Remove as.segsites function

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: coala
-Version: 0.5.4
+Version: 0.6.0
 License: MIT + file LICENSE
 Title: A Framework for Coalescent Simulation
 Authors@R: c(

NAMESPACE

@@ -3,8 +3,6 @@
 S3method("+",coalmodelpart)
 S3method("[",segsites)
 S3method(as.matrix,segsites)
-S3method(as.segsites,default)
-S3method(as.segsites,list)
 S3method(conv_to_ms_arg,default)
 S3method(conv_to_ms_arg,files_feat)
 S3method(conv_to_ms_arg,growth)
@@ -74,7 +72,6 @@ export(activate_ms)
 export(activate_msms)
 export(activate_scrm)
 export(activate_seqgen)
-export(as.segsites)
 export(calc_sumstats_from_data)
 export(check_model)
 export(coal_model)

NEWS.md

@@ -1,8 +1,9 @@
-coala 0.5.4
+coala 0.6.0
 ===========
 
 * Removes the option to import data import via PopGenome, as PopGenome is not on 
-  CRAN anymore.
+  CRAN anymore. Also removes the `as.segsites` function, as it does not do anything
+  anymore without the PopGenome import option (#205).
 
 
 

R/model.R

@@ -5,6 +5,7 @@
 #' can be simulated using the \code{\link[=simulate.coalmodel]{simulate}} function.
 #'
 #' @inheritParams feat_sample
+#' @aliases coalmodelpart
 #' @param sample_size Defines the number of populations and the number of
 #'   individual sampled from each population. Given as an integer vector where
 #'   each entry gives the number of individuals sampled from the corresponding

R/segsites.R

@@ -26,7 +26,6 @@
 #'
 #' @name segsites
 #' @author Paul Staab
-#' @seealso For converting biological data to segsites: \code{\link{as.segsites}}
 #' @examples
 #' snps <- matrix(c(1, 0, 0,
 #'                  1, 1, 0,
@@ -117,34 +116,3 @@ create_locus_trio <- function(left, middle, right) {
                     check = FALSE)
   })
 }
-
-
-#' Convert genetic data to coala's internal format
-#'
-#' This function can be used to convert the genomic data formats used in other
-#' packages to calculate coala's segregating sites object. This is useful for
-#' calculating the summary statistics of biological data using the
-#' \code{\link{calc_sumstats_from_data}} function.
-#'
-#' Currently, only the package \pkg{PopGenome} is supported, see
-#' \code{\link{as.segsites.GENOME}} for details.
-#'
-#' @param data The data object that is converted.
-#' @param ... Additional arguments specific for the used package.
-#'
-#' @return A list of segregating sites objects.
-#' @seealso Further instructions are provided in the `coala-data-import` vignette
-#' @seealso For information about segsites: \code{\link{segsites}}
-#' @export
-as.segsites <- function(data, ...) UseMethod("as.segsites")
-
-#' @export
-as.segsites.default <- function(data, ...) { #nolint
-  stop("Unknown data format")
-}
-
-#' @export
-as.segsites.list <- function(data, ...) { #nolint
-  assert_that(all(vapply(data, is_segsites, logical(1))))
-  data
-}

R/sumstat.R

@@ -143,10 +143,7 @@ calc_sumstats_from_sim <- function(seg_sites, trees, files, model,
 #' @param model The coala model. The summary statistics present in this model
 #'   will be calculated. The model should fit to the data, in particular
 #'   regarding the number of loci and haploids.
-#' @param segsites_list Either a list of \code{segsites} objects, or an object
-#'   that can be converted using \code{\link{as.segsites}}. It is possible
-#'   to specify additional argument for the conversion using the \code{...}
-#'   argument.
+#' @param segsites_list A list of \code{segsites} objects
 #' @param tree_list Not yet implemented.
 #' @param trios If your model is using locus trios, then you
 #'   can create these by combining individual loci. This is a list that defines
@@ -155,8 +152,7 @@ calc_sumstats_from_sim <- function(seg_sites, trees, files, model,
 #'   summary statistics is locus in the provided data that corresponds to the
 #'   number. If three numbers are provided, the locus for calculation is created
 #'   by combining the corresponding three loci from the given data.
-#' @param ... Additional arguments that will be passed to
-#'   \code{\link{as.segsites}}.
+#' @param ... Ignored
 #' @export
 #' @examples
 #' segsites <- create_segsites(matrix(c(1, 0, 0,
@@ -195,7 +191,6 @@ calc_sumstats_from_data <- function(model,
   }
 
   if (!is.null(segsites_list)) {
-    segsites_list <- as.segsites(segsites_list, ...)
     if (!all(vapply(segsites_list, is_segsites, logical(1)))) {
       stop("Incorrect or missing data in list of segregating sites")
     }