version 1.5.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tabula
 Title: Analysis, Seriation and Visualization of Archaeological Count
         Data
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: 
     c(person(given = "Nicolas",
              family = "Frerebeau",
@@ -59,7 +59,7 @@ Suggests: covr (>= 3.3.1), khroma (>= 1.3.0), knitr, magrittr (>= 1.5),
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Collate: 'utilities.R' 'AllClasses.R' 'AllGenerics.R' 'coerce.R'
         'data.R' 'date.R' 'deprecate.R' 'extract.R' 'index-diversity.R'
         'index-heterogeneity.R' 'index-rarefaction.R'
@@ -69,12 +69,12 @@ Collate: 'utilities.R' 'AllClasses.R' 'AllGenerics.R' 'coerce.R'
         'refine.R' 'seriation.R' 'seriate.R' 'show.R' 'statistics.R'
         'tabula-package.R' 'test.R' 'validate.R' 'zzz.R'
 NeedsCompilation: no
-Packaged: 2020-01-14 10:53:21 UTC; nicolas
+Packaged: 2020-03-19 11:12:43 UTC; nicolas
 Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
   Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>),
   Matthew Peeples [ctb] (<https://orcid.org/0000-0003-4496-623X>),
   Ben Marwick [ctb] (<https://orcid.org/0000-0001-7879-4531>),
   Anne Philippe [ctb],
   Jean-Baptiste Fourvel [ctb] (<https://orcid.org/0000-0002-1061-4642>)
 Repository: CRAN
-Date/Publication: 2020-01-16 13:20:02 UTC
+Date/Publication: 2020-03-19 11:40:03 UTC

MD5

@@ -1,7 +1,7 @@
-0e85aab82c300170945593ce013c9379 *DESCRIPTION
+c5f6d6b015be80db9f9225ed1f4725be *DESCRIPTION
 a3681dd5b56fdf5fca15b93274a43d5a *NAMESPACE
-6e9267559049ad57501c1c5ef469b908 *NEWS.md
-ca47214f2e174c3feee199162a0f577d *R/AllClasses.R
+f1a769332596548e5e11d1fcffd280fa *NEWS.md
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 dbf00f11ecea3a15c775c7c90d4aee16 *R/AllGenerics.R
 e820192dff9dae8fc9687b76a1b9ec16 *R/coerce.R
 9a2b9d364f9a84b7361b82c7b0e157e6 *R/data.R
@@ -22,36 +22,36 @@ f1f4ff6c193007d270a8776e50500c57 *R/plot-prepare.R
 b2d37ee2edf9a983ce64bd597cc0b4bb *R/plot-rank.R
 27d353f4e2ce9fe35ac322259f51d760 *R/plot-spot.R
 647ea627090cd7612251f01881b27c53 *R/plot-time.R
-facbea74321a059204c97be0417e4ad0 *R/refine.R
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 a2dc04a0d74d00c65db71de21831d3a9 *R/seriate.R
 2c4bd3063481471ad3fac36f5405a0bf *R/seriation.R
 4f7516c4c5f31e23d479f636e604e6d0 *R/show.R
 9bf41f0771a6f7c5b771dbbcf0c413ee *R/statistics.R
-f11c877004ece8ed56c47e11e7ec7dcb *R/tabula-package.R
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 8200cd88ac020159b0577b4e7cea0271 *R/test.R
 0080df68abc0c927576dd4c6f947d61d *R/utilities.R
-6e0f277215c8c4bccd8f2e515bd5ff50 *R/validate.R
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 b328eef7a85da57bd494614a4b571aa0 *R/zzz.R
-f08286f5ec43eebb20c1f60d281ceb7f *README.md
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 4c7ca12004ee42aa7eae2c932bed529e *data/boves.rda
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 e76a64149c1be068929e9ee0ce9775e7 *inst/examples/ex-plot_bar.R
@@ -65,15 +65,15 @@ f57496df0d5884b62f09f2bd22af4eb2 *inst/examples/ex-seriation.R
 9a398311352c5a595514585ab1aae2c3 *inst/examples/ex-similarity.R
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@@ -86,47 +86,47 @@ daaf06c58d7066b2be5484941f628f76 *man/figures/README-plot-time-1.png
 dfd9a02a33a942eac8985964e7b986b6 *man/figures/README-similarity-brainerd-1.png
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 5c4fb2f495aa6a45e711855a6c11198d *tests/figs/plots/rank-count-log-x.svg
@@ -135,10 +135,10 @@ c52f4d91a71dfe82b5602c96b6578a60 *tests/figs/plots/rank-count-log-xy.svg
 7318cdf99cbe48bdd4b67e4ee3adc19e *tests/figs/plots/rank-count-log-yx.svg
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 37752bced6e62be9a270180dc71fb92e *tests/testthat.R

