Skip to content

phyr

Model Based Phylogenetic Analysis

v1.1.3 · Nov 11, 2025 · GPL-3
CRAN GitHub Mirror

Description

A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).

Downloads

10.6K

Last 30 days

1213th

31.3K

Last 90 days

133.8K

Last year

Trend: +3.6% (30d vs prior 30d)

CRAN Check Status

6 NOTE
8 OK
Show all 14 flavors
Flavor Status
r-devel-linux-x86_64-debian-clang NOTE
r-devel-linux-x86_64-debian-gcc NOTE
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 NOTE
r-oldrel-macos-arm64 NOTE
r-oldrel-macos-x86_64 NOTE
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 NOTE
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (8 non-OK)
NOTE r-devel-linux-x86_64-debian-clang

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-linux-x86_64-debian-gcc

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-windows-x86_64

compiled code

File 'phyr/libs/x64/phyr.dll':
  Found non-API call to R: 'R_UnboundValue'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
NOTE r-oldrel-macos-arm64

installed package size

installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE r-oldrel-macos-x86_64

installed package size

installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE r-patched-linux-x86_64

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.

Check History

NOTE 8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 6, 2026
NOTE r-devel-linux-x86_64-debian-clang

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-linux-x86_64-debian-gcc

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-windows-x86_64

compiled code

File 'phyr/libs/x64/phyr.dll':
  Found non-API call to R: 'R_UnboundValue'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
NOTE r-patched-linux-x86_64

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘INLA’
ERROR 8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 4, 2026
NOTE r-devel-linux-x86_64-debian-clang

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
ERROR r-devel-linux-x86_64-debian-gcc

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-windows-x86_64

compiled code

File 'phyr/libs/x64/phyr.dll':
  Found non-API call to R: 'R_UnboundValue'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
NOTE r-patched-linux-x86_64

compiled code

File ‘phyr/libs/phyr.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘INLA’
NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘INLA’

Reverse Dependencies (2)

imports

rr2

suggests

phylosem

Dependency Network

Dependencies Reverse dependencies ape Rcpp Matrix dplyr lme4 nloptr gridExtra mvtnorm latticeExtra tidyr rr2 phylosem phyr

Version History

new 1.1.3 Mar 10, 2026
updated 1.1.3 ← 1.1.0 diff Nov 10, 2025
updated 1.1.0 ← 1.0.2 diff Dec 17, 2020
updated 1.0.2 ← 1.0.1 diff Nov 12, 2019
updated 1.0.1 ← 1.0.0 diff Nov 9, 2019
new 1.0.0 Oct 23, 2019