Using new RcppTskit names

Author: gregorgorjanc

NAMESPACE

@@ -1,7 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(tc_xptr_summary2)
-export(ts_xptr_num_individuals2)
+export(rtsk_table_collection_summary2)
+export(rtsk_treeseq_get_num_individuals2)
 import(RcppTskit)
 importFrom(methods,is)
 useDynLib(RcppTskitTestLinking, .registration = TRUE)

R/RcppExports.R

@@ -8,25 +8,26 @@
 #' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
 #' ts <- RcppTskit::ts_load(ts_file)
 #' ts$num_individuals()
-#' ts_xptr_num_individuals2(ts$pointer)
+#' RcppTskit:::rtsk_treeseq_get_num_individuals(ts$xptr)
+#' rtsk_treeseq_get_num_individuals2(ts$xptr)
 #' @export
-ts_xptr_num_individuals2 <- function(ts) {
-    .Call(`_RcppTskitTestLinking_ts_xptr_num_individuals2`, ts)
+rtsk_treeseq_get_num_individuals2 <- function(ts) {
+    .Call(`_RcppTskitTestLinking_rtsk_treeseq_get_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:::tc_load(ts_file)
+#' RcppTskit:::rtsk_table_collection_summary(tc)
+#' rtsk_table_collection_summary(tc)
 #' tc <- RcppTskit::TableCollection$new(ts_file)
-#' RcppTskit:::tc_xptr_summary(tc$pointer)
-#' tc_xptr_summary2(tc$pointer) # a bit simpler at this stage ...
+#' RcppTskit:::rtsk_table_collection_summary(tc$xptr)
+#' rtsk_table_collection_summary2(tc$xptr)
 #' @export
-tc_xptr_summary2 <- function(tc) {
-    .Call(`_RcppTskitTestLinking_tc_xptr_summary2`, tc)
+rtsk_table_collection_summary2 <- function(tc) {
+    .Call(`_RcppTskitTestLinking_rtsk_table_collection_summary2`, tc)
 }
 

README.md

@@ -85,12 +85,16 @@ $tables
 # This demo package implemented the same function
 # that is available in RcppTskit, but since we here
 # focus just on C++ code, we have to work with the
-# pointer object (externalptr) `ts$pointer` and
+# pointer object (externalptr) `ts$xptr` and
 # not with the tree sequence object (TreeSequence) `ts`
-> ts_xptr_num_individuals2(ts$pointer)
+> RcppTskit:::rtsk_treeseq_get_num_individuals(ts$xptr)
+[1] 8
+> rtsk_treeseq_get_num_individuals2(ts$xptr)
 [1] 8
 ```
 
+See also
+
 ## Wrap up
 
 Hopefully this demo package shows you sufficiently well on how

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

@@ -10,32 +10,32 @@ Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
 Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
-// ts_xptr_num_individuals2
-int ts_xptr_num_individuals2(const SEXP ts);
-RcppExport SEXP _RcppTskitTestLinking_ts_xptr_num_individuals2(SEXP tsSEXP) {
+// rtsk_treeseq_get_num_individuals2
+int rtsk_treeseq_get_num_individuals2(const SEXP ts);
+RcppExport SEXP _RcppTskitTestLinking_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(ts_xptr_num_individuals2(ts));
+    rcpp_result_gen = Rcpp::wrap(rtsk_treeseq_get_num_individuals2(ts));
     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) {
+// rtsk_table_collection_summary2
+Rcpp::List rtsk_table_collection_summary2(const SEXP tc);
+RcppExport SEXP _RcppTskitTestLinking_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
 }
 
 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},
+    {"_RcppTskitTestLinking_rtsk_treeseq_get_num_individuals2", (DL_FUNC) &_RcppTskitTestLinking_rtsk_treeseq_get_num_individuals2, 1},
+    {"_RcppTskitTestLinking_rtsk_table_collection_summary2", (DL_FUNC) &_RcppTskitTestLinking_rtsk_table_collection_summary2, 1},
     {NULL, NULL, 0}
 };
 

man/ts_xptr_num_individuals2.Rd man/rtsk_treeseq_get_num_individuals2.Rdman/ts_xptr_num_individuals2.Rd renamed to man/rtsk_treeseq_get_num_individuals2.Rd

@@ -9,11 +9,12 @@
 //' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
 //' ts <- RcppTskit::ts_load(ts_file)
 //' ts$num_individuals()
-//' ts_xptr_num_individuals2(ts$pointer)
+//' RcppTskit:::rtsk_treeseq_get_num_individuals(ts$xptr)
+//' rtsk_treeseq_get_num_individuals2(ts$xptr)
 //' @export
 // [[Rcpp::export]]
-int ts_xptr_num_individuals2(const SEXP ts) {
-  RcppTskit_treeseq_xptr ts_xptr(ts);
+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));
 }
 
@@ -22,16 +23,13 @@ int ts_xptr_num_individuals2(const SEXP ts) {
 //' @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$pointer) # a bit simpler at this stage ...
+//' tc <- RcppTskit:::tc_load(ts_file)
+//' RcppTskit:::rtsk_table_collection_summary(tc$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,
@@ -43,8 +41,9 @@ 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));
 }