version 1.0.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynutils
 Type: Package
 Title: Common Functionality for the 'dynverse' Packages
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(
     person(
       "Robrecht", 
@@ -28,23 +28,17 @@ BugReports: https://github.com/dynverse/dynutils/issues
 LazyData: TRUE
 RoxygenNote: 6.1.1
 Depends: R (>= 3.0.0)
-Imports: assertthat, crayon, devtools, desc, dplyr, glue, magrittr,
-        methods, purrr, Rcpp, stringr, testthat, tibble, tidyr
-Suggests: ggplot2, hdf5r, knitr, Matrix, readr, rmarkdown
+Imports: assertthat, crayon, desc, dplyr, magrittr, Matrix, methods,
+        proxyC, purrr, Rcpp, remotes, stringr, tibble
+Suggests: ggplot2, hdf5r, knitr, readr, rmarkdown, testthat
 LinkingTo: Rcpp
 Encoding: UTF-8
 VignetteBuilder: knitr
-Collate: 'RcppExports.R' 'add_class.R' 'assertions.R'
-        'inherit_default_params.R' 'calculate_distance.R'
-        'calculate_mean.R' 'check_packages.R' 'expand_matrix.R'
-        'extend_with.R' 'h5.R' 'install_packages.R' 'mapdf.R' 'news.R'
-        'package.R' 'pritt.R' 'random_time_string.R' 'safe_tempdir.R'
-        'scaling.R' 'tibble.R'
 NeedsCompilation: yes
-Packaged: 2019-03-21 16:52:55 UTC; rcannood
+Packaged: 2019-05-02 11:44:22 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: 2019-03-21 17:20:03 UTC
+Date/Publication: 2019-05-02 12:10:03 UTC

