RemoveNACases {zoolog}

Remove Cases Missing All Measurements

Description

Function to remove the table rows for which all measurements of interest are non-available (NA). A particular list of measurement names can be explicitly provided or selected by a common initial pattern. The default setting removes the rows with no log-ratio available.

Usage

RemoveNACases(data, measureNames = NULL, prefix = logPrefix)

Arguments

data

A dataframe with the input measurements.

measureNames

A vector of characters with the list of measurements to be considered for missing values. If NULL (default), all measurements starting by prefix are considered.

prefix

A character string with the initial pattern to select the list of measurements. The default is given by the internal variable logPrefix. It is in effect only when measureNames = NULL.

Value

A dataframe with the same columns as the input dataframe but removing the rows with missing values for all measurements in the list.

Examples

## Read an example dataset:
dataFile <- system.file("extdata", "dataValenzuelaLamas2008.csv.gz",
                        package = "zoolog")
dataExample <- utils::read.csv2(dataFile,
                                na.strings = "",
                                encoding = "UTF-8")
## We can observe the first lines (excluding some columns for visibility):
head(dataExample)[, -c(6:20,32:64)]

## Remove the cases not including any measurement present in the reference.
refMeasureNames <- unique(reference$Combi$Measure)
refMeasureNames
dataExamplePruned <- RemoveNACases(dataExample,
                                   measureNames = refMeasureNames)
## The first lines of the output data frame show at least one available
## measurement value in the selected list:
head(dataExamplePruned)[, -c(6:20,32:64)]

## If we compute first the log-ratios
dataExampleWithLogs <- LogRatios(dataExample)
## the cases not including any log-ratio can be removed with the
## default logPrefix
dataExampleWithLogsPruned <- RemoveNACases(dataExampleWithLogs)
head(dataExampleWithLogsPruned)[, -c(6:20,32:64)]