SCARE is a C++ program designed for inferences on a model of remating and sperm displacement. It makes use of multilocus genetic data on mothers and a sample of their offspring. The details of the model and the algorithm SCARE uses can be found in Jones and Clark 2002, "Bayesian Sperm Competition Estimates". The model has 2 parameters: alpha, the remating parameter (questions about alpha?), and beta, the parameter governing sperm displacement. Alpha is assumed to be between 0 and 6, Beta is assumed to be between 0.5 and 1. SCARE uses MCMC to generate 10,000 samples from the joint posterior of these 2 quantitites. A summary of the posterior is also produced. Download SCARE.
For users of Mac OS X, you can download an executable: main.exe. In the terminal environment, set the file to be an executable with "chmod a+x main.exe". You should then be able to run the program with the command "./main.exe< YourInputFile".
SCARE Input
A scare input file has the following format. First the random seed is
listed. Then, the number of broods in the data set is listed. (A brood
consists of a mother and a sample of her offspring.) Next, the number
of loci is listed followed by a list of 0's and 1's, 1 for each locus.
These indicate which (if any) loci are X linked. Following these
parameters that pertain to the whole data set is a listing for each
brood. First, the number of offspring for that brood, then the
mother's genotype, then the genotype for each offspring. Missing
genotypes should be denoted by zeros (both alleles should be zeros.)
Sample input file with 20 broods and 1 autosomal
locus.
Sample input file with 2 broods, 2
autosomal loci.
SCARE Output The posterior samples produced by SCARE are sent to standard output, and a summary of the results is placed in the file "summary.out" (Note that running the program will overwrite any file named "summary.out" already in the directory.) The summary gives an estimate of the posterior mean for each parameter. It also gives the number of posterior samples falling into each of several bins. The bins divide up the prior support region: the prior on alpha is uniform between 1 and 6, and is divided into bins of length 0.1. The prior on beta is uniform between 0.5 and 1, and is divided into bins of length 0.01. Thus there are potentially 2500 counts to report; however, only rows and columns that actually have posterior samples are included. Sample output generated by the 20 brood input file given above: summary.out, standard output.
SCARE Warnings SCARE sends warnings to the standard output under 2 conditions. If any offspring's genotype is incompatible with its mother's genotype, a warning is generated but the program continues on. There is also a maximum number of fathers per brood, 25. If this is exceeded, a warning is generated and the program will crash. (This should only happen if the offspring genotypes dictate that at least this many father's are necessary. In most cases, this warning is a sign of an error in the input file.) If any other problems are encountered, please send your input file and a description of the problem to m.b.jones@massey.ac.nz