version 1.0.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynutils
 Type: Package
-Title: Common Functions for the Dynverse Packages
-Version: 0.1.0
+Title: Common Functionality for the 'dynverse' Packages
+Version: 1.0.0
 Authors@R: c(
     person(
       "Robrecht", 
@@ -19,26 +19,27 @@ Authors@R: c(
     )
   )
 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>.
+  Provides common functionality for the 'dynverse' packages. 
+  'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
+  For more information, check out <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
+Suggests: ggplot2, knitr, readr, rmarkdown
 LinkingTo: Rcpp
+VignetteBuilder: knitr
 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'
+        'calculate_distance.R' 'check_packages.R' 'expand_matrix.R'
+        'extend_with.R' 'install_packages.R' 'mapdf.R' 'package.R'
+        'pritt.R' 'random_time_string.R' 'scaling.R' 'tibble.R'
 NeedsCompilation: yes
-Packaged: 2018-06-24 12:41:04 UTC; rcannood
+Packaged: 2018-07-18 12:41:55 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
+Date/Publication: 2018-07-18 13:10:09 UTC

MD5

@@ -1,49 +1,61 @@
-160299d0627fd1b4937e2e8180938520 *DESCRIPTION
-7fd1cd0ad39b2c648625195a33d2a7cb *NAMESPACE
-559e9bffb8bf1e8f6fa2bee69eb30f4e *R/RcppExports.R
-30b96236f20a33e753cd9e30df10a17d *R/add_class.R
+608cf24991008f2856a87421858392aa *DESCRIPTION
+8aca8bbc89cc03f8c11d846303914aa7 *NAMESPACE
+15b3317475a4dc79ee837baf020b4210 *R/RcppExports.R
+6f7fc8ddd74f0326bf2b59a523681cf7 *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
+d12293c4bf7b1a545afd8a8772ef9160 *R/check_packages.R
+ebced609202a59d493b476c3aac3fe8d *R/expand_matrix.R
+85c44df9d66d900d3faffeda2bdb4cbf *R/extend_with.R
+7b04594ee09c9b479b8ac5bd1863546e *R/inherit_default_params.R
+d3bdc879cc8de54ca1297fde2536702b *R/install_packages.R
+aaabb9fde3b05e2ed4a51753235b6157 *R/mapdf.R
+3255589fcaed67404498fb0983713ab5 *R/package.R
+15faad85abe90be3921dcaa156de86bd *R/pritt.R
+37bf34c1b1fb077abcc7cb9156a84f38 *R/random_time_string.R
+f8dd8af76a7ac011a43271821a80d626 *R/scaling.R
+c57520019a9bd779737ce37dbd3e5451 *R/tibble.R
+0914edf25fcf8d667015bf5c6d2ec43b *README.md
+d4d8b29b95540d27d4550c4896a1d62d *build/vignette.rds
+8207888e7b8d50bd61ed53aeaa43c008 *inst/NEWS
+552e6e0c1e70efca10b3db1994bc4786 *inst/doc/functionality.R
+59e4d8087b619be25f5a83fd1846e261 *inst/doc/functionality.Rmd
+d4d77130edd4c4694254a000e806d296 *inst/doc/functionality.html
+c3db2b03d9fad3aa6837b3f565dfdebd *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
+3252699f0111548d1c5865b259fc6045 *man/check_packages.Rd
+413271f77bb57611aeb016fa8f4d5e85 *man/dynutils.Rd
+7709555d2461d3fdc0754ff9ed78c279 *man/expand_matrix.Rd
+3018e1eb12824f76075b195fe12a4916 *man/extend_with.Rd
+9aaed213184b39633d36df275e873813 *man/extract_row_to_list.Rd
+740e7a7bf33786b1c8cefcf8ded17610 *man/inherit_default_params.Rd
+92547389f18931a8166951634e019577 *man/install_packages.Rd
+c75c1e1f49dbefd8590f7424587ad69b *man/list_as_tibble.Rd
+aaa833eaa967c4031572cff9760ea88a *man/mapdf.Rd
+62bd4790a9a678a2922a0b80a60ed606 *man/pritt.Rd
+d030ba9674691137199ba8be588b2986 *man/project_to_segments.Rd
+2cf7693dbaf3302c64209d7336c447d5 *man/random_time_string.Rd
+3ebf0627b766e627129d9ea56bc4e725 *man/scale_minmax.Rd
+796b56abcd3919f503ddecb80735ea9a *man/scale_quantile.Rd
+f9110f58085b0ae3ca4bc37b1bec76c9 *man/scale_uniform.Rd
+32b3de681b6aeb351f1e91ff7add5e2b *man/tibble_as_list.Rd
+69ab276f79857e48416d5cbb4eacd9ed *src/RcppExports.cpp
 c44a23e08f260ed4006b531a0eecc561 *src/calculate_distance.cpp
+fa89e1f21fd5ca27ac892f4ba8ba9c7c *src/project_to_segments.cpp
 645f970b5add7df4c3623df1e9c09778 *tests/testthat.R
 90070d56ee12b1460c344b2a4dd11d46 *tests/testthat/test-add_class.R
-88e6091b676fd212af7b8092ac5b00a2 *tests/testthat/test-calculate_distance.R
+1d3471e3c4f0726a5a3cf2f65a33e807 *tests/testthat/test-calculate_distance.R
+dbb99d66a04da64c942eeb3d2aad76a4 *tests/testthat/test-check_packages.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
+d993460d1ce3623f3edcff631b8f5b9f *tests/testthat/test-install_packages.R
+756bcdea5c45ef09d977a958b55c2695 *tests/testthat/test-mapdf.R
 d1f8057d6b406af20752b9a0a963107a *tests/testthat/test-pritt.R
+12b22a50c13f031e04cafada2045e5eb *tests/testthat/test-project_to_segments.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
+14eb963310f7d37419f201073a91a6ed *tests/testthat/test-tibble.R
+59e4d8087b619be25f5a83fd1846e261 *vignettes/functionality.Rmd

