Supplement 1. MATLAB files used for data generation, parameter estimation, and results analysis.

Name: Supplement 1. MATLAB files used for data generation, parameter estimation, and results analysis.
Published: 2016-08-05T01:44:42+00:00
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: nest-survival, nest-monitoring interval, biased estimates, transition probabilities, Markov chain, Mayfield model, multistate models, Environmental Science, Ecology

dataset

posted on 2016-08-05, 01:44 authored by Matthew A. Etterson, Richard S. Bennett

File List

MayfieldMC.zip -- zip file containing all seven MATLAB functions for data generation, parameter estimation, and output processing.

GenNests.m -- simulates nest-discovery data under a 2-stage nest cycle.

GenObs.m -- generates monitoring data on sets of nests generated using
the function 'GenNests.m'.

MayfieldMC.m -- computes the likelihoods of a set of observations using the
Markov Chain formulation.

EstimateTransFreq.m -- estimates the joint distributins of hatching and age:
Pr(H,a) and fledging and age: Pr(F,b) for a given set of observations.

RunSim.m -- otpimizes the Mayfield Markov Chain in 'MayfieldMC.mat'.

DailyBar.m -- calculates bias, asymptotic standard error, and standard %deviation of daily survival estimates using output from the function 'RunSim.mat'. It also generates grouped 2-d bar graphs, as used in manuscript.

OverallBar.m -- calculates bias, asymptotic standard error, and standard deviation of overall success estimates using output from the function 'RunSim.mat'. It also generates grouped 2-d bar graphs, as used in manuscript.

Description

The file MayfieldMC.zip contains 7 MATLAB functions used to perform the simulations described in this manuscript. The files GenNests.m, and GenObs.m are used to simulate sets of nests and observations on those nests. The file MayfieldMC.m estimates maximum likelihood values for daily survival estimates for a two-stage nest-survival model. It uses EstimateTransFreq.m to estimate hatching and fledging distributions on a set of nests given a set of observations on those nests. The file RunSim.m will perform the sequences of data generation and survival estimation described in the main text. The two remaining files DailyBar.m, OverallBar.m, were used to generate Fig. 2 and the figures in Appendix D using the output files from RunSim.m. Additional documentation and information on usage is contained in comments within the files.