Package 'hipecR'

Calculate person age

Description

This function calculates the age of a person by given birthdate and the end date

Usage

tar_age(birth_date, x_date)

Arguments

birth_date	A date value, e.g. "1974-11-23".
x_date	A date value until the age lasts, e.g. "2023-02-16".

Value

A numeric value in (years)

Examples

tar_age("1974-11-23", "2023-02-16")

---

Create Animated Bar Chart

Description

This function creates an animated bar chart with customizable colors and orientation. The resulting GIF can be saved to a specified filename.

Usage

tar_animbar(
  x,
  filename = "my_animated_bar",
  color1 = "steelblue1",
  color2 = "purple3",
  title = "%",
  horizontal = FALSE,
  total = 100,
  fps = 24,
  base_duration = 15,
  output_dir = tempdir(),
  overwrite = FALSE,
  ask = interactive()
)

Arguments

x	An integer indicating the value for the bar chart.
filename	A string specifying the name of the output file (default: "my_animated_bar").
color1	A string specifying the color for the first part of the bar (default: "steelblue1").
color2	A string specifying the color for the second part of the bar (default: "purple3").
title	A string specifying the title suffix for the animation (default: percent sign).
horizontal	A logical value indicating whether the bar chart should be horizontal (default: FALSE).
total	An integer indicating the maximum value for the bar chart scale (default: 100).
fps	Frames per second for the animation (default: 24).
base_duration	Base duration (seconds) for a full-scale animation (default: 15).
output_dir	Output directory for the GIF (default: temporary directory).
overwrite	Logical; overwrite an existing GIF (default: FALSE).
ask	Logical; if TRUE, prompt when file exists (default: interactive()).

Details

This function generates an animated bar chart with customizable colors and orientation. The resulting GIF can be saved to a specified filename.

Value

Invisible path to the generated GIF file.

Examples

if (interactive() && requireNamespace("gifski", quietly = TRUE)) {
  tar_animbar(x = 10, filename = "a3", color1 = "gold", color2 = "purple3",
              horizontal = TRUE, total = 10, fps = 5, base_duration = 1,
              output_dir = tempdir(), overwrite = TRUE, ask = FALSE)
  tar_animbar(x = 5, filename = "a4", color1 = "steelblue", color2 = "purple3",
              horizontal = FALSE, total = 10, fps = 5, base_duration = 1,
              output_dir = tempdir(), overwrite = TRUE, ask = FALSE)
  tar_animbar(x = 3, filename = "rapido_LRR", horizontal = FALSE, total = 10,
              fps = 5, base_duration = 1, output_dir = tempdir(),
              overwrite = TRUE, ask = FALSE)
}

---

Calculating BMI (kg/m^2)

Description

Calculating BMI (kg/m^2)

Usage

tar_bmi(weight, height)

Arguments

weight	Numeric, kg
height	Numeric, cm

Value

body mass index BMI

Examples

tar_bmi(weight = 100, height = 190)

---

Body surface area calculator in m^2 (DuBois and DuBois formula)

Description

This function calculates the body surface area with the DuBois method. DuBois D. A formula to estimate the approximate surface area if height and body mass are known. Arch Intern Med 1916;17:863-71.

Usage

tar_bsa(height, weight)

Arguments

height	A numeric value in cm
weight	A numeric value in kg

Value

A numeric value in m^2

Examples

tar_bsa(height = 180, weight = 80) # ~1.996421 m^2

---

Cast registry data

Description

Coerce raw input into a one-row data frame with registry fields.

Usage

tar_cast_data(data)

Arguments

data	A list or data frame with registry fields.

Value

A one-row data frame with standard column types.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

NA counter

Description

Counts NA values across columns.

Usage

tar_count_na(df)

Arguments

df	A data frame or tibble.

Value

A named numeric vector with NA counts per column.

Examples

if(interactive()){
 tar_count_na(mtcars)
 }

---

Count Top Categories in a Factor

Description

This function transforms the specified factor variable within a dataframe to lump all but the top n most frequent levels into an 'Other' category and then computes the count of each level.

Usage

tar_count_top(df, var, n = 5)

Arguments

df	A data frame containing the variable to be manipulated.
var	The variable (unquoted) within the data frame.
n	The number of top levels to keep before lumping others into 'Other'; default is 5.

Details

This function leverages 'dplyr' for data manipulation and 'forcats' for managing factor levels. It is particularly useful in data summarization where the focus is on the most frequent categories.

Value

A dataframe showing the count of each level including 'Other' for all lumped lesser categories.

