version 1.0.7

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynutils
 Type: Package
 Title: Common Functionality for the 'dynverse' Packages
-Version: 1.0.6
+Version: 1.0.7
 Authors@R: c(
     person(
       "Robrecht", 
@@ -25,20 +25,19 @@ Description:
 License: MIT + file LICENSE
 URL: https://github.com/dynverse/dynutils
 BugReports: https://github.com/dynverse/dynutils/issues
-LazyData: TRUE
 RoxygenNote: 7.1.1
 Depends: R (>= 3.0.0)
 Imports: assertthat, crayon, desc, dplyr, magrittr, Matrix, methods,
         proxyC, purrr, Rcpp, remotes, stringr, tibble
-Suggests: ggplot2, hdf5r, knitr, readr, rmarkdown, testthat
+Suggests: covr, ggplot2, hdf5r, knitr, readr, rmarkdown, testthat
 LinkingTo: Rcpp
 Encoding: UTF-8
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2021-03-22 11:24:41 UTC; rcannood
+Packaged: 2021-09-02 08:33:19 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: 2021-03-22 12:50:02 UTC
+Date/Publication: 2021-09-04 05:40:02 UTC

MD5

@@ -1,17 +1,17 @@
-e85f0a385a230b840f7734c355b000fe *DESCRIPTION
+cfaac4514a25c22522d50186d25d3da0 *DESCRIPTION
 ef3d9f056adaa322680184035912700f *LICENSE
 246edeab46c29b2a202d37070ffd69ba *NAMESPACE
-740331d8390bf198d01e8f7179407410 *NEWS.md
+5c9dbde5719e9fb33f6d81c9470867ef *NEWS.md
 dcdf2491b0e62a545623862a87d55529 *R/RcppExports.R
 6f7fc8ddd74f0326bf2b59a523681cf7 *R/add_class.R
 93ee58dfa8e9d0165a0aadbc62cfb01a *R/assertions.R
-0b5393640d6dcc30c10bb5b9fb657769 *R/calculate_distance.R
+bb6beeb3505b07b1e77e64718f3da1d2 *R/calculate_distance.R
 d6aa6f13af04adf14f579e08fc13d984 *R/calculate_mean.R
 e2b7b0caa56d6a39e5f74f05f1ba7546 *R/check_packages.R
 cdbbf9a1f8aea5c2df485b414eed39ad *R/development.R
 ebced609202a59d493b476c3aac3fe8d *R/expand_matrix.R
 aa0987fdaaa50b3bf720eef589eb9cbe *R/extend_with.R
-a13cca47e183757563216d56990fc82c *R/h5.R
+c589a1bec773c845c2229d0a547c230c *R/h5.R
 56ddd7a01d957f768e214bf3ff7d1286 *R/inherit_default_params.R
 54d7dba8e284ec639517ca1e31b66a83 *R/install_packages.R
 ad9da1318face1a62868506526ccb6b2 *R/mapdf.R
@@ -23,17 +23,17 @@ ad9da1318face1a62868506526ccb6b2 *R/mapdf.R
 3a163b578e254a622a259fb15598b87a *R/sparse_matrix.R
 ed5a6e94e1159f1aafdcfc1c82c27d49 *R/spearman_rank_sparse.R
 508280137e6c0eb4d37a5872de6ab486 *R/tibble.R
-e495e1e5c90fd817b8bfd8f0ebac5fc5 *README.md
-41c17df5a2b8275f015aa70cfd66b3e2 *build/vignette.rds
+4c7e41556e9fa4e748e25989f462b8b8 *README.md
+97438e22f9f6789b6c35f75e506e56ab *build/vignette.rds
 a60b55d68196751eae1016f1871240de *inst/doc/functionality.R
 fd437c3c797311ac07d31ffd0e74d86c *inst/doc/functionality.Rmd
-e8266682d3b17561ce09aa97af7c1a54 *inst/doc/functionality.html
+4f7d145fcbf87ea6aa77b79cc43edf02 *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
-0ac64cbde50d7bd409ca44d05c56366b *man/calculate_distance.Rd
+2096ec04355b4f0e3a9ddd0bf91b9a47 *man/calculate_distance.Rd
 5b35a6f332946299b91d087180993a29 *man/calculate_mean.Rd
 3252699f0111548d1c5865b259fc6045 *man/check_packages.Rd
 8119f54576526e375c65967172a35730 *man/deprecated.Rd
@@ -61,7 +61,7 @@ f9110f58085b0ae3ca4bc37b1bec76c9 *man/scale_uniform.Rd
 8cbb41dad70d4291c45362bc92d95fec *man/switch_devel.Rd
 ee0bba1b16667c4ea72c209f54ea9fa5 *man/test_h5_installation.Rd
 32b3de681b6aeb351f1e91ff7add5e2b *man/tibble_as_list.Rd
-8a2437afa3a3e6b7be52294db68ef331 *src/RcppExports.cpp
+c22eef051e327bc12147066a9237d35c *src/RcppExports.cpp
 fa89e1f21fd5ca27ac892f4ba8ba9c7c *src/project_to_segments.cpp
 eab0faf9e93b86fab93ff7f4b4dc4234 *src/spearman_rank_sparse.cpp
 e98edf1dd851bb968f099085613e1641 *tests/testthat.R
@@ -72,14 +72,14 @@ e98edf1dd851bb968f099085613e1641 *tests/testthat.R
 dbb99d66a04da64c942eeb3d2aad76a4 *tests/testthat/test-check_packages.R
 7485242237d66f602ee1126cbe4000c2 *tests/testthat/test-expand_matrix.R
 8faa7d5a28c69f65e45e8ff451fc705b *tests/testthat/test-extend_with.R
-6b476ee9c8230218a976b0abc9457fbf *tests/testthat/test-h5.R
+057e29b12553afd78ba1f7b0ca48a03f *tests/testthat/test-h5.R
 5ce31da95e0ab2cae64f31550e6957c1 *tests/testthat/test-inherit_default_params.R
 eb500b1fea1726787b4e1cc25de6caa0 *tests/testthat/test-mapdf.R
-87086196556352c60f0e8a21d5e13e02 *tests/testthat/test-news.R
+900fd5789d675deb11cbb4c5072259e4 *tests/testthat/test-news.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
+360a3ba04634c17bb988f9fbe1c19f90 *tests/testthat/test-tibble.R
 fd437c3c797311ac07d31ffd0e74d86c *vignettes/functionality.Rmd

