version 0.1.0

DESCRIPTION

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+Package: dynutils
+Type: Package
+Title: Common Functions for the Dynverse Packages
+Version: 0.1.0
+Authors@R: c(
+    person(
+      "Robrecht", 
+      "Cannoodt", 
+      email = "rcannood@gmail.com", 
+      role = c("aut", "cre"),
+      comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")
+    ),
+    person(
+      "Wouter", 
+      "Saelens", 
+      email = "wouter.saelens@ugent.be", 
+      role = c("aut"), 
+      comment = c(ORCID = "0000-0002-7114-6248", github = "zouter")
+    )
+  )
+Description: 
+  Provides a common functionality for the dynverse packages. 
+  Dynverse is created to support the development, execution, and benchmarking of trajectory inference methods.
+  For more information, see <https://github.com/dynverse/dynverse>.
+License: GPL-3
+LazyData: TRUE
+RoxygenNote: 6.0.1
+Depends: R (>= 3.0.0)
+Imports: crayon, devtools, desc, dplyr, glue, magrittr, methods,
+        processx, purrr, Rcpp, stringr, testthat, tibble, tidyr
+LinkingTo: Rcpp
+Collate: 'RcppExports.R' 'add_class.R' 'inherit_default_params.R'
+        'calculate_distance.R' 'expand_matrix.R' 'extend_with.R'
+        'install_packages.R' 'package.R' 'pritt.R'
+        'random_time_string.R' 'run_until_exit.R' 'scaling.R'
+        'tibble.R'
+NeedsCompilation: yes
+Packaged: 2018-06-24 12:41:04 UTC; rcannood
+Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
+    rcannood),
+  Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
+Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
+Repository: CRAN
+Date/Publication: 2018-06-24 14:07:55 UTC

MD5

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+160299d0627fd1b4937e2e8180938520 *DESCRIPTION
+7fd1cd0ad39b2c648625195a33d2a7cb *NAMESPACE
+559e9bffb8bf1e8f6fa2bee69eb30f4e *R/RcppExports.R
+30b96236f20a33e753cd9e30df10a17d *R/add_class.R
+e3850008f88dd058ab181e539a5c50d6 *R/calculate_distance.R
+0f487a73cab63061f96224412030a45e *R/expand_matrix.R
+9a35a257fed55e02d97c629a50add7ad *R/extend_with.R
+1799b09d5fd7efef74826bfc3f941e1b *R/inherit_default_params.R
+07154a189a5cb37288feb45a608f9a53 *R/install_packages.R
+804c2119fd58eebf877dc70df4c2ef30 *R/package.R
+2caaac611f00a3c04d56ea872171f578 *R/pritt.R
+28910897cf6c132d3244396d44c3cf29 *R/random_time_string.R
+286706fca7f4e4d3fff835a740c429e3 *R/run_until_exit.R
+9cb7cbe0086cfb38c03c9873305f1913 *R/scaling.R
+550683d4b4e4c47e74ebcf7538ff0f94 *R/tibble.R
+8b370792756e494e0cec32034d7b3e8b *README.md
+3d00986de3d8d541714a7dd58f3a2ce0 *man/add_class.Rd
+b5ac523861808607b014847cb3797765 *man/apply_minmax_scale.Rd
+64174b3e65b65ce84ce3293ae492f994 *man/apply_quantile_scale.Rd
+3bef0a231eef2816e0a263a1e4a2242c *man/apply_uniform_scale.Rd
+6771faace1ff701049356a61c23bad7e *man/calculate_distance.Rd
+bca985c7d6c2e02cd94152865c08f9aa *man/check_packages.Rd
+09abf5e13b450bc468bdb12786252548 *man/dynutils.Rd
+bdef8b65413518dfe3eb5198f56999cc *man/expand_matrix.Rd
+39511ee494f98c86ef0c814408a895f2 *man/extend_with.Rd
+5f8774f6b38947d6cd9342c01d6d0d9a *man/extract_row_to_list.Rd
+477a87afa99a1d7fab80ad6de6bad480 *man/inherit_default_params.Rd
+705111d76df76b2dee7e84ac28436829 *man/install_packages.Rd
+cdcecfb50415bd66de2de57fc0859613 *man/list_as_tibble.Rd
+78ae11d4f9fd66d62a142b48a0c2d4e7 *man/pritt.Rd
+7fdcbd475956fbd310599893c985d802 *man/random_time_string.Rd
+e40429d5ea63f5668a626fe44b3158ad *man/run_until_exit.Rd
+ab9f5a1c1ab3a0848d9d8aba7b32e7fa *man/scale_minmax.Rd
+2d96623cf5d66cd92fb5505d58373356 *man/scale_quantile.Rd
+42596f98342158554f6e89171e3a5df2 *man/scale_uniform.Rd
+674deaa0bac0516c48694763b0db986b *src/RcppExports.cpp
+c44a23e08f260ed4006b531a0eecc561 *src/calculate_distance.cpp
+645f970b5add7df4c3623df1e9c09778 *tests/testthat.R
+90070d56ee12b1460c344b2a4dd11d46 *tests/testthat/test-add_class.R
+88e6091b676fd212af7b8092ac5b00a2 *tests/testthat/test-calculate_distance.R
+7485242237d66f602ee1126cbe4000c2 *tests/testthat/test-expand_matrix.R
+8faa7d5a28c69f65e45e8ff451fc705b *tests/testthat/test-extend_with.R
+5ce31da95e0ab2cae64f31550e6957c1 *tests/testthat/test-inherit_default_params.R
+8877b963ff0ac63ef9d85918d715ce49 *tests/testthat/test-install_packages.R
+d1f8057d6b406af20752b9a0a963107a *tests/testthat/test-pritt.R
+15ff28feffad09aff3b062301884d6a4 *tests/testthat/test-random_time_string.R
+e74119145832bd5f34f17638ef62070b *tests/testthat/test-run_until_exit.R
+bacf3a9c91b28b7ab6ff90784e38ee69 *tests/testthat/test-scaling.R
+e8f3614bd73b1b86237c96d5ae9888ac *tests/testthat/test-tibble.R

