Add phyloregion r package

common/r-packages.scm

@@ -266,4 +266,100 @@
         "Estimating time to the common ancestor for a beneficial allele")
       (description
         "This package uses carriers and non-carriers of a beneficial mutation to estimate the time to the common ancester.")
-      (license #f))))
\ No newline at end of file
+      (license #f))))
+
+(define-public r-clustmixtype
+  (package
+    (name "r-clustmixtype")
+    (version "0.2-15")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "clustMixType" version))
+        (sha256
+          (base32 "1m43xhqc7jcdj1h5nlp0daz99s1nfss7rwwjn7qqf1hvscblyp3s"))))
+    (properties `((upstream-name . "clustMixType")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcolorbrewer r-tibble))
+    (home-page "https://cran.r-project.org/package=clustMixType")
+    (synopsis "k-Prototypes Clustering for Mixed Variable-Type Data")
+    (description
+      "This package provides functions to perform k-prototypes partitioning clustering
+for mixed variable-type data according to Z.Huang (1998): Extensions to the
+k-Means Algorithm for Clustering Large Data Sets with Categorical Variables,
+Data Mining and Knowledge Discovery 2, 283-304, <DOI:10.1023/A:1009769707641>.")
+    (license gpl2+)))
+
+(define-public r-betapart
+  (package
+    (name "r-betapart")
+    (version "1.5.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "betapart" version))
+        (sha256
+          (base32 "1m2rykch2vhh90s08s9s2kmmrxhp9ik32s5zkdw8991cbw2j7n68"))))
+    (properties `((upstream-name . "betapart")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-ape
+            r-dosnow
+            r-fastmatch
+            r-foreach
+            r-geometry
+            r-itertools
+            r-picante
+            r-rcdd
+            r-snow))
+    (home-page "https://cran.r-project.org/package=betapart")
+    (synopsis
+      "Partitioning Beta Diversity into Turnover and Nestedness Components")
+    (description
+      "This package provides functions to compute pair-wise dissimilarities (distance
+matrices) and multiple-site dissimilarities, separating the turnover and
+nestedness-resultant components of taxonomic (incidence and abundance based),
+functional and phylogenetic beta diversity.")
+    (license gpl2+)))
+
+(define-public r-phyloregion
+  (package
+    (name "r-phyloregion")
+    (version "1.0.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "phyloregion" version))
+        (sha256
+          (base32 "161pjy66vhpjwc4h9q4jiqpyzn0v4nawx8ahspjpc7a376rk5552"))))
+    (properties `((upstream-name . "phyloregion")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-ape
+            r-betapart
+            r-clustmixtype
+            r-colorspace
+            r-dismo
+            r-igraph
+            r-matrix
+            r-phangorn
+            r-randomforest
+            r-raster
+            r-rgdal
+            r-rgeos
+            r-sp
+            r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/darunabas/phyloregion")
+    (synopsis "Biogeographic Regionalization and Macroecology")
+    (description
+      "Computational infrastructure for biogeography, community ecology, and
+biodiversity conservation (Daru et al.  2020) <doi:10.1111/2041-210X.13478>.  It
+is based on the methods described in Daru et al. (2020)
+<doi:10.1038/s41467-020-15921-6>.  The original conceptual work is described in
+Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of
+biogeographical regionalization.  Additionally, the package contains fast and
+efficient functions to compute more standard conservation measures such as
+phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and
+global endangerment, as well as compositional turnover (e.g., beta diversity).")
+    (license agpl3+)))
\ No newline at end of file