optimizationResult-class: Class containing optimization results.

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Class containing optimization results.

Description

Objects from this class contain optimization results resulting from design of experiment (DoE).

Usage

optimizedParameters(object, paramSet = NULL, DoEIteration = NULL)

optimizedObject(object, paramSet = NULL)

scores(object, paramSet = NULL, DoEIteration = NULL)

experimentInfo(object, paramSet, DoEIteration)

## S4 method for signature 'optimizationResult'
algorithm(obj)

## S4 method for signature 'optimizationResult'
length(x)

## S4 method for signature 'optimizationResult'
lengths(x, use.names = FALSE)

## S4 method for signature 'optimizationResult'
show(object)

## S4 method for signature 'optimizationResult,missing'
plot(
  x,
  paramSet,
  DoEIteration,
  paramsToPlot = NULL,
  maxCols = NULL,
  type = "contour",
  image = TRUE,
  contours = "colors",
  ...
)

## S4 method for signature 'optimizationResult'
optimizedParameters(object, paramSet = NULL, DoEIteration = NULL)

## S4 method for signature 'optimizationResult'
optimizedObject(object, paramSet = NULL)

## S4 method for signature 'optimizationResult'
scores(object, paramSet = NULL, DoEIteration = NULL)

## S4 method for signature 'optimizationResult'
experimentInfo(object, paramSet, DoEIteration)

Arguments

paramSet	Numeric index of the parameter set (i.e. the first parameter set gets index ‘⁠1⁠’). For some methods optional: if NULL the best will be selected.
DoEIteration	Numeric index specifying the DoE iteration within the specified paramSet. For some methods optional: if NULL the best will be selected.
obj, x, object	An optimizationResult object.
use.names	Ignored.
paramsToPlot	Which parameters relations should be plot. If NULL all will be plot. Alternatively, a list containing one or more character vectors specifying each two parameters that should be plotted. Finally, if only one pair should be plotted, can be a character vector specifying both parameters.
maxCols	Multiple parameter pairs are plotted in a grid. The maximum number of columns can be set with this argument. Set to NULL for no limit.
type	The type of plots to be generated: "contour", "image" or "persp". The equally named functions will be called for plotting.
image	Passed to contour (if type="contour").
contours	Passed to persp (if type="persp").
...	Further arguments passed to contour, image or persp (depending on type).

Details

Objects from this class are returned by optimizeFeatureFinding and optimizeFeatureGrouping.

Methods (by generic)

• algorithm(optimizationResult): Returns the algorithm that was used for finding features.

• length(optimizationResult): Obtain total number of experimental design iterations performed.

• lengths(optimizationResult): Obtain number of experimental design iterations performed for each parameter set.

• show(optimizationResult): Shows summary information for this object.

• plot(x = optimizationResult, y = missing): Generates response plots for all or a selected set of parameters.

• optimizedParameters(optimizationResult): Returns parameter set yielding optimal results. The paramSet and DoEIteration arguments can be NULL.

• optimizedObject(optimizationResult): Returns the object (i.e. a features or featureGroups object) that was generated with optimized parameters. The paramSet argument can be NULL.

• scores(optimizationResult): Returns optimization scores. The paramSet and DoEIteration arguments can be NULL.

• experimentInfo(optimizationResult): Returns a list with optimization information from an DoE iteration.

Slots

algorithm

A character specifying the algorithm that was optimized.

paramSets

A list with detailed results from each parameter set that was tested.

bestParamSet

Numeric index of the parameter set yielding the best response.

Examples

## Not run: 
# ftOpt is an optimization object.

# plot contour of all parameter pairs from the first parameter set/iteration.
plot(ftOpt, paramSet = 1, DoEIteration = 1)

# as above, but only plot two parameter pairs
plot(ftOpt, paramSet = 1, DoEIteration = 1,
     paramsToPlot = list(c("mzPPM", "chromFWHM"), c("chromFWHM", "chromSNR")))

# plot 3d perspective plots
plot(ftOpt, paramSet = 1, DoEIteration = 1, type = "persp")

## End(Not run)

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.