NAMESPACE

@@ -15,12 +15,21 @@ export(inherit_default_params)
 export(install_packages)
 export(list_as_tibble)
 export(manhattan_distance)
+export(mapdf)
+export(mapdf_chr)
+export(mapdf_dbl)
+export(mapdf_dfc)
+export(mapdf_dfr)
+export(mapdf_int)
+export(mapdf_lgl)
 export(pritt)
+export(project_to_segments)
 export(random_time_string)
-export(run_until_exit)
 export(scale_minmax)
 export(scale_quantile)
 export(scale_uniform)
+export(tibble_as_list)
+export(walkdf)
 import(dplyr)
 import(methods)
 import(stringr)
@@ -35,18 +44,25 @@ importFrom(magrittr,"%<>%")
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,"%>%")
+importFrom(purrr,as_mapper)
+importFrom(purrr,discard)
 importFrom(purrr,keep)
 importFrom(purrr,map)
+importFrom(purrr,map_at)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
 importFrom(purrr,map_df)
+importFrom(purrr,map_dfc)
+importFrom(purrr,map_dfr)
+importFrom(purrr,map_if)
 importFrom(purrr,map_int)
 importFrom(purrr,map_lgl)
 importFrom(purrr,set_names)
+importFrom(purrr,walk)
 importFrom(stats,cor)
 importFrom(stats,quantile)
-importFrom(stats,setNames)
 importFrom(testthat,expect_equal)
+importFrom(testthat,expect_false)
 importFrom(testthat,expect_is)
 importFrom(testthat,expect_named)
 importFrom(utils,installed.packages)

R/RcppExports.R

@@ -9,3 +9,31 @@ euclidean_distance <- function(x, y) {
     .Call('_dynutils_euclidean_distance', PACKAGE = 'dynutils', x, y)
 }
 
