glm_pres_abs: Fit a Generalized Linear Models on presence/absence data

In polehalieutique/demerstem: This package aims to falicitate Fish stock assessement for west african partners involved in the EU DEMERSTEM project

Fit a Generalized Linear Models on presence/absence data

Description

glm_pres_abs returns a presence/absence GLM model. It can run a StepAIC if specified. It runs the GLMs, plot the residuals analysis graphs and return the GLM outputs.

Usage

glm_pres_abs(
  tableau_pres,
  parameters,
  formula_select,
  summary = FALSE,
  type = 2
)

Arguments

tableau_pres	table of presence and absence data, coming as the output of table_pres_abs
parameters	list of parameters to test
formula_select	if "auto", the function select which formula as the lowest AIC. Else, run the selected formula.
summary	To show residuals plots.
type	To study marginal effects with Anova type III in case of interaction

Value

glm_pres_abs can either return the best GLM model based on AIC comparison, or return the outputs of the GLM based on the formula given in formula_select

Examples

data(tableau_sc)
list_param <- c("annee", "saison")
table_ex <- table_pres_abs(tableau_sc, esp="PSEUDOTOLITHUS ELONGATUS", list_param=c("annee", "saison"), espece_id='nom_taxonomique', var_eff_list=c("surface_chalutee"), catch_col='total_capture', limit=0.0001)
param <- param_use(table_ex, list_param)

for (i in 1:length(param)){
table_ex[,param[i]] <- as.factor(table_ex[,param[i]])
table_ex[,param[i]] <- droplevels(table_ex[,param[i]])
contrasts(table_ex[,param[i]]) <- contr.sum(levels(table_ex[,param[i]]))
}

glm_pres_abs(table_ex, param, formula_select = "auto")

polehalieutique/demerstem documentation built on Aug. 4, 2024, 5:12 a.m.