NEWS.md

@@ -1,8 +1,16 @@
+# dynutils 1.0.7
+
+ * MINOR CHANGE `calculate_distance()`: Convert matrices to CsparseMatrix instead of dgCMatrix.
+
+ * MINOR CHANGE `calculate_distance()`: Pass through the `diag` argument to proxyC.
+
+ * BUG FIX unit test: Order of attributes is not relevant.
+
 # dynutils 1.0.6
 
-* MINOR CHANGE `calculate_distance()`: Allow for many more distance measures.
+ * MINOR CHANGE `calculate_distance()`: Allow for many more distance measures.
 
-* BUG FIX: Import `desc::desc()` where needed.
+ * BUG FIX: Import `desc::desc()` where needed.
 
 # dynutils 1.0.5 (2020-02-21)
 

R/calculate_distance.R

@@ -6,6 +6,8 @@
 #' @param y (Optional) a numeric matrix, dense or sparse, with `nrow(x) == nrow(y)`.
 #' @param method Which distance method to use. Options are: `"cosine"`, `"pearson"`, `"spearman"`, `"euclidean"`, and `"manhattan"`.
 #' @param margin Which margin to use for the pairwise comparison. 1 => rowwise, 2 => columnwise.
+#' @param diag if `TRUE`, only compute diagonal elements of the similarity/distance matrix; useful when comparing corresponding rows or columns of 'x' and 'y'.
+#' @param drop0 if `TRUE`, zero values are removed regardless of min_simil or rank.
 #'
 #' @export
 #'
@@ -27,7 +29,9 @@ calculate_distance <- function(
   y = NULL,
   method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
              "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski"),
-  margin = 1
+  margin = 1,
+  diag = FALSE,
+  drop0 = FALSE
 ) {
   method <- match.arg(method)
   input <- .process_input_matrices(x = x, y = y, margin = margin)
@@ -36,15 +40,15 @@ calculate_distance <- function(
 
   dis <-
     if (method %in% c("cosine", "pearson", "spearman")) {
-      sim <- calculate_similarity(x = x, y = y, method = method, margin = 2)
+      sim <- calculate_similarity(x = x, y = y, method = method, margin = 2, diag = diag, drop0 = drop0)
 
       if (method == "cosine") {
         1 - 2 * acos(sim) / pi
       } else {
         1 - (sim + 1) / 2
       }
     } else {
-      proxyC::dist(x = x, y = y, method = method, margin = 2)
+      proxyC::dist(x = x, y = y, method = method, margin = 2, diag = diag, drop0 = drop0)
     }
 
   if (is.null(y)) {
@@ -65,7 +69,9 @@ calculate_similarity <- function(
   x,
   y = NULL,
   margin = 1,
-  method = c("spearman", "pearson", "cosine")
+  method = c("spearman", "pearson", "cosine"),
+  diag = FALSE,
+  drop0 = FALSE
 ) {
   method <- match.arg(method)
   input <- .process_input_matrices(x = x, y = y, margin = margin)
@@ -83,7 +89,7 @@ calculate_similarity <- function(
     method <- "correlation"
   }
 
