compressing chronogram database with 'xz'

phylotastic · Jun 18, 2022 · f17b129 · LunaSare · Jan 8, 2024 · f17b129
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.6.3
-Date: 2022-06-09 06:48:13 UTC
-SHA: 40287aa21bc8cec52ccc21e676a222ba2f7768bc
+Version: 0.6.4
+Date: 2022-06-13 05:40:15 UTC
+SHA: 672d4ba276afb5c4bade87cc67c7b6034c7cbcb3
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: datelife
 Title: Scientific Data on Time of Lineage Divergence for Your Taxa
-Version: 0.6.4
+Version: 0.6.5
 Maintainer: Luna L. Sanchez Reyes <[email protected]>
 Authors@R: c(
   person("Brian", "O'Meara", email = "[email protected]", role=c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -4,9 +4,11 @@
 DONE:
 -->
 
-# datelife 0.6.4
-  - data: updated `opentree_chronograms` object. It now has 253 chronograms from Open Tree of Life
-  - examples: set to not run most examples
+# datelife 0.6.5
+  - data: 
+    - updated `opentree_chronograms` object. It now has 253 chronograms from Open Tree of Life and uses "xz" compression. 
+  - examples: 
+    - set to not test examples
   - functions:
     - added functions `matrix_to_table` and `matrices_to_table` that go from a matrix of patristic distances to a table of taxon name pairs and respective node ages.
     - bug fix on `use_calibrations_bladj` that used element $present_calibrations instead of $matched_calibrations

diff --git a/R/opentree_chronograms.R b/R/opentree_chronograms.R
@@ -4,7 +4,7 @@
 #'
 #' @name opentree_chronograms
 #' @docType data
-#' @format A list of four elements, containing data from OpenTree of Life chronograms
+#' @format A list of four elements, containing data from Open Tree of Life chronograms
 #' \describe{
 #'   \item{authors}{A list of lists of author names of the original studies that
 #'     published chronograms in the Open Tree of Life database.}
@@ -26,8 +26,8 @@
 #' remotes::install_github("ROpenSci/bibtex")'
 #' opentree_chronograms <- get_opentree_chronograms()
 #' opentree_chronograms$update <- Sys.time()
-#' opentree_chronograms$version <- '0.6.2'
-#' usethis::use_data(opentree_chronograms, overwrite = T)
+#' opentree_chronograms$version <- '2022.01.28'
+#' usethis::use_data(opentree_chronograms, overwrite = T, compress = "xz")
 #' and updated with update_datelife_cache()
 "opentree_chronograms"
 

diff --git a/R/tree_fix_brlen.R b/R/tree_fix_brlen.R
@@ -1,7 +1,7 @@
 # functions to fix negative or null branch lengths from an ultranetric treem, and to add dates of missing taxa at random
 
 #' Take a tree with branch lengths and fix negative or zero length branches.
-#' @param tree A tree either as a newick character string or as a phylo object
+#' @param tree A tree either as a newick character string or as a `phylo` object.
 #' @param fixing_criterion A character vector specifying the type of branch length to be fixed: "negative" or "zero" (the number 0 is also allowed).
 #' @param fixing_method A character vector specifying the method to fix branch lengths: "bladj", "mrbayes" or a number to be assigned to all branches meeting fixing_criterion
 #' @param ultrametric Boolean indicating whether to force ultrametric or not.

diff --git a/R/tree_processing.R b/R/tree_processing.R
@@ -135,7 +135,8 @@ phylo_check <- function(phy = NULL, brlen = FALSE, dated = FALSE) {
   }
 }
 
-#' Checks if a tree is a phylo class object otherwise it uses input_process. Additionally it can check if tree is a chronogram with phylo_check
+#' Checks if a tree is a phylo class object otherwise it uses input_process.
+#' Additionally it can check if tree is a chronogram with phylo_check
 #' @inheritParams tree_fix_brlen
 #' @inheritDotParams phylo_check -phy
 #' @return If tree is correctly formatted, it returns a `phylo` object.

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 [![CRAN
 status](https://www.r-pkg.org/badges/version/datelife)](https://CRAN.R-project.org/package=datelife)
 ![GitHub R package
-version](https://img.shields.io/github/r-package/v/phylotastic/datelife?color=pink&label=GitHub)
+version](https://img.shields.io/github/r-package/v/phylotastic/datelife?color=green&label=GitHub)
 [![R-CMD-check](https://github.com/phylotastic/datelife/workflows/R-CMD-check/badge.svg)](https://github.com/phylotastic/datelife/actions)
 [![codecov](https://codecov.io/gh/phylotastic/datelife/branch/master/graph/badge.svg)](https://app.codecov.io/gh/phylotastic/datelife)
 [![Github Open
@@ -20,6 +20,8 @@ Issues](https://img.shields.io/github/issues-closed-raw/phylotastic/datelife.svg
 [![NSF-1458603](https://img.shields.io/badge/NSF-1458603-white.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1458603)
 [![NSF-0905606](https://img.shields.io/badge/NSF-0905606-white.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=0905606)
 [![NSF-1458572](https://img.shields.io/badge/NSF-1458572-white.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1458572)
+[![CRAN RStudio mirror
+downloads](https://cranlogs.r-pkg.org/badges/datelife)](https://www.r-pkg.org/pkg/datelife)
 <!-- badges: end -->
 
