Merge pull request #122 from gregorgorjanc/gregorgorjanc/issue120

Added rtsk_individual_table_add_row() and tc.individual_table_add_row()

Author: bryo-han

RcppTskit/NEWS.md

@@ -28,6 +28,9 @@ and releases adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html
 - Added `TableCollection$build_index()` to build indexes and
   `TableCollection$drop_index()` to drop indexes.
 - Added ``TableCollection$num_*()` getters for the number of rows in the tables.
+- Added `rtsk_individual_table_add_row()` and
+  `TableCollection$individual_table_add_row()` to append individual rows from
+  \code{R}, mirroring `tsk_individual_table_add_row()`.
 - TODO
 
 ### Changed

RcppTskit/R/Class-TableCollection.R

@@ -143,6 +143,55 @@ TableCollection <- R6Class(
       rtsk_table_collection_get_num_individuals(self$xptr)
     },
 
+    #' @description Add a row to the individuals table.
+    #' @param flags integer flags for the new individual.
+    #' @param location numeric vector with the location of the new individual.
+    #' @param parents integer vector with parent individual IDs (0-based).
+    #' @param metadata for the new individual; accepts \code{NULL},
+    #'   a raw vector, or a character of length 1.
+    #' @details See the \code{tskit Python} equivalent at
+    #'   \url{https://tskit.dev/tskit/docs/stable/python-api.html#tskit.IndividualTable.add_row}.
+    #'   The function casts inputs to the expected class.
+    #' @return Integer row ID (0-based) of the newly added individual.
+    #' @examples
+    #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
+    #' tc <- tc_load(ts_file)
+    #' n_before <- tc$num_individuals()
+    #' new_id <- tc$individual_table_add_row()
+    #' new_id <- tc$individual_table_add_row(location = c(5, 8))
+    #' new_id <- tc$individual_table_add_row(flags = 0L)
+    #' new_id <- tc$individual_table_add_row(parents = c(0L, 2L))
+    #' new_id <- tc$individual_table_add_row(metadata = "abc")
+    #' new_id <- tc$individual_table_add_row(metadata = charToRaw("cba"))
+    #' n_after <- tc$num_individuals()
+    individual_table_add_row = function(
+      flags = 0L,
+      location = NULL,
+      parents = NULL,
+      metadata = NULL
+    ) {
+      if (is.null(metadata)) {
+        metadata_raw <- NULL
+      } else if (is.raw(metadata)) {
+        metadata_raw <- metadata
+      } else if (
+        is.character(metadata) && length(metadata) == 1L && !is.na(metadata)
+      ) {
+        metadata_raw <- charToRaw(metadata)
+      } else {
+        stop(
+          "metadata must be NULL, a raw vector, or a length-1 non-NA character string!"
+        )
+      }
+      rtsk_individual_table_add_row(
+        tc = self$xptr,
+        flags = as.integer(flags),
+        location = if (is.null(location)) NULL else as.numeric(location),
+        parents = if (is.null(parents)) NULL else as.integer(parents),
+        metadata = metadata_raw
+      )
+    },
+
     #' @description Get the number of nodes in a table collection.
     #' @return A signed 64 bit integer \code{bit64::integer64}.
     #' @examples

RcppTskit/R/RcppExports.R

@@ -203,6 +203,10 @@ rtsk_table_collection_metadata_length <- function(tc) {
     .Call(`_RcppTskit_rtsk_table_collection_metadata_length`, tc)
 }
 
+rtsk_individual_table_add_row <- function(tc, flags = 0L, location = NULL, parents = NULL, metadata = NULL) {
+    .Call(`_RcppTskit_rtsk_individual_table_add_row`, tc, flags, location, parents, metadata)
+}
+
 test_tsk_bug_assert_c <- function() {
     invisible(.Call(`_RcppTskit_test_tsk_bug_assert_c`))
 }
@@ -235,3 +239,7 @@ test_rtsk_table_collection_build_index_forced_error <- function(tc) {
     invisible(.Call(`_RcppTskit_test_rtsk_table_collection_build_index_forced_error`, tc))
 }
 
+test_rtsk_individual_table_add_row_forced_error <- function(tc) {
+    invisible(.Call(`_RcppTskit_test_rtsk_individual_table_add_row_forced_error`, tc))
+}
+

