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Integrating Phylogenies and Ecology

v1.8.2 · Jun 10, 2020 · GPL-2
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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
r-oldrel-windows-x86_64 NOTE
r-patched-linux-x86_64 NOTE
r-release-linux-x86_64 NOTE
r-release-macos-arm64 NOTE
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r-release-windows-x86_64 NOTE
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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checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
NOTE r-devel-macos-arm64

Rd files

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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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) traitgram.Rd:14: Escaped LaTeX specials: \$
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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 ?
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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-oldrel-macos-x86_64

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checkRd: (-1) IvesGodfray.Rd:12: 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 ?
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checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 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
...[truncated]...
vard.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

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
...[truncated]...
vard.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-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
...[truncated]...
atrix.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-fedora-gcc

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 ?
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...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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-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
...[truncated]...
atrix.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: \$ \$

Reverse Dependencies (19)

depends

idar

imports

CommEcol DAMOCLES PCPS betapart bivariatemaps pez recluster

suggests

RRphylo canaper cati ecolottery enveomics.R fishtree microeco pctax phylospatial phyr treestats

Dependency Network

Dependencies Reverse dependencies ape vegan nlme idar CommEcol DAMOCLES PCPS betapart bivariatemaps pez recluster RRphylo canaper cati ecolottery enveomics.R fishtree microeco +4 more reverse deps picante

Version History

new 1.8.2 Mar 10, 2026
updated 1.8.2 ← 1.8.1 diff Jun 9, 2020
updated 1.8.1 ← 1.8 diff Feb 12, 2020
updated 1.8 ← 1.7 diff Mar 20, 2019
updated 1.7 ← 1.6-2 diff May 13, 2018
updated 1.6-2 ← 1.6-1 diff Mar 4, 2014
updated 1.6-1 ← 1.6-0 diff Oct 31, 2013
updated 1.6-0 ← 1.5-2 diff May 30, 2013
updated 1.5-2 ← 1.5-1 diff Oct 8, 2012
updated 1.5-1 ← 1.4-2 diff Oct 1, 2012
updated 1.4-2 ← 1.4-1 diff Sep 21, 2012
updated 1.4-1 ← 1.3-0 diff Sep 3, 2012
updated 1.3-0 ← 1.2-0 diff Apr 23, 2011
updated 1.2-0 ← 1.1-1 diff Jul 23, 2010
updated 1.1-1 ← 1.1-0 diff May 21, 2010
updated 1.1-0 ← 1.0-1 diff Apr 9, 2010
updated 1.0-1 ← 1.0-0 diff Mar 3, 2010
updated 1.0-0 ← 0.7-2 diff Feb 14, 2010
updated 0.7-2 ← 0.7-1 diff Oct 26, 2009
updated 0.7-1 ← 0.7-0 diff Jul 2, 2009