Package 'lulab.utils'

check_cha

Description

Check for missing values for character columns

Usage

check_cha(col, df, verbose = TRUE)

Arguments

col	a character variable name
df	a data.frame
verbose	logical, controlling the output

Details

This function is used to check the distribution of character variables in the data frame.

Value

a distribution table of the character variable in the data frame

Author(s)

Zhen Lu

Examples

data("melanoma", package = "boot")
melanoma2 <- melanoma
check_cha('status', melanoma2)
# or
mapply(check_cha,'status', MoreArgs= list(melanoma2))

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check_wget

Description

Check if wget is installed

Usage

check_wget()

Details

This function is used to check if wget is installed on the system.

Value

a logical value indicating whether wget is installed

Author(s)

Zhen Lu

Examples

check_wget()

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extract_logistic_model

Description

Extract results from a fitted model.

Usage

extract_logistic_model(
  model,
  markers_name,
  n_independent_metabolites,
  digits,
  effective_size,
  case_size,
  control_size,
  outcome_name
)

Arguments

model	The fitted logistic model object.
markers_name	A character vector of marker names.
n_independent_metabolites	The number of independent metabolites.
digits	The number of decimal places to round to.
effective_size	A numeric vector containing effective sample sizes.
case_size	The number of cases.
control_size	The number of controls.
outcome_name	The name of the outcome variable.

Details

This function extracts relevant results from a fitted logistic model and formats them for reporting.

Value

A named vector containing the extracted results.

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round2

Description

Round a number to a specified number of decimal places.

Usage

round2(x, digits = 0)

Arguments

x	The numeric input to be rounded.
digits	The number of decimal places to round to, Default: digits

Details

This function rounds the input number to the specified number of decimal places.

Value

The rounded numeric value.

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Make a Table 1 summary

Description

Create a stratified Table 1, save it as an Excel workbook, and return the table as a data frame.

Usage

Table1(df, ycol, xcol, xlabels = NULL, result_dir, verbose = TRUE)

Arguments

df	A data frame.
ycol	A single character string naming the grouping variable.
xcol	A character vector naming variables to summarize.
xlabels	Optional labels for the groups. Defaults to the observed levels of ycol.
result_dir	Directory where Table1.xlsx will be saved.
verbose	Logical; if TRUE, print the output path.

Value

A data frame containing the rendered Table 1.

Author(s)

Zhen Lu

Examples

data("melanoma", package = "boot")
melanoma2 <- melanoma
melanoma2$status <- factor(
  melanoma2$status,
  levels = c(2, 1, 3),
  labels = c("Alive", "Melanoma death", "Non-melanoma death")
)
Table1(
  df = melanoma2,
  ycol = "status",
  xcol = c("time", "age", "sex"),
  result_dir = tempdir()
)

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test_mirror

Description

Test speed of CRAN mirror

Usage

test_mirror(region, verbose = TRUE)

Arguments

region	a character string, the region of the CRAN mirror, e.g. 'China'
verbose	logical, controlling the output

Details

This function is used to test the speed of CRAN mirror.

Value

a data.frame with the name, URL, and download time of the fastest CRAN mirror

Author(s)

Zhen Lu

Examples

test_mirror('China')

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use_wget

Description

Use wget to download files

Usage

use_wget(use = TRUE)

Arguments

use	a logical value, controlling the download method

Details

This function is used to set the download method.

Value

a logical value indicating whether wget is used

Author(s)

Zhen Lu

Examples

use_wget(use = TRUE)
getOption("download.file.method")
getOption("download.file.extra") 
test_url <- "https://eternallybored.org/misc/wget/1.21.4/64/wget.exe"
test_destfile <- tempfile()
download.file(test_url, destfile = test_destfile)

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