Assert none of the arguments of a function are null.

Description

Checks all the arguments in the parent function and makes sure that none of them are NULL

Usage

check_args(ignore, select)

Arguments

Examples

myfunc <- function(verbose = get_opts("verbose"), b = get_opts("b")){
  check_args()
}

set_opts(verbose = 1)
## this will throw an error, suggesting b is not defined properly
try(myfunc())

fix_column_names

Description

removes special chars from names

Usage

fix_column_names(x, char = "_")

Arguments

fix_names

Description

Replace special characters in column names of a data.frame

Usage

fix_names(x, char = "_")

Arguments

See Also

make.names

Create tables in LaTeX, HTML, Markdown and reStructuredText

Description

This is a very simple table generator. It is simple by design. It is not intended to replace any other R packages for making tables. This is a trimmed down version of the original kable function in knitr package. Please refer to knitr's kable function for details.

Usage

kable(
  x,
  format,
  digits = getOption("digits"),
  row.names = NA,
  col.names = colnames(x),
  align,
  caption = NULL,
  escape = TRUE,
  ...
)

Arguments

Author(s)

Yihui Xie http://yihui.org

Setting/loading and extracting various options into the environment

Description

• set_opts(): set options into a custom envir

• get_opts(): extract options

• load_opts(): Read a tab delimited file using read_sheet or toml file and load them as options using set_opts

• new_opts(): create a options manager to be included in a pacakge

• print.opts(): print pkg options as a pretty table

Usage

load_opts(x, check = TRUE, envir = opts, verbose = TRUE, .parse = TRUE, ...)

load_toml(toml, .remove_period = T, envir = envir, verbose = T)

new_opts(envir = new.env())

get_opts(x, envir = opts, .use.names = FALSE)

set_opts(..., .dots, .parse = TRUE, envir = opts)

## S3 method for class 'opts'
print(x, ...)

Arguments

Details

Integrating params in a package:

create a options manager:

opts_mypkg = new_opts()

The object opts_mypkg is a list of a few functions, which set, fetch and load options (using a isolated environment). Here are a few examples:

Set some options:

opts_mypkg$set(version = '0.1', name = 'mypkg')

Fetch ALL options:

opts_mypkg$get() OR opts_mypkg$get("version") to fetch a specific option.

Loading configuration files:

load_opts() OR opts_pkg$load():

There are cases when options and params are actually paths to scripts or other apps or folders etc. In such cases it might be useful to quickly check if these paths exists on the system. As such, load_opts() automatically checks params ending with path|dir|exe (if check=TRUE).

For example, values for variables like mypath, my_path, tool_exe, etc would be check if they exists and a warning would be shown if they don't exist.

Below is a list example options, retrieved via

get_opts():

|name          |value            |
|default_regex |(.*)             |
|my_conf_path  |~/flowr/conf     |
|my_dir        |path/to/a/folder |
|my_path       |~/flowr          |
|my_tool_exe   |/usr/bin/ls      |

See Also

read_sheet

read_sheet

read_sheet load_opts

Examples

## Set options
opts = set_opts(flow_run_path = "~/mypath")
#OR
opts = set_opts(.dots = list(flow_run_path = "~/mypath"))

## printing options, this is internally called by get_opts()
print(opts)

## Fetch options
get_opts()
get_opts("flow_run_path")

## Load options from a file
fl = system.file("conf/params.conf", package = "params")
load_opts(fl)


## Create a options manager:
opts_mypkg = new_opts()
## this provides three functions
opts_mypkg$set(version = '0.1', name = 'mypkg')
opts_mypkg$load(fl)
opts_mypkg$get()

## Additionally, one has the options of using braces ({{}})
## do define nested options:

set_opts(first = "John", last = "Doe", full = "{{first}} {{last}}")

default opts

Description

default opts

Usage

opts

Format

An object of class environment of length 6.

Parse options to expand {{variable}} into their respective values

Description

This function is internally called by set_opts and load_opts

Usage

parse_opts(lst, envir)

Arguments

Read/Write sheets (automatically detect the file type and work accordingly)

Description

Read/Write sheets (automatically detect the file type and work accordingly)

write_sheet requires version 0.3.1.

• tsv, txt, conf, def: assumed to be tab-delimited

• csv: assumed to be comma delimited

• xlsx: microsoft excel, uses openxlsx to read the sheet. Also, it removes extra columns which often creep into excel files.

Usage

read_sheet(
  x,
  id_column,
  start_row = 1,
  sheet = 1,
  ext,
  header = TRUE,
  verbose = FALSE,
  ...
)

write_sheet(x, file, ext, type = "", ...)

Arguments

Details

Note: for excel sheets:

• If id_column is missing, default if first column

• If sheet is missing, it automatically reads the first sheet

Some important default values for tsv and csv files:

stringsAsFactors = FALSE,comment.char = '#', strip.white=TRUE, blank.lines.skip=TRUE

Examples

## read a excel sheet
sheet = read_sheet(system.file("extdata/example.xlsx", package = "params"))

## read a comma separated sheet
csv = read_sheet(system.file("extdata/example.csv", package = "params"))

## read a tab separate sheet
tsv = read_sheet(system.file("extdata/example.tsv", package = "params"))


# write sheets -------

## Not run: 
# throws a R CMD check note - don't run
## write a comma separated sheet
write_sheet(sheet, "example.csv")

## write a tab separated sheet
write_sheet(sheet, "example.tsv")

## write an excel separated sheet
write_sheet(sheet, "example.xlsx")

## End(Not run)