qtl2scan: Genome Scans for QTL Experiments

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

.bayes_int_plain <- function(lod, pos, prob) {
    .Call(`_qtl2scan_R_bayes_int_plain`, lod, pos, prob)
}

calc_ll_binreg_eigenchol <- function(X, y, maxit = 100L, tol = 1e-6) {
    .Call(`_qtl2scan_calc_ll_binreg_eigenchol`, X, y, maxit, tol)
}

calc_ll_binreg_eigenqr <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_ll_binreg_eigenqr`, X, y, maxit, tol, qr_tol)
}

calc_coef_binreg_eigenqr <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_binreg_eigenqr`, X, y, maxit, tol, qr_tol)
}

calc_coefSE_binreg_eigenqr <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_binreg_eigenqr`, X, y, maxit, tol, qr_tol)
}

fit_binreg_eigenqr <- function(X, y, se = TRUE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit_binreg_eigenqr`, X, y, se, maxit, tol, qr_tol)
}

calc_ll_binreg_weighted_eigenchol <- function(X, y, weights, maxit = 100L, tol = 1e-6) {
    .Call(`_qtl2scan_calc_ll_binreg_weighted_eigenchol`, X, y, weights, maxit, tol)
}

calc_ll_binreg_weighted_eigenqr <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_ll_binreg_weighted_eigenqr`, X, y, weights, maxit, tol, qr_tol)
}

calc_coef_binreg_weighted_eigenqr <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_binreg_weighted_eigenqr`, X, y, weights, maxit, tol, qr_tol)
}

calc_coefSE_binreg_weighted_eigenqr <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_binreg_weighted_eigenqr`, X, y, weights, maxit, tol, qr_tol)
}

fit_binreg_weighted_eigenqr <- function(X, y, weights, se = TRUE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit_binreg_weighted_eigenqr`, X, y, weights, se, maxit, tol, qr_tol)
}

calc_ll_binreg_weighted <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_ll_binreg_weighted`, X, y, weights, maxit, tol, qr_tol)
}

calc_coef_binreg_weighted <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_binreg_weighted`, X, y, weights, maxit, tol, qr_tol)
}

calc_coefSE_binreg_weighted <- function(X, y, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_binreg_weighted`, X, y, weights, maxit, tol, qr_tol)
}

fit_binreg_weighted <- function(X, y, weights, se = TRUE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit_binreg_weighted`, X, y, weights, se, maxit, tol, qr_tol)
}

calc_ll_binreg <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_ll_binreg`, X, y, maxit, tol, qr_tol)
}

calc_coef_binreg <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_binreg`, X, y, maxit, tol, qr_tol)
}

calc_coefSE_binreg <- function(X, y, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_binreg`, X, y, maxit, tol, qr_tol)
}

fit_binreg <- function(X, y, se = TRUE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit_binreg`, X, y, se, maxit, tol, qr_tol)
}

.find_peaks <- function(lod, threshold, peakdrop) {
    .Call(`_qtl2scan_R_find_peaks`, lod, threshold, peakdrop)
}

.find_peaks_and_lodint <- function(lod, threshold, peakdrop, drop) {
    .Call(`_qtl2scan_R_find_peaks_and_lodint`, lod, threshold, peakdrop, drop)
}

.find_peaks_and_bayesint <- function(lod, pos, threshold, peakdrop, prob) {
    .Call(`_qtl2scan_R_find_peaks_and_bayesint`, lod, pos, threshold, peakdrop, prob)
}

fit1_binary_addcovar <- function(genoprobs, pheno, addcovar, weights, se = FALSE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit1_binary_addcovar`, genoprobs, pheno, addcovar, weights, se, maxit, tol, qr_tol)
}

fit1_binary_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, se = TRUE, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_fit1_binary_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, se, maxit, tol, qr_tol)
}

fit1_hk_addcovar <- function(genoprobs, pheno, addcovar, weights, se = FALSE, tol = 1e-12) {
    .Call(`_qtl2scan_fit1_hk_addcovar`, genoprobs, pheno, addcovar, weights, se, tol)
}

fit1_hk_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, se = TRUE, tol = 1e-12) {
    .Call(`_qtl2scan_fit1_hk_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, se, tol)
}

fit1_pg_addcovar <- function(genoprobs, pheno, addcovar, eigenvec, weights, se = FALSE, tol = 1e-12) {
    .Call(`_qtl2scan_fit1_pg_addcovar`, genoprobs, pheno, addcovar, eigenvec, weights, se, tol)
}

