generate_vital_rate_coefs: Generate coefficients for obtaining vital rates

In cxr: A Toolbox for Modelling Species Coexistence in R

Generate coefficients for obtaining vital rates

Description

Any vital rate is a function of several parameters, potentially including interactions or environmental effects. This function generates the coefficients for these parameters, so that users do not have to introduce them all manually in a 'param' list. Coefficients can be generated from a random sampling of a normal distribution with specified mean and standard deviation, or they can be retrieved from a model object that accepts a 'tidy' function from the broom/broom.mixed packages. This is because coefficients for vital rates can be understood as coefficients from statistical regressions.

Usage

generate_vital_rate_coefs(
  param,
  sp = NULL,
  sites = NULL,
  vital.rate = NULL,
  vr.coef = NULL,
  mean.coef = NULL,
  sd.coef = NULL,
  glm.object = NULL,
  glm.coef.equivalence = NULL
)

Arguments

param	the original list with the structure of species, sites, vital rates to calculate, and parameters affecting them. See the function 'build_param'
sp	number or character of the species to calculate coefficients for. If empty, all species are assumed.
sites	number or character of the sites to calculate coefficients for. If empty, all sites are assumed.
vital.rate	character giving the vital rate to calculate coefficients for. If empty, all vital rates are assumed.
vr.coef	character giving a specific coefficient to calculate. If empty, all coefficients are assumed.
mean.coef	optional numeric value, mean for sampling coefficient values
sd.coef	optional numeric value, standard deviation for sampling coefficient values
glm.object	optional model object/coef table
glm.coef.equivalence	if a glm table is provided and its names differ from the 'param' data structure, you can include a named list in which names are the names from 'param' and its elements are the equivalent names from the glm table

Details

In the current version, we assume that the model coefficients come from a logistic regression with binomial family. Otherwise, the function will probably not fail, but the coefficients will not be interpretable and the results in terms of obtaining the actual vital rates from these will be meaningless.

Also note that you need to take care manually of the signs of the coefficients, if entered through mean/sd pairs.

Value

the updated parameter list

cxr documentation built on Oct. 27, 2023, 1:08 a.m.