Package 'edar'

Copy files and rename with date

Description

Copy files to destination and rename with date and a tag as desired.

Usage

fc(..., des = "", tag = "", td = TRUE)

Arguments

...	⁠<chr>⁠ A vector of file paths of the source files to copy and rename.
des	⁠<chr>⁠ Destination folder. "." to rename files at the current location.
tag	⁠<chr>⁠ Tag to the filename.
td	⁠<lgl>⁠ TRUE to add today (yymmdd) to the filename.

Value

A logical vector indicating if the operation succeeded for each of the files.

Examples

## Not run: 
# Copy a file to home directory
tmp = tempdir()
fc("f1.R","f2.R",des=tmp)

## End(Not run)

---

flextable wrapper

Description

Sugar function for default flextable output.

Usage

ft(d, fnote = NULL, ttl = NULL, sig = 8, dig = 2, src = 0, omit = "")

Arguments

d	⁠<dfr>⁠ A data frame.
fnote	⁠<chr>⁠ Footnote.
ttl	⁠<chr>⁠ Title.
sig	⁠<int>⁠ Number of significant digits to compute.
dig	⁠<int>⁠ Number of decimal places to display.
src	⁠<int>⁠ Either 1 or 2 to add source label over 1 or 2 lines.
omit	⁠<chr>⁠ Text to omit from the source label.

Value

A flextable object.

Examples

mtcars |> head() |> ft()
mtcars |> head() |> ft(src=1)
mtcars |> head() |> ft("Footnote")
mtcars |> head() |> ft("Footnote",src=1)
mtcars |> head() |> ft(sig=2,dig=1)

---

flextable defaults

Description

Sugar function to set flextable defaults. The arguments are passed to flextable::set_flextable_defaults().

Usage

ft_def(
  show = FALSE,
  font = "Calibri Light",
  fsize = 10,
  pad = 3,
  na = "",
  nan = "",
  ...
)

Arguments

show	⁠<lgl>⁠ TRUE to show values after the update.
font	⁠<chr>⁠ Font family - for font.family.
fsize	⁠<int>⁠ Font size (in point) - for font.size.
pad	⁠<int>⁠ Padding space around text - for padding.
na	⁠<chr>⁠ A value to display instead of NA - for na_str
nan	⁠<chr>⁠ A value to display instead of NaN - for nan_str
...	Additional arguments to pass to flextable::set_flextable_defaults()

Value

A list containing previous default values.

See Also

flextable::set_flextable_defaults().

Examples

## Not run: 
ft_def()

## End(Not run)

---

Geometric coefficient of variation

Description

Compute geometric coefficient of variation (GCV)

Usage

geo_cv(x)

Arguments

x	⁠<num>⁠ A vector of values.

Value

Geometric coefficient of variation

Examples

geo_cv(rlnorm(10))

---

Geometric mean

Description

Compute geometric mean.

Usage

geo_mean(x)

Arguments

x	⁠<num>⁠ A vector of values.

Value

Geometric mean.

Examples

geo_mean(rlnorm(10))

---

Geometric standard deviation

Description

Compute geometric standard deviation (GSD)

Usage

geo_sd(x)

Arguments

x	⁠<num>⁠ A vector of values.

Value

Geometric standard deviation

Examples

geo_sd(rlnorm(10))

---

Box plot wrapper for categorical covariates

Description

Create box plots for a chosen variable by all discrete covariates in a dataset. Numeric variables will be dropped, except the chosen variable to plot.

Usage

ggbox(d, var, cats, alpha = 0.1, show = TRUE, nsub = TRUE, ...)

Arguments

d	⁠<dfr>⁠ A data frame.
var	⁠<var>⁠ A variable to plot as unquoted name.
cats	⁠<var>⁠ Optional. Categorical variables to plot as a vector of unquoted names.
alpha	⁠<num>⁠ Alpha value for ggplot2::geom_jitter.
show	⁠<lgl>⁠ TRUE to show data using ggplot2::geom_jitter.
nsub	⁠<lgl>⁠ Show number of observations.
...	Additional arguments for ggplot2::geom_boxplot.