Examples

if(interactive()){
  data <- data.frame(color = c("red", "blue", "green", "blue", "blue", "red", "yellow", "red"))
  print(tar_count_top(data, color, n = 2))
 }

---

Create registry record

Description

Add a new record to the in-memory 'responses' data frame.

Usage

tar_create_data(data)

Arguments

data	A named list or data frame with registry fields.

Value

Invisible NULL.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Create default registry record

Description

Return an empty default registry record.

Usage

tar_create_default_record()

Value

A one-row data frame with default values.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

tar_dateinput

Description

Handles date format in Austrian HIPEC Registry(c)

Usage

tar_dateInput(inputId, label)

Arguments

inputId	character
label	character

Details

Wraps shinyWidgets::airDatepickerInput with fixed defaults.

Value

A date input in dd-MM-yyyy format.

See Also

airDatepicker

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Delete registry record

Description

Delete a record from 'responses' by id.

Usage

tar_delete_data(data)

Arguments

data	A list or data frame containing an 'id' field.

Value

Invisible NULL.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Look-up function for DGAV registry IDs/names

Description

This function takes a data frame 'df' and a vector of key values 'mykeyvalues'. It returns an unnamed vector of corresponding results by performing lookups in the data frame.

Usage

tar_dgav_lookup(df, mykeyvalues)

Arguments

df	data frame with Name and azl number
mykeyvalues	is a vector containing the key values to be looked up in the data frame. These key values can be either numeric or character strings. The function processes each key value individually to determine if it matches entries in the specified columns of the data frame

Value

a key or value, depending on what is wanted

Examples

# Example data
df <- data.frame(
  Name = c("Hans", "Maria", "Franz HUBER"),
  azl = c("1006341612", "1040405318", "1060707219"),
  stringsAsFactors = FALSE
)

tar_dgav_lookup(df, "HUBER")       # Should return "1060707219"
tar_dgav_lookup(df, "huber")       # Should also return "1060707219"
tar_dgav_lookup(df, "Franz")       # Should return "1060707219"
tar_dgav_lookup(df, 1006341612)  # Should return "Hans"
tar_dgav_lookup(df, c(1006341612, 1040405318)) # Should return "Hans"  "Maria"

# Function to handle inputs for data frame

---

Create a combined flag plot

Description

This function downloads flag images of specified countries, combines them vertically with spaces in between, and saves the combined image to a file.

Usage

tar_flag(
  countries,
  name,
  output_dir = tempdir(),
  overwrite = FALSE,
  ask = interactive()
)

Arguments

countries	A character vector of country codes (ISO 3166\-1 alpha\-2).
name	A character string for the name of the study. This will be used to construct the output file name.
output_dir	A directory for the output file (default: temporary directory).
overwrite	Logical; overwrite an existing PNG (default: FALSE).
ask	Logical; if TRUE, prompt when file exists (default: interactive()).

Value

Invisible path to the saved PNG file.

Examples

if (interactive()) {
  tar_flag(c("nl", "se", "es", "si", "dk", "no", "us"), "rapido")
  tar_flag(c("at", "de"), "demo", output_dir = tempdir(), overwrite = TRUE)
}

---

Add Footnote to Graph and Save as PNG

Description

This function takes a 'grViz' graph object, adds a footnote with specified style and text, and saves the graph along with the footnote as a PNG file. The PNG file is named based on the graph object name.

Usage

tar_footnote(
  graph,
  style,
  string,
  filename = NULL,
  output_dir = tempdir(),
  overwrite = FALSE,
  ask = interactive()
)

Arguments

graph	A 'grViz' graph object.
style	A character string specifying the CSS style for the footnote.
string	A character string specifying the footnote text.
filename	Optional output filename (without extension). Defaults to the variable name of 'graph' if possible.
output_dir	Output directory (default: temporary directory).
overwrite	Logical; overwrite an existing PNG (default: FALSE).
ask	Logical; if TRUE, prompt when file exists (default: interactive()).

Value

None. The function saves a PNG file in the working directory.

Examples

if (interactive() && requireNamespace("DiagrammeR", quietly = TRUE)) {
graph <- DiagrammeR::grViz("
digraph {
graph [layout = dot]
node [shape = box]
a [label = 'A']
b [label = 'B']
a -> {b}
}
")

style <- "color: grey; font-family: Arial; text-align: left; font-size: 10px;"
string <- paste(
  "CNCT = Consolidation Chemotherapy,",
  "CRT = Chemoradiotherapy,",
  "CT = Chemotherapy,",
  "INCT = Induction Chemotherapy,",
  "SCRT = Short-course Radiotherapy,",
  "TME = Total Mesorectal Excision,",
  "WW = Watch and Wait,",
  sep = " "
)

tar_footnote(graph, style, string)
}

---

Get next registry ID

Description

Get the next numeric ID based on the 'responses' data frame.

