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birp (version 0.0.5)

Testing for Population Trends Using Low-Cost Ecological Count Data

Description

A Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) , and the file 'AUTHORS' for a list of copyright holders and contributors.

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Install

install.packages('birp')

Monthly Downloads

2

Version

0.0.5

License

GPL (>= 2)

Maintainer

Madleina Caduff

Last Published

July 12th, 2025

Functions in birp (0.0.5)

.createObjBirp.birp

Function to create an object of type birp

Plot posterior distributions of gamma parameters

print.birp_data

Print a birp_data object Prints a summary of a birp_data object, including the number of methods, locations, control-intervention (CI) groups, and timepoints, as well as the names or identifiers for each.

Function to open a file and generate error message if it was not found

.openPosteriorPlot.birp

Function to open an empty plot for plotting the posterior probabilities

Summary method for birp objects

.addToList.birp

Function to convert an argument to a string and add it to a list if necessary

summary.birp_data

Summarize a birp_data object

Simulate Data for BIRP Models Generates simulated count data using the BIRP model framework with user-defined parameters.

plot_epoch_pair

Plot joint posterior of two gamma parameters

Plot Posterior Trend Estimates

.calculateRho.birp

Function to calculate rho

Print a birp object

Plot MCMC Traces and Posterior Densities

.getEpochStarts.birp

Function to get the start of each epoch, including for a hypothetical epoch after the last epoch

.getLabelGamma.birp

Function to generate a nice axis label with greek gamma and subscript

.checkFile.birp

Function to check if a file exists and generate error message if it was not found

tools:::Rd_package_title("birp")

birp_from_command_line

Create a birp Object from Command-Line Output Files

birp_data_from_file

Create a birp_data Object from File(s)

Create a birp_data Object from Count and Effort Matrices

birp_data_from_data_frame

Create a 'birp_data' Object from a Data Frame or List of Data Frames

Assess whether a Poisson model can replace the Negative Binomial model

Create a birp Object

.addLegendMultiGamma.birp

Function to add legend to plot denoting gammas

.addTextSingleGamma.birp

Function to add text box to plot denoting P(gamma > 0 | n) or P(gamma < 0 | n) for single gammas

.plotShadingPolygon.birp

Function to add a hatched polygon to a plot

Plot a birp_data Object

.validate.birp_data

This function check if a birp_data object is valid

simulate_birp_from_results

This function simulates a birp_data object using all parameter estimates, dimensionality (methods, locations, timepoints) and the total number of counts nu_ij of a birp object

.getDataAllMethods.birp_data

This function reads data for all methods into a list