fit1_pg_intcovar <- function(genoprobs, pheno, addcovar, intcovar, eigenvec, weights, se = TRUE, tol = 1e-12) {
    .Call(`_qtl2scan_fit1_pg_intcovar`, genoprobs, pheno, addcovar, intcovar, eigenvec, weights, se, tol)
}

interpolate_map <- function(oldpos, oldmap, newmap) {
    .Call(`_qtl2scan_interpolate_map`, oldpos, oldmap, newmap)
}

find_intervals <- function(pos, map, tol = 1e-8) {
    .Call(`_qtl2scan_find_intervals`, pos, map, tol)
}

fit_linreg_eigenchol <- function(X, y, se) {
    .Call(`_qtl2scan_fit_linreg_eigenchol`, X, y, se)
}

calc_coef_linreg_eigenchol <- function(X, y) {
    .Call(`_qtl2scan_calc_coef_linreg_eigenchol`, X, y)
}

calc_coefSE_linreg_eigenchol <- function(X, y) {
    .Call(`_qtl2scan_calc_coefSE_linreg_eigenchol`, X, y)
}

calc_rss_eigenchol <- function(X, y) {
    .Call(`_qtl2scan_calc_rss_eigenchol`, X, y)
}

calc_fitted_linreg_eigenchol <- function(X, y) {
    .Call(`_qtl2scan_calc_fitted_linreg_eigenchol`, X, y)
}

fit_linreg_eigenqr <- function(X, y, se, tol = 1e-12) {
    .Call(`_qtl2scan_fit_linreg_eigenqr`, X, y, se, tol)
}

calc_coef_linreg_eigenqr <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_linreg_eigenqr`, X, y, tol)
}

calc_coefSE_linreg_eigenqr <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_linreg_eigenqr`, X, y, tol)
}

calc_rss_eigenqr <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_rss_eigenqr`, X, y, tol)
}

calc_fitted_linreg_eigenqr <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_fitted_linreg_eigenqr`, X, y, tol)
}

calc_mvrss_eigenchol <- function(X, Y) {
    .Call(`_qtl2scan_calc_mvrss_eigenchol`, X, Y)
}

calc_mvrss_eigenqr <- function(X, Y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_mvrss_eigenqr`, X, Y, tol)
}

calc_resid_eigenchol <- function(X, Y) {
    .Call(`_qtl2scan_calc_resid_eigenchol`, X, Y)
}

calc_resid_eigenqr <- function(X, Y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_resid_eigenqr`, X, Y, tol)
}

calc_rss_linreg <- function(X, Y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_rss_linreg`, X, Y, tol)
}

calc_coef_linreg <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_coef_linreg`, X, y, tol)
}

calc_coefSE_linreg <- function(X, y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_coefSE_linreg`, X, y, tol)
}

calc_resid_linreg <- function(X, Y, tol = 1e-12) {
    .Call(`_qtl2scan_calc_resid_linreg`, X, Y, tol)
}

calc_resid_linreg_3d <- function(X, P, tol = 1e-12) {
    .Call(`_qtl2scan_calc_resid_linreg_3d`, X, P, tol)
}

fit_linreg <- function(X, y, se = TRUE, tol = 1e-12) {
    .Call(`_qtl2scan_fit_linreg`, X, y, se, tol)
}

Rcpp_eigen_decomp <- function(A) {
    .Call(`_qtl2scan_Rcpp_eigen_decomp`, A)
}

Rcpp_eigen_rotation <- function(K, y, X) {
    .Call(`_qtl2scan_Rcpp_eigen_rotation`, K, y, X)
}

Rcpp_calc_logdetXpX <- function(X) {
    .Call(`_qtl2scan_Rcpp_calc_logdetXpX`, X)
}

Rcpp_calcLL <- function(hsq, Kva, y, X, reml = TRUE, logdetXpX = NA_real_) {
    .Call(`_qtl2scan_Rcpp_calcLL`, hsq, Kva, y, X, reml, logdetXpX)
}

Rcpp_fitLMM <- function(Kva, y, X, reml = TRUE, check_boundary = TRUE, logdetXpX = NA_real_, tol = 1e-4) {
    .Call(`_qtl2scan_Rcpp_fitLMM`, Kva, y, X, reml, check_boundary, logdetXpX, tol)
}

Rcpp_fitLMM_mat <- function(Kva, Y, X, reml = TRUE, check_boundary = TRUE, logdetXpX = NA_real_, tol = 1e-4) {
    .Call(`_qtl2scan_Rcpp_fitLMM_mat`, Kva, Y, X, reml, check_boundary, logdetXpX, tol)
}

