wpeR (version 0.1.0)

check_sampledata: Check and prepare genetic sample metadata

Description

Verifies the consistency of columns in the genetic sample metadata and prepares it for use with other functions in the wpeR package. The function ensures that the provided data is properly formatted and conforms to the standards of functions that make up the wpeR package.

Usage

check_sampledata(
  Sample,
  Date,
  AnimalRef,
  GeneticSex,
  lat,
  lng,
  SType,
  extraCols = NULL
)

Value

A data frame with at least 7 columns and a number of rows equal to the length of the input vector. Each column corresponds to one of the input parameters. If the function executes without warnings or errors, the result from check_sampledata() can be used as an input parameter for other functions within this package: get_colony(), get_ped(), org_fams()

and plot_table().

Arguments

Sample

A vector of sample unique identifier codes.

Date

A vector of sample collection dates in 'YYYY-MM-DD' format.

AnimalRef

A vector of identifier codes of the particular individual that the sample belongs to.

GeneticSex

A vector of genetic sex information ('F' for female, 'M' for male, NA for unknown).

lat

A vector of latitude coordinates in the WGS84 coordinate system (EPSG: 4326).

lng

A vector of longitude coordinates in the WGS84 coordinate system (EPSG: 4326).

SType

A vector of sample types eg.: scat, hair, tissue.

extraCols

A vector of extra column names that the user wants to include in sampledata data frame (see Details).

Details

By specifying the extraCols parameter additional information can be included in the sampledata dataframe. Such additional information is not required for the functioning of the wpeR package functions, but can be useful to the user when interpreting results. When including additional columns the function inputs (Sample, Date, AnimalRef...) have to be defined as a vector extracted from data frame column (eg. Sample = dataframe$column) and the extraCols parameter is defined, as a vector of column names form the same data frame (eg. extraCols = c(column1, column2, column3)).

Examples

sampledata <- check_sampledata(
  Sample = wolf_samples$Sample,
  Date = wolf_samples$Date,
  AnimalRef = wolf_samples$AnimalRef,
  GeneticSex = wolf_samples$GeneticSex,
  lat = wolf_samples$lat,
  lng = wolf_samples$lng,
  SType = wolf_samples$SType
)