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Permit compilation with Nullable::operatorT() #4

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178 changes: 89 additions & 89 deletions R/RcppExports.R
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Original file line number Diff line number Diff line change
@@ -1,89 +1,89 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#' Calculate IBD probabilities
#'
#' Calculate IBD probabilities for different types of populations.
#'
#' IBD probabilities can be calculated for many different types of populations.
#' In the following table all supported populations are listed. Note that the
#' value of x in the population types is variable, with its maximum value
#' depicted in the last column.
#'
#' | __Population type__ | __Cross__ | __Description__ | __max. x__ |
#' | ------ | ----------------- | -------------------------------------- | --- |
#' | DH | biparental | doubled haploid population | |
#' | Fx | biparental | Fx population (F1, followed by x-1 generations of selfing) | 8 |
#' | FxDH | biparental | Fx, followed by DH generation | 8 |
#' | BCx | biparental | backcross, second parent is recurrent parent | 9 |
#' | BCxDH | biparental | BCx, followed by DH generation | 9 |
#' | BC1Sx | biparental | BC1, followed by x generations of selfing | 7 |
#' | BC1SxDH | biparental | BC1, followed by x generations of selfing and DH | 6 |
#' | C3 | three-way | three way cross: (AxB) x C | |
#' | C3DH | three-way | C3, followed by DH generation | |
#' | C3Sx | three-way | C3, followed by x generations of selfing | 7 |
#' | C3SxDH | three-way | C3, followed by x generations of selfing and DH generation | 6 |
#' | C4 | four-way | four-way cross: (AxB) x (CxD) | |
#' | C4DH | four-way | C4, followed by DH generation | |
#' | C4Sx | four-way | C4, followed by x generations of selfing | 6 |
#' | C4SxDH | four-way | C4, followed by x generations of selfing and DH generation | 6 |
#'
#' @param popType A character string indicating the type of population. One of
#' DH, Fx, FxDH, BCx, BCxDH, BC1Sx, BC1SxDH, C3, C3DH, C3Sx, C3SxDH, C4, C4DH,
#' C4Sx, C4SxDH (see Details).
#' @param markerFile A character string indicating the location of the file with
#' genotypic information for the population. The file should be in
#' tab-delimited format with a header containing marker names.
#' @param mapFile A character string indicating the location of the map file
#' for the population. The file should be in tab-delimited format. It should
#' consist of exactly three columns, marker, chromosome and position. There
#' should be no header. The positions in the file should be in centimorgan.
#' @param evalPos A data.frame with evaluation positions to which the
#' calculations should be limited.
#' @param evalDist An optional numerical value indicating the maximum
#' distance for marker positions. Extra markers will be added based on the
#' value of \code{grid}.
#' @param grid Should the extra markers that are added to assure the a
#' maximum distince of \code{evalDist} be on a grid (\code{TRUE}) or in between
#' marker existing marker positions (\code{FALSE}).
#' @param verbose Should messages indicating the progress of the process be
#' printed?
#'
#' @returns An object of class \code{IBDprob}, a \code{list} with five elements,
#' \describe{
#' \item{map}{a \code{data.frame} with chromosome and position of the markers.}
#' \item{markers}{a 3-dimensional \code{array} of IBD probabilities with
#' genotypes, markers and parents as array dimensions.}
#' \item{parents}{the parents.}
#' \item{popType}{the population type.}
#' }
#'
#' @examples
#' ## Compute IBD probabilities for Steptoe Morex.
#' SxMIBD <- calcIBD(popType = "DH",
#' markerFile = system.file("extdata/SxM", "SxM_geno.txt",
#' package = "statgenIBD"),
#' mapFile = system.file("extdata/SxM", "SxM_map.txt",
#' package = "statgenIBD"))
#'
#' ## Check summary.
#' summary(SxMIBD)
#'
#' ## Compute IBD probabilities for Steptoe Morex.
#' ## Add extra evaluation positions in between exiting marker positions
#' ## to assure evaluation positions are at most 5 cM apart.
#' SxMIBD_Ext <- calcIBD(popType = "DH",
#' markerFile = system.file("extdata/SxM", "SxM_geno.txt",
#' package = "statgenIBD"),
#' mapFile = system.file("extdata/SxM", "SxM_map.txt",
#' package = "statgenIBD"),
#' evalDist = 5)
#'
#' ## Check summary.
#' summary(SxMIBD_Ext)
#'
#' @export
