inputMunch {modEvA}

Munch inputs into 'obs' and 'pred' vectors

Description

This function is used internally by many other functions in this package to check and extract the 'obs' and 'pred' vectors from the user inputs.

Usage

inputMunch(model = NULL, obs = NULL, pred = NULL, rm.dup = FALSE, na.rm = FALSE,
verbosity = 2)

Arguments

model

a binary-response model object of class "glm", "gam", "gbm", "randomForest" or "bart". If this argument is provided, 'obs' and 'pred' will be extracted with mod2obspred. Alternatively, you can input the 'obs' and 'pred' arguments (e.g. for external test data) instead of 'model'.

obs

alternatively to 'model' and together with 'pred', a numeric vector of observed presences (1) and absences (0) of a binary response variable. Alternatively (and if 'pred' is a 'SpatRaster'), a two-column matrix or data frame containing, respectively, the x (longitude) and y (latitude) coordinates of the presence points, in which case the 'obs' vector will be extracted with ptsrast2obspred. This argument is ignored if 'model' is provided.

pred

alternatively to 'model' and together with 'obs', a vector with the corresponding predicted values of presence probability, habitat suitability, environmental favourability or alike. Must be of the same length and in the same order as 'obs'. Alternatively (and if 'obs' is a set of point coordinates), a 'SpatRaster' map of the predicted values for the entire evaluation region, in which case the 'pred' vector will be extracted with ptsrast2obspred. This argument is ignored if 'model' is provided.

rm.dup

logical argument to be passed to ptsrast2obspred indicating whether repeated points within the same pixel should be removed. The default is FALSE.

na.rm

logical argument indicating whether to remove (with a warning saying how many) rows with NA in any of the resulting 'obs' or 'pred' values. The default is FALSE.

verbosity

integer value indicating the amount of messages to display. Defaults to 2, for the maximum amount of messages.

Value

This function returns a two-column data frame containing the 'obs' and 'pred' values, or an error message if inputs are not as required.

Author(s)

A. Marcia Barbosa