diff --git a/DESCRIPTION b/DESCRIPTION index f36700d..f4dfb69 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: coala -Version: 0.1.0.9001 -Date: 2015-07-17 +Version: 0.1.1.9000 +Date: 2015-07-31 License: MIT + file LICENSE Title: A Framework for Coalescent Simulation Authors@R: c( diff --git a/NEWS b/NEWS index 13c5d3e..2c94aac 100644 --- a/NEWS +++ b/NEWS @@ -1,7 +1,8 @@ coala 0.1.1.9000 ---------------- -* Add MCMF summary statistic (). +* Add MCMF summary statistic (#94). + coala 0.1.1 diff --git a/R/RcppExports.R b/R/RcppExports.R index 37c4900..5a791e3 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -33,14 +33,14 @@ calc_jsfs <- function(seg_sites, pop1, pop2) { .Call('coala_calc_jsfs', PACKAGE = 'coala', seg_sites, pop1, pop2) } -calc_nucleotide_div <- function(seg_sites, individuals) { - .Call('coala_calc_nucleotide_div', PACKAGE = 'coala', seg_sites, individuals) -} - calc_mcmf <- function(seg_sites, individuals, has_trios = TRUE) { .Call('coala_calc_mcmf', PACKAGE = 'coala', seg_sites, individuals, has_trios) } +calc_nucleotide_div <- function(seg_sites, individuals) { + .Call('coala_calc_nucleotide_div', PACKAGE = 'coala', seg_sites, individuals) +} + unphase_segsites <- function(seg_sites, ploidy, samples_per_ind) { .Call('coala_unphase_segsites', PACKAGE = 'coala', seg_sites, ploidy, samples_per_ind) } diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index ead9b19..eab379a 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -84,28 +84,28 @@ BEGIN_RCPP return __result; END_RCPP } -// calc_nucleotide_div -NumericVector calc_nucleotide_div(List seg_sites, const NumericVector individuals); -RcppExport SEXP coala_calc_nucleotide_div(SEXP seg_sitesSEXP, SEXP individualsSEXP) { +// calc_mcmf +NumericVector calc_mcmf(const List seg_sites, const NumericVector individuals, const bool has_trios); +RcppExport SEXP coala_calc_mcmf(SEXP seg_sitesSEXP, SEXP individualsSEXP, SEXP has_triosSEXP) { BEGIN_RCPP Rcpp::RObject __result; Rcpp::RNGScope __rngScope; - Rcpp::traits::input_parameter< List >::type seg_sites(seg_sitesSEXP); + Rcpp::traits::input_parameter< const List >::type seg_sites(seg_sitesSEXP); Rcpp::traits::input_parameter< const NumericVector >::type individuals(individualsSEXP); - __result = Rcpp::wrap(calc_nucleotide_div(seg_sites, individuals)); + Rcpp::traits::input_parameter< const bool >::type has_trios(has_triosSEXP); + __result = Rcpp::wrap(calc_mcmf(seg_sites, individuals, has_trios)); return __result; END_RCPP } -// calc_mcmf -NumericVector calc_mcmf(const List seg_sites, const NumericVector individuals, const bool has_trios); -RcppExport SEXP coala_calc_mcmf(SEXP seg_sitesSEXP, SEXP individualsSEXP, SEXP has_triosSEXP) { +// calc_nucleotide_div +NumericVector calc_nucleotide_div(List seg_sites, const NumericVector individuals); +RcppExport SEXP coala_calc_nucleotide_div(SEXP seg_sitesSEXP, SEXP individualsSEXP) { BEGIN_RCPP Rcpp::RObject __result; Rcpp::RNGScope __rngScope; - Rcpp::traits::input_parameter< const List >::type seg_sites(seg_sitesSEXP); + Rcpp::traits::input_parameter< List >::type seg_sites(seg_sitesSEXP); Rcpp::traits::input_parameter< const NumericVector >::type individuals(individualsSEXP); - Rcpp::traits::input_parameter< const bool >::type has_trios(has_triosSEXP); - __result = Rcpp::wrap(calc_mcmf(seg_sites, individuals, has_trios)); + __result = Rcpp::wrap(calc_nucleotide_div(seg_sites, individuals)); return __result; END_RCPP } diff --git a/src/stat_omegaprime.cpp b/src/stat_mcmf.cpp similarity index 97% rename from src/stat_omegaprime.cpp rename to src/stat_mcmf.cpp index 5dbefef..b2190df 100644 --- a/src/stat_omegaprime.cpp +++ b/src/stat_mcmf.cpp @@ -14,7 +14,7 @@ void maxsplit(const NumericMatrix ss, std::map m; unsigned int key; - int max_key_value = std::pow(2, individuals.size()); + unsigned int max_key_value = std::pow(2, individuals.size()); for (int snp = 0; snp < ss.ncol(); ++snp) { if (trio_locus_vec[snp] != trio_locus) continue;