Value

A ggplot object.

Examples

d = mtcars |> mutate(across(c(am,carb,cyl,gear,vs),factor))
d |> ggbox(mpg)
d |> ggbox(mpg,alpha=0.5)
d |> ggbox(mpg,show=FALSE)
d |> ggbox(mpg,nsub=FALSE)
d |> ggbox(mpg,c(cyl,vs))

---

Histogram wrapper for continuous covariates

Description

Create histograms for all numeric variables in a dataset. Non-numeric variables will be dropped.

Usage

gghist(d, cols, bins = 30, nsub = TRUE, ...)

Arguments

d	⁠<dfr>⁠ A data frame.
cols	⁠<var>⁠ Optional. Columns to plot as a vector of unquoted names.
bins	⁠<int>⁠ Number of bins.
nsub	⁠<lgl>⁠ Show number of observations.
...	Additional arguments for ggplot2::geom_histogram.

Value

A ggplot object.

Examples

iris |> gghist()
iris |> gghist(c(Sepal.Width,Sepal.Length))

---

Save ggplot with output path

Description

Save ggplot with output path

Usage

ggout(plt, fpath, lab = "", omit = "", ...)

Arguments

plt	A ggplot object.
fpath	⁠<chr>⁠ File path to save output and add to label.
lab	⁠<chr>⁠ Custom label to use instead of fpath.
omit	⁠<chr>⁠ Text to omit from the label.
...	Other arguments to pass to ggplot2::ggsave().

Value

The file path of the output.

See Also

ggplot2::ggsave()

Examples

## Not run: 
fpath = "../output.png"
iris |> gghist() |> ggout(fpath)

## End(Not run)

---

Add source file label to a ggplot object

Description

Add a label with the current source file path and run time to a ggplot object.

Usage

ggsrc(plt, span = 1, size = 8, col = "grey55", lab = NULL, omit = "")

Arguments

plt	A ggplot object.
span	⁠<num>⁠ Number of lines: either 1 or 2.
size	⁠<num>⁠ Text size.
col	⁠<chr>⁠ Colour of the text.
lab	⁠<chr>⁠ Custom label to use instead of the default.
omit	⁠<chr>⁠ Text to omit from the label.

Value

A ggplot object with the added label.

Examples

p = mtcars |> ggxy(mpg,hp)
p |> ggsrc()
p |> ggsrc(lab="My label")
p |> ggsrc(lab="My label",omit="My ")

---

Time-profile plot wrapper

Description

Create plots for time profile data such as PK and PD plots.

Usage

ggtpp(
  d,
  x,
  y,
  id,
  ...,
  nsub = TRUE,
  logx = FALSE,
  logy = FALSE,
  alpha_point = 0.2,
  alpha_line = 0.1,
  xlab = NULL,
  ylab = NULL,
  ttl = NULL,
  sttl = NULL,
  cap = NULL
)

Arguments

d	⁠<dfr>⁠ A data frame.
x, y	⁠<var>⁠ Variables for x- and y-axis as unquoted names
id	⁠<var>⁠ Variable for grouping ID such as subject ID as unquoted name.
...	Arguments to pass to ggplot2::aes for additional mapping.
nsub	⁠<lgl>⁠ TRUE to show number of subjects as per id in caption.
logx, logy	⁠<lgl>⁠ TRUE to log x- and y-axis.
alpha_point	⁠<num>⁠ Alpha value for ggplot2::geom_point.
alpha_line	⁠<num>⁠ Alpha value for ggplot2::geom_line.
xlab, ylab	⁠<chr>⁠ Labels for x- and y-axis.
ttl, sttl, cap	⁠<chr>⁠ Title. Subtitle. Caption.

Value

A ggplot object.

Examples

Theoph |> ggtpp(x=Time,y=conc,id=Subject)

---

Violin plot wrapper for categorical covariates

Description

Create violin plots for a chosen variable by all discrete covariates in a dataset. Numeric variables will be dropped, except the chosen variable to plot.

