Depend on RcppTskit 0.3.0

Author: gregorgorjanc

DESCRIPTION

@@ -10,10 +10,10 @@ Depends:
     R (>= 4.0.0)
 Imports:
     methods,
-    RcppTskit (>= 0.2.0)
+    RcppTskit (>= 0.3.0)
 LinkingTo:
     Rcpp (>= 0.12.10),
-    RcppTskit (>= 0.2.0)
+    RcppTskit (>= 0.3.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(tc_xptr_summary2)
 export(ts_xptr_num_individuals2)
 import(RcppTskit)
 importFrom(methods,is)

R/RcppExports.R

@@ -14,3 +14,19 @@ ts_xptr_num_individuals2 <- function(ts) {
     .Call(`_RcppTskitTestLinking_ts_xptr_num_individuals2`, ts)
 }
 
+#' @title Summarise `tskit` table collection
+#' @param tc an external pointer to a \code{tsk_table_collection_t} object.
+#' @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)
+#' tc_xptr_summary2(tc) # a bit simpler at this stage ...
+#' tc <- RcppTskit::TableCollection$new(ts_file)
+#' RcppTskit:::tc_xptr_summary(tc$pointer)
+#' tc_xptr_summary2(tc$pointer) # a bit simpler at this stage ...
+#' @export
+tc_xptr_summary2 <- function(tc) {
+    .Call(`_RcppTskitTestLinking_tc_xptr_summary2`, tc)
+}
+

man/tc_xptr_summary2.Rd

@@ -21,9 +21,21 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// tc_xptr_summary2
+Rcpp::List tc_xptr_summary2(const SEXP tc);
+RcppExport SEXP _RcppTskitTestLinking_tc_xptr_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));
+    return rcpp_result_gen;
+END_RCPP
+}
 
 static const R_CallMethodDef CallEntries[] = {
     {"_RcppTskitTestLinking_ts_xptr_num_individuals2", (DL_FUNC) &_RcppTskitTestLinking_ts_xptr_num_individuals2, 1},
+    {"_RcppTskitTestLinking_tc_xptr_summary2", (DL_FUNC) &_RcppTskitTestLinking_tc_xptr_summary2, 1},
     {NULL, NULL, 0}
 };
 

src/RcppExports.cpp

@@ -16,3 +16,35 @@ int ts_xptr_num_individuals2(const SEXP ts) {
   RcppTskit_treeseq_xptr ts_xptr(ts);
   return static_cast<int>(tsk_treeseq_get_num_individuals(ts_xptr));
 }
+
+//' @title Summarise `tskit` table collection
+//' @param tc an external pointer to a \code{tsk_table_collection_t} object.
+//' @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)
+//' tc_xptr_summary2(tc) # a bit simpler at this stage ...
+//' tc <- RcppTskit::TableCollection$new(ts_file)
+//' RcppTskit:::tc_xptr_summary(tc$pointer)
+//' tc_xptr_summary2(tc$pointer) # a bit simpler at this stage ...
+//' @export
+// [[Rcpp::export]]
+Rcpp::List tc_xptr_summary2(const SEXP tc) {
+  RcppTskit_table_collection_xptr tc_xptr(tc);
+  const tsk_table_collection_t *tables = tc_xptr;
+  return Rcpp::List::create(
+      Rcpp::_["num_provenances"] = tables->provenances.num_rows,
+      Rcpp::_["num_populations"] = tables->populations.num_rows,
+      Rcpp::_["num_migrations"] = tables->migrations.num_rows,
+      Rcpp::_["num_individuals"] = tables->individuals.num_rows,
+      Rcpp::_["num_nodes"] = tables->nodes.num_rows,
+      Rcpp::_["num_edges"] = tables->edges.num_rows,
+      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));
+}