MD5

@@ -1,82 +1,87 @@
-46d72619891f80e043d8a40802cb4bec *DESCRIPTION
-89555237b6aec86140edd1967341e7c8 *NAMESPACE
-15b3317475a4dc79ee837baf020b4210 *R/RcppExports.R
+9e39d9ff3019724fe6b35e9e12b17a4b *DESCRIPTION
+f42d7052d35f6c9f8fcf33e29af3b169 *NAMESPACE
+dcdf2491b0e62a545623862a87d55529 *R/RcppExports.R
 6f7fc8ddd74f0326bf2b59a523681cf7 *R/add_class.R
 93ee58dfa8e9d0165a0aadbc62cfb01a *R/assertions.R
-e3850008f88dd058ab181e539a5c50d6 *R/calculate_distance.R
+0567136a0ea7179450e01daec3b56c88 *R/calculate_distance.R
 d6aa6f13af04adf14f579e08fc13d984 *R/calculate_mean.R
 d12293c4bf7b1a545afd8a8772ef9160 *R/check_packages.R
+bb24825b695c9f4273d1d94742b42bfa *R/development.R
 ebced609202a59d493b476c3aac3fe8d *R/expand_matrix.R
-85c44df9d66d900d3faffeda2bdb4cbf *R/extend_with.R
-bdd21bbee0e41746786b7fc234149c91 *R/h5.R
-7b04594ee09c9b479b8ac5bd1863546e *R/inherit_default_params.R
-c609af265ed22262b84876038a06b074 *R/install_packages.R
-3d1b74d29cd7cee98c0e149d0f718aa0 *R/mapdf.R
-49a3aa3a25b0f1afe4f2185cf0f57fd6 *R/news.R
-05be96ce07e81cae3f2a8d73069161a2 *R/package.R
-15faad85abe90be3921dcaa156de86bd *R/pritt.R
+aa0987fdaaa50b3bf720eef589eb9cbe *R/extend_with.R
+a13cca47e183757563216d56990fc82c *R/h5.R
+56ddd7a01d957f768e214bf3ff7d1286 *R/inherit_default_params.R
+10578fb8a2f46f5ecb3b982175fa2b2f *R/install_packages.R
+ad9da1318face1a62868506526ccb6b2 *R/mapdf.R
+ef3df5c1091735c9c9a712004957c78f *R/news.R
+c97a751e3b56aaea353a18eac7be3c4f *R/package.R
 37bf34c1b1fb077abcc7cb9156a84f38 *R/random_time_string.R
 9b4d1d09be1a4744441026f362c8ac80 *R/safe_tempdir.R
-f8dd8af76a7ac011a43271821a80d626 *R/scaling.R
-1a382f59e99865b7c0941c3fbddf5218 *R/tibble.R
-d152f7d60b76ea693ea9ddded6eec80d *README.md
-3bee9bf2edeafb3a833b4e20407e5590 *build/vignette.rds
-d9142a46db8d94b3a24478b9f7399d87 *inst/NEWS
-6f26e5be2469401a56c320b66d751f8b *inst/NEWS.md
-800e36dd32e2746ac28770868dc03b5a *inst/doc/functionality.R
-dcfa0ef794ab3e314a0e1b253fd0674d *inst/doc/functionality.Rmd
-afc2e58a2e937d07dce30de0893a099c *inst/doc/functionality.html
+84177816e09c42df4cfb3348882c7cef *R/scaling.R
+3a163b578e254a622a259fb15598b87a *R/sparse_matrix.R
+ed5a6e94e1159f1aafdcfc1c82c27d49 *R/spearman_rank_sparse.R
+508280137e6c0eb4d37a5872de6ab486 *R/tibble.R
+14b0374fdcb108355c447c634393d610 *README.md
+62552cf79a790d98f992f24c9b160324 *build/vignette.rds
+2df7a652027d6216f1deffcb18cb216a *inst/NEWS
+34740d7dd1cb5c8681b992358e9aec11 *inst/NEWS.md
+c28ffd40aaf548dc3c35eec3f4f56de3 *inst/doc/functionality.R
+9ea7d77f2b021d331860e5d4ac87d4b8 *inst/doc/functionality.Rmd
+78540f76ffbabc8b831ac0d9a1228156 *inst/doc/functionality.html
 c3db2b03d9fad3aa6837b3f565dfdebd *man/add_class.Rd
 6bc340f4659bf12f836063f6dbdd2329 *man/all_in.Rd
 b5ac523861808607b014847cb3797765 *man/apply_minmax_scale.Rd
 64174b3e65b65ce84ce3293ae492f994 *man/apply_quantile_scale.Rd
 3bef0a231eef2816e0a263a1e4a2242c *man/apply_uniform_scale.Rd
-6771faace1ff701049356a61c23bad7e *man/calculate_distance.Rd
-e9a3ffa5050a8b94a10a881d52d2b409 *man/calculate_mean.Rd
+2a41ba64ac7e6974373c798d81c51322 *man/calculate_distance.Rd
+5b35a6f332946299b91d087180993a29 *man/calculate_mean.Rd
 3252699f0111548d1c5865b259fc6045 *man/check_packages.Rd
-e24bb86a09016228bc6f52eb27c457e1 *man/dynutils.Rd
+8119f54576526e375c65967172a35730 *man/deprecated.Rd
+3833f3de1b175491d2117bde300549cc *man/dynutils.Rd
 7709555d2461d3fdc0754ff9ed78c279 *man/expand_matrix.Rd
 3018e1eb12824f76075b195fe12a4916 *man/extend_with.Rd
 7613b5995b078d708cc26c1a5d2d9b88 *man/extract_row_to_list.Rd
+b13a5533db06c4565c8025ec07416d90 *man/figures/dependencies.png