Usage

tar_get_next_id()

Value

Integer ID.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Registry field metadata

Description

Create a named vector of fields and labels for the registry.

Usage

tar_get_table_metadata(variable = fieldsAll, label = label_names)

Arguments

variable	Character vector of field names. Default: fieldsAll.
label	Character vector of labels. Default: label_names.

Details

Expects 'variable' and 'label' to be the same length.

Value

A list with element 'fields', a named character vector.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Adjust Theme Sizes in ggplot2

Description

This function adjusts the sizes of various theme elements in a ggplot2 plot. It takes a single argument which is the base size for geom_text, and it calculates the theme sizes based on this.

Usage

tar_ggplot_font_size(geom_text_size = 7)

Arguments

geom_text_size

The base size for text elements in 'geom_text'. Default is 7.

Details

Always add the same size as in geom_text, then all fonts will have the same size. Default size is 7. If there is no geom_text we can control the font size of axis, legend, title and text with this function.

Value

A 'theme' object that can be added to a ggplot.

References

The formula is from here: https://stackoverflow.com/questions/25061822/ggplot-geom-text-font-size-control

Examples

library(ggplot2)
p <- ggplot(mtcars, aes(factor(vs), y = mpg, fill = factor(am))) +
  geom_bar(stat = "identity", position = "dodge") +
  labs(title = "my_title") +
  tar_ggplot_font_size(10)
print(p)

---

Display both the head and tail of a dataframe or tibble

Description

This function returns the first 'nh' = n head and last 'nt' = n tail rows of a dataframe or tibble. Row numbers from the original data are preserved as row names in the result.

Usage

tar_head_tail(data, nh = 5, nt = 5)

Arguments

data	A data frame or tibble whose head and tail you wish to view.
nh	An integer specifying the number of rows from the start of 'data' to display. Default is 5.
nt	An integer specifying the number of rows from the end of 'data' to display. Default is 5.

Value

A dataframe composed of the first 'nh' and last 'nt' rows of the input data. The row numbers from the original data are used as row names in the result.

See Also

rownames

Examples

if(interactive()){
 # Generate example data
 df <- data.frame(A = 1:10, B = 11:20)
 tar_head_tail(df, nh = 3, nt = 2)
 }

---

Imputates outliers and shows 4 different method plots

Description

Imputates outliers and shows 4 different method plots

Usage

tar_impute_outlier(df, variable)

Arguments

df	data frame or tibble where the numeric variable lives
variable	Numeric variable column in the data frame

Value

4 plots with mean, median, mode and capping imputation

Examples

if (interactive()) {
  tar_impute_outlier(mtcars, mpg)
}

---

Short Installer

Description

Helper that returns an 'install.packages()' command for a package name.

Usage

tar_install(x)

Arguments

x	The name of the package you want to install.

Details

This function uses non-standard evaluation to allow you to specify the package name unquoted.

Value

A character string with the corresponding 'install.packages()' command.

Examples

tar_install(dplyr)

---

Plot Survival Curves and Save with Median Annotations

Description

This function fits a survival model, plots the survival curves, and annotates median survival times. The plot can optionally be saved to file.

Usage

tar_median_survival(
  df,
  var,
  time_col = "time",
  status_col = "status",
  output_file = NULL
)

Arguments

df	A data frame containing the survival data.
var	A variable used for grouping the survival curves.
time_col	A string specifying the name of the column representing time.
status_col	A string specifying the name of the column representing status.
output_file	Optional output path for saving the plot. If 'NULL' (default), the function does not write a file.

Value

A 'ggsurvplot' object (invisibly). Optionally writes a PNG file.

Examples

# Example dataset
df_survival <- structure(
  list(
    status = c(1, 0, 1, 1, 1, 1, 0, 1, 1, 0),
    primorgan = structure(
      c(1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L),
      levels = c("Colon", "Rectum"),
      class = "factor"
    ),
    sex = structure(
      c("male", "female", "male", "male", "male",
        "male", "male", "male", "male", "female"),
      label = "Gender"
    ),
    time = c(4.26, 49.52, 18.05, 11.04, 47.67, 8.03, 76.2, 15.44, 22.74, 50.64),
    subtype = structure(
      c(2L, 1L, 2L, 3L, 2L, 3L, 1L, 1L, 1L, 2L),
      levels = c("adenocarcinoma", "mucinous", "signet ring cell"),
      label = "Histological subtype",
      class = "factor"
    )
  ),
  row.names = c(NA, -10L),
  class = c("tbl_df", "tbl", "data.frame")
)

tar_median_survival(
  df = df_survival,
  var = sex,
  time_col = "time",
  status_col = "status",
  output_file = file.path(tempdir(), "survival_sex.png")
)

---

tar_oneline

Description

Creates a one-liner from a multiline code example in the clipboard.

