diff --git a/.Rbuildignore b/.Rbuildignore index 52cdf487..b57faadf 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,7 +7,6 @@ ^cran-comments\.md$ ^CRAN-RELEASE$ ^LICENSE\.md$ -^NEWS\.Rmd$ ^README\.Rmd$ ^data-raw$ ^doc$ @@ -17,6 +16,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^\.github$ -^\.covrignore$ ^paper\.md$ ^paper\.bib$ diff --git a/.covrignore b/.covrignore deleted file mode 100644 index 08e998d6..00000000 --- a/.covrignore +++ /dev/null @@ -1,2 +0,0 @@ -^\R\deprecate\.R$ -^\R\zzz\.R$ diff --git a/DESCRIPTION b/DESCRIPTION index 511ec0e3..b1d1e0a8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: tabula Title: Analysis, Seriation and Visualization of Archaeological Count Data -Version: 1.3.0.9000 +Version: 1.4.0 Authors@R: c(person(given = "Nicolas", family = "Frerebeau", diff --git a/NEWS.Rmd b/NEWS.Rmd deleted file mode 100644 index ab508ad8..00000000 --- a/NEWS.Rmd +++ /dev/null @@ -1,121 +0,0 @@ ---- -output: github_document -header-includes: - - \usepackage{amsmath} - - \usepackage{amssymb} -editor_options: - chunk_output_type: console ---- - - - -```{r, echo = FALSE, message=FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>" -) -``` - -## tabula `r utils::packageVersion("tabula")` (`r Sys.Date()`) - -## tabula 1.3.0 (release date: 2019-09-20) -### New classes and methods -* `Matrix` this S4 class is now the superclass of all matrix-like classes. -* `AbundanceMatrix` this virtual S4 class is defined as the superclass of `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix`. -* `SpaceTime` this S4 class represents space-time informations. -* `as_*()` coerce a `matrix` or `data.frame` to a `CountMatrix`, `FrequencyMatrix`, `IncidenceMatrix`, `OccurrenceMatrix` or `SimilarityMatrix`. -* `date_event()` replaces `dateEvent()`. -* `date_mcd()` allows Mean Ceramic Date estimation. -* `get_dates()` and `set_dates<-` allow to extract and replace chronological informations in `AbundanceMatrix` objects. -* `plot_bertin()` and `plot_ford()` replace `plotBar()`. -* `plot_date()` replaces `plotDate()`. -* `plot_date()` gained a method for `AbundanceMatrix` objects. -* `plot_heatmap()` replaces `plotMatrix()`. -* `plot_rank()` replaces `plotRank()`. -* `plot_spot()` replaces `plotSpot()`. -* `plot_time()` produces an abundance *vs.* time graph. -* `refine_dates()` and `refine_seriation()` replace `refine()`. -* `seriate_reciprocal()` and `seriate_correspondance()` replace `seriate()`. -* `test_diversity()` allows Shannon diversity test. -* `test_fit()` produces a Frequency Increment Test. - -### Bugfixes & changes -* `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix` now also contain the `SpaceTime` class. -* Deprecate `plotBar()`, `plotMatrix()`, `plotRank()`, `plotSpot()`, `refine()`, `seriate()`. -* Remove `dateEvent()`. -* Empty rows/columns are removed prior to CA seriation to avoid error in `svd()`. - -### Enhancements -* Add the Merzbach ceramics dataset. -* The `plot_date()` method for `DateModel` objects now allows to display an activity or a tempo plot. - -### Internals -* Reduce required R version to 3.2. -* Error handling has been revised and error messages have been harmonized. -* Refer to {ggplot2} functions using `::` (stop importing the entire package). -* Use {vdiffr} to test graphical output. -* Replace `FactoMinerR::CA()` with `ca::ca()` (this avoids having to install all {FactoMineR} dependencies when only one function is used). -* Remove {dplyr} from the imported packages, move {magrittr} to suggested packages. - -### Experimental -* When a `Matrix` object is first created, an identifier (UUID v4) is generated with `generate_uuid()`. This ID is preserved when coercing to another class. This makes it possible to identify objects representing the same initial data and associate them with the results of specific computations. -* `get_coordinates()` and `set_coordinates<-` allow to extract and replace spatial informations in `AbundanceMatrix` objects. -* `get_features()` allows to convert an `AbundanceMatrix` object to a `data.frame`. It is intended for compatibility with the {sf} package. - -## tabula 1.2.0 (release date: 2019-03-20) -### New classes and methods -* The function `dateEvent()` allows to compute chronological models as described in Bellanger and Husi (2006). -* `DateModel` this S4 class stores the results of `dateEvent()`. -* `SimilarityMatrix` this S4 class represents a (dis)similarity matrix. -* `plotDate()` method for `DateModel` objects. -* `plotSpot()` methods for `SimilarityMatrix` and `OccurrenceMatrix` objects. -* `[` operators for several classes. - -### Bugfixes & changes -* `OccurrenceMatrix` now stores the number of times each pair of taxa occurs together in at least one sample. -* `similarity()` now returns an object of class `SimilarityMatrix`. -* `plotBar()` no longer add confidence interval by default. -* Remove useless accessors. - -### Enhancements -* `similarity()` gained a new estimator: binomial co-occurrence assessment method (similarity between types). -* `seriate()` gained a new argument to pass a `BootCA` object. - -### Internals -* Add an optional progress bars with {pbapply} in long running functions. - -## tabula 1.1.0 (release date: 2018-12-30) -### Bugfixes & changes -* `similarity()` now returns a symmetric matrix. - -### Enhancements -* `richness()` gained new estimators: - * For abundance data: Chao1, bias-corrected Chao1, improved Chao1 and Abundance-based Coverage Estimator (ACE). - * For replicated incidence data: Chao2, bias-corrected Chao2, improved Chao2 and Incidence-based Coverage Estimator (ICE). - -### Internals -* Add references in the `Description` field of the DESCRIPTION file. -* Split the documentation for alpha-diversity measures. -* Split the documentation for beta-diversity measures. - -## tabula 1.0.0 (release date: 2018-12-03) - -* Initial version on CRAN - -### New classes and methods -* `BootCA` this S4 class stores partial bootstrap CA-based seriation results. -* `[[` operators acting on `PermutationOrder` and `BootCA` to extract parts. - -### Bugfixes & changes -* `refine()` method for `CountMatrix` now use `stats::rmultinorm()` for partial bootstrap CA. - -### Enhancements -* Add the Zuni and Mississippi ceramics datasets. -* `similarity()` gained a new estimator: the Brainerd-Robinson coefficient of similarity. - -### Internals -* Add a vignette for matrix seriation. - -## tabula 0.9.0 (release date: 2018-11-16) - -* First release. diff --git a/NEWS.md b/NEWS.md index 4b13d6d7..2435dfc4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,163 +1,128 @@ +## tabula 1.4.0 +* Published in the [*Journal of Open Source Software*](https://doi.org/10.21105/joss.01821). +### New classes and methods +* `DiversityIndex`, `HeterogeneityIndex`, `EvennessIndex` and `RichnessIndex` S4 classes represent diversity index. +* `index_heterogeneity()` replaces `diversity()`. +* `index_evenness()` replaces `evenness()`. +* `index_richness()` replaces `richness()`. +* `index_composition()` allows to estimate asymptotic species richness. +* `plot_diversity()` produces a diversity *vs.* sample size graph and allow to compare estimates with simulated assemblages. +* Add replacement methods for the `*Matrix` classes. +### Bugfixes & changes +* Deprecate `diversity()`, `evenness()` and `richness()`. +### Internals +* Display progress bars only if `interactive()` is `TRUE` and {pbapply} is installed. - - - - -## tabula 1.3.0 +## tabula 1.3.0 (release date: 2019-09-20) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3455385.svg)](https://doi.org/10.5281/zenodo.3455385) ### New classes and methods - - - `Matrix` this S4 class is now the superclass of all matrix-like - classes. - - `AbundanceMatrix` this virtual S4 class is defined as the superclass - of `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix`. - - `SpaceTime` this S4 class represents