Use new RcppTskit names

Author: gregorgorjanc

NAMESPACE

@@ -79,6 +79,8 @@ export(randCross)
 export(randCross2)
 export(reduceGenome)
 export(resetPop)
+export(rtsk_table_collection_summary2)
+export(rtsk_treeseq_get_num_individuals2)
 export(runMacs)
 export(runMacs2)
 export(sampleHaplo)
@@ -105,7 +107,6 @@ export(solveRRBLUP_EM)
 export(solveRRBLUP_EM2)
 export(solveRRBLUP_EM3)
 export(solveUVM)
-export(tc_xptr_summary2)
 export(usefulness)
 export(varA)
 export(varAA)

R/RcppExports.R

@@ -378,14 +378,25 @@ MaCS <- function(args, maxSites, inbred, ploidy, nThreads, seed) {
 #' @return A list.
 #' @examples
 #' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
-#' tc <- RcppTskit:::tc_xptr_load(ts_file)
-#' RcppTskit:::tc_xptr_summary(tc)
-#' AlphaSimR:::tc_xptr_summary2(tc) # a bit simpler at this stage ...
-#' tc <- RcppTskit::TableCollection$new(ts_file)
-#' RcppTskit:::tc_xptr_summary(tc$pointer)
-#' AlphaSimR:::tc_xptr_summary2(tc$pointer) # a bit simpler at this stage ...
+#' tc <- RcppTskit:::tc_load(ts_file)
+#' RcppTskit:::rtsk_table_collection_summary(tc$xptr)
+#' rtsk_table_collection_summary2(tc$xptr)
 #' @export
-tc_xptr_summary2 <- function(tc) {
-    .Call(`_AlphaSimR_tc_xptr_summary2`, tc)
+rtsk_table_collection_summary2 <- function(tc) {
+    .Call(`_AlphaSimR_rtsk_table_collection_summary2`, tc)
+}
+
+#' @title Get number of individuals in tree sequence
+#' @param ts an external pointer to a \code{tsk_treeseq_t} object.
+#' @return integer number of individuals.
+#' @examples
+#' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
+#' ts <- RcppTskit::ts_load(ts_file)
+#' ts$num_individuals()
+#' RcppTskit:::rtsk_treeseq_get_num_individuals(ts$xptr)
+#' rtsk_treeseq_get_num_individuals2(ts$xptr)
+#' @export
+rtsk_treeseq_get_num_individuals2 <- function(ts) {
+    .Call(`_AlphaSimR_rtsk_treeseq_get_num_individuals2`, ts)
 }
 

man/tc_xptr_summary2.Rd man/rtsk_table_collection_summary2.Rdman/tc_xptr_summary2.Rd renamed to man/rtsk_table_collection_summary2.Rd

@@ -860,14 +860,25 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// tc_xptr_summary2
-Rcpp::List tc_xptr_summary2(const SEXP tc);
-RcppExport SEXP _AlphaSimR_tc_xptr_summary2(SEXP tcSEXP) {
+// rtsk_table_collection_summary2
+Rcpp::List rtsk_table_collection_summary2(const SEXP tc);
+RcppExport SEXP _AlphaSimR_rtsk_table_collection_summary2(SEXP tcSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const SEXP >::type tc(tcSEXP);
-    rcpp_result_gen = Rcpp::wrap(tc_xptr_summary2(tc));
+    rcpp_result_gen = Rcpp::wrap(rtsk_table_collection_summary2(tc));
+    return rcpp_result_gen;
+END_RCPP
+}
+// rtsk_treeseq_get_num_individuals2
+int rtsk_treeseq_get_num_individuals2(const SEXP ts);
+RcppExport SEXP _AlphaSimR_rtsk_treeseq_get_num_individuals2(SEXP tsSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const SEXP >::type ts(tsSEXP);
+    rcpp_result_gen = Rcpp::wrap(rtsk_treeseq_get_num_individuals2(ts));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -928,7 +939,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"_AlphaSimR_getNumThreads", (DL_FUNC) &_AlphaSimR_getNumThreads, 0},
     {"_AlphaSimR_packHaplo", (DL_FUNC) &_AlphaSimR_packHaplo, 3},
     {"_AlphaSimR_MaCS", (DL_FUNC) &_AlphaSimR_MaCS, 6},
-    {"_AlphaSimR_tc_xptr_summary2", (DL_FUNC) &_AlphaSimR_tc_xptr_summary2, 1},
+    {"_AlphaSimR_rtsk_table_collection_summary2", (DL_FUNC) &_AlphaSimR_rtsk_table_collection_summary2, 1},
+    {"_AlphaSimR_rtsk_treeseq_get_num_individuals2", (DL_FUNC) &_AlphaSimR_rtsk_treeseq_get_num_individuals2, 1},
     {NULL, NULL, 0}
 };
 

