Data and code for "Accounting for observation biases associated with counts of young when estimating fecundity: case study on the arboreal-nesting red kite (Milvus milvus)", Sollmann, R., Adenot, N., Spakovszky, P., Windt, J., Mattsson, B.J. (2024), PCJ.
All code necessary to implement the estimation simulations and population projections described in the above references manuscript
DOI repository: https://doi.org/10.5281/zenodo.10245802
DOI publication: https://doi.org/10.24072/pcjournal.436
This repository contains the following scripts (folder R) :
Parameter estimation simulations.R: R code to generate imperfect and perfect counts (of nestlings) and fit the models described under Q1-Q3 in the above referenced manuscript, estimating average number of nestlings while accounting for false negative and false positive observation error
Simulation summaries and plots.R: R code to summarize simulation output and create plots
Population projection.R: R code to implement population projection described in the above referenced manuscript and produce plots
It further contains the following model code files (folder R) :
Nimble model code.R: Nimble model code for the models described in the manuscript and used in the estimation simulation
It further contains the following data files (folder data-raw) :
datmat.rds: Matrix with empirical observations of nestling counts, rows are true counts (climb counts), columns corresponding uncertain ground counts; values in cells correspond to number of nests with particular combination of true and uncertain count.
Pnest.scenarios.rds: Matrix with values of pi (probability a nest contains 1-4 nestlings); true input values, expected observed values based on uncertain (ground) counts only; estimated values from all scenarios investigated under Q3 (see main text for details)
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Fitting models requires the R package Nimble. Please see publication for version information and R scripts for additional packages used in processing data.