space-time informations. - - `as_*()` coerce a `matrix` or `data.frame` to a `CountMatrix`, - `FrequencyMatrix`, `IncidenceMatrix`, `OccurrenceMatrix` or - `SimilarityMatrix`. - - `date_event()` replaces `dateEvent()`. - - `date_mcd()` allows Mean Ceramic Date estimation. - - `get_dates()` and `set_dates<-` allow to extract and replace - chronological informations in `AbundanceMatrix` objects. - - `plot_bertin()` and `plot_ford()` replace `plotBar()`. - - `plot_date()` replaces `plotDate()`. - - `plot_date()` gained a method for `AbundanceMatrix` objects. - - `plot_heatmap()` replaces `plotMatrix()`. - - `plot_rank()` replaces `plotRank()`. - - `plot_spot()` replaces `plotSpot()`. - - `plot_time()` produces an abundance *vs.* time graph. - - `refine_dates()` and `refine_seriation()` replace `refine()`. - - `seriate_reciprocal()` and `seriate_correspondance()` replace - `seriate()`. - - `test_diversity()` allows Shannon diversity test. - - `test_fit()` produces a Frequency Increment Test. +* `Matrix` S4 class is now the superclass of all matrix-like classes. +* `AbundanceMatrix` virtual S4 class is defined as the superclass of `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix`. +* `SpaceTime` S4 class represents space-time informations. +* `as_*()` coerce a `matrix` or `data.frame` to a `CountMatrix`, `FrequencyMatrix`, `IncidenceMatrix`, `OccurrenceMatrix` or `SimilarityMatrix`. +* `date_event()` replaces `dateEvent()`. +* `date_mcd()` allows Mean Ceramic Date estimation. +* `get_dates()` and `set_dates<-` allow to extract and replace chronological informations in `AbundanceMatrix` objects. +* `plot_bertin()` and `plot_ford()` replace `plotBar()`. +* `plot_date()` replaces `plotDate()`. +* `plot_date()` gained a method for `AbundanceMatrix` objects. +* `plot_heatmap()` replaces `plotMatrix()`. +* `plot_rank()` replaces `plotRank()`. +* `plot_spot()` replaces `plotSpot()`. +* `plot_time()` produces an abundance *vs.* time graph. +* `refine_dates()` and `refine_seriation()` replace `refine()`. +* `seriate_reciprocal()` and `seriate_correspondance()` replace `seriate()`. +* `test_diversity()` allows Shannon diversity test. +* `test_fit()` produces a Frequency Increment Test. ### Bugfixes & changes - - - `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix` now also - contain the `SpaceTime` class. - - Deprecate `plotBar()`, `plotMatrix()`, `plotRank()`, `plotSpot()`, - `refine()`, `seriate()`. - - Remove `dateEvent()`. - - Empty rows/columns are removed prior to CA seriation to avoid error - in `svd()`. +* `CountMatrix`, `FrequencyMatrix` and `IncidenceMatrix` now also contain the `SpaceTime` class. +* Deprecate `plotBar()`, `plotMatrix()`, `plotRank()`, `plotSpot()`, `refine()`, `seriate()`. +* Remove `dateEvent()`. +* Empty rows/columns are removed prior to CA seriation to avoid error in `svd()`. ### Enhancements - - - Add the Merzbach ceramics dataset. - - The `plot_date()` method for `DateModel` objects now allows to - display an activity or a tempo plot. +* Add the Merzbach ceramics dataset. +* The `plot_date()` method for `DateModel` objects now allows to display an activity or a tempo plot. ### Internals - - - Reduce required R version to 3.2. - - Error handling has been revised and error messages have been - harmonized. - - Refer to {ggplot2} functions using `::` (stop importing the entire - package). - - Use {vdiffr} to test graphical output. - - Replace `FactoMinerR::CA()` with `ca::ca()` (this avoids having to - install all {FactoMineR} dependencies when only one function is - used). - - Remove {dplyr} from the imported packages, move {magrittr} to - suggested packages. +* Reduce required R version to 3.2. +* Error handling has been revised and error messages have been harmonized. +* Refer to {ggplot2} functions using `::` (stop importing the entire package). +* Use {vdiffr} to test graphical output. +* Replace `FactoMinerR::CA()` with `ca::ca()` (this avoids