Usage

ggvio(d, var, cats, alpha = 0.1, show = TRUE, nsub = TRUE, ...)

Arguments

d	⁠<dfr>⁠ A data frame.
var	⁠<var>⁠ A variable to plot as unquoted name.
cats	⁠<var>⁠ Optional. Categorical variables to plot as a vector of unquoted names.
alpha	⁠<num>⁠ Alpha value for ggplot2::geom_jitter.
show	⁠<lgl>⁠ TRUE to show data using ggplot2::geom_jitter.
nsub	⁠<lgl>⁠ Show number of observations.
...	Additional arguments for ggplot2::geom_violin.

Value

A ggplot object.

Examples

d = mtcars |> mutate(across(c(am,carb,cyl,gear,vs),factor))
d |> ggvio(mpg)
d |> ggvio(mpg,alpha=0.5)
d |> ggvio(mpg,show=FALSE)
d |> ggvio(mpg,nsub=FALSE)
d |> ggvio(mpg,c(cyl,vs))

---

XY scatter plot wrapper

Description

Create basic XY scatter plot for quick data exploration. Default to show Pearson correlation coefficient with p-value using ggpubr::stat_cor(). For more complex plots, it is recommended to use ggplot2::ggplot2 directly.

Usage

ggxy(
  d,
  x,
  y,
  ...,
  lm = TRUE,
  se = TRUE,
  cor = TRUE,
  pv = 0.001,
  nsub = TRUE,
  legend = TRUE,
  asp = 1
)

Arguments

d	⁠<dfr>⁠ A data frame.
x, y	⁠<var>⁠ Variables for x- and y-axis as unquoted names.
...	Arguments to pass to ggplot2::aes() for additional mapping.
lm	⁠<lgl>⁠ TRUE to add regression line from linear model.
se	⁠<lgl>⁠ TRUE to show standard error with the regression line.
cor	⁠<lgl>⁠ TRUE to show Pearson correlation coefficient with p-value.
pv	⁠<dbl>⁠ Precision of p-value, e.g., 0.001 to show 3 decimal places, NULL for no rounding.
nsub	⁠<lgl>⁠ Show number of observations.
legend	⁠<lgl>⁠ TRUE to show legend.
asp	⁠<num>⁠ For aspect.ratio in ggplot2::theme().

Value

A ggplot object.

See Also

ggpubr::stat_cor()

Examples

mtcars |> ggxy(wt,hp)
mtcars |> ggxy(wt,hp,col=factor(gear))
mtcars |> ggxy(wt,hp,col=factor(gear),legend=FALSE)
mtcars |> ggxy(wt,hp,col=factor(gear),pch=factor(am))
mtcars |> ggxy(wt,hp,nsub=FALSE)
mtcars |> ggxy(wt,hp,pv=NULL)
mtcars |> ggxy(wt,hp,lm=FALSE)
mtcars |> ggxy(wt,hp,se=FALSE)
mtcars |> ggxy(wt,hp,cor=FALSE)

---

Generate hex colour codes

Description

Generate a vector of hex colour codes for the desired number of colours. Colours are generated by evenly splitting hue in the range ⁠[0,360]⁠ in the HCL colour space using grDevices::hcl. The output is meant to follow the default colours used in ggplot2::ggplot2.

Usage

hexn(n, show = FALSE)

Arguments

n	⁠<int>⁠ Number of colours to output.
show	⁠<lgl>⁠ TRUE to show the output colours.

Value

A vector of hex colour codes that can be used for plotting.

Examples

hexn(6,FALSE)
hexn(4,TRUE)

---

kable wrapper

Description

Sugar function for default kable output.

Usage

kb(d, fnote = NULL, cap = NULL, sig = 8, dig = 2, src = 0, omit = "")

Arguments

d	⁠<dfr>⁠ A data frame.
fnote	⁠<chr>⁠ Footnote.
cap	⁠<chr>⁠ Caption.
sig	⁠<int>⁠ Number of significant digits to compute.
dig	⁠<int>⁠ Number of decimal places to display.
src	⁠<int>⁠ Either 1 or 2 to add source label over 1 or 2 lines.
omit	⁠<chr>⁠ Text to omit from the source label.