man/rtsk_treeseq_get_num_individuals2.Rd

@@ -16,16 +16,13 @@
 //' @return A list.
 //' @examples
 //' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
-//' tc <- RcppTskit:::tc_xptr_load(ts_file)
-//' RcppTskit:::tc_xptr_summary(tc)
-//' AlphaSimR:::tc_xptr_summary2(tc) # a bit simpler at this stage ...
-//' tc <- RcppTskit::TableCollection$new(ts_file)
-//' RcppTskit:::tc_xptr_summary(tc$pointer)
-//' AlphaSimR:::tc_xptr_summary2(tc$pointer) # a bit simpler at this stage ...
+//' tc <- RcppTskit:::tc_load(ts_file)
+//' RcppTskit:::rtsk_table_collection_summary(tc$xptr)
+//' rtsk_table_collection_summary2(tc$xptr)
 //' @export
 // [[Rcpp::export]]
-Rcpp::List tc_xptr_summary2(const SEXP tc) {
-  RcppTskit_table_collection_xptr tc_xptr(tc);
+Rcpp::List rtsk_table_collection_summary2(const SEXP tc) {
+  rtsk_table_collection_t tc_xptr(tc);
   const tsk_table_collection_t *tables = tc_xptr;
   return Rcpp::List::create(
       Rcpp::_["num_provenances"] = tables->provenances.num_rows,
@@ -37,8 +34,25 @@ Rcpp::List tc_xptr_summary2(const SEXP tc) {
       Rcpp::_["num_sites"] = tables->sites.num_rows,
       Rcpp::_["num_mutations"] = tables->mutations.num_rows,
       Rcpp::_["sequence_length"] = tables->sequence_length,
-      Rcpp::_["has_reference_sequence"] = tc_xptr_has_reference_sequence(tc),
-      Rcpp::_["time_units"] = tc_xptr_time_units(tc),
-      Rcpp::_["file_uuid"] = tc_xptr_file_uuid(tc),
-      Rcpp::_["has_index"] = tc_xptr_has_index(tc));
+      Rcpp::_["has_reference_sequence"] =
+          rtsk_table_collection_has_reference_sequence(tc),
+      Rcpp::_["time_units"] = rtsk_table_collection_get_time_units(tc),
+      Rcpp::_["file_uuid"] = rtsk_table_collection_get_file_uuid(tc),
+      Rcpp::_["has_index"] = rtsk_table_collection_has_index(tc));
+}
+
+//' @title Get number of individuals in tree sequence
+//' @param ts an external pointer to a \code{tsk_treeseq_t} object.
+//' @return integer number of individuals.
+//' @examples
+//' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
+//' ts <- RcppTskit::ts_load(ts_file)
+//' ts$num_individuals()
+//' RcppTskit:::rtsk_treeseq_get_num_individuals(ts$xptr)
+//' rtsk_treeseq_get_num_individuals2(ts$xptr)
+//' @export
+// [[Rcpp::export]]
+int rtsk_treeseq_get_num_individuals2(const SEXP ts) {
+  rtsk_treeseq_t ts_xptr(ts);
+  return static_cast<int>(tsk_treeseq_get_num_individuals(ts_xptr));
 }