calcIBD <- function(popType, markerFile, mapFile, evalPos = NULL, evalDist = NULL, grid = TRUE, verbose = FALSE) {
.Call(`_statgenIBD_calcIBD`, popType, markerFile, mapFile, evalPos, evalDist, grid, verbose)
}
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' Calculate IBD probabilities
#'
#' Calculate IBD probabilities for different types of populations.
#'
#' IBD probabilities can be calculated for many different types of populations.
#' In the following table all supported populations are listed. Note that the
#' value of x in the population types is variable, with its maximum value
#' depicted in the last column.
#'
#' | __Population type__ | __Cross__ | __Description__ | __max. x__ |
#' | ------ | ----------------- | -------------------------------------- | --- |
#' | DH | biparental | doubled haploid population | |
#' | Fx | biparental | Fx population (F1, followed by x-1 generations of selfing) | 8 |
#' | FxDH | biparental | Fx, followed by DH generation | 8 |
#' | BCx | biparental | backcross, second parent is recurrent parent | 9 |
#' | BCxDH | biparental | BCx, followed by DH generation | 9 |
#' | BC1Sx | biparental | BC1, followed by x generations of selfing | 7 |
#' | BC1SxDH | biparental | BC1, followed by x generations of selfing and DH | 6 |
#' | C3 | three-way | three way cross: (AxB) x C | |
#' | C3DH | three-way | C3, followed by DH generation | |
#' | C3Sx | three-way | C3, followed by x generations of selfing | 7 |
#' | C3SxDH | three-way | C3, followed by x generations of selfing and DH generation | 6 |
#' | C4 | four-way | four-way cross: (AxB) x (CxD) | |
#' | C4DH | four-way | C4, followed by DH generation | |
#' | C4Sx | four-way | C4, followed by x generations of selfing | 6 |
#' | C4SxDH | four-way | C4, followed by x generations of selfing and DH generation | 6 |
#'
#' @param popType A character string indicating the type of population. One of
#' DH, Fx, FxDH, BCx, BCxDH, BC1Sx, BC1SxDH, C3, C3DH, C3Sx, C3SxDH, C4, C4DH,
#' C4Sx, C4SxDH (see Details).
#' @param markerFile A character string indicating the location of the file with
#' genotypic information for the population. The file should be in
#' tab-delimited format with a header containing marker names.
#' @param mapFile A character string indicating the location of the map file
#' for the population. The file should be in tab-delimited format. It should
#' consist of exactly three columns, marker, chromosome and position. There
#' should be no header. The positions in the file should be in centimorgan.
#' @param evalPos A data.frame with evaluation positions to which the
#' calculations should be limited.
#' @param evalDist An optional numerical value indicating the maximum
#' distance for marker positions. Extra markers will be added based on the
#' value of \code{grid}.
#' @param grid Should the extra markers that are added to assure the a
#' maximum distince of \code{evalDist} be on a grid (\code{TRUE}) or in between
#' marker existing marker positions (\code{FALSE}).
#' @param verbose Should messages indicating the progress of the process be
#' printed?
#'
#' @returns An object of class \code{IBDprob}, a \code{list} with five elements,
#' \describe{
#' \item{map}{a \code{data.frame} with chromosome and position of the markers.}
#' \item{markers}{a 3-dimensional \code{array} of IBD probabilities with
#' genotypes, markers and parents as array dimensions.}
#' \item{parents}{the parents.}
#' \item{popType}{the population type.}
#' }
#'
#' @examples
#' ## Compute IBD probabilities for Steptoe Morex.
#' SxMIBD <- calcIBD(popType = "DH",
#' markerFile = system.file("extdata/SxM", "SxM_geno.txt",
#' package = "statgenIBD"),
#' mapFile = system.file("extdata/SxM", "SxM_map.txt",
#' package = "statgenIBD"))
#'
#' ## Check summary.
#' summary(SxMIBD)
#'
#' ## Compute IBD probabilities for Steptoe Morex.
#' ## Add extra evaluation positions in between exiting marker positions
#' ## to assure evaluation positions are at most 5 cM apart.
#' SxMIBD_Ext <- calcIBD(popType = "DH",
#' markerFile = system.file("extdata/SxM", "SxM_geno.txt",
#' package = "statgenIBD"),
#' mapFile = system.file("extdata/SxM", "SxM_map.txt",
#' package = "statgenIBD"),
#' evalDist = 5)
#'
#' ## Check summary.
#' summary(SxMIBD_Ext)
#'
#' @export
calcIBD <- function(popType, markerFile, mapFile, evalPos = NULL, evalDist = NULL, grid = TRUE, verbose = FALSE) {
.Call(`_statgenIBD_calcIBD`, popType, markerFile, mapFile, evalPos, evalDist, grid, verbose)
}

