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Integrating Phylogenies and Ecology

v1.8.2 · Jun 10, 2020 · GPL-2

Description

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

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r-devel-macos-arm64 NOTE
r-devel-windows-x86_64 NOTE
r-oldrel-macos-arm64 NOTE
r-oldrel-macos-x86_64 NOTE
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Check details (16 non-OK)
NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Steven W. Kembel <steve.kembel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Steven", "W."),
                      family = "Kembel",
                      role = c("aut", "cre"),
                      email = "steve.kembel@gmail.com"),
               person(given = c("David", "D."),
                      family = "Ackerly",
                      role = "aut",
                      email = "dackerly@berkeley.edu"),
               person(given = c("Simon", "P."),
                      family = "Blomberg",
                      role = "aut",
                      email = "s.blomberg1@uq.edu.au"),
               person(given = c("Will", "K."),
                      family = "Cornwell",
                      role = "aut",
                      email = "cornwell@zoology.ubc.ca"),
               person(given = c("Peter", "D."),
                      family = "Cowan",
                      role = "aut",
                      email = "pdc@berkeley.edu"),
               person(given = c("Matthew", "R."),
                      family = "Helmus",
                      role = "aut",
                      email = "mrhelmus@wisc.edu"),
               person(given = "Helene",
                      family = "Morlon",
                      role = "aut",
                      email = "morlon.helene@gmail.com"),
               person(given = c("Campbell", "O."),
                      family = "Webb",
                      role = "aut",
                      email = "cwebb@oeb.harvard.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Steven W. Kembel <steve.kembel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Steven", "W."),
                      family = "Kembel",
                      role = c("aut", "cre"),
                      email = "steve.kembel@gmail.com"),
               person(given = c("David", "D."),
                      family = "Ackerly",
                      role = "aut",
                      email = "dackerly@berkeley.edu"),
               person(given = c("Simon", "P."),
                      family = "Blomberg",
                      role = "aut",
                      email = "s.blomberg1@uq.edu.au"),
               person(given = c("Will", "K."),
                      family = "Cornwell",
                      role = "aut",
                      email = "cornwell@zoology.ubc.ca"),
               person(given = c("Peter", "D."),
                      family = "Cowan",
                      role = "aut",
                      email = "pdc@berkeley.edu"),
               person(given = c("Matthew", "R."),
                      family = "Helmus",
                      role = "aut",
                      email = "mrhelmus@wisc.edu"),
               person(given = "Helene",
                      family = "Morlon",
                      role = "aut",
                      email = "morlon.helene@gmail.com"),
               person(given = c("Campbell", "O."),
                      family = "Webb",
                      role = "aut",
                      email = "cwebb@oeb.harvard.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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NOTE r-devel-windows-x86_64

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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-oldrel-macos-arm64

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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-oldrel-macos-x86_64

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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
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NOTE r-oldrel-windows-x86_64

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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
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Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Steven W. Kembel <steve.kembel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Steven", "W."),
                      family = "Kembel",
                      role = c("aut", "cre"),
                      email = "steve.kembel@gmail.com"),
               person(given = c("David", "D."),
                      family = "Ackerly",
                      role = "aut",
                      email = "dackerly@berkeley.edu"),
       
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Steven W. Kembel <steve.kembel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Steven", "W."),
                      family = "Kembel",
                      role = c("aut", "cre"),
                      email = "steve.kembel@gmail.com"),
               person(given = c("David", "D."),
                      family = "Ackerly",
                      role = "aut",
                      email = "dackerly@berkeley.edu"),
       
NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-release-macos-arm64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?

Reverse Dependencies (20)

depends

Dependency Network

Dependencies Reverse dependencies ape vegan nlme EcoIndR idar CommEcol DAMOCLES PCPS betapart bivariatemaps pez recluster RRphylo canaper cati ecolottery enveomics.R fishtree +5 more reverse deps picante

Version History

new 1.8.2 Mar 10, 2026