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

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.