 21c38d6edb23eb7766127edfb805d2cc *man/has_names.Rd
-740e7a7bf33786b1c8cefcf8ded17610 *man/inherit_default_params.Rd
-92547389f18931a8166951634e019577 *man/install_packages.Rd
+e7578523a6fa518bfb8ed4c7def2a0ea *man/inherit_default_params.Rd
+7882b49fc121c84cc4ce635266e3392f *man/install_packages.Rd
 ffb5cc4ea8eb2cc74b8881ee03793acc *man/is_bounded.Rd
 b9518d93e55a498b29be70221d67e209 *man/is_single_numeric.Rd
-51180651c2f54cbec26e4cd894ff2ea7 *man/is_sparse.Rd
+9c390e87ca76ed1d225baea185e4b038 *man/is_sparse.Rd
 c75c1e1f49dbefd8590f7424587ad69b *man/list_as_tibble.Rd
-4126dd0f30b3a7b6d7ff96db14a57528 *man/mapdf.Rd
-62bd4790a9a678a2922a0b80a60ed606 *man/pritt.Rd
-d030ba9674691137199ba8be588b2986 *man/project_to_segments.Rd
+accf4b9c8028a260b70a2e76e0c5cc04 *man/mapdf.Rd
+2b3a023bd618893c84f8145c2396ae97 *man/project_to_segments.Rd
 2cf7693dbaf3302c64209d7336c447d5 *man/random_time_string.Rd
 924b15280c2637b60a75a439b96da664 *man/read_h5.Rd
 b0cb95b27f4369b40ec09cdb98029c5d *man/recent_news.Rd
 4709d575d5fa06a874efac612a29ee78 *man/safe_tempdir.Rd
 3ebf0627b766e627129d9ea56bc4e725 *man/scale_minmax.Rd
 796b56abcd3919f503ddecb80735ea9a *man/scale_quantile.Rd
 f9110f58085b0ae3ca4bc37b1bec76c9 *man/scale_uniform.Rd
+8cbb41dad70d4291c45362bc92d95fec *man/switch_devel.Rd
+ee0bba1b16667c4ea72c209f54ea9fa5 *man/test_h5_installation.Rd
 32b3de681b6aeb351f1e91ff7add5e2b *man/tibble_as_list.Rd
 59b1b0efb62d2254a11478b3434b8e3a *man/update_news.Rd
-69ab276f79857e48416d5cbb4eacd9ed *src/RcppExports.cpp
-c44a23e08f260ed4006b531a0eecc561 *src/calculate_distance.cpp
+8a2437afa3a3e6b7be52294db68ef331 *src/RcppExports.cpp
 fa89e1f21fd5ca27ac892f4ba8ba9c7c *src/project_to_segments.cpp
-645f970b5add7df4c3623df1e9c09778 *tests/testthat.R
+eab0faf9e93b86fab93ff7f4b4dc4234 *src/spearman_rank_sparse.cpp
+e98edf1dd851bb968f099085613e1641 *tests/testthat.R
 90070d56ee12b1460c344b2a4dd11d46 *tests/testthat/test-add_class.R
 35e9b56c7825d520e904f7fefc4bc561 *tests/testthat/test-assertions.R
-1d3471e3c4f0726a5a3cf2f65a33e807 *tests/testthat/test-calculate_distance.R
+a5d7131e9d3de2744e212f172e6b6c4a *tests/testthat/test-calculate_distance.R
 6361031d09fa22e6b4cc5e705e13c726 *tests/testthat/test-calculate_mean.R
 dbb99d66a04da64c942eeb3d2aad76a4 *tests/testthat/test-check_packages.R
 7485242237d66f602ee1126cbe4000c2 *tests/testthat/test-expand_matrix.R
 8faa7d5a28c69f65e45e8ff451fc705b *tests/testthat/test-extend_with.R
-c33799ef844aa1d9a1f3500f5e88b748 *tests/testthat/test-h5.R
+6b476ee9c8230218a976b0abc9457fbf *tests/testthat/test-h5.R
 5ce31da95e0ab2cae64f31550e6957c1 *tests/testthat/test-inherit_default_params.R
-5a0b8841cae5fd25cd22193bb97735b3 *tests/testthat/test-install_packages.R
-ddab0c82ed76e18043f565728e5d9743 *tests/testthat/test-mapdf.R
+f665360485a47a68db1c5e78f4419139 *tests/testthat/test-install_packages.R
+eb500b1fea1726787b4e1cc25de6caa0 *tests/testthat/test-mapdf.R
 d1a8a626c25752cab51675892ff9597f *tests/testthat/test-news.R
-d1f8057d6b406af20752b9a0a963107a *tests/testthat/test-pritt.R
 12b22a50c13f031e04cafada2045e5eb *tests/testthat/test-project_to_segments.R
 15ff28feffad09aff3b062301884d6a4 *tests/testthat/test-random_time_string.R
 af921049e7a8a884810b545563e80928 *tests/testthat/test-safe_tempdir.R
 bacf3a9c91b28b7ab6ff90784e38ee69 *tests/testthat/test-scaling.R
+5494b68645ab4526138202e62385dea5 *tests/testthat/test-spearman_rank_sparse.R
 fc042589bc13e4175521bb1d10631436 *tests/testthat/test-tibble.R
-dcfa0ef794ab3e314a0e1b253fd0674d *vignettes/functionality.Rmd
+9ea7d77f2b021d331860e5d4ac87d4b8 *vignettes/functionality.Rmd