Usage

tar_oneline()

Value

A character vector with the reformatted one-line code.

See Also

tidy_source

Examples

if (interactive()) {
  # Your multiline string
  # copy this code
  numericInput(
    "Register_Nr",
    "Nr.",
    min = 0,
    max = 20,
    step = 1,
    value = 0
  )
  # then apply
  tar_oneline()
}

---

Set Pillar Print Minimum

Description

This function sets the 'pillar.print_min' option in R. This option controls globally the minimum number of data to print in tibbles. In contrast to data frames, in tibbles only 10 lines are shown except you use print(n=...). But you have to add it each time. tar_print can be use once globally and changed whenever necessayr!

Usage

tar_print(value = 50)

Arguments

value

A single non-negative integer for the minimum number of rows shown of a tibble in the console. Defaults to 50.

Value

Invisible null. The function is called for its side effect of setting an option.

References

The formula is from here: https://stackoverflow.com/questions/77708674/is-there-a-global-option-to-adjust-the-default-setting-of-tibbles-that-displays

Examples

tar_print(100)  # Set the pillar.print_min option to 100
tar_print()     # Set the pillar.print_min option back to default (50)

---

Peritoneal Surface Area Calculation

Description

This function calculates 1 the given height and weight. It's used as a factor for further calculations.

Usage

tar_psa(height, weight)

Arguments

height	A numeric value representing the height in cm.
weight	A numeric value representing the weight in kg.

Value

A numeric value representing 1

Examples

tar_psa(180, 80) # Expected output: 199.6421 cm^2

---

Read registry data

Description

Return the in-memory 'responses' data frame, if present.

Usage

tar_read_data()

Value

A data frame or NULL if not available.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Update registry record

Description

Update an existing record in 'responses' by row name.

Usage

tar_update_data(data)

Arguments

data	A named list or data frame with registry fields.

Value

Invisible NULL.

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Update Shiny inputs from record

Description

Push a registry record into Shiny input controls.

Usage

tar_update_inputs(data, session)

Arguments

data	A one-row data frame with registry fields.
session	Shiny session.

Value

Invisible NULL.

See Also

updateTextInput, updateNumericInput, updateDateInput

Examples

if(interactive()){
 #EXAMPLE1
 }

---

tar_WellPanel

Description

Creates a shinydashboard box equivalent with shiny

Usage

tar_WellPanel(n)

Arguments

n	integer the gives the number of months in follow-up

Details

Builds a wellPanel containing follow-up inputs for the given month.

Value

returns a wellpanel a quasi shinydashboard box (without ShinyDashboard)

Examples

if(interactive()){
 #EXAMPLE1
 }

---

Convert a Windows Path to a WSL Path

Description

Converts a Windows path (for example, C:/Users/... or C:\Users\...) into a WSL path (/mnt/c/Users/... by default). Optionally copies the converted path to the clipboard.

Usage

tar_wsl_pfad(path = getwd(), copy_to_clipboard = TRUE, mount_root = "/mnt")

Arguments

path	A single Windows path string. Defaults to getwd().
copy_to_clipboard	Logical. If TRUE, try to copy the resulting WSL path to the clipboard.
mount_root	Mount root used by WSL. Defaults to "/mnt".

Value

A single character string with the converted WSL path.

Examples

tar_wsl_pfad("C:/Users/tarka/project", copy_to_clipboard = FALSE)
tar_wsl_pfad("C:\\Users\\tarka\\project", copy_to_clipboard = FALSE)

---

Convert "yes" and "no" to 1 and 0

Description

This function takes a vector and converts all instances of "yes" to 1, "no" to 0, and leaves other values as NA. It's useful for converting categorical "yes"/"no" responses into a numeric format that can be used in statistical analysis.

Usage

tar_yes_no(x)

Arguments

x	A vector containing elements to be converted. Elements should be character strings potentially including "yes" and "no".

Value

A numeric vector where "yes" is replaced with 1, "no" with 0, and other values with NA.

Examples

test_vector <- c("yes", "no", "maybe", "yes", "no")
tar_yes_no(test_vector)

---