 # Welcome to DateLife’s R package GitHub repository!
@@ -95,7 +97,7 @@ the accompanying paper:
 O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K,
 Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2022).
 <em>datelife: Scientific Data on Time of Lineage Divergence for Your
-Taxa</em>. R package version 0.6.2,
+Taxa</em>. R package version 0.6.4,
 <a href="https://doi.org/10.5281/zenodo.593938">https://doi.org/10.5281/zenodo.593938</a>.
 </p>
 <p>

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,10 +1,8 @@
-## New submission v 0.6.4
+## New submission v 0.6.5
 This is a new submission where I have:
 
-* addressed note on package size: The package hosts a database of 4.7Mb that is needed to run main functions
-* Removed unnecessary "if (interactive())" from examples
-* Fixed R code problem by useing `inherits` instead of if() conditions comparing class() to string
-* Fixed examples that were failing in some Linux environments.
+* compressed database with "xz" compression, so the package size is now under 5 Mb
+* started the process of moving database object and functions used to create it to its own package
 
 ### Test environments:
 
@@ -20,24 +18,10 @@ This is a new submission where I have:
   - R 4.3 Under development (2022-06-08 r82470)
 
 ### Results
-0 errors ✔ | 0 warnings ✔ | 4 notes ✖
+0 errors ✔ | 0 warnings ✔ | 3 notes ✖
 
 * Note 1
 
-```
-checking installed package size ... NOTE
-    installed size is 6.1Mb
-    sub-directories of 1Mb or more:
-      data         4.7Mb
-```
-
-**Comments**: <br/>
-The package is hosting a database (`data/opentree_chronograms.rda`), increasing the size of the data dir.
-This database is needed to run main functions.
-
-
-* Note 2
-
 ```
 ❯ checking package dependencies ... NOTE
   Packages suggested but not available for checking: 'msa', 'Biostrings'
@@ -50,7 +34,7 @@ This database is needed to run main functions.
 **Comments**: <br/>
 All the packages imported are needed for the datelife workflow.
 
-* Note 3
+* Note 2
 
 ```
 Possibly misspelled words in DESCRIPTION:
@@ -76,7 +60,7 @@ Possibly misspelled words in DESCRIPTION:
 **Comments**: <br/>
 None of these word are misspelled
 
-* Note 4
+* Note 3
 
 ```
 Found the following (possibly) invalid DOIs:

diff --git a/data/opentree_chronograms.rda b/data/opentree_chronograms.rda
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/Getting_started_with_datelife.html b/docs/articles/Getting_started_with_datelife.html
diff --git a/docs/articles/fringiliidae.html b/docs/articles/fringiliidae.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   Getting_started_with_datelife: Getting_started_with_datelife.html
   fringiliidae: fringiliidae.html
-last_built: 2022-06-13T05:35Z
+last_built: 2022-06-20T07:28Z
 urls:
   reference: http://phylotastic.org/datelife/reference
   article: http://phylotastic.org/datelife/articles

diff --git a/docs/reference/birds_and_cats.html b/docs/reference/birds_and_cats.html
diff --git a/docs/reference/build_grove_list.html b/docs/reference/build_grove_list.html
diff --git a/docs/reference/build_grove_matrix.html b/docs/reference/build_grove_matrix.html
diff --git a/docs/reference/check_conflicting_calibrations.html b/docs/reference/check_conflicting_calibrations.html
diff --git a/docs/reference/check_ott_input.html b/docs/reference/check_ott_input.html
diff --git a/docs/reference/choose_cluster.html b/docs/reference/choose_cluster.html
diff --git a/docs/reference/classification_paths_from_taxonomy.html b/docs/reference/classification_paths_from_taxonomy.html
diff --git a/docs/reference/clean_ott_chronogram.html b/docs/reference/clean_ott_chronogram.html
diff --git a/docs/reference/clean_taxon_info_children.html b/docs/reference/clean_taxon_info_children.html
diff --git a/docs/reference/clean_tnrs.html b/docs/reference/clean_tnrs.html
diff --git a/docs/reference/cluster_patristicmatrix.html b/docs/reference/cluster_patristicmatrix.html
diff --git a/docs/reference/congruify_and_check.html b/docs/reference/congruify_and_check.html
diff --git a/docs/reference/congruify_and_mrca_multiPhylo.html b/docs/reference/congruify_and_mrca_multiPhylo.html