plot_trend: Plot estimated population trend

In FRBCesab/popbayes: Bayesian Model to Estimate Population Trends from Counts Series

Plot estimated population trend

Description

This function plots a panel of two graphics for one BUGS model (previously generated by fit_trend()):

• on the left side, the population trend estimated by the Bayesian model (blue line) with the 95% CI (gray envelop). Dots (with intervals) represent converted counts passed to the model (with the 95% CI);

• on the right side, a bar plot of estimated relative growth rates (r) by date. Dark bars are real estimated r.

Usage

plot_trend(series, title = TRUE, path = ".", path_fig = ".", save = FALSE)

Arguments

series	a character string. The count series name (can be retrieved by running list_series()).
title	a logical. If TRUE (default) a title (series name) is added.
path	a character string. The directory in which count series (and BUGS outputs) have been saved by the function format_data() (and by fit_trend()).
path_fig	a character string. The directory where to save the plot (if save = TRUE). This directory must exist and can be an absolute or a relative path.
save	a logical. If TRUE (default is FALSE) the plot is saved in path_fig.

Value

No return value.

Examples

## Load Garamba raw dataset ----
file_path <- system.file("extdata", "garamba_survey.csv", 
                         package = "popbayes")
                         
garamba <- read.csv(file = file_path)

## Create temporary folder ----
temp_path <- tempdir()

## Format dataset ----
garamba_formatted <- popbayes::format_data(
  data              = garamba, 
  path              = temp_path,
  field_method      = "field_method",
  pref_field_method = "pref_field_method",
  conversion_A2G    = "conversion_A2G",
  rmax              = "rmax")

## Select one serie ----
a_buselaphus <- popbayes::filter_series(garamba_formatted, 
                                        location = "Garamba",
                                        species  = "Alcelaphus buselaphus")

## Fit population trends (requires JAGS) ----
a_buselaphus_mod <- popbayes::fit_trend(a_buselaphus, path = temp_path)

## Plot estimated population trend ----
popbayes::plot_trend(series = "garamba__alcelaphus_buselaphus", 
                     path   = temp_path)

FRBCesab/popbayes documentation built on Jan. 26, 2024, 12:13 p.m.