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gregorgorjanc merged 2 commits into from
Apr 6, 2026
Merged

Polishing docs #134

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b4608da
Polish docs from PR #126
gregorgorjanc Apr 6, 2026
10517e4
Ignoring jarl warnings for internal functions in docs
gregorgorjanc Apr 6, 2026
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17 changes: 8 additions & 9 deletions RcppTskit/R/Class-TableCollection.R
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Original file line number Diff line number Diff line change
Expand Up @@ -205,10 +205,10 @@ TableCollection <- R6Class(
#' @description Add a row to the nodes table.
#' @param flags integer flags for the new node.
#' @param time numeric time value for the new node.
#' @param population integer population row ID (0-based, or \code{-1});
#' \code{NULL} maps to \code{-1}.
#' @param individual integer individual row ID (0-based, or \code{-1});
#' \code{NULL} maps to \code{-1}.
#' @param population integer population row ID (0-based);
#' use \code{-1} if not known - \code{NULL} maps to \code{-1}.
#' @param individual integer individual row ID (0-based);
#' use \code{-1} if not known - \code{NULL} maps to \code{-1}.
#' @param metadata for the new node; accepts \code{NULL},
#' a raw vector, or a character of length 1.
#' @details See the \code{tskit Python} equivalent at
Expand Down Expand Up @@ -285,17 +285,16 @@ TableCollection <- R6Class(
#' @examples
#' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
#' tc <- tc_load(ts_file)
#' parent <- 0L
#' child <- 1L
#' child <- tc$node_table_add_row(time = 0.0)
#' n_before <- tc$num_edges()
#' new_id <- tc$edge_table_add_row(
#' left = 0, right = 1, parent = parent, child = child
#' left = 0, right = 50, parent = 16L, child = child
#' )
#' new_id <- tc$edge_table_add_row(
#' left = 1, right = 2, parent = parent, child = child, metadata = "abc"
#' left = 50, right = 75, parent = 17L, child = child, metadata = "abc"
#' )
#' new_id <- tc$edge_table_add_row(
#' left = 2, right = 3, parent = parent, child = child, metadata = charToRaw("cba")
#' left = 75, right = 100, parent = 18L, child = child, metadata = charToRaw("cba")
#' )
#' n_after <- tc$num_edges()
edge_table_add_row = function(
Expand Down
26 changes: 12 additions & 14 deletions RcppTskit/man/TableCollection.Rd
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57 changes: 36 additions & 21 deletions RcppTskit/src/RcppTskit.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1246,18 +1246,20 @@ Rcpp::List rtsk_table_collection_metadata_length(const SEXP tc) {
// @param flags passed to \code{tskit C}.
// @param location numeric vector with the location of the new individual
// (can be \code{NULL}).
// @param parents integer vector with parent individual IDs
// @param parents integer vector with parent individual IDs (0-based)
// (can be \code{NULL}).
// @param metadata raw vector with metadata bytes
// (can be \code{NULL}).
// @details This function calls
// \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_individual_table_add_row}
// on the individuals table of \code{tc}.
// @return The 0-based row ID of the newly added individual.
// @return The row ID (0-based) of the newly added individual.
// @examples
// ts_file <- system.file("examples/test.trees", package = "RcppTskit")
// tc_xptr <- RcppTskit:::rtsk_table_collection_load(ts_file)
// n_before <- RcppTskit:::rtsk_table_collection_get_num_individuals(tc_xptr)
// m_before
// <- RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$individuals
// tc_py <- RcppTskit:::rtsk_table_collection_r_to_py(tc_xptr)
// tc_py$individuals$max_rows
// tc_py$individuals["flags"]
Expand All @@ -1279,8 +1281,13 @@ Rcpp::List rtsk_table_collection_metadata_length(const SEXP tc) {
// new_id <- RcppTskit:::rtsk_individual_table_add_row(tc = tc_xptr, flags = 3L,
// location = c(2, 11), parents = c(1L, 3L), metadata = charToRaw("abc"))
// n_after <- RcppTskit:::rtsk_table_collection_get_num_individuals(tc_xptr)
// new_id == as.integer(n_before) && n_after == n_before + 3L
// tc_py <- RcppTskit:::rtsk_table_collection_r_to_py(tc_xptr)
// m_after <-
// RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$individuals
// new_id == n_after - 1L
// n_after == n_before + 3L
// m_after == m_before + 3L
// tc_py <-
// RcppTskit:::rtsk_table_collection_r_to_py(tc_xptr)
// tc_py$individuals$max_rows
// tc_py$individuals["flags"]
// tc_py$individuals["location"]
Expand Down Expand Up @@ -1340,18 +1347,21 @@ int rtsk_individual_table_add_row(
// \code{tsk_table_collection_t} object.
