delta_glm: Delta coupling of 2 GLMs

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

Delta coupling of 2 GLMs

Description

delta_glm realize the delta-coupling using the 2 precedents GLMs, extract the year factor, calculate the AI and display the plots.

Usage

delta_glm(
  tab_pres,
  tab_ia,
  esp,
  title,
  list_param,
  var_eff_list,
  espece_id,
  catch_col,
  limit,
  formula_select_pres,
  formula_select_ia,
  repartition = 0,
  temporal_factor = 0,
  data_type
)

Arguments

tab_pres	input dataset table used for pres/abs model
tab_ia	input dataset table used for ia model
esp	exact name of the studied species
title	title will be displayed in the plots
list_param	list of the tested parameters
var_eff_list	list of the possible fishing effort column
espece_id	exact name of the column indicating the species
catch_col	exact name of the column indicating the catches
limit	percentage representing the limit value under which the modality is removed
formula_select_pres	specify the final prese/abs model
formula_select_ia	specify the final abundance model
repartition	Surface by region strata (can be absolute value)
data_type	Specify the type of data for the combining of different data_type
temporal_facto	If other than annual and on a smaller time step (seasonal, quarter...). That way biomass mean will be calculated in this time step for each year

Examples

data(tableau_sc)
tableau_sc_GIN <- tableau_sc %>% mutate(bathymetrie = case_when(
  profond_deb >= 05  & profond_deb <=10 ~ "5-10m",
  profond_deb > 10 & profond_deb <=15 ~ "10-15m",
 profond_deb > 15 & profond_deb <= 30 ~ "15-30m"
))


repartition <- as.data.frame(cbind(bathymetrie = c("5-10m", "10-15m", "15-30m"),
                                  proportion = c(661.5, 1009.3, 2872.3)))

repartition$proportion <- as.numeric(repartition$proportion)

delta_IA <- delta_glm(tab_pres = tableau_sc_GIN, tab_ia = tableau_sc_GIN, esp="PSEUDOTOLITHUS ELONGATUS", title="1st Try",
                      list_param=c("annee", "bathymetrie"), var_eff_list=c("surface_chalutee"), espece_id='nom_taxonomique',
                      catch_col='total_capture', limit=0.0001,
                      formula_select_pres = "presence ~ annee + bathymetrie",
                      formula_select_ia = "log(i_ab) ~ annee + bathymetrie",
                      repartition = repartition,
                      data_type = "SC")

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