having to install all {FactoMineR} dependencies when only one function is used). +* Remove {dplyr} from the imported packages, move {magrittr} to suggested packages. ### Experimental - - - When a `Matrix` object is first created, an identifier (UUID v4) is - generated with `generate_uuid()`. This ID is preserved when coercing - to another class. This makes it possible to identify objects - representing the same initial data and associate them with the - results of specific computations. - - `get_coordinates()` and `set_coordinates<-` allow to extract and - replace spatial informations in `AbundanceMatrix` objects. - - `get_features()` allows to convert an `AbundanceMatrix` object to a - `data.frame`. It is intended for compatibility with the {sf} - package. +* When a `Matrix` object is first created, an identifier (UUID v4) is generated with `generate_uuid()`. This ID is preserved when coercing to another class. This makes it possible to identify objects representing the same initial data and associate them with the results of specific computations. +* `get_coordinates()` and `set_coordinates<-` allow to extract and replace spatial informations in `AbundanceMatrix` objects. +* `get_features()` allows to convert an `AbundanceMatrix` object to a `data.frame`. It is intended for compatibility with the {sf} package. ## tabula 1.2.0 (release date: 2019-03-20) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2600844.svg)](https://doi.org/10.5281/zenodo.2600844) ### New classes and methods - - - The function `dateEvent()` allows to compute chronological models as - described in Bellanger and Husi (2006). - - `DateModel` this S4 class stores the results of `dateEvent()`. - - `SimilarityMatrix` this S4 class represents a (dis)similarity - matrix. - - `plotDate()` method for `DateModel` objects. - - `plotSpot()` methods for `SimilarityMatrix` and `OccurrenceMatrix` - objects. - - `[` operators for several classes. +* The function `dateEvent()` allows to compute chronological models as described in Bellanger and Husi (2006). +* `DateModel` this S4 class stores the results of `dateEvent()`. +* `SimilarityMatrix` this S4 class represents a (dis)similarity matrix. +* `plotDate()` method for `DateModel` objects. +* `plotSpot()` methods for `SimilarityMatrix` and `OccurrenceMatrix` objects. +* `[` operators for several classes. ### Bugfixes & changes - - - `OccurrenceMatrix` now stores the number of times each pair of taxa - occurs together in at least one sample. - - `similarity()` now returns an object of class `SimilarityMatrix`. - - `plotBar()` no longer add confidence interval by default. - - Remove useless accessors. +* `OccurrenceMatrix` now stores the number of times each pair of taxa occurs together in at least one sample. +* `similarity()` now returns an object of class `SimilarityMatrix`. +* `plotBar()` no longer add confidence interval by default. +* Remove useless accessors. ### Enhancements - - - `similarity()` gained a new estimator: binomial co-occurrence - assessment method (similarity between types). - - `seriate()` gained a new argument to pass a `BootCA` object. +* `similarity()` gained a new estimator: binomial co-occurrence assessment method (similarity between types). +* `seriate()` gained a new argument to pass a `BootCA` object. ### Internals - - - Add an optional progress bars with {pbapply} in long running - functions. +* Add an optional progress bars with {pbapply} in long running functions. ## tabula 1.1.0 (release date: 2018-12-30) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2529084.svg)](https://doi.org/10.5281/zenodo.2529084) ### Bugfixes & changes - - - `similarity()` now returns a symmetric matrix. +* `similarity()` now returns a symmetric matrix. ### Enhancements - - - `richness()` gained new estimators: - - For abundance data: Chao1, bias-corrected Chao1, improved Chao1 - and Abundance-based Coverage Estimator (ACE). - - For replicated incidence data: Chao2, bias-corrected Chao2, - improved Chao2 and Incidence-based Coverage Estimator (ICE). +* `richness()` gained new estimators: +* For abundance data: Chao1, bias-corrected Chao1, improved Chao1 and Abundance-based Coverage Estimator (ACE). +* For replicated incidence data: Chao2, bias-corrected Chao2, improved Chao2 and Incidence-based Coverage Estimator (ICE). ### Internals - - - Add references in the `Description` field of the DESCRIPTION file. - - Split the documentation for alpha-diversity measures. - - Split the documentation for beta-diversity measures. +* Add references in the `Description` field of the DESCRIPTION file. +* Split the documentation for alpha-diversity measures. +* Split the documentation for beta-diversity measures. ## tabula 1.0.0 (release date: 2018-12-03) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1881131.svg)](https://doi.org/10.5281/zenodo.1881131) - - Initial version on CRAN +* Initial version on CRAN ### New classes and methods - - - `BootCA` this S4 class stores partial bootstrap CA-based seriation - results. - - `[[` operators acting on `PermutationOrder` and `BootCA` to extract - parts. +* `BootCA` this S4 class stores partial bootstrap CA-based seriation results. +* `[[` operators acting on `PermutationOrder` and `BootCA` to extract parts. ### Bugfixes & changes - - - `refine()` method for `CountMatrix` now use `stats::rmultinorm()` - for partial bootstrap CA. +* `refine()` method for `CountMatrix` now use `stats::rmultinorm()` for partial bootstrap CA. ### Enhancements - - - Add the Zuni and Mississippi ceramics datasets. - - `similarity()` gained a new estimator: the Brainerd-Robinson - coefficient of similarity. +* Add the Zuni and Mississippi ceramics datasets. +* `similarity()` gained a new estimator: the Brainerd-Robinson coefficient of similarity. ### Internals - - - Add a vignette for matrix seriation. +* Add a vignette for matrix seriation. ## tabula 0.9.0 (release date: 2018-11-16) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1489945.svg)](https://doi.org/10.5281/zenodo.1489945) - - First release. +* Beta release. diff --git a/R/tabula-package.R b/R/tabula-package.R index 078c4ad6..aed70d63 100644 --- a/R/tabula-package.R +++ b/R/tabula-package.R @@ -2,16 +2,17 @@ #' \tabular{ll}{ #' \strong{Package:} \tab tabula \cr #' \strong{Type:} \tab Package \cr -#' \strong{Version:} \tab 1.3.0 \cr +#' \strong{Version:} \tab 1.4.0 \cr #' \strong{License:} \tab GPL-3 \cr -#' \strong{DOI:} \tab \href{https://doi.org/10.5281/zenodo.1489944}{10.5281/zenodo.1489944} +#' \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 #' } #' @author #' \strong{Full list of authors and contributors} (alphabetic order) #' #' \tabular{ll}{ -#' Nicolas Frerebeau \tab \emph{Université Bordeaux Montaigne, France} \cr #' Jean-Baptiste Fourvel \tab \emph{CNRS, France} \cr +#' Nicolas Frerebeau \tab \emph{Université Bordeaux Montaigne, France} \cr #' Brice Lebrun \tab \emph{Aix-Marseille Université, France} \cr #' Ben Marwick \tab \emph{University of Washington, USA} \cr #' Matthew Peeples \tab \emph{Arizona State University, USA} \cr @@ -38,9 +39,12 @@ # See https://github.com/tidyverse/magrittr/issues/29 if(getRversion() >= "2.15.1") utils::globalVariables(c(".")) +#' @importFrom ca ca +#' @importFrom ggplot2 ggplot aes coord_fixed element_blank element_rect +#' element_text facet_wrap geom_line geom_path geom_point geom_tile labs +#' scale_size_area scale_x_continuous scale_x_discrete scale_x_log10 +#' scale_y_continuous scale_y_discrete scale_y_log10 theme #' @importFrom methods as callNextMethod new setClass setClassUnion setGeneric #' setMethod validObject -#' @importFrom ca ca -#' @importFrom ggplot2 ggplot aes geom_path geom_point labs scale_x_log10 #' @importFrom rlang .data NULL diff --git a/README.Rmd b/README.Rmd index f4221596..a1aac2cb 100644 --- a/README.Rmd +++ b/README.Rmd @@ -209,8 +209,7 @@ plot_date(model, type = "tempo", select = "LZ1105") + ```{r diversity} mississippi %>% as_count() %>% - diversity(simplify = TRUE) %>% - head() + index_heterogeneity(method = "shannon") ## Test difference in Shannon diversity between assemblages ## (returns a matrix of adjusted p values) diff --git a/README.md b/README.md index 73802827..2d569c50 100644 --- a/README.md +++ b/README.md @@ -176,7 +176,7 @@ incidence <- IncidenceMatrix(data = sample(0:1, 400, TRUE, c(0.6, 0.4)), # Correspondance analysis-based seriation (indices <- seriate_reciprocal(incidence, margin = c(1, 2))) #> Permutation order for matrix seriation: -#> Matrix ID: a3257479-d188-48e1-9720-1c64c20f0509 +#> Matrix ID: 9639e796-f714-402c-baa6-35541d7e1b96 #> 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 #> Method: reciprocal @@ -240,15 +240,29 @@ referred to as indices of *heterogeneity*): ``` r mississippi %>% as_count() %>% - diversity(simplify = TRUE) %>% - head() -#> berger brillouin mcintosh shannon simpson -#> 10-P-1 0.4052288 1.1572676 0.4714431 1.2027955 0.3166495 -#> 11-N-9 0.6965699 0.7541207 0.2650711 0.7646565 0.5537760 -#> 11-N-1 0.6638526 0.9192403 0.2975381 0.9293974 0.5047209 -#> 11-O-10 0.6332288 0.8085445 0.2990830 0.8228576 0.5072514 -#> 11-N-4 0.6034755 0.7823396 0.2997089 0.7901428 0.5018826 -#> 13-N-5 0.4430380 0.9442803 0.4229570 0.9998430 0.3823434 + index_heterogeneity(method = "shannon") +#> +#> index +#> 10-P-1 1.2027955 +#> 11-N-9 0.7646565 +#> 11-N-1 0.9293974 +#> 11-O-10 0.8228576 +#> 11-N-4 0.7901428 +#> 13-N-5 0.9998430 +#> 13-N-4 1.2051989 +#> 13-N-16 1.1776226 +#> 13-O-11 1.1533432 +#> 13-O-10 1.2884172 +#> 13-P-1 1.1725355 +#> 13-P-8 1.5296294 +#> 13-P-10 1.7952443 +#> 13-O-7 1.1627477 +#> 13-O-5 1.0718463 +#> 13-N-21 0.9205717 +#> 12-O-5 1.1751002 +#> Holden Lake 0.7307620 +#> 13-N-15 1.1270126 +#> 12-N-3 1.0270291 ## Test difference in Shannon diversity between assemblages ## (returns a matrix of adjusted p values) diff --git a/codemeta.json b/codemeta.json index 66e923b3..cde9f5df 100644 --- a/codemeta.json +++ b/codemeta.json @@ -5,8 +5,8 @@ ], "@type": "SoftwareSourceCode", "identifier": "tabula", - "description": "An easy way to examine archaeological count data. This package provides a convenient and reproducible toolkit for relative and absolute dating and analysis of (chronological) patterns. It includes functions for matrix seriation (reciprocal ranking, CA-based seriation), chronological modeling and dating of archaeological assemblages and/or objects. Beyond these, the package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). The package make it easy to visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.", - "name": "tabula: Analysis, Seriation and Visualization of Archaeological Count Data", + "description": "An easy way to examine archaeological count data. This package \n provides a convenient and reproducible toolkit for relative and absolute \n dating and analysis of (chronological) patterns. It includes functions for \n matrix seriation (reciprocal ranking, CA-based seriation), chronological \n modeling and dating of archaeological assemblages and/or objects. \n Beyond these, the package provides several tests and measures of diversity: \n heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), \n richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), \n turnover and similarity (Brainerd-Robinson, etc.). \n The package make it easy to visualize count data and statistical thresholds: \n rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.", + "name": "tabula: Analysis, Seriation and Visualization of Archaeological\n Count Data", "codeRepository": "http://github.com/nfrerebeau/tabula", "relatedLink": [ "http://tabula.archaeo.science", @@ -15,14 +15,14 @@ ], "issueTracker": "http://github.com/nfrerebeau/tabula/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.3.0", + "version": "1.4.