-  sim <- proxyC::simil(x = x, y = y, method = method, margin = 2)
+  sim <- proxyC::simil(x = x, y = y, method = method, margin = 2, diag = diag, drop0 = drop0)
 
   # fixes due to rounding errors
   if (method %in% c("pearson", "spearman", "cosine")) {
@@ -105,11 +111,11 @@ list_similarity_methods <- function() eval(formals(calculate_similarity)$method)
 #' @importFrom methods as
 .process_input_matrices <- function(x, y, margin) {
   if (is.data.frame(x)) x <- as.matrix(x)
-  if (is.matrix(x)) x <- as(x, "dgCMatrix")
+  if (is.matrix(x)) x <- as(x, "CsparseMatrix")
 
   if (!is.null(y)) {
     if (is.data.frame(y)) y <- as.matrix(y)
-    if (is.matrix(y)) y <- as(y, "dgCMatrix")
+    if (is.matrix(y)) y <- as(y, "CsparseMatrix")
   }
 
   assert_that(

R/h5.R

@@ -166,7 +166,7 @@ write_h5_ <- function(x, file_h5, path) {
   if (is.null(x)) {
     hdf5r::h5attr(subfile, "object_class") <- "null"
   } else if (is_sparse(x)) {
-    ipx <- as(x, "dgCMatrix")
+    ipx <- as(x, "CsparseMatrix")
     hdf5r::h5attr(subfile, "object_class") <- "sparse_matrix"
     subfile[["i"]] <- ipx@i
     subfile[["p"]] <- ipx@p

README.md

@@ -25,17 +25,22 @@ list of changes.
 
 <!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
 
+### Recent changes in dynutils 1.0.7
+
+-   MINOR CHANGE `calculate_distance()`: Convert matrices to
+    CsparseMatrix instead of dgCMatrix.
+
+-   MINOR CHANGE `calculate_distance()`: Pass through the `diag`
+    argument to proxyC.
+
+-   BUG FIX unit test: Order of attributes is not relevant.
+
 ### Recent changes in dynutils 1.0.6
 
 -   MINOR CHANGE `calculate_distance()`: Allow for many more distance
     measures.
 
-### Recent changes in dynutils 1.0.5 (2020-02-21)
-
--   BUG FIX `install_packages()`: will not try to install packages when
-    the session is not interactive.
-
--   LICENSE: Change to MIT.
+-   BUG FIX: Import `desc::desc()` where needed.
 
 ## Dynverse dependencies
 

inst/doc/functionality.html

@@ -39,6 +39,7 @@
 pre > code.sourceCode { white-space: pre; position: relative; }
 pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
 div.sourceCode { margin: 1em 0; }
 pre.sourceCode { margin: 0; }
@@ -363,13 +364,13 @@ <h2>Manipulation of vectors</h2>
 <div id="random_time_string-generates-a-string-very-likely-to-be-unique" class="section level3">
 <h3><code>random_time_string</code>: Generates a string very likely to be unique</h3>
 <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">random_time_string</span>(<span class="st">&quot;test&quot;</span>)</span>
-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210322_122440__test__syYeN626jT&quot;</span></span>
+<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210902_103319__test__syYeN626jT&quot;</span></span>
 <span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a><span class="fu">random_time_string</span>(<span class="st">&quot;test&quot;</span>)</span>
-<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210322_122440__test__e6MCnXcJM7&quot;</span></span>
+<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210902_103319__test__e6MCnXcJM7&quot;</span></span>
 <span id="cb20-6"><a href="#cb20-6" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb20-7"><a href="#cb20-7" aria-hidden="true" tabindex="-1"></a><span class="fu">random_time_string</span>(<span class="st">&quot;test&quot;</span>)</span>
-<span id="cb20-8"><a href="#cb20-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210322_122440__test__9pFJ5mxS3R&quot;</span></span></code></pre></div>
+<span id="cb20-8"><a href="#cb20-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;20210902_103319__test__9pFJ5mxS3R&quot;</span></span></code></pre></div>
 </div>
 </div>
 <div id="tibble-helpers" class="section level2">
@@ -384,7 +385,7 @@ <h3><code>list_as_tibble</code>: Convert a list of lists to a tibble whilst reta
 <span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a>tib <span class="ot">&lt;-</span> <span class="fu">list_as_tibble</span>(li)</span>
 <span id="cb21-7"><a href="#cb21-7" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb21-8"><a href="#cb21-8" aria-hidden="true" tabindex="-1"></a>tib</span>
-<span id="cb21-9"><a href="#cb21-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 2 x 4</span></span>
+<span id="cb21-9"><a href="#cb21-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 2 × 4</span></span>
 <span id="cb21-10"><a href="#cb21-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;       a b      c      .object_class</span></span>
 <span id="cb21-11"><a href="#cb21-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   &lt;dbl&gt; &lt;list&gt; &lt;chr&gt;  &lt;list&gt;       </span></span>
 <span id="cb21-12"><a href="#cb21-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1     1 &lt;fn&gt;   parrot &lt;chr [2]&gt;    </span></span>
@@ -475,7 +476,7 @@ <h2>File helpers</h2>
 <div id="safe_tempdir-create-an-empty-temporary-directory-and-return-its-path" class="section level3">
 <h3><code>safe_tempdir</code>: Create an empty temporary directory and return its path</h3>
 <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">safe_tempdir</span>(<span class="st">&quot;samson&quot;</span>)</span>
-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;/tmp/RtmpYk0E8W/file1b5c4b27ef332b/samson&quot;</span></span></code></pre></div>
+<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;/tmp/RtmpPYnzSd/file3def077bad0e06/samson&quot;</span></span></code></pre></div>
 </div>
 </div>
 <div id="assertion-helpers" class="section level2">