// @param flags passed to \code{tskit C}.
// @param time numeric time value for the new node.
// @param population integer population row ID (0-based, or \code{-1}).
// @param individual integer individual row ID (0-based, or \code{-1}).
// @param population integer population row ID (0-based);
// use \code{-1} if not known.
// @param individual integer individual row ID (0-based);
// use \code{-1} if not known.
// @param metadata raw vector with metadata bytes
// (can be \code{NULL}).
// @details This function calls
// \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_node_table_add_row}
// on the nodes table of \code{tc}.
// @return The 0-based row ID of the newly added node.
// @return The row ID (0-based) of the newly added node.
// @examples
// ts_file <- system.file("examples/test.trees", package = "RcppTskit")
// tc_xptr <- RcppTskit:::rtsk_table_collection_load(ts_file)
// n_before <- RcppTskit:::rtsk_table_collection_get_num_nodes(tc_xptr)
// m_before <- RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$nodes
// tc_py <- RcppTskit:::rtsk_table_collection_r_to_py(tc_xptr)
// tc_py$nodes$max_rows
// tc_py$nodes["flags"]
Expand All @@ -1370,7 +1380,10 @@ int rtsk_individual_table_add_row(
// metadata = charToRaw("abc")
// )
// n_after <- RcppTskit:::rtsk_table_collection_get_num_nodes(tc_xptr)
// new_id == as.integer(n_before) && n_after == n_before + 3L
// m_after <- RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$nodes
// new_id == n_after - 1L
// n_after == n_before + 4L
// m_after == m_before + 3L
// tc_py <- RcppTskit:::rtsk_table_collection_r_to_py(tc_xptr)
// tc_py$nodes$max_rows
// tc_py$nodes["flags"]
Expand Down Expand Up @@ -1428,27 +1441,29 @@ int rtsk_node_table_add_row(
// @details This function calls
// \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_edge_table_add_row}
// on the edges table of \code{tc}.
// @return The 0-based row ID of the newly added edge.
// @return The row ID (0-based) of the newly added edge.
// @examples
// ts_file <- system.file("examples/test.trees", package = "RcppTskit")
// tc_xptr <- RcppTskit:::rtsk_table_collection_load(ts_file)
// parent <- 0L
// child <- 1L
// child <- rtsk_node_table_add_row(tc_xptr, time = 0.0)
// n_before <- RcppTskit:::rtsk_table_collection_get_num_edges(tc_xptr)
// m_before <-
// RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)[["edges"]] new_id
// <- RcppTskit:::rtsk_edge_table_add_row(
// tc = tc_xptr, left = 0, right = 1, parent = parent, child = child
// m_before <- RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$edges
// new_id <- RcppTskit:::rtsk_edge_table_add_row(
// tc = tc_xptr, left = 0, right = 50, parent = 16L, child = child
// )
// new_id <- RcppTskit:::rtsk_edge_table_add_row(
// tc = tc_xptr, left = 1, right = 2, parent = parent, child = child,
// metadata = charToRaw("abc")
// tc = tc_xptr, left = 50, right = 75, parent = 17L, child = child,
// metadata = "abc"
// )
// new_id <- RcppTskit:::rtsk_edge_table_add_row(
// tc = tc_xptr, left = 75, right = 100, parent = 18L, child = child,
// metadata = charToRaw("cba")
// )
// n_after <- RcppTskit:::rtsk_table_collection_get_num_edges(tc_xptr)
// m_after <-
// RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)[["edges"]] new_id
// == as.integer(n_before) && n_after == n_before + 2L && m_after == m_before +
// 3L
// m_after <- RcppTskit:::rtsk_table_collection_metadata_length(tc_xptr)$edges
// new_id == n_after - 1L
// n_after == n_before + 3L
// m_after == m_before + 3L
// [[Rcpp::export]]
int rtsk_edge_table_add_row(
const SEXP tc, const double left, const double right, const int parent,
Expand Down
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