids_save("example", layout = "half portrait", device = "png")
thekids_save("example", layout = "full landscape", device = "png")

thekids_save("example", layout = c("half landscape", "half portrait"))
thekids_save("example", device = c("png", "pdf"))

## End(Not run)

---

Function to display the available colours in The Kids palette

Description

Displays the colour palette for The Kids, including their hex codes.

Usage

thekids_showpalette()

---

The Kids themed table output

Description

A function that accepts tabular data, in a range of formats, and outputs an object of class flextable() (intended) for display in html and word documents.

Usage

thekids_table(
  x,
  fontsize = 10,
  fontsize_header = 11,
  line_spacing = 1.5,
  padding = 2.5,
  colour = "midnightblue",
  highlight = NULL,
  highlight_colour = NULL,
  zebra = FALSE,
  font_family = "Barlow",
  fallback_font_family = "sans",
  date_fix = TRUE,
  ...
)

Arguments

x	a table, typically a data.frame, tibble, or output from gtsummary.
fontsize	the font size for text in the body of the table, defaults to 8 (passed through to set_flextable_defaults).
fontsize_header	the font size for text in the header of the table, defaults to 10.
line_spacing	line spacing for the table, defaults to 1.5 (passed through to set_flextable_defaults).
padding	padding around all four sides of the text within the cell, defaults to 2.5 (passed through to set_flextable_defaults).
colour	a named colour, hex code or one of the colours from The Kids palette, see thekids_colours for available colour names.
highlight	A numeric vector indicating which rows to highlight. Defaults to NULL, meaning no rows are highlighted.
highlight_colour	Colour used when highlighting rows for both highlight and zebra. If NULL, a 50% tint of the main colour argument is used.
zebra	controls alternating highlighting of rows, logical or integer (defaults to FALSE); if TRUE, alternate each row's background with colour; if an integer, alternate row blocks of this size are highlighted; if negative, this will invert the sequence of highlighted blocks; (defaults to FALSE)
font_family	string containing the font family to apply to the table. Default "Barlow".
fallback_font_family	fallback font family if font_family is does not exist. Default is "sans".
date_fix	re-wraps date objects to strictly occupy one line, instead of splitting (defaults to TRUE).
...	other parameters passed through to set_flextable_defaults.

Details

The purpose of this function is easily coerce many different table structures in a consistent format (look and feel), with The Kids branding applied, that ultimately will look nice in either an html or word output.

Default settings produce a relatively compact table, to avoid reports becoming excessively lengthy.

The output can be piped (⁠%>%⁠) into further flextable() functions for advance customisation of the appearance.

Currently the function works well with input in the form of data frames, tibbles, dplyr pipes (think summarise()), gtsummary, and kable outputs.

For a more thorough example, see the vignette.

Value

a flextable class object that will display in both html and word output

Note

Errors may be encountered if the input to the function (kable/gtsummary/flextable) has already received a lot of processing (merging cells, aesthetic changes). The intention is that these things would occur after running thekids_table().

Font family must be installed at a system level, otherwise the default ("sans") will be applied.

Pre-specified formatting applied to 'flextable' objects (ahead of thekids_table()) may not carry over as expected. Please consider using thekids_table() in place of an explicit flextable() call, because our function already coerces the table to a flextable object.

Examples

## Not run: 

head(mtcars, 10) %>%
  thekids_table(colour = "Saffron")


mtcars %>%
  select(cyl, mpg, hp, wt, gear) %>%
  group_by(cyl, gear) %>%
  summarise(mean_mpg = mean(mpg),
            mean_hp = mean(hp),
            mean_wt = mean(wt)) %>%
  thekids_table(colour = "CelestialBlue", highlight = c(4:6),
                padding.left = 20, padding.right = 20)

## End(Not run)

---

Apply Institute Theming to ggplot2 Plots

Description

This function applies a custom theme to ggplot2 plots, incorporating specific fonts and colours to align with the institute's visual identity.

Usage

thekids_theme(
  base_size = 11,
  base_family = NULL,
  base_line_size = base_size/22,
  base_rect_size = base_size/22,
  strip_colour = "midnightblue",
  scale_colour_type = lifecycle::deprecated(),
  scale_fill_type = lifecycle::deprecated(),
  colour_theme = lifecycle::deprecated(),
  fill_theme = lifecycle::deprecated(),
  rev_colour = lifecycle::deprecated(),
  rev_fill = lifecycle::deprecated(),
  fig_dpi = 300,
  ...
)

theme_thekids(
  base_size = 11,
  base_family = NULL,
  base_line_size = base_size/22,
  base_rect_size = base_size/22,
  strip_colour = "midnightblue",
  scale_colour_type = lifecycle::deprecated(),
  scale_fill_type = lifecycle::deprecated(),
  colour_theme = lifecycle::deprecated(),
  fill_theme = lifecycle::deprecated(),
  rev_colour = lifecycle::deprecated(),
  rev_fill = lifecycle::deprecated(),
  fig_dpi = 300,
  ...
)

Arguments

base_size	The base font size, given in points. Default is 11.
base_family	The base font family used for the text (default Barlow). Most Google Fonts are supported (see Note).
base_line_size	The base size for line elements (e.g., axis lines, grid lines). Calculated as base_size/22 by default.
base_rect_size	The base size for rect elements (e.g., plot background, legend keys). Calculated as base_size/22 by default.
strip_colour	A named colour from the list of The Kids colours, see thekids_colours for available colour names. Note that only the main colour names are accepted because the 50% tint is always used.
scale_colour_type	Deprecated. Use viridis_pal instead.
scale_fill_type	Deprecated. Use viridis_pal instead.
colour_theme	Deprecated. Use viridis_pal instead.
fill_theme	Deprecated. Use viridis_pal instead.
rev_colour	Deprecated. Use viridis_pal instead.
rev_fill	Deprecated. Use viridis_pal instead.
fig_dpi	Base DPI for figure. Only applicable when Barlow font family (default) is not selected.
...	Miscellaneous arguments necessary for parameter aliasing, etc.

