Part C

Part C--use "cat" utility to reassemble into a zipped folder containing the complete code and data files

EstimationPrograms_FormattedInputFiles

See the ReadMe for further details. These are the input files formatted for each analysis program and are the population samples under analysis

Part B

Part B--use "cat" utility to reassemble into a zipped folder containing the complete code and data files

CoNe_IBD50_OutputFiles

CoNe Ne estimation output files for IBD scenarios with true Ne = 50. See the same readme for other input/output files for naming conventions

TypeI_ErrorTest_SireUnbalanced

R code to run the error testing of the unbalanced half-sib sire model over 1000 replicate datasets

NemoReplicates

Zipped file containing the 1000 simulated replicate datasets from Nemo used for type I error testing

TypeI_ErrorTest_DamUnbalanced

R code to run the error testing of the unbalanced half-sib dam model over 1000 replicate datasets

ProgramOutputFilesFor_Colony_Estim_MLNe_NeEstimator_ONeSamp_TMVP

These are the Ne estimates output by the various programs. See the readme for file naming conventions. Because of their large size, CoNe output files are stored separately

Ne5000_IdealRawPopulationFiles

These are the "true" population files for ideal (isolation) populations of size 5000 simulated from Nemo. They contain all individuals and many extra loci, from which these were sampled to obtain the inputs used in analyses (see Program_InputFiles). Temporal samplers used two time points, from which the files here are identified as belonging to generation 0 or generation 1

TypeI_ErrorTest_DamBalanced

R code to run the error testing of the balanced half-sib dam model over 1000 replicate datasets