MorphoRegions (version 0.1.0)

process_measurements: Process vertebra measurements

Description

process_measurements() initializes the analysis workflow by processing a dataset of vertebra measurements into an object usable by MorphoRegions. Such processing includes identifying the vertebra indices and the measurements and filling in missing values.

Usage

process_measurements(data, pos = 1L, measurements, fillNA = TRUE)

Value

A regions_data object, which is a list of data.frames (one for each specimen) with attributes containing metadata.

Arguments

data

a data.frame containing a column of vertebra indices and measurements for each vertebra, or a list thereof for multiple specimens.

pos

the name or index of the variable in data containing the vertebra indices. Default is to use the first column.

measurements

the names or indices of the variables in data containing the relevant vertebra measurements. If unspecified, will use all variables other than that specified in pos.

fillNA

logical; whether to fill in missing values using a simple linear imputation. Default is TRUE. See Details.

Details

Any rows with missing values for all measurements will be removed. When missing values in non-removed rows are present and fillNA is set to TRUE, process_measurements() fills them in if the sequence of missing values is no greater than 2 in length. For numeric variables, it uses a linear interpolation, and for categorical variables, it fills in the missing values with the surrounding non-missing values if they are identical and leaves them missing otherwise. Otherwise, missing values are left as they are.

When a list of data frames is supplied to data, only the variables named in measurements that are common across datasets will be stored as measurement variables.

See Also

svdPCO() for computing principal coordinate axes from processed vertebra data.

Examples

# Process dataset; vertebra index in "Vertebra" column
data("alligator")

alligator_data <- process_measurements(alligator,
                                       pos = "Vertebra")

# Process multiple datasets; vertebra index in first column
data("porpoise")

porpoise_data <- process_measurements(list(porpoise1,
                                           porpoise2,
                                           porpoise3),
                                      pos = 1)