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(add_class)
+export(apply_minmax_scale)
+export(apply_quantile_scale)
+export(apply_uniform_scale)
+export(calculate_distance)
+export(check_packages)
+export(correlation_distance)
+export(euclidean_distance)
+export(expand_matrix)
+export(extend_with)
+export(extract_row_to_list)
+export(inherit_default_params)
+export(install_packages)
+export(list_as_tibble)
+export(manhattan_distance)
+export(pritt)
+export(random_time_string)
+export(run_until_exit)
+export(scale_minmax)
+export(scale_quantile)
+export(scale_uniform)
+import(dplyr)
+import(methods)
+import(stringr)
+import(tibble)
+import(tidyr)
+importFrom(desc,desc_get_remotes)
+importFrom(devtools,install_cran)
+importFrom(devtools,install_github)
+importFrom(glue,glue)
+importFrom(magrittr,"%$%")
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,set_colnames)
+importFrom(magrittr,set_rownames)
+importFrom(purrr,"%>%")
+importFrom(purrr,keep)
+importFrom(purrr,map)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
+importFrom(purrr,map_df)
+importFrom(purrr,map_int)
+importFrom(purrr,map_lgl)
+importFrom(purrr,set_names)
+importFrom(stats,cor)
+importFrom(stats,quantile)
+importFrom(stats,setNames)
+importFrom(testthat,expect_equal)
+importFrom(testthat,expect_is)
+importFrom(testthat,expect_named)
+importFrom(utils,installed.packages)
+importFrom(utils,setRepositories)
+useDynLib(dynutils)

R/RcppExports.R

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+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+manhattan_distance <- function(x, y) {
+    .Call('_dynutils_manhattan_distance', PACKAGE = 'dynutils', x, y)
+}
+
+euclidean_distance <- function(x, y) {
+    .Call('_dynutils_euclidean_distance', PACKAGE = 'dynutils', x, y)
+}
+

R/add_class.R

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+#' Add class to object whilst keeping the old classes
+#'
+#' @inheritParams base::class
+#' @param class A character vector naming classes
+#'
+#' @export
+add_class <- function(x, class) {
+  class(x) <- c(class, class(x))
+  x
+}