NAMESPACE

@@ -12,20 +12,23 @@ export(calculate_distance)
 export(calculate_geometric_mean)
 export(calculate_harmonic_mean)
 export(calculate_mean)
+export(calculate_similarity)
 export(check_packages)
 export(correlation_distance)
 export(euclidean_distance)
 export(expand_matrix)
 export(extend_with)
 export(extract_row_to_list)
+export(get_h5_test_data)
 export(has_names)
 export(inherit_default_params)
 export(install_packages)
 export(is_bounded)
 export(is_single_numeric)
 export(is_sparse)
 export(list_as_tibble)
-export(manhattan_distance)
+export(list_distance_methods)
+export(list_similarity_methods)
 export(mapdf)
 export(mapdf_chr)
 export(mapdf_dbl)
@@ -34,7 +37,6 @@ export(mapdf_dfr)
 export(mapdf_int)
 export(mapdf_lat)
 export(mapdf_lgl)
-export(pritt)
 export(project_to_segments)
 export(random_time_string)
 export(read_h5)
@@ -44,33 +46,42 @@ export(safe_tempdir)
 export(scale_minmax)
 export(scale_quantile)
 export(scale_uniform)
+export(switch_cran)
+export(switch_devel)
+export(switch_master)
+export(test_h5_installation)
 export(tibble_as_list)
 export(update_news)
 export(walkdf)
 export(write_h5)
 export(write_h5_)
-import(dplyr)
-import(methods)
-import(stringr)
-import(tibble)
-import(tidyr)
+importFrom(Matrix,t)
 importFrom(Rcpp,evalCpp)
 importFrom(assertthat,"%has_name%")
 importFrom(assertthat,"on_failure<-")
-importFrom(desc,desc_get_remotes)
-importFrom(devtools,install_cran)
-importFrom(devtools,install_github)
-importFrom(glue,glue)
+importFrom(assertthat,assert_that)
+importFrom(crayon,bold)
+importFrom(crayon,green)
+importFrom(crayon,red)
+importFrom(dplyr,enquo)
+importFrom(dplyr,n)
+importFrom(dplyr,slice)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
+importFrom(methods,as)
+importFrom(methods,formalArgs)
+importFrom(methods,is)
+importFrom(proxyC,dist)
+importFrom(proxyC,simil)
 importFrom(purrr,"%>%")
 importFrom(purrr,"%||%")
 importFrom(purrr,as_mapper)
 importFrom(purrr,discard)
 importFrom(purrr,keep)
 importFrom(purrr,map)
+importFrom(purrr,map2)
 importFrom(purrr,map_at)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
@@ -82,12 +93,18 @@ importFrom(purrr,map_int)
 importFrom(purrr,map_lgl)
 importFrom(purrr,set_names)
 importFrom(purrr,walk)
-importFrom(stats,cor)
+importFrom(remotes,install_cran)
 importFrom(stats,quantile)
-importFrom(testthat,expect_equal)
-importFrom(testthat,expect_false)
-importFrom(testthat,expect_is)
-importFrom(testthat,expect_named)
+importFrom(stats,runif)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_match)
+importFrom(stringr,str_pad)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_subset)
+importFrom(tibble,as_tibble)
+importFrom(tibble,lst)
+importFrom(tibble,tibble)
 importFrom(utils,installed.packages)
 importFrom(utils,setRepositories)
 useDynLib(dynutils)

R/RcppExports.R

@@ -1,14 +1,6 @@
 # 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)
-}
-
 #' Project a set of points to to set of segments
 #'
 #' Finds the projection index for a matrix of points \code{x}, when
@@ -37,3 +29,7 @@ project_to_segments <- function(x, segment_start, segment_end) {
     .Call('_dynutils_project_to_segments', PACKAGE = 'dynutils', x, segment_start, segment_end)
 }
 
+spearman_rank_sparse_rcpp <- function(x, p, nrow) {
+    .Call('_dynutils_spearman_rank_sparse_rcpp', PACKAGE = 'dynutils', x, p, nrow)
+}
+