NEWS.md

@@ -1,4 +1,10 @@
-## tabula 1.5.0
+## tabula 1.5.1
+## Bugfixes & changes
+* CRAN pacakge check warning (r-devel) has been fixed (use a `stringsAsFactors = FALSE` default).
+
+## tabula 1.5.0 (CRAN release date: 2020-01-16)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3612110.svg)](https://doi.org/10.5281/zenodo.3612110)
+
 ### Internals
 * Depend on {arkhe}.
 

R/AllClasses.R

@@ -262,13 +262,13 @@ setMethod(
 
     .Object@id <- if (missing(id)) arkhe:::generate_uuid() else id
     if (missing(rows)) {
-      rows <- list(id = factor(), x = numeric(0), y = numeric(0))
+      rows <- list(id = character(0), x = numeric(0), y = numeric(0))
     } else {
       rows
     }
     .Object@rows <- rows
     if (missing(columns)) {
-      columns <- list(id = factor(), x = numeric(0), y = numeric(0))
+      columns <- list(id = character(0), x = numeric(0), y = numeric(0))
     } else {
       columns
     }

R/refine.R

@@ -33,11 +33,12 @@ setMethod(
     id_rows <- rep(names(hull_rows),
                    times = vapply(hull_rows, nrow, numeric(1)))
     rows <- do.call(rbind.data.frame, hull_rows)
-    rows <- cbind.data.frame(id = id_rows, rows)
+    rows <- data.frame(id = id_rows, rows, stringsAsFactors = FALSE)
+
     id_cols <- rep(names(hull_columns),
                    times = vapply(hull_columns, nrow, numeric(1)))
     cols <- do.call(rbind.data.frame, hull_columns)
-    cols <- cbind.data.frame(id = id_cols, cols)
+    cols <- data.frame(id = id_cols, cols, stringsAsFactors = FALSE)
 
     .BootCA(
       id = arkhe::get_id(object),

R/tabula-package.R

@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  \strong{Package:} \tab tabula \cr
 #'  \strong{Type:} \tab Package \cr
-#'  \strong{Version:} \tab 1.5.0 \cr
+#'  \strong{Version:} \tab 1.5.1 \cr
 #'  \strong{License:} \tab GPL-3 \cr
 #'  \strong{DOI:} \tab \href{https://doi.org/10.5281/zenodo.1489944}{10.5281/zenodo.1489944} \cr
 #'  \strong{JOSS:} \tab \href{https://doi.org/10.21105/joss.01821}{10.21105/joss.01821} \cr

R/validate.R

@@ -89,7 +89,7 @@ setValidity(
       arkhe:::catch_conditions(arkhe:::check_length(rows, 3)),
       arkhe:::catch_conditions(arkhe:::check_lengths(rows)),
       arkhe:::catch_conditions(arkhe:::check_names(rows, c("id", "x", "y"))),
-      arkhe:::catch_conditions(arkhe:::check_type(rows[[1]], "integer")),
+      arkhe:::catch_conditions(arkhe:::check_type(rows[[1]], "character")),
       arkhe:::catch_conditions(arkhe:::check_type(rows[[2]], "numeric")),
       arkhe:::catch_conditions(arkhe:::check_type(rows[[3]], "numeric")),
       unlist(lapply(
@@ -103,7 +103,7 @@ setValidity(
       arkhe:::catch_conditions(arkhe:::check_length(columns, 3)),
       arkhe:::catch_conditions(arkhe:::check_lengths(columns)),
       arkhe:::catch_conditions(arkhe:::check_names(columns, c("id", "x", "y"))),
-      arkhe:::catch_conditions(arkhe:::check_type(columns[[1]], "integer")),
+      arkhe:::catch_conditions(arkhe:::check_type(columns[[1]], "character")),
       arkhe:::catch_conditions(arkhe:::check_type(columns[[2]], "numeric")),
       arkhe:::catch_conditions(arkhe:::check_type(columns[[3]], "numeric")),
       unlist(lapply(

