new function

NAMESPACE

@@ -13,5 +13,6 @@ export(read_loci)
 export(read_parameters)
 export(read_population)
 export(read_speciome)
+export(read_traits)
 export(rm_plural_colnames)
 importFrom(magrittr,"%>%")

R/read_traits.R

@@ -0,0 +1,45 @@
+#' Read trait-wise data
+#'
+#' Wrapper around \code{read_speciome} for variables with one value per
+#' trait per time point.
+#'
+#' @param root Path to the simulation folder
+#' @param variables Vector of names of variable to read (will be interpreted using \code{interpret_variable_names})
+#'
+#' @return A tibble containing the simulation data
+#'
+#' @note The function will read "time.dat" as an extra variable, no need to
+#' supply it.
+#'
+#' @seealso \code{read_speciome}
+#'
+#' @examples
+#'
+#' root <- system.file("extdata", "sim-example", package = "speciomer")
+#' read_traits(root, "trait_Fst")
+#'
+#' @export
+
+read_traits <- function(root, variables) {
+
+  # Add a trait prefix to the variable names if needed
+  variables <- interpret_variable_names(variables, type = "trait")
+
+  # Parametrization
+  ncols <- rep(1, length(variables))
+  variables <- c("time", variables)
+  ncols <- c(-3, ncols)
+
+  # Read trait-wise data
+  data <- read_speciome(root, variables, ncols = ncols)
+
+  # Remove the prefix "trait", now redundant
+  colnames(data) <- stringr::str_remove(colnames(data), "trait_")
+
+  # Add a trait identifier
+  data <- data %>%
+    tibble::add_column(trait = rep(seq(3), nrow(data) / 3), .after = "time")
+
+  return(data)
+
+}

tests/testthat/test_read_traits.R

@@ -0,0 +1,9 @@
+root <- system.file("extdata", "sim-example", package = "speciomer")
+
+test_that("Read trait-wise data", {
+
+  data <- read_traits(root, "Cst")
+  ntimes <- length(read_binary(paste0(root, "/time.dat")))
+  expect_equal(nrow(data), 3 * ntimes)
+
+})