.lod_int_plain <- function(lod, drop) {
    .Call(`_qtl2scan_R_lod_int_plain`, lod, drop)
}

find_matching_cols <- function(mat, tol = 1e-12) {
    .Call(`_qtl2scan_find_matching_cols`, mat, tol)
}

find_lin_indep_cols <- function(mat, tol = 1e-12) {
    .Call(`_qtl2scan_find_lin_indep_cols`, mat, tol)
}

formX_intcovar <- function(probs, addcovar, intcovar, position, has_intercept = TRUE) {
    .Call(`_qtl2scan_formX_intcovar`, probs, addcovar, intcovar, position, has_intercept)
}

expand_genoprobs_intcovar <- function(probs, intcovar) {
    .Call(`_qtl2scan_expand_genoprobs_intcovar`, probs, intcovar)
}

weighted_matrix <- function(mat, weights) {
    .Call(`_qtl2scan_weighted_matrix`, mat, weights)
}

weighted_3darray <- function(array, weights) {
    .Call(`_qtl2scan_weighted_3darray`, array, weights)
}

matrix_x_matrix <- function(X, Y) {
    .Call(`_qtl2scan_matrix_x_matrix`, X, Y)
}

matrix_x_vector <- function(X, y) {
    .Call(`_qtl2scan_matrix_x_vector`, X, y)
}

matrix_x_3darray <- function(X, A) {
    .Call(`_qtl2scan_matrix_x_3darray`, X, A)
}

.pick_marker_subset <- function(pos, min_d, weights) {
    .Call(`_qtl2scan_pick_marker_subset`, pos, min_d, weights)
}

random_int <- function(n, low, high) {
    .Call(`_qtl2scan_random_int`, n, low, high)
}

get_permutation <- function(n) {
    .Call(`_qtl2scan_get_permutation`, n)
}

permute_nvector <- function(n_perm, x) {
    .Call(`_qtl2scan_permute_nvector`, n_perm, x)
}

permute_ivector <- function(n_perm, x) {
    .Call(`_qtl2scan_permute_ivector`, n_perm, x)
}

permute_nvector_stratified <- function(n_perm, x, strata, n_strata = -1L) {
    .Call(`_qtl2scan_permute_nvector_stratified`, n_perm, x, strata, n_strata)
}

permute_ivector_stratified <- function(n_perm, x, strata, n_strata = -1L) {
    .Call(`_qtl2scan_permute_ivector_stratified`, n_perm, x, strata, n_strata)
}

scan_binary_onechr <- function(genoprobs, pheno, addcovar, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr`, genoprobs, pheno, addcovar, maxit, tol, qr_tol)
}

scan_binary_onechr_weighted <- function(genoprobs, pheno, addcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr_weighted`, genoprobs, pheno, addcovar, weights, maxit, tol, qr_tol)
}

scan_binary_onechr_intcovar_highmem <- function(genoprobs, pheno, addcovar, intcovar, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr_intcovar_highmem`, genoprobs, pheno, addcovar, intcovar, maxit, tol, qr_tol)
}

scan_binary_onechr_intcovar_weighted_highmem <- function(genoprobs, pheno, addcovar, intcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr_intcovar_weighted_highmem`, genoprobs, pheno, addcovar, intcovar, weights, maxit, tol, qr_tol)
}

scan_binary_onechr_intcovar_lowmem <- function(genoprobs, pheno, addcovar, intcovar, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr_intcovar_lowmem`, genoprobs, pheno, addcovar, intcovar, maxit, tol, qr_tol)
}

scan_binary_onechr_intcovar_weighted_lowmem <- function(genoprobs, pheno, addcovar, intcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scan_binary_onechr_intcovar_weighted_lowmem`, genoprobs, pheno, addcovar, intcovar, weights, maxit, tol, qr_tol)
}

scan_hk_onechr_nocovar <- function(genoprobs, pheno, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_nocovar`, genoprobs, pheno, tol)
}

scan_hk_onechr <- function(genoprobs, pheno, addcovar, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr`, genoprobs, pheno, addcovar, tol)
}

scan_hk_onechr_weighted <- function(genoprobs, pheno, addcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_weighted`, genoprobs, pheno, addcovar, weights, tol)
}