Details

The function determines the operating system and selects appropriate font names for Windows or other systems. It applies a minimal theme with custom settings for plot title, axis title, and strip text, using the 'Barlow Semi Condensed' font family. It also adjusts color scales using the 'viridis' package.

For a more thorough example, see the vignette.

Value

A list of ggplot2 theme elements and scale adjustments.

Note

If a Google font has not been loaded with the package, thekids_theme will load this function on your behalf.

Supported Google Fonts are those that exist in sysfonts::font_families_google().

Examples

## Not run: 
# Install the required fonts first (see below)
# Example usage with ggplot2
library(ggplot2)

p <- ggplot(mtcars, aes(x = mpg, y = wt, col = factor(cyl))) +
  geom_point() +
  thekids_theme() +
  scale_colour_thekids()

print(p)

p2 <- ggplot(mtcars, aes(x = factor(cyl), y = wt, fill = factor(cyl))) +
  geom_col() +
  thekids_theme() +
  scale_fill_thekids(palette='tint50', reverse=TRUE)

print(p2)

## End(Not run)
## Not run: 
# Install the required fonts first (see below)
# Example usage with ggplot2
library(ggplot2)

p <- ggplot(mtcars, aes(x = mpg, y = wt, col = factor(cyl))) +
  geom_point() +
  theme_thekids() +
  scale_colour_thekids()

print(p)

p2 <- ggplot(mtcars, aes(x = factor(cyl), y = wt, fill = factor(cyl))) +
  geom_col() +
  theme_thekids() +
  scale_fill_thekids(palette='tint50', reverse=TRUE)

print(p2)

## End(Not run)

---

Apply a variable dictionary to a dataset. Each column is replaced with a new name and a corresponding label attribute is applied.

Description

Apply a variable dictionary to a dataset. Each column is replaced with a new name and a corresponding label attribute is applied.

Usage

update_columns(
  data,
  dict,
  old = NULL,
  new = NULL,
  label = NULL,
  reorder = FALSE
)

Arguments

data	A data.frame-like object
dict	A data.frame-like object or .csv file path (.csv, .txt, .xlsx, .rds). Should have 3 columns specifying: old names, new names, and labels.
old	Column name in dict with old column names (default "old")
new	Column name in dict with new column names (default "new")
label	Column name in dict with human-readable labels (default "label")
reorder	Logical, default FALSE. If TRUE, columns listed in the dictionary will be reordered according to the order they appear in the dictionary. Columns not referenced in the dictionary remain at the end in their original order.

Value

A data.frame with renamed columns and labels applied

Examples

data("data_patient", package = "thekidsbiostats")

# 1) Create a data dictionary and formulate some cleaned column names, assign to `dict` object
dict <- make_column_dict(data_patient, auto_clean = TRUE, quiet = FALSE)

# 2) Apply column names to data, assign to `data_patient_clean`
data_patient_clean <- update_columns(data_patient, dict = dict)

---

variable_labels

Description

Apply variable labels to a data frame per the REDCap data dictionary. If there is no variable label associated with a column then is lable will be the same as the column's name.

Apply variable labels to a data frame per the REDCap data dictionary. If there is no variable label associated with a column then is label will be the same as the column's name.

Usage

variable_labels(d, dict)

variable_labels(d, dict)

Arguments

d	REDCap import
dict	REDCap data dictionary

Value

character vector (length ncol(d)) of REDCap Field Labels per the data dictionary

data frame with variable labels

Examples

## Not run: 

dat <- tibble(var = 1)

dictionary <- tibble(`Variable / Field Name` = "var", `Field Label` = "Label")

dat <- labelled::set_variable_labels(dat, .labels = variable_labels(dat, dictionary))


## End(Not run)

## Not run: 

dat <- tibble(var = 1, var2___1 = 1, var2___2 = 0)
dictionary <- tibble(`Variable / Field Name` = c("var", "var2"),
                     `Field Label` = c("Label for field 'Var'", NA),
                     `Field Type` = c(NA, "checkbox"),
                     `Choices, Calculations, OR Slider Labels` =
                       c(NA, "1, First checkbox label | 2, Second checkbox label"))

dat <- variable_labels(dat, dictionary)
View(dat)


## End(Not run)

---

yesno_vars

Description

yesno_vars

Usage

yesno_vars(d)

Arguments

d	a data frame object

Value

a character vector of columns that are factors with levels: c("Yes", "No")

Examples

## Not run: 

dat <- tibble(var = factor(c("Yes", "Yes", "No", "Yes"), levels = c("Yes", "No")))

yesno_vars(dat)

mutate(dat, across(yesno_vars(dat), ~case_when(. == "Yes" ~ TRUE, . == "No" ~ FALSE, TRUE ~ NA)))


## End(Not run)

---