src/RcppExports.cpp

@@ -5,6 +5,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // project_to_segments
 List project_to_segments(NumericMatrix x, NumericMatrix segment_start, NumericMatrix segment_end);
 RcppExport SEXP _dynutils_project_to_segments(SEXP xSEXP, SEXP segment_startSEXP, SEXP segment_endSEXP) {

tests/testthat/test-h5.R

@@ -27,7 +27,7 @@ test_that("is_sparse works", {
 
   m <- Matrix::Matrix(matrix(c(1:10)), sparse = FALSE)
   expect_false(is_sparse(m))
-  expect_true(is_sparse(methods::as(m, "dgCMatrix")))
+  expect_true(is_sparse(methods::as(m, "CsparseMatrix")))
   expect_false(is_sparse(methods::as(m, "dgeMatrix")))
 })
 

tests/testthat/test-news.R

@@ -8,32 +8,32 @@ on.exit(unlink(dir_loc, recursive = TRUE))
 description <- paste0(dir_loc, "/DESCRIPTION")
 news_md <- paste0(dir_loc, "/NEWS.md")
 
-readr::write_lines(c("Package: testing"), description)
-
-readr::write_lines(c(
-  "# testing 0.1.1 (2019-01-02)",
-  " * BUG FIX: Fixing a lot of bugs!",
-  "",
-  "# testing 0.1.0 (2019-01-01)",
-  " * FUNCTIONALITY: Oh man I implemented so many things today!",
-  "   I am so smart, I am so smart",
-  "   https://media0.giphy.com/media/vLruErVSYGx8s/giphy.gif?cid=3640f6095c939f916374546263a8a301",
-  "",
-  "# testing 0.0.1 (2018-12-31)",
-  " * INITIAL RELEASE: super useful package!"
-), news_md)
-
 test_that("update_news works", {
+  # check for description
+  expect_error(detect_package_folder(path = dir_loc), regexp = "Could not find DESCRIPTION file")
+  readr::write_lines(c("Package: testing"), description)
+
+  # check for news
+  expect_error(find_news(path = dir_loc), regexp = "does not have a NEWS.md")
+  readr::write_lines(c(
+    "# testing 0.1.1 (2019-01-02)",
+    " * BUG FIX: Fixing a lot of bugs!",
+    "",
+    "# testing 0.1.0 (2019-01-01)",
+    " * FUNCTIONALITY: Oh man I implemented so many things today!",
+    "   I am so smart, I am so smart",
+    "   https://media0.giphy.com/media/vLruErVSYGx8s/giphy.gif?cid=3640f6095c939f916374546263a8a301",
+    "",
+    "# testing 0.0.1 (2018-12-31)",
+    " * INITIAL RELEASE: super useful package!"
+  ), news_md)
+
+  # read news contents
   recent_news <- recent_news(path = dir_loc, 2)
 
+  # check contents
   expect_is(recent_news, "character")
   expect_true(any(grepl("testing 0.1.1", recent_news)))
   expect_false(any(grepl("testing 0.0.1", recent_news)))
-
-  file.remove(news_md)
-  expect_error(find_news(path = dir_loc), regexp = "does not have a NEWS.md")
-
-  file.remove(description)
-  expect_error(detect_package_folder(path = dir_loc), regexp = "Could not find DESCRIPTION file")
 })
 

tests/testthat/test-tibble.R

@@ -17,13 +17,7 @@ tib <- tibble(
 test_that("list_as_tibble works", {
   tib2 <- list_as_tibble(li)
 
-  expect_equal(attributes(tib2), attributes(tib))
-
-  expect_equal(tib2$a, tib$a)
-  expect_equal(tib2$b, tib$b)
-  expect_equal(tib2$c, tib$c)
-  expect_equal(tib2$d, tib$d)
-  expect_equal(tib2$.object_class, tib$.object_class)
+  expect_equal(tib, tib2)
 })
 
 test_that("tibble_as_list works", {