R: Corrections

6.3.corrections {pems.utils}

R Documentation

Corrections

Description

Corrections are a special subset of functions which by default write over the elements that they recalculate.

Usage


correctInput(input = NULL, ..., data = NULL,
         correction = NULL)

zeroNegatives(input = NULL, ..., data = NULL, 
         screen = FALSE)

correctBaseline(x, ..., data = NULL, output = "ans")

#associated

calcPack2(input, ..., settings = NULL, data = NULL)

Arguments

`input`	(Required data series typically vectors) The input to use when makin a correction. This is typically a vector or element in either a `data.frame` or `pems` object.
`x`	(For `correctBaseline`) (Required data series typically vectors) The input to use when makin a correction. This is typically a vector or element in either a `data.frame` or `pems` object.
`...`	(Optional) Other arguments, typically passed on.
`data`	(Optional `data.frame` or `pems` object) The data source if either a `data.frame` or `pems` object is being used.
`correction`	(For `correctInput`, required function) The correction operation to apply to `input`. This is typically a function or function name (as character string).
`screen`	(For `zeroNegatives`, logical) If the user intends screening the correction before applying it, this should be set to `TRUE`.
`output`	(character) Where options exists for the function output, the required output. For `correctBaseline`, current options: `'ans'` (the default) and `'diagnostic'`.
`settings`	(For `calcPack2`, list) Any arguments to be used as settings when handling `pems.elements`. Unless developing functions, this can typically be ignored.

Details

correctInput is a general correction handlers. It accepts an input and a function, correction, which it applies to input.

zeroNegatives resets any negative values in an input to zero.

correctBaseline attempts to correct the baseline of a supplied data (pems.element vector) time-series. Baseline corrections are carried out using methods from the baseline package. See Below.

calcPack2 is an alternative version of calcPack. See associated help for details.

Value

With the exception of calcPack2, all the above functions generate input corrections.

correctBaseline returns the supplied data time-series (x) after applying the requested baseline correction (see below).

Note

By default, corrections return results in the format of the input. So: If inputs are supplied as vectors, the answer is returned as a vector; If inputs are supplied in a pems object, that pems object is returned with the answer added in. This behaviour is enabled by the default output = "special". Output type can be forced by declaring ouput in the function call. Options "input", "data.frame" and "pems" return vectors, data.frames and pems objects, respectively.

Unlike other calculations, corrections automatically replace the associated input, unless prevented (using overwrite = FALSE).

This function management is handled by calcChecks and calcPack. These are front and back end calc... function add-ins that anyone can use as a 'minimal code' means of integrating third-party and pems.utils functions.

See calcChecks documentation for details.

correctBaseline is a recent transfer from sleeper.service. It uses baseline functions to provide 'best guess' baseline corrections.

By default, it applies:

baseline(..., method="rollingBall", wm=50, ws=50)

Please Note the 'best guess': As baseline corrections are based statistical estimates of likely baselines rather than actual measures of drift these should be treated as estimates.

Unit management is by convertUnits. See associated help documentation for details.

Author(s)

Karl Ropkins

References

baseline:

Kristian Hovde Liland and Bjorn-Helge Mevik (2015). baseline: Baseline Correction of Spectra. R package version 1.2-1. https://CRAN.R-project.org/package=baseline

Examples


###########
##example 1 
###########

#basic usage

zeroNegatives(-10:10) #etc

[Package pems.utils version 0.2.29.1 Index]