80 changes: 40 additions & 40 deletions src/RcppExports.cpp
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Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
// Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif
// calcIBD
List calcIBD(CharacterVector& popType, CharacterVector& markerFile, CharacterVector& mapFile, Nullable<DataFrame&> evalPos, Nullable<NumericVector&> evalDist, const bool& grid, const bool& verbose);
RcppExport SEXP _statgenIBD_calcIBD(SEXP popTypeSEXP, SEXP markerFileSEXP, SEXP mapFileSEXP, SEXP evalPosSEXP, SEXP evalDistSEXP, SEXP gridSEXP, SEXP verboseSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< CharacterVector& >::type popType(popTypeSEXP);
Rcpp::traits::input_parameter< CharacterVector& >::type markerFile(markerFileSEXP);
Rcpp::traits::input_parameter< CharacterVector& >::type mapFile(mapFileSEXP);
Rcpp::traits::input_parameter< Nullable<DataFrame&> >::type evalPos(evalPosSEXP);
Rcpp::traits::input_parameter< Nullable<NumericVector&> >::type evalDist(evalDistSEXP);
Rcpp::traits::input_parameter< const bool& >::type grid(gridSEXP);
Rcpp::traits::input_parameter< const bool& >::type verbose(verboseSEXP);
rcpp_result_gen = Rcpp::wrap(calcIBD(popType, markerFile, mapFile, evalPos, evalDist, grid, verbose));
return rcpp_result_gen;
END_RCPP
}
static const R_CallMethodDef CallEntries[] = {
{"_statgenIBD_calcIBD", (DL_FUNC) &_statgenIBD_calcIBD, 7},
{NULL, NULL, 0}
};
RcppExport void R_init_statgenIBD(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
// Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#include <RcppArmadillo.h>
#include <Rcpp.h>

using namespace Rcpp;

#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// calcIBD
List calcIBD(CharacterVector& popType, CharacterVector& markerFile, CharacterVector& mapFile, Nullable<DataFrame> evalPos, Nullable<NumericVector> evalDist, const bool& grid, const bool& verbose);
RcppExport SEXP _statgenIBD_calcIBD(SEXP popTypeSEXP, SEXP markerFileSEXP, SEXP mapFileSEXP, SEXP evalPosSEXP, SEXP evalDistSEXP, SEXP gridSEXP, SEXP verboseSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< CharacterVector& >::type popType(popTypeSEXP);
Rcpp::traits::input_parameter< CharacterVector& >::type markerFile(markerFileSEXP);
Rcpp::traits::input_parameter< CharacterVector& >::type mapFile(mapFileSEXP);
Rcpp::traits::input_parameter< Nullable<DataFrame> >::type evalPos(evalPosSEXP);
Rcpp::traits::input_parameter< Nullable<NumericVector> >::type evalDist(evalDistSEXP);
Rcpp::traits::input_parameter< const bool& >::type grid(gridSEXP);
Rcpp::traits::input_parameter< const bool& >::type verbose(verboseSEXP);
rcpp_result_gen = Rcpp::wrap(calcIBD(popType, markerFile, mapFile, evalPos, evalDist, grid, verbose));
return rcpp_result_gen;
END_RCPP
}

static const R_CallMethodDef CallEntries[] = {
{"_statgenIBD_calcIBD", (DL_FUNC) &_statgenIBD_calcIBD, 7},
{NULL, NULL, 0}
};

RcppExport void R_init_statgenIBD(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
6 changes: 3 additions & 3 deletions src/calcIBD.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -99,8 +99,8 @@ using namespace ibd;
List calcIBD(CharacterVector& popType,
CharacterVector& markerFile,
CharacterVector& mapFile,
Nullable<DataFrame&> evalPos = R_NilValue,
Nullable<NumericVector&> evalDist = R_NilValue,
Nullable<DataFrame> evalPos = R_NilValue,
Nullable<NumericVector> evalDist = R_NilValue,
const bool& grid = true,
const bool& verbose = false)
{
Expand All @@ -126,7 +126,7 @@ List calcIBD(CharacterVector& popType,
_poptype,
Rcpp::as<std::string>(markerFile),
Rcpp::as<std::string>(mapFile),
evalPos,
Rcpp::DataFrame(evalPos),
max_step_size,
grid,
verbose);
Expand Down