scan_hk_onechr_intcovar_highmem <- function(genoprobs, pheno, addcovar, intcovar, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_intcovar_highmem`, genoprobs, pheno, addcovar, intcovar, tol)
}

scan_hk_onechr_intcovar_weighted_highmem <- function(genoprobs, pheno, addcovar, intcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_intcovar_weighted_highmem`, genoprobs, pheno, addcovar, intcovar, weights, tol)
}

scan_hk_onechr_intcovar_lowmem <- function(genoprobs, pheno, addcovar, intcovar, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_intcovar_lowmem`, genoprobs, pheno, addcovar, intcovar, tol)
}

scan_hk_onechr_intcovar_weighted_lowmem <- function(genoprobs, pheno, addcovar, intcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_hk_onechr_intcovar_weighted_lowmem`, genoprobs, pheno, addcovar, intcovar, weights, tol)
}

scan_pg_onechr <- function(genoprobs, pheno, addcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_pg_onechr`, genoprobs, pheno, addcovar, eigenvec, weights, tol)
}

scan_pg_onechr_intcovar_highmem <- function(genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_pg_onechr_intcovar_highmem`, genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol)
}

scan_pg_onechr_intcovar_lowmem <- function(genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scan_pg_onechr_intcovar_lowmem`, genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol)
}

scanblup <- function(genoprobs, pheno, addcovar, se, reml, tol = 1e-12) {
    .Call(`_qtl2scan_scanblup`, genoprobs, pheno, addcovar, se, reml, tol)
}

scancoef_binary_addcovar <- function(genoprobs, pheno, addcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_binary_addcovar`, genoprobs, pheno, addcovar, weights, maxit, tol, qr_tol)
}

scancoef_binary_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_binary_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, maxit, tol, qr_tol)
}

scancoefSE_binary_addcovar <- function(genoprobs, pheno, addcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_binary_addcovar`, genoprobs, pheno, addcovar, weights, maxit, tol, qr_tol)
}

scancoefSE_binary_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, maxit = 100L, tol = 1e-6, qr_tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_binary_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, maxit, tol, qr_tol)
}

scancoef_hk_addcovar <- function(genoprobs, pheno, addcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_hk_addcovar`, genoprobs, pheno, addcovar, weights, tol)
}

scancoef_hk_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_hk_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, tol)
}

scancoefSE_hk_addcovar <- function(genoprobs, pheno, addcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_hk_addcovar`, genoprobs, pheno, addcovar, weights, tol)
}

scancoefSE_hk_intcovar <- function(genoprobs, pheno, addcovar, intcovar, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_hk_intcovar`, genoprobs, pheno, addcovar, intcovar, weights, tol)
}

scancoef_pg_addcovar <- function(genoprobs, pheno, addcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_pg_addcovar`, genoprobs, pheno, addcovar, eigenvec, weights, tol)
}

scancoef_pg_intcovar <- function(genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoef_pg_intcovar`, genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol)
}

scancoefSE_pg_addcovar <- function(genoprobs, pheno, addcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_pg_addcovar`, genoprobs, pheno, addcovar, eigenvec, weights, tol)
}

scancoefSE_pg_intcovar <- function(genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol = 1e-12) {
    .Call(`_qtl2scan_scancoefSE_pg_intcovar`, genoprobs, pheno, addcovar, intcovar, eigenvec, weights, tol)
}

.calc_sdp <- function(geno) {
    .Call(`_qtl2scan_calc_sdp`, geno)
}

.invert_sdp <- function(sdp, n_str) {
    .Call(`_qtl2scan_invert_sdp`, sdp, n_str)
}

.alleleprob_to_snpprob <- function(alleleprob, sdp, interval, on_map) {
    .Call(`_qtl2scan_alleleprob_to_snpprob`, alleleprob, sdp, interval, on_map)
}

genocol_to_snpcol <- function(n_str, sdp) {
    .Call(`_qtl2scan_genocol_to_snpcol`, n_str, sdp)
}

.genoprob_to_snpprob <- function(genoprob, sdp, interval, on_map) {
    .Call(`_qtl2scan_genoprob_to_snpprob`, genoprob, sdp, interval, on_map)
}

Xgenocol_to_snpcol <- function(n_str, sdp) {
    .Call(`_qtl2scan_Xgenocol_to_snpcol`, n_str, sdp)
}

.Xgenoprob_to_snpprob <- function(genoprob, sdp, interval, on_map) {
    .Call(`_qtl2scan_Xgenoprob_to_snpprob`, genoprob, sdp, interval, on_map)
}