haplo.em.control {haplo.stats} | R Documentation |
This function creates a list of parameters that control the EM algorithm based on progressive insertion of loci. Non-default parameters for the EM algorithm can be set as parameters passed to haplo.em.control.
haplo.em.control(loci.insert.order=NULL, insert.batch.size = 6, min.posterior = 1e-07, tol = 1e-05, max.iter=500, random.start=0, n.try = 10, iseed=NULL, max.haps.limit = 2e6, verbose=0)
loci.insert.order |
Numeric vector with specific order to insert the loci. If this value is NULL, the insert oder will be in sequential order (1, 2, ..., No. Loci). |
insert.batch.size |
Number of loci to be inserted in a single batch. |
min.posterior |
Minimum posterior probability of haplotype pair, conditional on observed marker genotypes. Posteriors below this minimum value will have their pair of haplotypes "trimmed" off the list of possible pairs. |
tol |
Default 1e-5 |
max.iter |
Maximum number of iterations allowed for the EM algorithm before it stops and prints an error. Default is 500. |
random.start |
If random.start = 0, then the inititial starting values of the posteriors for the first EM attempt will be based on assuming equal posterior probabilities (conditional on genotypes). If random.start = 1, then the initial starting values of the first EM attempt will be based on assuming a uniform distribution for the initial posterior probabilities. |
n.try |
Number of times to try to maximize the lnlike by the EM algorithm. The first try will use, as initial starting values for the posteriors, either equal values or uniform random variables, as determined by random.start. All subsequent tries will use uniform random values as initial starting values for the posterior probabilities. |
iseed |
An integer or a saved copy of .Random.seed. This allows simulations to be reproduced by using the same initial seed. |
max.haps.limit |
The maximum number of haplotypes for which memory is allocated. |
verbose |
Logical, if [T]rue, print lots of debug messages to the screen. If [F]alse, default, do not print any messages. It is best to use verbose=F. |
The default is to use n.try = 10. If this takes too much time, it may be worthwhile to decrease n.try. Other tips for computing haplotype frequencies for a large number of loci, particularly if some have many alleles, is to decrease the batch size (insert.batch.size), increase the memory (max.haps.limit).
A list of the parameters passed to the function.
# This is how it is used within haplo.score # > score.gauss <- haplo.score(resp, geno, trait.type="gaussian", # > em.control=haplo.em.control(insert.batch.size = 2, n.try=1))