create_params_colonyV2: Create COLONY, Version 2.0.6.5 Input files
In zakrobinson/RSibPurge: A convenient R-interface for COLONY Version 2.0.6.5

Description Usage Arguments Value Author(s)

Create input file for Colony, Version 2.0.6.5. Author Of COLONY: Jinliang Wang, Institute of Zoology, Zoological Society of London

create_params_colonyV2(projectname = "test1", project_path = getwd(),
  offspring_alleles, geno = T, nCode = NULL, rand_seed = 1234,
  update_allelefreq = 0, Dio_Mono = 2, inbred = 0,
  haplodiploid = 0, monogamy_M = 0, monogamy_F = 0, clones = 0,
  FS_scaling = 1, FS_prior = 0, FS_prior_M = NA, FS_prior_F = NA,
  nRuns = 1, RunLength = 2, likelihood = 1, precision = 3,
  alle_drop = 0, false_alle = 0.005)

`projectname`	a text string that describes the Colony run "project".
`project_path`	a directory where input and output files will be stored.
`offspring_alleles`	a data frame with individual IDs in the first column and alleles or genotypes following.
`geno`	Logical if offspring_alleles are in genotype per column format versus allele per column format.
`nCode`	if geno=T then how many digits are the genotypes coded in (i.e. 12 heterzygote has a nCode of 2)
`rand_seed`	Seed for random number generator
`update_allelefreq`	an indicator of value 1 (or 0) to instruct Colony to (or not to) update allele frequencies during the simulated annealing process in searching for the ML configuration.
`Dio_Mono`	a value of either 2 or 1 to indicate dioecious species or monoecious species.
`inbred`	a value of either 0 or 1 to indicate the absence or presence of inbreeding.
`haplodiploid`	a value of either 0 or 1 to indicate diploid species or haplodiploid species.
`monogamy_M`	an indicator value (0 or 1) to specify whether males are polygamous (=0) or monogamous (=1).
`monogamy_F`	an indicator value (0 or 1) to specify whether females are polygamous (=0) or monogamous (=1).
`clones`	an indicator value (1 or 0) to specify whether clones (or duplicated individuals) are to be inferred (=1) or not (=0).
`FS_scaling`	an indicator value (1 or 0) to specify whether full sibship size is to be scaled (=1) or not (=0).
`FS_prior_M`	give an indicator value of 0, 1, 2 or 3 to indicate no sibship prior, weak sibship prior, medium sibship prior or strong sibship prior for males.
`FS_prior_F`	give an indicator value of 0, 1, 2 or 3 to indicate no sibship prior, weak sibship prior, medium sibship prior or strong sibship prior for females.
`nRuns`	Provide a value for the number of replicate runs for the dataset (project)
`RunLength`	Give a value of 1, 2, 3, 4 to indicate short, medium, long, very long run
`likelihood`	Give an indicated value of 0, 1 or 2 to tell Colony to use the pairwise-likelihood score (PLS), full likelihood (FL), or the FL and PLS combined (FPLS) method.
`precision`	Give an indicated value of 0/1/2/3 to use Low/Medium/High/VeryHigh precision in calculating the full likelihood.
`alle_drop`	allele dropout rate.
`fasle_alle`	other typing error rate.