Installation
To install this package:
devtools::install_github("daijiang/phyr")
# or install from binary file (may not be the latest version)
# macOS
install.packages("https://raw.githubusercontent.com/daijiang/phyr/master/phyr_1.0.3.tgz", repos = NULL)
# Windows
install.packages("https://raw.githubusercontent.com/daijiang/phyr/master/phyr_0.1.6.zip", repos = NULL)Main functions
The phyr package has three groups of functions:
- community phylogenetic diversity metrics (alpha:
psv,psr,pse, etc. and beta:pcd), which were included in thepicantepackage originally. They were updated with c++ to improve speed. - models to estimate correlation between functional traits while
accounting for phylogenetic relationships (
cor_phylo), which was included in theapepackage originally. It has new syntax, much improved performance (c++), and bootstrapping option. - phylogenetic generalized linear mixed models (
pglmm), which was originally included in thepezpackage. It has new model formula syntax that allows straightforward model set up, a faster version of maximum likelihood implementation via c++, and a Bayesian model fitting framework based on INLA.- We hope the model formula proposed here can be used to
standardize PGLMMs set up across different tools (e.g.
brmsfor Stan). - PGLMM for comparative data (
pglmm.compare), which was originally fromape::binaryPGLMM()but has more features.
- We hope the model formula proposed here can be used to
standardize PGLMMs set up across different tools (e.g.
Usage examples of pglmm()
pglmm use similar syntax as lme4::lmer to specify random terms: add
__ (two underscores) at the end of grouping variable (e.g. sp) to
specify both phylogenetic and non-phylogenetic random terms; use
(1|sp__@site) to specify nested term (i.e. species phylogenetic matrix
V_sp nested within the diagonal of site matrix I_site) to test
phylogenetic overdispersion or underdispersion. This should be the most
commonly used one and is equal to kronecker(I_site, V_sp).
We can also use a second phylogeny for bipartite questions. For example,
(1|parasite@host__) will be converted to kronecker(V_host, I_parasite); (1|parasite__@host__) will be converted to
kronecker(V_host, V_parasite).
For details about model formula, see documentation ?phyr::pglmm. More
application examples can be found in Ives 2018
Chapter 4.
library(phyr)library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
comm = comm_a
comm$site = row.names(comm)
dat = tidyr::gather(comm, key = "sp", value = "freq", -site) %>%
left_join(envi, by = "site") %>%
left_join(traits, by = "sp")
dat$pa = as.numeric(dat$freq > 0)
head(dat)
## site sp freq sand shade precip tmin sla veg.height
## 1 s3293 Acer_rubrum 0 80.75 20.9 1.902397 0.1288019 294 170.5
## 2 s3294 Acer_rubrum 3 83.36 45.1 1.902397 0.1288019 294 170.5
## 3 s3295 Acer_rubrum 8 88.83 58.9 1.922669 -0.1061756 294 170.5
## 4 s3296 Acer_rubrum 0 91.24 19.7 1.922669 -0.1061756 294 170.5
## 5 s3297 Acer_rubrum 0 90.04 56.6 1.922669 -0.1061756 294 170.5
## 6 s3299 Acer_rubrum 15 81.87 87.0 1.899665 0.1736423 294 170.5
## disp.mode pa
## 1 Wind 0
## 2 Wind 1
## 3 Wind 1
## 4 Wind 0
## 5 Wind 0
## 6 Wind 1
# phy-LMM
test1 = phyr::pglmm(freq ~ 1 + shade + (1|sp__) + (1|site) + (1|sp__@site),
data = dat, family = "gaussian", REML = FALSE,
cov_ranef = list(sp = phylotree))
## Warning: Drop species from the phylogeny that are not in the variable sp
test1
## Linear mixed model fit by maximum likelihood
##
## Call:freq ~ 1 + shade
##
## logLik AIC BIC
## -463.3 940.6 956.5
##
## Random effects:
## Variance Std.Dev
## 1|sp 7.345e-01 0.8570105
## 1|sp__ 1.800e-04 0.0134157
## 1|site 1.035e-07 0.0003217
## 1|sp__@site 2.138e-05 0.0046238
## residual 3.261e+00 1.8058430
##
## Fixed effects:
## Value Std.Error Zscore Pvalue
## (Intercept) -0.1911039 0.3920853 -0.4874 0.625972
## shade 0.0226917 0.0067263 3.3736 0.000742 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# phy-GLMM
test2 = phyr::pglmm(pa ~ 1 + shade + (1|sp__) + (1|site) + (1|sp__@site),
data = dat, family = "binomial", REML = FALSE,
cov_ranef = list(sp = phylotree))
## Warning: Drop species from the phylogeny that are not in the variable sp
test2
## Generalized linear mixed model for binomial data fit by maximum likelihood
##
## Call:pa ~ 1 + shade
##
##
## Random effects:
## Variance Std.Dev
## 1|sp 1.786e-06 0.001336
## 1|sp__ 4.441e-01 0.666389
## 1|site 4.496e-06 0.002120
## 1|sp__@site 8.689e-06 0.002948
##
## Fixed effects:
## Value Std.Error Zscore Pvalue
## (Intercept) -2.0835724 0.5744500 -3.6271 0.0002867 ***
## shade 0.0165916 0.0087165 1.9035 0.0569784 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# bipartite
tree_site = ape::rtree(n = n_distinct(dat$site), tip.label = sort(unique(dat$site)))
z_bipartite = phyr::pglmm(freq ~ 1 + shade + (1|sp__) + (1|site__) +
(1|sp__@site) + (1|sp@site__) + (1|sp__@site__),
data = dat, family = "gaussian",REML = TRUE,
cov_ranef = list(sp = phylotree, site = tree_site))
## Warning: Drop species from the phylogeny that are not in the variable sp
z_bipartite
## Linear mixed model fit by restricted maximum likelihood
##
## Call:freq ~ 1 + shade
##
## logLik AIC BIC
## -466.0 952.1 974.8
##
## Random effects:
## Variance Std.Dev
## 1|sp 1.648e-02 0.128377
## 1|sp__ 1.173e+00 1.082923
## 1|site 2.792e-02 0.167098
## 1|site__ 8.659e-03 0.093052
## 1|sp__@site 1.965e+00 1.401671
## 1|sp@site__ 7.968e-02 0.282273
## 1|sp__@site__ 8.041e-05 0.008967
## residual 9.625e-01 0.981064
##
## Fixed effects:
## Value Std.Error Zscore Pvalue
## (Intercept) -0.127328 0.815075 -0.1562 0.8759
## shade 0.019393 0.011889 1.6311 0.1029Licenses
Licensed under the GPL-3 license.
Contributing
Contributions are welcome. You can provide comments and feedback or ask questions by filing an issue on Github here or making pull requests.
Code of conduct
Please note that the 'phyr' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.