README.md

@@ -68,7 +68,7 @@ remotes::install_github("nfrerebeau/tabula")
 ``` r
 # Load packages
 library(tabula)
-#> Loading required package: codex
+#> Loading required package: arkhe
 
 library(khroma)
 library(ggplot2)
@@ -92,7 +92,7 @@ must be saved in its own column and each observation (sample/case) must
 be saved in its own row.
 
 These new classes are of simple use, please refer to the documentation
-of the [**codex**](https://github.com/nfrerebeau/codex) package where
+of the [**arkhe**](https://github.com/nfrerebeau/arkhe) package where
 these classes are defined.
 
 ### Visualization
@@ -150,7 +150,7 @@ incidence <- IncidenceMatrix(data = sample(0:1, 400, TRUE, c(0.6, 0.4)),
 # Get seriation order on rows and columns
 # Correspondance analysis-based seriation
 (indices <- seriate_reciprocal(incidence, margin = c(1, 2)))
-#> <PermutationOrder: 4bffe51c-75f2-4bc3-a2d0-7c005a75b349>
+#> <PermutationOrder: 2116a2a1-18fa-4b40-b68b-37906e31a8c6>
 #> Permutation order for matrix seriation:
 #> - Row order: 1 4 20 3 9 16 19 10 13 2 11 7 17 5 6 18 14 15 8 12...
 #> - Column order: 1 16 9 4 8 14 3 20 13 2 6 18 7 17 5 11 19 12 15 10...
@@ -216,7 +216,7 @@ referred to as indices of *heterogeneity*):
 mississippi %>%
   as_count() %>%
   index_heterogeneity(method = "shannon")
-#> <HeterogeneityIndex: 05b1f084-1042-4314-b597-72a5b9bb6d79>
+#> <HeterogeneityIndex: bdd1c08f-43f6-4396-a7ae-484565a00345>
 #> - Method: shannon
 #>             size     index
 #> 10-P-1       153 1.2027955

inst/doc/bibliography.R

@@ -1,4 +1,4 @@
-## ----setup, include = FALSE----------------------------------------------
+## ----setup, include = FALSE---------------------------------------------------
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"

inst/doc/bibliography.html

@@ -1,19 +1,18 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
 
 <head>
 
 <meta charset="utf-8" />
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
-<meta name="viewport" content="width=device-width, initial-scale=1">
+<meta name="viewport" content="width=device-width, initial-scale=1" />
 
 <meta name="author" content="N. Frerebeau" />
 
-<meta name="date" content="2020-01-14" />
+<meta name="date" content="2020-03-19" />
 
 <title>Bibliography</title>
 
@@ -33,9 +32,6 @@
 font-size: 14px;
 line-height: 1.35;
 }
-#header {
-text-align: center;
-}
 #TOC {
 clear: both;
 margin: 0 0 10px 10px;
@@ -203,7 +199,8 @@
 code > span.co { color: #888888; font-style: italic; } 
 code > span.ot { color: #007020; } 
 code > span.al { color: #ff0000; font-weight: bold; } 
-code > span.fu { color: #900; font-weight: bold; }  code > span.er { color: #a61717; background-color: #e3d2d2; } 
+code > span.fu { color: #900; font-weight: bold; } 
+code > span.er { color: #a61717; background-color: #e3d2d2; } 
 </style>
 
 
@@ -219,7 +216,7 @@
 <h1 class="title toc-ignore">Bibliography</h1>
 <h3 class="subtitle">Comprehensive list of references cited in the package</h3>
 <h4 class="author">N. Frerebeau</h4>
-<h4 class="date">2020-01-14</h4>
+<h4 class="date">2020-03-19</h4>