Merge branch 'master' into staging

1 files changed, 442 insertions, 11 deletions

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 749eed8b57..6ce0ed1424 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1,10 +1,13 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
+;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
+;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
+;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,6 +38,252 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
+(define-public r-tidyverse
+  (package
+    (name "r-tidyverse")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tidyverse" version))
+       (sha256
+        (base32
+         "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-cli" ,r-cli)
+       ("r-crayon" ,r-crayon)
+       ("r-dbplyr" ,r-dbplyr)
+       ("r-dplyr" ,r-dplyr)
+       ("r-forcats" ,r-forcats)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-haven" ,r-haven)
+       ("r-hms" ,r-hms)
+       ("r-httr" ,r-httr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-lubridate" ,r-lubridate)
+       ("r-magrittr" ,r-magrittr)
+       ("r-modelr" ,r-modelr)
+       ("r-purrr" ,r-purrr)
+       ("r-readr" ,r-readr)
+       ("r-readxl" ,r-readxl)
+       ("r-reprex" ,r-reprex)
+       ("r-rlang" ,r-rlang)
+       ("r-rstudioapi" ,r-rstudioapi)
+       ("r-rvest" ,r-rvest)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://tidyverse.tidyverse.org")
+    (synopsis "Install and load packages from the \"Tidyverse\"")
+    (description
+     "The @code{tidyverse} is a set of packages that work in harmony because
+they share common data representations and API design.  This package is
+designed to make it easy to install and load multiple tidyverse packages in a
+single step.")
+    (license license:gpl3)))
+
+(define-public r-rvest
+  (package
+    (name "r-rvest")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rvest" version))
+       (sha256
+        (base32
+         "04mv99z8dixywx96kfy4215g6ib23s7qvd77hcf9pxqxzcvqhvhd"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-httr" ,r-httr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-selectr" ,r-selectr)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://github.com/hadley/rvest")
+    (synopsis "Simple web scraping for R")
+    (description
+     "@code{r-rvest} helps you scrape information from web pages.  It is
+designed to work with @code{magrittr} to make it easy to express common web
+scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
+    (license license:gpl3)))
+
+(define-public r-selectr
+  (package
+    (name "r-selectr")
+    (version "0.3-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "selectr" version))
+       (sha256
+        (base32
+         "0kdrj64rqg4z6hg92y9r2h602a2i73r5rnlpg23ys33d5d32n8jy"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-stringr" ,r-stringr)))
+    (home-page "https://sjp.co.nz/projects/selectr/")
+    (synopsis "Translate CSS selectors to XPath expressions")
+    (description
+     "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
+expression.  This allows you to use CSS selectors when working with the XML
+package as it can only evaluate XPath expressions.  Also provided are
+convenience functions useful for using CSS selectors on XML nodes.  This
+package is a port of the Python package @code{cssselect}.")
+    (license license:bsd-3)))
+
+(define-public r-reprex
+  (package
+    (name "r-reprex")
+    (version "0.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reprex" version))
+       (sha256
+        (base32
+         "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-callr" ,r-callr)
+       ("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-whisker" ,r-whisker)))
+    (home-page "https://github.com/tidyverse/reprex")
+    (synopsis "Prepare reproducible R code examples for sharing")
+    (description
+     "This package provides a convenience wrapper that uses the
+@code{rmarkdown} package to render small snippets of code to target formats
+that include both code and output.  The goal is to encourage the sharing of
+small, reproducible, and runnable examples on code-oriented websites or email.
+@code{reprex} also extracts clean, runnable R code from various common formats,
+such as copy/paste from an R session.")
+    (license license:expat)))
+
+(define-public r-callr
+  (package
+    (name "r-callr")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "callr" version))
+       (sha256
+        (base32
+         "0m51p39vfwldxv6h8x4y9w3laf8q9bldhfqhlcrlx3xhy3irb1bp"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-crayon" ,r-crayon)
+       ("r-debugme" ,r-debugme)
+       ("r-r6" ,r-r6)
+       ("r-testthat" ,r-testthat)))
+    (home-page "https://github.com/r-lib/callr#readme")
+    (synopsis "Call R from R")
+    (description
+     "It is sometimes useful to perform a computation in a separate R process,
+without affecting the current R process at all.  This packages does exactly
+that.")
+    (license license:expat)))
+
+(define-public r-readxl
+  (package
+    (name "r-readxl")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "readxl" version))
+       (sha256
+        (base32
+         "1bf7gxw9r11m4llyymplxiaa4gzgyj4bwmwad5in756pzq3jzmpv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cellranger" ,r-cellranger)
+       ("r-rcpp" ,r-rcpp)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://readxl.tidyverse.org")
+    (synopsis "Read Excel files")
+    (description
+     "This package lets you import Excel files into R.  It supports
+@file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
+the embedded @code{RapidXML} C++ library.")
