R/deprecated.R

In xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

#' @title Deprecated functions in \pkg{rphenoscape}.
#' @description The functions listed below are deprecated and will become defunct in
#'   the near future. When possible, alternative functions with identical or similar
#'   functionality are mentioned. Where the signature of the alternative (new) 
#'   function differs significantly from that of the deprecated one, help pages for
#'   the deprecated functions are available at \code{help("<function>-deprecated")}.
#' @name rphenoscape-deprecated
#' @keywords internal
NULL

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_iri}:
#' For `pk_get_iri()` use [get_term_iri()] instead.
#' @keywords internal
#' @export
pk_get_iri <- function(...) {
  .Deprecated("get_term_iri")
  get_term_iri(...)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_study_list}:
#' For `pk_get_study_list()` use [get_studies()] instead. Note that `get_studies()`
#' returns an empty result set if nothing was found, in contrast to `pk_get_study_list`,
#' which returns FALSE in that case (and prints a message).
#' @keywords internal
#' @export
pk_get_study_list <- function(...) {
  .Deprecated("get_studies")
  res <- get_studies(...)
  if (length(res) == 0) {
    mssg(T, "No study found in database.")
    invisible(FALSE)
  } else
    res
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_taxon_class}:
#' For `pk_taxon_class()` use [term_classification()] with as="taxon" instead.
#' Note that `pk_taxon_class()` defaults verbose to TRUE instead of FALSE as
#' `term_classification()` does. Also `pk_taxon_class()` return value has the legacy `@id` name.
#' @keywords internal
#' @export
pk_taxon_class <- function(x, verbose=TRUE) {
  .Deprecated("term_classification")
  term_classification_raw(x, as = "taxon", verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_anatomical_class}:
#' For `pk_anatomical_class()` use [term_classification()] with as="anatomy" instead.
#' Note that `pk_anatomical_class()` defaults verbose to TRUE instead of FALSE as
#' `term_classification()` does. Also `pk_anatomical_class()` return value has the legacy `@id` name.
#' @keywords internal
#' @export
pk_anatomical_class <- function(x, verbose=TRUE) {
  .Deprecated("term_classification")
  term_classification_raw(x, as = "anatomy", verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_phenotype_class}:
#' For `pk_phenotype_class()` use [term_classification()] with as="pato" instead.
#' Note that `pk_phenotype_class()` defaults verbose to TRUE instead of FALSE as
#' `term_classification()` does. Also `pk_phenotype_class()` return value has the legacy `@id` name.
#' @keywords internal
#' @export
pk_phenotype_class <- function(x, verbose=TRUE) {
  .Deprecated("term_classification")
  term_classification_raw(x, as = "pato", verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_ontotrace_xml}:
#' For `pk_get_ontotrace_xml()` use [get_ontotrace_data()] instead.
#' @keywords internal
#' @export
pk_get_ontotrace_xml <- function(taxon, entity,
                                 relation = 'part of',
                                 variable_only = TRUE,
                                 strict = TRUE) {
  .Deprecated("get_ontotrace_data")
  get_ontotrace_data(taxon, entity, relation, variable_only, strict)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_study_xml}:
#' For `pk_get_study_xml()` use [get_study_data()] instead.
#' Note that `pk_get_study_xml()` maintains legacy functionality of displaying messages. `get_study_data()`
#' has a verbose argument to control displaying messages.
#' @keywords internal
#' @export
pk_get_study_xml <- function(study_ids) {
  .Deprecated("get_study_data")
  get_study_data(study_ids, verbose = TRUE)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_is_descendant}:
#' For `pk_is_descendant()` use [is_descendant()] instead.
#' @keywords internal
#' @export
pk_is_descendant <- function(term, candidates, includeRels = c("none", "part_of")) {
  .Deprecated("is_descendant")
  is_descendant(term, candidates, includeRels)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_is_ancestor}:
#' For `pk_is_ancestor()` use [is_ancestor()] instead.
#' @keywords internal
#' @export
pk_is_ancestor <- function(term, candidates, includeRels = c("none", "part_of")) {
  .Deprecated("is_ancestor")
  is_ancestor(term, candidates, includeRels)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_taxon_detail}:
#' For `pk_taxon_detail()` use [taxon_info()] instead.
#' @keywords internal
#' @export
pk_taxon_detail <- function(term, verbose=FALSE) {
  .Deprecated("taxon_info")
  taxon_info(term, verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_anatomical_detail}:
#' For `pk_anatomical_detail()` use [anatomy_term_info()] instead.
#' @keywords internal
#' @export
pk_anatomical_detail <- function(term, verbose=FALSE) {
  .Deprecated("anatomy_term_info")
  anatomy_term_info(term, verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_phenotype_detail}:
#' For `pk_phenotype_detail()` use [phenotypic_quality_term_info()] instead.
#' @keywords internal
#' @export
pk_phenotype_detail <- function(term, verbose=FALSE) {
  .Deprecated("phenotypic_quality_term_info")
  phenotypic_quality_term_info(term, verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_gene_detail}:
#' For `pk_gene_detail()` use [gene_info()] instead.
#' @keywords internal
#' @export
pk_gene_detail <- function(term, taxon = NA, verbose=FALSE) {
  .Deprecated("gene_info")
  gene_info(term, taxon, verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_is_extinct}:
#' For `pk_is_extinct()` use [is_extinct()] instead.
#' @keywords internal
#' @export
pk_is_extinct <- function(taxon, verbose = FALSE) {
  .Deprecated("is_extinct")
  is_extinct(taxon, verbose)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_ontotrace}:
#' For `pk_get_ontotrace()` use [get_char_matrix()] instead.
#' @keywords internal
#' @export
pk_get_ontotrace <- function(nex) {
  .Deprecated("get_char_matrix")
  get_char_matrix(nex)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_ontotrace_meta}:
#' For `pk_get_ontotrace_meta()` use [get_char_matrix_meta()] instead.
#' @keywords internal
#' @export
pk_get_ontotrace_meta <- function(nex) {
  .Deprecated("get_char_matrix_meta")
  get_char_matrix_meta(nex)
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_study}:
#' For `pk_get_study()` use [get_char_matrix()] with lapply instead.
#' Note that `pk_get_study()` always displays messages instead of using the
#'  verbose parameter as `get_char_matrix()` does.
#' @keywords internal
#' @export
pk_get_study <- function(nexmls) {
  .Deprecated("get_char_matrix")
  lapply(nexmls, function(nex) get_char_matrix(nex, otus_id = FALSE, states_as_labels = TRUE, verbose = TRUE))
}

#' @rdname rphenoscape-deprecated
#' @section \code{pk_get_study_meta}:
#' For `pk_get_study_meta()` use [get_char_matrix_meta()] with lapply instead.
#' @keywords internal
#' @export
pk_get_study_meta <- function(nexmls) {
  .Deprecated("get_char_matrix_meta")
  lapply(nexmls, function(nex) get_char_matrix_meta(nex))
}