Value

A kable object.

Examples

mtcars |> head() |> kb()
mtcars |> head() |> kb(src=1)
mtcars |> head() |> kb("Footnote")
mtcars |> head() |> kb("Footnote",src=1)
mtcars |> head() |> kb(sig=2,dig=1)

---

Generate source file label

Description

Generate a label with the current source file path and run time, assuming that the source file is in the current working directory. In interactive sessions, the function is designed to work in a script file in RStudio and uses rstudioapi to get the file path. It will return empty if run in the console directly.

Usage

label_src(span = 1, omit = "", tz = TRUE, fname = FALSE)

Arguments

span	⁠<int>⁠ Number of lines: either 1 or 2.
omit	⁠<chr>⁠ Text to omit from the label.
tz	⁠<lgl>⁠ FALSE to exclude time stamp.
fname	⁠<lgl>⁠ TRUE to return the file name only.

Value

A label showing the source file path with a time stamp.

Examples

label_src()
label_src(tz=FALSE)
label_src(fname=TRUE)

---

Generate time stamp label

Description

Generate a label with a time stamp indicating the run time.

Usage

label_tz(omit = "")

Arguments

omit	⁠<chr>⁠ Text to omit from the label.

Value

A label with time stamp.

Examples

label_tz()

---

Summarise continuous variables by group

Description

Summarise all continuous variables by group. Non-numeric variables will be dropped.

Usage

summ_by(
  d,
  cols,
  ...,
  pct = c(0.25, 0.75),
  geo = FALSE,
  xname = "",
  view = FALSE
)

Arguments

d	⁠<dfr>⁠ A data frame.
cols	⁠<var>⁠ Optional. Columns to summarise as unquoted names.
...	⁠<var>⁠ Optional. Columns to group by as unquoted names.
pct	⁠<num>⁠ A vector of two indicating the percentiles to compute.
geo	⁠<lgl>⁠ TRUE to add geometric mean and standard devaition.
xname	⁠<chr>⁠ Characters to omit in output column names.
view	⁠<lgl>⁠ TRUE to print output as flextable.

Value

A data frame of summarised variables.

Examples

d = mtcars |> dplyr::mutate(vs=factor(vs), am=factor(am))
d |> summ_by()
d |> summ_by(geo=TRUE)
d |> summ_by(pct=c(0.1,0.9))
d |> summ_by(mpg)
d |> summ_by(mpg,vs)
d |> summ_by(mpg,vs,am)
d |> summ_by(c(mpg,disp))
d |> summ_by(c(mpg,disp),vs)
d |> summ_by(c(mpg,disp),vs,xname="mpg_")
# Grouping without column selection is possible but rarely useful in large dataset
d |> summ_by(,vs)

---

Summarise categorical variables

Description

Summarise all categorical variables. Numeric variables will be dropped.

Usage

summ_cat(d, ..., var, view = FALSE)

Arguments

d	⁠<dfr>⁠ A data frame.
...	⁠<var>⁠ Optional. Columns to summarise.
var	⁠<var/int>⁠ (name or index) Optional. A variable to extract as a data frame.
view	⁠<lgl>⁠ TRUE to show output as flextable.

Value

A list containing summaries for all categorical variables or a data frame showing the summary of a selected variable.

Examples

d = mtcars |> dplyr::mutate(dplyr::across(c(cyl,vs,am,gear,carb),factor))
d |> summ_cat()
d |> summ_cat(cyl,vs)
d |> summ_cat(var=cyl)
d |> summ_cat(var=1)

---

Table wrapper for two variables

Description

Wrapper function to produce summary tables for two variables.

Usage

tab2v(d, x, y)

Arguments

d	⁠<dfr>⁠ A data frame.
x, y	⁠<var>⁠ Variables to tabulate.

Value

A tabyl object.

Examples

# example code
mtcars |> tab2v(vs,cyl)
mtcars |> tab2v(vs,am)
mtcars |> tab2v(vs,am)
mtcars |> tab2v(vs,gear)

---