Package options

These options are best set via ir_options() and queried via ir_get_option(). However, the base functions options() and getOption() work as well but require an isoreader2. prefix (the package name and a dot) for the option name. Setting an option to a value of NULL means that the default is used. ir_get_options() is available as an additional convenience function to retrieve a subset of options with a regular expression pattern.

Usage

ir_options(...)

ir_get_options(pattern = NULL)

ir_get_option(x)

Arguments

...

set package options, syntax identical to options()

pattern

to retrieve multiple options (as a list) with a shared pattern

x

name of the specific option to retrieve

Functions

• ir_options(): set/get option values

• ir_get_options(): get a subset of option values that fit a pattern

• ir_get_option(): retrieve the current value of one option (option must be defined for the package)

Options for the isoreader2 package

• aggregators: data aggregators for pulling data out of raw files. The list of available aggregators is accessible via ir_get_option("aggregators"). Individiual aggregators are available via the shortcut helper function ir_get_aggregator("standard"). Register new/overwrite existing aggregators via ir_register_aggregator().

• debug: turn on debug mode

• auto_use_ansi: whether to automatically enable correct rendering of stylized (ansi) output in HTML reports from notebooks that call library(isoir). Can be turned off by calling isoir::ir_options(auto_use_ansi = FALSE) before call library(isoir).

Examples

# All default options
ir_get_options()
#> $aggregators
#> $aggregators$minimal
#> ────────────────────────────── Aggregator minimal ──────────────────────────────
#> Dataset metadata:
#>  → file_name = as.character(sub(file_name, pattern = "\\.[^.]+$", replacement =
#> ""))
#>  → analysis = as.integer(analysis)
#>  → timestamp = as.POSIXct(timestamp)
#> Dataset traces:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → time.s = as.numeric(time.s)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> Dataset cycles:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → cycle = as.integer(cycle)
#>  → type = as.character(type)
#>  → mass = as.character(mass)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> Dataset scans:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → x = as.numeric(x)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> 
#> $aggregators$standard
#> ────────────────────────────── Aggregator standard ─────────────────────────────
#> Dataset metadata:
#>  → file_name = as.character(sub(file_name, pattern = "\\.[^.]+$", replacement =
#> ""))
#>  → analysis = as.integer(analysis)
#>  → timestamp = as.POSIXct(timestamp)
#>  → (.*) = as.character(all_matches("(.*)"))
#> Dataset traces:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → time.s = as.numeric(time.s)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> Dataset cycles:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → cycle = as.integer(cycle)
#>  → type = as.character(type)
#>  → mass = as.character(mass)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> Dataset scans:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → x = as.numeric(x)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#> 
#> $aggregators$extended
#> ────────────────────────────── Aggregator extended ─────────────────────────────
#> Dataset metadata:
#>  → file_name = as.character(sub(file_name, pattern = "\\.[^.]+$", replacement =
#> ""))
#>  → analysis = as.integer(analysis)
#>  → timestamp = as.POSIXct(timestamp)
#>  → (.*) = as.character(all_matches("(.*)"))
#> Dataset traces:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → time.s = as.numeric(time.s)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#>  → channel = as.integer(channel)
#>  → config = as.integer(config)
#> Dataset cycles:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → cycle = as.integer(cycle)
#>  → type = as.character(type)
#>  → mass = as.character(mass)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#>  → channel = as.integer(channel)
#> Dataset scans:
#>  → analysis = as.integer(analysis)
#>  → species = as.character(species)
#>  → mass = as.character(mass)
#>  → x = as.numeric(x)
#>  → (intensity\\..*) = as.numeric(all_matches("(intensity\\..*)"))
#>  → channel = as.integer(channel)
#> Dataset resistors:
#>  → species = as.character(species)
#>  → config = as.integer(config)
#>  → channel = as.integer(channel)
#>  → mass = as.character(mass)
#>  → cup = as.integer(cup)
#>  → resistance.Ohm = as.numeric(resistance.Ohm)
#>  → nominal.Ohm = as.numeric(nominal.Ohm)
#> 
#> 
#> $debug
#> [1] FALSE
#> 
#> $auto_use_ansi
#> [1] TRUE
#>