+    ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
+    ;; 'rapidxml' which is Boost.
+    (license (list license:gpl3 license:bsd-2 license:boost1.0))))
+
+(define-public r-modelr
+  (package
+    (name "r-modelr")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "modelr" version))
+       (sha256
+        (base32
+         "1rqw0b583vp107zqp4h3wj51dvv4hb3wszfr1f5f48xassc53f95"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-lazyeval" ,r-lazyeval)
+       ("r-magrittr" ,r-magrittr)
+       ("r-purrr" ,r-purrr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/tidyverse/modelr")
+    (synopsis "Helper functions for modelling in pipelines")
+    (description
+     "Functions for modelling that help you seamlessly integrate modelling
+into a pipeline of data manipulation and visualisation.")
+    (license license:gpl3)))
+
+(define-public r-haven
+  (package
+    (name "r-haven")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "haven" version))
+       (sha256
+        (base32
+         "1fkcvsrnw8waqwggv0aydbvbi99x5kp9g78xfxj4w6s3xvdzcysz"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-forcats" ,r-forcats)
+       ("r-hms" ,r-hms)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readr" ,r-readr)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://haven.tidyverse.org")
+    (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
+    (description
+     "This package lets you mport foreign statistical formats into R via the
+embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
+    (license license:expat)))
+
+(define-public r-amap
+  (package
+    (name "r-amap")
+    (version "0.8-14")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "amap" version))
+              (sha256
+               (base32
+                "1dz37z9v4zvyvqrs4xvpfv468jwvpxav60qn2w0049bw8llj6xdl"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
+    (synopsis "Another multidimensional analysis package")
+    (description "This package provides tools for clustering and principal
+component analysis (with robust methods, and parallelized functions).")
+    (license license:gpl2+)))
+
 (define-public r-ape
   (package
     (name "r-ape")
@@ -131,6 +380,27 @@ inspired by Python's Literal String Interpolation (PEP-0498) and
 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
     (license license:expat)))
 
+(define-public r-pastecs
+  (package
+   (name "r-pastecs")
+   (version "1.3.21")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "pastecs" version))
+            (sha256
+             (base32
+              "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-boot" ,r-boot)))
+   (home-page "http://www.sciviews.org/pastecs")
+   (synopsis "Analysis of space-time ecological series")
+   (description
+    "This package provides functions for regulation, decomposition and analysis
+of space-time series.  The @code{pastecs} library is a PNEC-Art4 and IFREMER
+initiative to bring PASSTEC 2000 functionalities to R.")
+   (license license:gpl2+)))
+
 (define-public r-plogr
   (package
     (name "r-plogr")
@@ -757,14 +1027,14 @@ or excesses over a high threshold.")
 (define-public r-lmtest
   (package
     (name "r-lmtest")
-    (version "0.9-35")
+    (version "0.9-36")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lmtest" version))
        (sha256
         (base32
-         "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
+         "0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-zoo" ,r-zoo)))
@@ -779,6 +1049,26 @@ tools for inference in parametric models are provided.")
     ;; Either version is okay
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-idr
+  (package
+    (name "r-idr")
+    (version "1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "idr" version))
+              (sha256
+               (base32
+                "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/idr/")
+    (synopsis "Irreproducible discovery rate")
+    (description
+     "This is a package for estimating the copula mixture model and plotting
+correspondence curves in \"Measuring reproducibility of high-throughput
+experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
+by Li, Brown, Huang, and Bickel")
+    (license license:gpl2+)))
+
 (define-public r-inline
   (package
     (name "r-inline")
@@ -1329,14 +1619,14 @@ created using basic graphics.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.4.3")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "119pc2jnxvm13cvd77c7d14p3bn68f4jm310vj3yfck40101n9if"))))
+         "081x87sy6dmfvkgwfjrl5ax51k77ciyzg9x3xql25vdi92rmwj3m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -1625,6 +1915,29 @@ University Press.  It provides smoothing methods for nonparametric regression
 and density estimation")
     (license license:gpl2+)))
 
+(define-public r-venndiagram
+  (package
+    (name "r-venndiagram")
+    (version "1.6.20")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "VennDiagram" version))
+              (sha256
+               (base32
+                "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
+    (properties `((upstream-name . "VennDiagram")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-futile-logger" ,r-futile-logger)))
+    (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
+    (synopsis "Generate High-Resolution Venn and Euler Plots")
+    (description
+     "This package provides a set of functions to generate high-resolution
+Venn and Euler plots.  It includes handling for several special cases,
+including two-case scaling, and extensive customization of plot shape and
+structure.")