+#' Project a set of points to to set of segments
+#'
+#' Finds the projection index for a matrix of points \code{x}, when
+#' projected onto a set of segments defined by \code{segment_start} and \code{segment_end}.
+#'
+#' @param x a matrix of data points.
+#' @param segment_start a matrix of segment start points.
+#' @param segment_end a matrix of segment end points.
+#'
+#' @return A list with components
+#'   \item{x_proj}{a matrix of projections of \code{x} onto the given segments.}
+#'   \item{segment}{the index of the segment a point is projected on}
+#'   \item{progression}{the progression of a projection along its segment}
+#'   \item{distance}{the distance from each point in \code{x} to its projection in \code{x_proj}}
+#'
+#' @examples
+#' x <- matrix(rnorm(50, 0, .5), ncol = 2)
+#' segfrom <- matrix(c(0, 1, 0, -1, 1, 0, -1, 0), ncol = 2, byrow = TRUE)
+#' segto <- segfrom / 10
+#' fit <- project_to_segments(x, segfrom, segto)
+#'
+#' str(fit) # examine output
+#'
+#' @export
+project_to_segments <- function(x, segment_start, segment_end) {
+    .Call('_dynutils_project_to_segments', PACKAGE = 'dynutils', x, segment_start, segment_end)
+}
+

R/add_class.R

@@ -4,6 +4,10 @@
 #' @param class A character vector naming classes
 #'
 #' @export
+#'
+#' @examples
+#' library(purrr)
+#' l <- list(important_number = 42) %>% add_class("my_list")
 add_class <- function(x, class) {
   class(x) <- c(class, class(x))
   x

R/check_packages.R

@@ -0,0 +1,16 @@
+#' Check which packages are installed
+#'
+#' @param ... A set of package names
+#'
+#' @export
+#'
+#' @importFrom utils installed.packages
+#'
+#' @examples
+#' check_packages("SCORPIUS", "dynutils")
+#' check_packages(c("princurve", "mlr", "tidyverse"))
+check_packages <- function(...) {
+  packages <- unlist(list(...))
+  installed_packages <- rownames(utils::installed.packages())
+  set_names(packages %in% installed_packages, packages)
+}

R/expand_matrix.R

@@ -6,6 +6,10 @@
 #' @param fill With what to fill missing data
 #'
 #' @export
+#'
+#' @examples
+#' x <- matrix(runif(12), ncol = 4, dimnames = list(c("a", "c", "d"), c("D", "F", "H", "I")))
+#' expand_matrix(x, letters[1:5], LETTERS[1:10], fill = 0)
 expand_matrix <- function(
   mat,
   rownames = NULL,

R/extend_with.R

@@ -4,9 +4,18 @@
 #' @param .class_name A class name to add
 #' @param ... Extra information in the list
 #'
-#' @importFrom testthat expect_is expect_named
+#' @importFrom testthat expect_is expect_named expect_false
 #'
 #' @export
+#'
+#' @examples
+#' library(purrr)
+#' l <- list(important_number = 42) %>% add_class("my_list")
+#' l %>% extend_with(
+#'   .class_name = "improved_list",
+#'   url = "https://github.com/dynverse/dynverse"
+#' )
+#' l
 extend_with <- function(
   object,
   .class_name,

R/inherit_default_params.R

@@ -7,25 +7,17 @@
 #' @export
 #'
 #' @examples
-#' fun1 <- function(a = 10, b = 7) {
-#'   runif(a, -b, b)
-#' }
-#'
-#' fun2 <- function(c = 9) {
-#'   2^c
-#' }
+#' 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)
+#'     list(x = fun1(a, b), y = fun2(c))
 #'   }
 #' )
 #'
-#' fun3(1, 2, 3)
-#' fun3()
+#' fun3
 inherit_default_params <- function(super_functions, fun) {
   if (is.function(super_functions)) {
     super_functions <- list(super_functions)