gibbsf90 | R Documentation |
The function uses the model formula language in R to describe the model and from this generates the files needed to do an analysis using gibbs2f90 software!
gibbsf90(formula, phen, ped = NULL, geno = NULL, map = NULL, idName,
diffVAR = NULL, nMaternal = NULL, weight = NULL, nIter = 1500,
burnIn = 500, thin = 5, missing = 0, covariate = 0, OPTeff = NULL,
OPTlist = NULL, intern = TRUE, Gcov = NULL, Rcov = NULL,
execute = TRUE, PED_DEPTH = 0, covAM = 1, covR = 1, useF = FALSE)
formula |
A two-sided linear formula object describing the fixed effects part of the model, with the responses on the left of a ~ operator (separated by | if more then one response) and the terms, separated by + operators, on the right. |
phen |
Name of phenotype file. |
ped |
Name of pedigree file |
geno |
Name of genotype file. |
map |
Name of map file. |
idName |
Identification name of animal's column. |
diffVAR |
List of the trait and their unique effect, if any. |
nMaternal |
Number of traits on maternal effect. By default nMaternal=0. |
weight |
name of the column (numeric) with a vector of weights, may be NULL. If weights is not NULL, the residual variance of each data-point is set to be proportional to the inverse of the squared-weight. |
nIter, burnIn, thin |
(integer) the number of iterations, burn-in and thinning. |
missing |
a integer specifying the missing value (default 0). |
covariate |
Name of covariate(s) if there is(are) any. |
OPTeff |
OPTIONAL effect, i.e., mat, pe, mpe. It is NULL if it is not given. |
OPTlist |
OPTIONAL effect. It is NULL if it is not given. |
intern |
a logical (not NA) which indicates whether to capture the output of the command as an R character vector. |
Gcov |
Genetic (co)variance. It is NULL if it is not given. |
Rcov |
Residual (co)variance. It is NULL if it is not given. |
execute |
Whether to run the gibbsf90. By default execute=TRUE. |
PED_DEPTH |
a integer specifying the depth of pedigree search. The default is 3, byt all pedigrees are loaded if it is set to 0. |
covAM |
type 0 if covariance between additive and maternal genetic effects must be fixed in zero, 1 otherwise. By default covAM=1. |
covR |
type 0 if residual covariance must be fixed in zero, 1 otherwise. By default covAM=1. |
useF |
logical value indicating whether inbreeding coefficient of this animal should be computed. Default is FALSE. |
gibbsf90 results.
Misztal I, Tsuruta S., Lourenco D., Aguilar I., Legarra A., Vitezica Z (2014). Manual for BLUPF90 family of programs. Available at: <http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=blupf90_all1.pdf>.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.