+    (license license:gpl2+)))
+
 (define-public r-vioplot
   (package
     (name "r-vioplot")
@@ -2288,16 +2601,16 @@ published results; and a routine for graphical display.")
 (define-public r-network
   (package
     (name "r-network")
-    (version "1.13.0")
+    (version "1.13.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "network" version))
        (sha256
         (base32
-         "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s"))))
+         "1bbkbqkqf1d7irfwh08c13c2pfypir1ssvlqrln83irqns1ikdv0"))))
     (build-system r-build-system)
-    (home-page "http://statnet.org/")
+    (home-page "https://statnet.org/")
     (synopsis "Classes for relational data")
     (description
      "This package provides tools to create and modify network objects.  The
@@ -2319,7 +2632,7 @@ supports arbitrary vertex/edge/graph attributes.")
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
-    (home-page "http://www.statnet.org")
+    (home-page "https://statnet.org")
     (synopsis "R scripts and utilities used by the Statnet software")
     (description "This package provides non-statistical utilities used by the
 software developed by the Statnet Project.")
@@ -2340,7 +2653,7 @@ software developed by the Statnet Project.")
     (propagated-inputs
      `(("r-network" ,r-network)
        ("r-statnet-common" ,r-statnet-common)))
-    (home-page "http://www.statnet.org")
+    (home-page "https://statnet.org")
     (synopsis "Tools for social network analysis")
     (description
      "This package provides a range of tools for social network analysis,
@@ -3273,3 +3586,121 @@ those functions to be used with time series including specifications that may
 contain lags, diffs and missing values.")
     ;; Any GPL version.
     (license license:gpl2+)))
+
+(define-public r-catdap
+  (package
+    (name "r-catdap")
+    (version "1.3.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "catdap" version))
+       (sha256
+        (base32
+         "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/catdap/")
+    (synopsis "Tools for categorical data analysis")
+    (description
+     "This package provides functions for analyzing multivariate data.
+Dependencies of the distribution of the specified variable (response
+variable) to other variables (explanatory variables) are derived and
+evaluated by the @dfn{Akaike Information Criterion} (AIC).")
+    (license license:gpl2+)))
+
+(define-public r-arules
+  (package
+    (name "r-arules")
+    (version "1.6-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "arules" version))
+       (sha256
+        (base32
+         "14gbq5k2zkx4wc7kkfazz313ngij89qp1xmyxfg3nq3v1s84c3sl"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)))
+    (home-page "https://github.com/mhahsler/arules")
+    (synopsis "Mining association rules and frequent itemsets")
+    (description
+     "This package provides an infrastructure for representing, manipulating
+and analyzing transaction data and patterns (frequent itemsets and association rules).
+It also provides C implementations of the association mining algorithms Apriori
+and Eclat.")
+    (license license:gpl3)))
+
+(define-public r-parsedate
+  (package
+    (name "r-parsedate")
+    (version "1.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "parsedate" version))
+       (sha256
+        (base32
+         "0mg7hbm3903iwvmpn51gjpaaq03rsp72hjb1g8h5g84r81iha002"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/gaborcsardi/parsedate")
+    (synopsis
+     "Recognize and parse dates in various formats")
+    (description
+     "This package provides three functions for dealing with dates:
+@code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
+time formats, @code{parse_date} parses dates in unspecified formats,
+and @code{format_iso_8601} formats a date in ISO 8601 format.")
+    (license license:gpl2)))
+
+(define-public r-abc-data
+  (package
+    (name "r-abc-data")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abc.data" version))
+       (sha256
+        (base32
+         "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
+    (properties `((upstream-name . "abc.data")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/abc.data/")
+    (synopsis "Data for Approximate Bayesian Computation (ABC) package")
+    (description
+     "This package contains data which are used by functions of the abc
+package which implements several @dfn{Approximate Bayesian Computation} (ABC)
+algorithms for performing parameter estimation, model selection, and
+goodness-of-fit.")
+    (license license:gpl3+)))
+
+(define-public r-abc
+  (package
+    (name "r-abc")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abc" version))
+       (sha256
+        (base32
+         "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abc-data" ,r-abc-data)
+       ("r-locfit" ,r-locfit)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-quantreg" ,r-quantreg)))
+    (home-page "https://cran.r-project.org/web/packages/abc/")
+    (synopsis "Tools for Approximate Bayesian Computation (ABC)")
+    (description
+     "This package implements several @dfn{Approximate Bayesian
+Computation} (ABC) algorithms for performing parameter estimation, model
+selection, and goodness-of-fit.  Cross-validation tools are also available for
+measuring the accuracy of ABC estimates, and to calculate the
+misclassification probabilities of different models.")
+    (license license:gpl3+)))