RcppTskit/inst/include/RcppTskit_public.hpp

@@ -57,5 +57,10 @@ void rtsk_table_collection_build_index(SEXP tc, int options = 0);
 void rtsk_table_collection_drop_index(SEXP tc, int options = 0);
 Rcpp::List rtsk_table_collection_summary(SEXP tc);
 Rcpp::List rtsk_table_collection_metadata_length(SEXP tc);
+int rtsk_individual_table_add_row(
+    SEXP tc, int flags = 0,
+    Rcpp::Nullable<Rcpp::NumericVector> location = R_NilValue,
+    Rcpp::Nullable<Rcpp::IntegerVector> parents = R_NilValue,
+    Rcpp::Nullable<Rcpp::RawVector> metadata = R_NilValue);
 
 #endif

RcppTskit/man/TableCollection.Rd

@@ -534,6 +534,21 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// rtsk_individual_table_add_row
+int rtsk_individual_table_add_row(const SEXP tc, const int flags, const Rcpp::Nullable<Rcpp::NumericVector> location, const Rcpp::Nullable<Rcpp::IntegerVector> parents, const Rcpp::Nullable<Rcpp::RawVector> metadata);
+RcppExport SEXP _RcppTskit_rtsk_individual_table_add_row(SEXP tcSEXP, SEXP flagsSEXP, SEXP locationSEXP, SEXP parentsSEXP, SEXP metadataSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const SEXP >::type tc(tcSEXP);
+    Rcpp::traits::input_parameter< const int >::type flags(flagsSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::Nullable<Rcpp::NumericVector> >::type location(locationSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::Nullable<Rcpp::IntegerVector> >::type parents(parentsSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::Nullable<Rcpp::RawVector> >::type metadata(metadataSEXP);
+    rcpp_result_gen = Rcpp::wrap(rtsk_individual_table_add_row(tc, flags, location, parents, metadata));
+    return rcpp_result_gen;
+END_RCPP
+}
 // test_tsk_bug_assert_c
 void test_tsk_bug_assert_c();
 RcppExport SEXP _RcppTskit_test_tsk_bug_assert_c() {
@@ -612,6 +627,16 @@ BEGIN_RCPP
     return R_NilValue;
 END_RCPP
 }
+// test_rtsk_individual_table_add_row_forced_error
+void test_rtsk_individual_table_add_row_forced_error(const SEXP tc);
+RcppExport SEXP _RcppTskit_test_rtsk_individual_table_add_row_forced_error(SEXP tcSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const SEXP >::type tc(tcSEXP);
+    test_rtsk_individual_table_add_row_forced_error(tc);
+    return R_NilValue;
+END_RCPP
+}
 
 static const R_CallMethodDef CallEntries[] = {
     {"_RcppTskit_test_validate_options", (DL_FUNC) &_RcppTskit_test_validate_options, 2},
@@ -661,6 +686,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_RcppTskit_rtsk_table_collection_drop_index", (DL_FUNC) &_RcppTskit_rtsk_table_collection_drop_index, 2},
     {"_RcppTskit_rtsk_table_collection_summary", (DL_FUNC) &_RcppTskit_rtsk_table_collection_summary, 1},
     {"_RcppTskit_rtsk_table_collection_metadata_length", (DL_FUNC) &_RcppTskit_rtsk_table_collection_metadata_length, 1},
+    {"_RcppTskit_rtsk_individual_table_add_row", (DL_FUNC) &_RcppTskit_rtsk_individual_table_add_row, 5},
     {"_RcppTskit_test_tsk_bug_assert_c", (DL_FUNC) &_RcppTskit_test_tsk_bug_assert_c, 0},
     {"_RcppTskit_test_tsk_bug_assert_cpp", (DL_FUNC) &_RcppTskit_test_tsk_bug_assert_cpp, 0},
     {"_RcppTskit_test_tsk_trace_error_c", (DL_FUNC) &_RcppTskit_test_tsk_trace_error_c, 0},
@@ -669,6 +695,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_RcppTskit_test_rtsk_treeseq_copy_tables_forced_error", (DL_FUNC) &_RcppTskit_test_rtsk_treeseq_copy_tables_forced_error, 1},
     {"_RcppTskit_test_rtsk_treeseq_init_forced_error", (DL_FUNC) &_RcppTskit_test_rtsk_treeseq_init_forced_error, 1},
     {"_RcppTskit_test_rtsk_table_collection_build_index_forced_error", (DL_FUNC) &_RcppTskit_test_rtsk_table_collection_build_index_forced_error, 1},
+    {"_RcppTskit_test_rtsk_individual_table_add_row_forced_error", (DL_FUNC) &_RcppTskit_test_rtsk_individual_table_add_row_forced_error, 1},
     {NULL, NULL, 0}
 };