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", - "version": "3.6.0", + "version": "3.6.1", "url": "https://r-project.org" }, - "runtimePlatform": "R version 3.6.0 (2019-04-26)", + "runtimePlatform": "R version 3.6.1 (2019-07-05)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -103,7 +103,7 @@ "@type": "SoftwareApplication", "identifier": "khroma", "name": "khroma", - "version": ">= 1.2.0", + "version": ">= 1.3.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -277,7 +277,7 @@ ], "citation": [ { - "@type": "SoftwareSourceCode", + "@type": "ScholarlyArticle", "datePublished": "2019", "author": [ { @@ -286,9 +286,20 @@ "familyName": "Frerebeau" } ], - "name": "{tabula}: Analysis, Seriation and Visualization of Archaeological Count Data", - "url": "https://doi.org/10.5281/zenodo.1489944", - "description": "R package version 1.3.0" + "name": "{tabula}: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data", + "identifier": "10.21105/joss.01821", + "@id": "https://doi.org/10.21105/joss.01821", + "sameAs": "https://doi.org/10.21105/joss.01821", + "isPartOf": { + "@type": "PublicationIssue", + "issueNumber": "4", + "datePublished": "2019", + "isPartOf": { + "@type": ["PublicationVolume", "Periodical"], + "volumeNumber": "39", + "name": "Journal of Open Source Software" + } + } } ] } diff --git a/cran-comments.md b/cran-comments.md index 11f83666..d4943711 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -9,7 +9,8 @@ 0 errors | 0 warnings | 1 note * Some links in the documentation point to articles behind paywalls that may return a 403 error. -* CRAN Package Check notes for v1.2.0 have been fixed. +* CRAN package check error with long doubles disabled has been fixed. +* CRAN package check notes have been fixed. ## Reverse dependencies diff --git a/inst/CITATION b/inst/CITATION index 0a74d1ff..3a3e08a9 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,19 +1,17 @@ citHeader("To cite tabula in publications use:") -citEntry(entry = "Manual", - title = "{tabula}: Analysis, Seriation and Visualization of Archaeological Count Data", +citEntry(entry = "Article", + title = "{tabula}: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data", author = c(person("Nicolas", "Frerebeau", role = "aut")), year = "2019", - organization = "Université Bordeaux Montaigne", - address = "Pessac, France", - note = "R package version 1.3.0", - url = "https://doi.org/10.5281/zenodo.1489944", + journal = "Journal of Open Source Software", + volume = "39", + number = "4", + doi = "10.21105/joss.01821", textVersion = paste("Frerebeau, Nicolas (2019).", - "tabula: Analysis, Seriation and Visualization of Archaeological Count Data.", - "R package version 1.3.0", - "Université Bordeaux Montaigne, Pessac, France.", - "DOI 10.5281/zenodo.1489944.", - "URL https://cran.r-project.org/package=tabula.") + "tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data.", + "Journal of Open Source Software,", + "DOI 10.21105/joss.01821.") ) diff --git a/man/tabula-package.Rd b/man/tabula-package.Rd index 1c2a15e6..d04d4c08 100644 --- a/man/tabula-package.Rd +++ b/man/tabula-package.Rd @@ -26,9 +26,10 @@ An easy way to examine archaeological count data. This package \tabular{ll}{ \strong{Package:} \tab tabula \cr \strong{Type:} \tab Package \cr - \strong{Version:} \tab 1.3.0 \cr + \strong{Version:} \tab 1.4.0 \cr \strong{License:} \tab GPL-3 \cr - \strong{DOI:} \tab \href{https://doi.org/10.5281/zenodo.1489944}{10.5281/zenodo.1489944} + \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 } } \seealso{ @@ -45,8 +46,8 @@ Useful links: \strong{Full list of authors and contributors} (alphabetic order) \tabular{ll}{ - Nicolas Frerebeau \tab \emph{Université Bordeaux Montaigne, France} \cr Jean-Baptiste Fourvel \tab \emph{CNRS, France} \cr + Nicolas Frerebeau \tab \emph{Université Bordeaux Montaigne, France} \cr Brice Lebrun \tab \emph{Aix-Marseille Université, France} \cr Ben Marwick \tab \emph{University of Washington, USA} \cr Matthew Peeples \tab \emph{Arizona State University, USA} \cr