version 1.2.0

cran · Mar 20, 2019 · 845ba32 · 845ba32
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: tabula
 Title: Analysis, Seriation and Visualization of Archaeological Count
         Data
-Version: 1.0.0
-Date: 2018-11-22
+Version: 1.2.0
+Date: 2019-03-19
 Authors@R: c(person("Nicolas", "Frerebeau",
-                    email = "data@archaeo.science",
+                    email = "nicolas.frerebeau@u-bordeaux-montaigne.fr",
                     role = c("aut", "cre"),
                     comment = c(ORCID = "https://orcid.org/0000-0001-5759-4944")),
              person("Brice", "Lebrun",
@@ -16,33 +16,37 @@ Authors@R: c(person("Nicolas", "Frerebeau",
                     role = c("ctb"),
                     comment = c(ORCID = "https://orcid.org/0000-0003-4496-623X"))
             )
-Maintainer: Nicolas Frerebeau <data@archaeo.science>
+Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
 Description: An easy way to examine archaeological count data (artifacts, faunal 
-    remains, etc.). This package includes several measures of diversity, e.g. 
-    richness, rarefaction, diversity, turnover, similarity, etc. It also 
-    provides matrix seriation methods for chronological modeling and dating. 
-    The package make it easy to visualize count data and statistical thresholds: 
-    rank/abundance plots, Ford and Bertin diagrams, etc.
+    remains, etc.). This package includes several measures of diversity: e.g. 
+    richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), diversity/dominance 
+    and evenness (Brillouin, Shannon, Simpson, etc.), turnover and similarity 
+    (Brainerd-Robinson, ...). Most of these methods are described and discussed 
+    in Maguran (1988) <doi:10.1007/978-94-015-7358-0>. It also provides matrix 
+    seriation methods (reciprocal ranking, CA-based seriation) for 
+    chronological modeling and dating. The package make it easy to visualize 
+    count data and statistical thresholds: rank/abundance plots, Ford (1972) 
+    <isbn:0913134082> and Bertin (1977) <isbn:2082111121> diagrams, etc.
 URL: http://github.com/nfrerebeau/tabula
 BugReports: http://github.com/nfrerebeau/tabula/issues
 Depends: R (>= 3.4)
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-Collate: 'utilities.R' 'tabula.R' 'AllClasses.R' 'AllGenerics.R'
-        'LogicalMatrix.R' 'NumericMatrix.R' 'index-richness.R'
-        'index-diversity.R' 'alpha-diversity.R' 'index-turnover.R'
-        'index-similarity.R' 'beta-diversity.R' 'data.R'
-        'method-seriation.R' 'statistics.R' 'plot.R' 'seriation.R'
+Collate: 'tabula.R' 'AllClasses.R' 'coerce.R' 'AllGenerics.R' 'data.R'
+        'date.R' 'diversity.R' 'extract.R' 'statistics.R' 'plot.R'
+        'rarefaction.R' 'refine.R' 'richness.R' 'seriation.R'
+        'seriate.R' 'show.R' 'similarity.R' 'turnover.R' 'utilities.R'
+        'validate.R' 'zzz.R'
 RoxygenNote: 6.1.1
-Suggests: testthat, knitr, rmarkdown
+Suggests: covr, khroma, knitr, pbapply, rmarkdown, testthat
 Imports: dplyr (>= 0.7), FactoMineR, ggplot2 (>= 3.0.0), grDevices,
-        magrittr, methods, rlang, stats, tidyr, utils
+        magrittr, methods, plyr, rlang, stats, tidyr, utils
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2018-11-22 17:10:58 UTC; nicolas
+Packaged: 2019-03-19 15:27:35 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>)
 Repository: CRAN
-Date/Publication: 2018-12-03 09:40:03 UTC
+Date/Publication: 2019-03-20 13:10:03 UTC
diff --git a/MD5 b/MD5
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diff --git a/NAMESPACE b/NAMESPACE
@@ -2,25 +2,28 @@
 
 export(CountMatrix)
 export(IncidenceMatrix)
+export(totals)
+exportMethods("[")
 exportMethods("[[")
-exportMethods(columns)
+exportMethods(dateEvent)
 exportMethods(diversity)
 exportMethods(evenness)
-exportMethods(method)
 exportMethods(permute)
 exportMethods(plotBar)
+exportMethods(plotDate)
 exportMethods(plotMatrix)
 exportMethods(plotRank)
 exportMethods(plotSpot)
 exportMethods(rarefaction)
 exportMethods(refine)
 exportMethods(richness)
-exportMethods(rows)
 exportMethods(seriate)
 exportMethods(similarity)
 exportMethods(totals)
 exportMethods(turnover)
+import(dplyr)
 import(ggplot2)
+import(tidyr)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(rlang,":=")
diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,43 @@
+# tabula 1.2.0
+
+* ADD: Belanger and Husi (2006) dating method (#3).
+* ADD: binomial co-occurrence assessment method (similarity between types).
+* ADD: 'SimilarityMatrix' S4 class to represent a (dis)similarity matrix.
+* ADD: 'plotSpot' method for 'SimilarityMatrix' object.
+* ADD: 'plotSpot' method for 'OccurrenceMatrix' object.
+* ADD: '[' methods for several classes.
+* FIX: 'similarity()' now returns a SimilarityMatrix object.
+* FIX: 'plotBar()' does not add confidence interval by default.
+* FIX: add an argument to 'seriate()' to pass a 'BootCA' object (#4).
+* FIX: add an optional progress bars with 'pbapply' in long running functions.
+* FIX: deprecate useless accessors.
+* FiX: 'OccurrenceMatrix' now stores the number of times each pair of taxa occurs together in at least one sample.
+
+# tabula 1.1.0
+
+* ADD: Chao1 estimator for abundance data.
+* ADD: Bias-corrected Chao1 estimator.
+* ADD: Improved Chao1 estimator.
+* ADD: Chao2 estimator for replicated incidence data.
+* ADD: Bias-corrected Chao2 estimator.
+* ADD: Improved Chao2 estimator.
+* ADD: Abundance-based Coverage Estimator (ACE).
+* ADD: Incidence-based Coverage Estimator (ICE).
+* FIX: 'similarity()' now returns a symmetric matrix.
+* FIX: add references in the 'Description' field of the DESCRIPTION file (#1).
+* FIX: split documentation for alpha-diversity measures.
+* FIX: split documentation for beta-diversity measures.
+
+# tabula 1.0.0
+
+* ADD: Brainerd-Robinson coefficient of similarity.
+* ADD: Zuni ceramics dataset.
+* ADD: Mississippi ceramics dataset.
+* ADD: 'BootCA' S4 class to store partial bootstrap CA results.
+* ADD: extract methods for PermutationOrder and BootCA.
+* ADD: vignette for matrix seriation.
+* FIX: use 'stats::rmultinorm()' for partial bootstrap CA.
+
+# tabula 0.9.0
+
+* First release.