Package 'cpmtools'

add.roxy

Description

adds roxygen documentation headers to the top on R function and optionally write this to a file in the R folder.

Usage

add.roxy(obj, file = FALSE)

Arguments

obj	the function to create documentation for
file	if TRUE write to file (R/function name.R), Default: FALSE

Value

TRUE if successful, FALSE if not

See Also

makeOxygen tidy_source

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

Paradox

Description

Functions to make pleasing doodles

Usage

canvas()

paradox(
  shape,
  dist = 0.05,
  reverse = FALSE,
  cols = colorRampPalette(c("red", "blue"))(40),
  debug = FALSE
)

paradoxes(shapes, dist = 0.05, cols = colorRampPalette(c("red", "blue"))(40))

scale_shape(shape, scale = 1, shift = 0)

Arguments

shape	a matrix with colums x and y definining a shape to doodle within, can be any closed polygon, but some shapes work better than others.
dist	the distance up the adjacent edge where each new line will be drawn, default 0.05
reverse	should the shape be drawn in reverse order (see examples)
cols	a palate of colours as a vector of strings interpretable as colours
debug	should debug messages be produces (default FALSE)
shapes	a list of shapes (polygons) to doodle within
scale	if scaling, how much to scale by
shift	if scaling, should the shape also be shifted and by how much

Value

displays a plot

Examples

if (interactive()) {

  triangle <- cbind(x = c(0, 1, .7), y = c(0, 0.1, 1))
  triangle2 <- cbind(x = c(0, 0, .7), y = c(0, 1, 1))

  square <- cbind(x = c(0, 1, 1, 0), y = c(0, 0, 1, 1))

  canvas()
  paradox(square, 0.03)

  canvas()
  paradox(triangle, 0.042)
  paradox(triangle2, 0.042)

  canvas()
  paradox(scale_shape(square, c(0.5, 1)), 0.03)
  paradox(scale_shape(square, c(0.5, 1), c(0.5, 0)), 0.05, reverse = TRUE)

  canvas()
  dist <- 0.02
  paradox(scale_shape(square, .5), dist)
  paradox(scale_shape(square, .5, c(0.5, 0)), dist, reverse = TRUE)
  paradox(scale_shape(square, .5, .5), dist)
  paradox(scale_shape(square, .5, c(0, 0.5)), dist, reverse = TRUE)

  canvas()
  dist <- 0.02
  paradox(scale_shape(square, .5), dist, reverse = TRUE)
  paradox(scale_shape(square, .5, c(0.5, 0)), dist, reverse = TRUE)
  paradox(scale_shape(square, .5, .5), dist, reverse = TRUE)
  paradox(scale_shape(square, .5, c(0, 0.5)), dist, reverse = TRUE)

  canvas()
  dist <- 0.02

  cols1 <- colorRampPalette(c("red", "blue"))(30)
  cols2 <- colorRampPalette(c("blue", "red"))(30)
  cols3 <- colorRampPalette(c("green", "purple"))(30)
  cols4 <- colorRampPalette(c("purple", "green"))(30)

  paradox(scale_shape(square, .5), dist,
    reverse = TRUE,
    cols = c(rbind(cols1, cols2, cols3, cols4))
  )
  paradox(scale_shape(square, .5, c(0.5, 0)), dist,
    reverse = FALSE,
    cols = c(rbind(cols3, cols4, cols1, cols2))
  )
  paradox(scale_shape(square, .5, .5), dist,
    reverse = FALSE,
    cols = c(rbind(cols1, cols2, cols3, cols4))
  )
  paradox(scale_shape(square, .5, c(0, 0.5)), dist,
    reverse = TRUE,
    cols = c(rbind(cols3, cols4, cols1, cols2))
  )
}

---

git_init

Description

FUNCTION_DESCRIPTION

Usage

git_init(path = ".", commit = TRUE)

Arguments

path	PARAM_DESCRIPTION, Default: '.'
commit	PARAM_DESCRIPTION, Default: TRUE

Details

DETAILS

Value

no return value

See Also

init,add,commit

Examples

if (interactive()) {
  # initialise a git repository and stage all files
  git_init(commit = FALSE)
}

---

installed_packages

Description

FUNCTION_DESCRIPTION

Usage

installed_packages()

Details

DETAILS

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

open_dir

Description

FUNCTION_DESCRIPTION

Usage

open_dir(dir = ".")

Arguments

dir	PARAM_DESCRIPTION, Default: '.'

Details

DETAILS

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

quick_help

Description

FUNCTION_DESCRIPTION

Usage

quick_help(person, project, path = getOption("cpmtools.quick_help_path"))

Arguments

person	PARAM_DESCRIPTION
project	PARAM_DESCRIPTION
path	PARAM_DESCRIPTION, Default: getOption("cpmtools.quick_help_path")

Details

DETAILS

Value

OUTPUT_DESCRIPTION

See Also

taf.skeleton init,add,commit

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

sourceTAF2

Description

FUNCTION_DESCRIPTION

Usage

sourceTAF2(script, quiet = FALSE)

Arguments

script	PARAM_DESCRIPTION
quiet	PARAM_DESCRIPTION, Default: FALSE

Details

DETAILS

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

taf_gitignore

Description

FUNCTION_DESCRIPTION

Usage

taf_gitignore(path = ".", append = FALSE)

Arguments

path	PARAM_DESCRIPTION, Default: '.'
append	PARAM_DESCRIPTION, Default: FALSE

Details

DETAILS

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

create a blank data set file

Description

description

Usage

taf_roxy(dataset)

Arguments

dataset

the name of the dataset that will be created

Details

DETAILS

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if (interactive()) {
  # EXAMPLE1
}

## End(Not run)

---

update_r_win

Description

FUNCTION_DESCRIPTION

Usage

update_r_win(check.only = TRUE)

Arguments

check.only

if TRUE R binaries are not downloaded and installed, only a check is performed

Value

OUTPUT_DESCRIPTION

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

---

Write SAM assesseent to a TAF json file

Description

Write a SAM assessment to a json file int the correct format to be uploaded to the TAF assessment results database

Usage

write_sam_upload(fit, dir = NULL)

Arguments

fit	a fitted object from a SAM model fit.
dir	an optional directory name.

---

write.taf.json

Description

FUNCTION_DESCRIPTION

Usage

write.taf.json(x, file = NULL, dir = NULL, ...)

Arguments

x	PARAM_DESCRIPTION
file	PARAM_DESCRIPTION, Default: NULL
dir	PARAM_DESCRIPTION, Default: NULL
...	PARAM_DESCRIPTION

Details

DETAILS

Value

no return value

See Also

read_json

---