disclapmix: Discrete Laplace Mixture Inference using the EM Algorithm
Version 1.6.2

Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).

Browse man pages Browse package API and functions Browse package files

AuthorMikkel Meyer Andersen and Poul Svante Eriksen
Date of publication2015-09-09 15:40:33
MaintainerMikkel Meyer Andersen <mikl@math.aau.dk>
LicenseGPL-2
Version1.6.2
URL http://dx.doi.org/10.1016/j.jtbi.2013.03.009 http://arxiv.org/abs/1304.2129
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("disclapmix")

Man pages

clusterdist: Calculate distance between clusters
clusterprob: Cluster origin probabilities for haplotypes
contributor_pairs: Contributor pairs from a 2 person mixture
danes: Y-STR haplotypes
disclapmix: Discrete Laplace mixture inference using the EM algorithm
disclapmixfit: Discrete Laplace mixture fit by the EM algorithm
disclapmix-package: Discrete Laplace mixture inference using the EM algorithm
generate_mixture: Generate a mixture
plot.disclapmixfit: Plot a disclapmixfit
predict.disclapmixfit: Predict from a disclapmixfit
print.disclapmixfit: Print a disclapmixfit
rank_contributor_pairs: Separate a 2 person mixture
simulate.disclapmixfit: Simulate from a disclapmixfit
summary.disclapmixfit: Summary of a disclapmixfit

Functions

INTERNAL_glmfit Source code
check_x Source code
check_y Source code
clusterdist Man page Source code
clusterprob Man page Source code
contributor_pairs Man page Source code
convert_coef_to_disclap_parameters Source code
convert_coef_to_disclap_parameters_internal Source code
convert_to_compact_db Source code
create_initial_y Source code
create_model_matrix Source code
create_response_vector Source code
danes Man page
disclapglm_deviance Source code
disclapglm_linkfun Source code
disclapglm_linkinv Source code
disclapglm_loglikeh Source code
disclapglm_mu_eta Source code
disclapglm_varfunc Source code
disclapmix Man page Source code
disclapmix-package Man page
disclapmixfit Man page
find_haplotype_in_matrix Source code
generate_mixture Man page Source code
get_AIC Source code
get_AICc Source code
get_BIC Source code
get_cand2_set Source code
get_loglikelihood_full Source code
get_loglikelihood_marginal Source code
get_rank Man page Source code
haplotype_diversity Source code
happrobsum_normalise Source code
happrobsum_within Source code
happrobsum_within_between Source code
happrobsum_within_between_binomial Source code
happrobsum_within_between_binomial_compact_dbs Source code
happrobsum_within_between_cache Source code
happrobsum_within_between_normalised Source code
move_centers Source code
plot.disclapmixfit Man page Source code
plot.ranked_contrib_pairs Man page Source code
predict.disclapmixfit Man page Source code
predict_clusterwise Source code
print.contrib_pairs Man page Source code
print.disclapmixfit Man page Source code
print.ranked_contrib_pairs Man page Source code
rank_contributor_pairs Man page Source code
rcpp_calculate_haplotype_probabilities Source code
rcpp_calculate_haplotype_probabilities_clusterwise Source code
rcpp_calculate_haplotype_probabilities_sum Source code
rcpp_calculate_haplotype_probabilities_sum_CLASS Source code
rcpp_calculate_haplotype_probabilities_sum_CLASS_Cache Source code
rcpp_calculate_haplotype_probabilities_sum_between Source code
rcpp_calculate_haplotype_probabilities_sum_binomial Source code
rcpp_calculate_haplotype_probabilities_sum_binomial_compact_dbs Source code
rcpp_calculate_vic Source code
rcpp_calculate_wic Source code
rcpp_create_design_matrix Source code
rcpp_create_new_weight_vector Source code
rcpp_create_response_vector Source code
rcpp_find_haplotype_in_matrix Source code
rcpp_hapsums_disclap_normalised Source code
rcpp_match_quantities Source code
rcpp_simulate Source code
simulate.disclapmixfit Man page Source code
summary.disclapmixfit Man page Source code
theta_weir Source code

Files

src
src/Makevars
src/helper.cpp
src/disclapfamily.cpp
src/happrobsum.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
demo
demo/00Index
demo/danes.R
NEWS
data
data/danes.txt.gz
R
R/mixture.R
R/disclapmix.R
R/clusterdist.R
R/RcppExports.R
R/clusterprob.R
R/proto_functions.R
R/helper.R
MD5
DESCRIPTION
man
man/disclapmix-package.Rd
man/disclapmixfit.Rd
man/clusterprob.Rd
man/rank_contributor_pairs.Rd
man/disclapmix.Rd
man/danes.Rd
man/summary.disclapmixfit.Rd
man/print.disclapmixfit.Rd
man/plot.disclapmixfit.Rd
man/simulate.disclapmixfit.Rd
man/contributor_pairs.Rd
man/generate_mixture.Rd
man/predict.disclapmixfit.Rd
man/clusterdist.Rd
disclapmix documentation built on May 19, 2017, 7:31 a.m.