R/calculate_distance.R

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+#' @importFrom testthat expect_is
+calculate_distance_preproc_x <- function(x) {
+  testthat::expect_is(x, c("matrix", "data.frame", "dgCMatrix"))
+  as.matrix(x)
+}
+
+#' @importFrom testthat expect_equal
+calculate_distance_preproc_y <- function(x, y) {
+  if (is.null(y)) y <- x
+  testthat::expect_equal(ncol(y), ncol(x))
+  calculate_distance_preproc_x(y)
+}
+
+calculate_distance_postproc_d <- function(x, y, d) {
+  dimnames(d) <- list(rownames(x), rownames(y))
+  d
+}
+
+#' Distance metrics
+#'
+#' Calculate (pairwise) distances between two matrices
+#'
+#' @param x A numeric matrix
+#' @param y (Optional) a numeric matrix, with \code{ncol(x) == ncol(y)}.
+#' @param method Distance method to use. Options are:
+#' \itemize{
+#'   \item euclidean: \code{\link{euclidean_distance}}
+#'   \item manhattan: \code{\link{manhattan_distance}}
+#'   \item spearman, pearson, or kendall: \code{\link{correlation_distance}}
+#' }
+#'
+#' @rdname calculate_distance
+#'
+#' @export
+#'
+#' @examples
+#' ## Generate two matrices with 50 and 100 samples
+#' x <- matrix(rnorm(50*10, mean = 0, sd = 1), ncol = 10)
+#' y <- matrix(rnorm(100*10, mean = 1, sd = 2), ncol = 10)
+#'
+#' dist_euclidean <- calculate_distance(x, y, method = "euclidean")
+#' dist_manhattan <- calculate_distance(x, y, method = "manhattan")
+#' dist_spearman <- calculate_distance(x, y, method = "spearman")
+#' dist_pearson <- calculate_distance(x, y, method = "pearson")
+#' dist_kendall <- calculate_distance(x, y, method = "kendall")
+calculate_distance <- function(
+  x,
+  y = NULL,
+  method = c("euclidean", "manhattan", "spearman", "pearson", "kendall")
+) {
+  method <- match.arg(method)
+
+  if (method == "euclidean") {
+    euclidean_distance(x, y)
+  } else if (method == "manhattan") {
+    manhattan_distance(x, y)
+  } else if (method %in% c("spearman", "pearson", "kendall")) {
+    correlation_distance(x, y, method = method)
+  }
+}
+
+#' @rdname calculate_distance
+#'
+#' @inheritParams stats::cor
+#'
+#' @importFrom stats cor
+#'
+#' @include inherit_default_params.R
+#'
+#' @export
+correlation_distance <- inherit_default_params(
+  list(stats::cor),
+  function(x, y, method, use) {
+    x <- calculate_distance_preproc_x(x)
+    y <- calculate_distance_preproc_y(x, y)
+
+    d <- 1 - (stats::cor(t(x), t(y), method = method, use = use) + 1) / 2
+
+    calculate_distance_postproc_d(x, y, d)
+  }
+)
+
+#' @rdname calculate_distance
+#'
+#' @export
+manhattan_distance <- function(x, y = NULL) {
+  x <- calculate_distance_preproc_x(x)
+  y <- calculate_distance_preproc_y(x, y)
+
+  d <- .Call('_dynutils_manhattan_distance', PACKAGE = 'dynutils', x, y)
+
+  calculate_distance_postproc_d(x, y, d)
+}
+
+#' @rdname calculate_distance
+#'
+#' @export
+euclidean_distance <- function(x, y = NULL) {
+  x <- calculate_distance_preproc_x(x)
+  y <- calculate_distance_preproc_y(x, y)
+
+  d <- .Call('_dynutils_euclidean_distance', PACKAGE = 'dynutils', x, y)
+
+  calculate_distance_postproc_d(x, y, d)
+}
+
+

R/expand_matrix.R

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+#' Expand a matrix with given rownames and colnames
+#'
+#' @param mat The matrix to expand
+#' @param rownames The desired rownames
+#' @param colnames The desired colnames
+#' @param fill With what to fill missing data
+#'
+#' @export
+expand_matrix <- function(
+  mat,
+  rownames = NULL,
+  colnames = NULL,
+  fill = 0
+) {
+  if (is.null(rownames)) {
+    rownames <- rownames(mat)
+  }
+  if (is.null(colnames)) {
+    colnames <- colnames(mat)
+  }
+  newmat <- matrix(
+    fill,
+    nrow = length(rownames),
+    ncol = length(colnames),
+    dimnames = list(rownames, colnames)
+  )
+  newmat[rownames(mat),colnames(mat)] <- mat
+  newmat
+}

R/extend_with.R

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+#' Extend an object
+#'
+#' @param object A list
+#' @param .class_name A class name to add
+#' @param ... Extra information in the list
+#'
+#' @importFrom testthat expect_is expect_named
+#'
+#' @export
+extend_with <- function(
+  object,
+  .class_name,
+  ...
+) {
+  testthat::expect_is(object, "list")
+  testthat::expect_is(.class_name, "character")
+
+  extension <- list(...)
+
+  if (is.null(names(extension)) && length(extension) == 1 && "list" %in% class(extension[[1]])) {
+    extension <- extension[[1]]
+  }
+
+  testthat::expect_is(extension, "list")
+  testthat::expect_named(extension)
+  testthat::expect_false(any(names(extension) == ""))
+
+  object[names(extension)] <- extension
+
+  add_class(object, .class_name)
+}

R/inherit_default_params.R

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+#' Inherit default parameters from a list of super functions
+#'
+#' @param super_functions A list of super functions of which \code{fun} needs to inherit the default parameters
+#' @param fun The function whose default parameters need to be overridden
+#'
+#' @return Function \code{fun}, but with the default parameters of the \code{super_functions}
+#' @export
+#'
+#' @examples
+#' fun1 <- function(a = 10, b = 7) {
+#'   runif(a, -b, b)
+#' }
+#'
+#' fun2 <- function(c = 9) {
+#'   2^c
+#' }
+#'
+#' fun3 <- inherit_default_params(
+#'   super = list(fun1, fun2),
+#'   fun = function(a, b, c) {
+#'     x <- fun1(a, b)
+#'     y <- fun2(c)
+#'     list(x = x, y = y)
+#'   }
+#' )
+#'
+#' fun3(1, 2, 3)
+#' fun3()
+inherit_default_params <- function(super_functions, fun) {
+  if (is.function(super_functions)) {
+    super_functions <- list(super_functions)
+  }
+  for (sup in super_functions) {
+    argsup <- intersect(formalArgs(fun), formalArgs(sup))
+    formals(fun)[argsup] <- formals(sup)[argsup]
+  }
+  fun
+}