dat.lim2014 | R Documentation |
Results from studies examining the association between maternal size, offspring size, and number of offsprings.
dat.lim2014
The object is a list containing data frames m_o_size
, m_o_fecundity
, o_o_unadj
, and o_o_adj
that contain the following columns and the corresponding phylogenetic trees called m_o_size_tree
, m_o_fecundity_tree
, o_o_unadj_tree
, and o_o_adj_tree
:
article | numeric | article id |
author | character | study author(s) |
year | numeric | publication year |
species | character | species |
amniotes | character | whether the species was amniotic |
environment | character | whether the species were wild or captive |
reprounit | character | whether the data were based on lifetime reproductive output or a single reproductive event (only in m_o_size and m_o_fecundity ) |
ri | numeric | correlation coefficient |
ni | numeric | sample size |
The object dat.lim2014
includes 4 datasets:
m_o_size | on the correlation between maternal size and offspring size |
m_o_fecundity | on the correlation between maternal size and number of offsprings |
o_o_unadj | on the correlation between offspring size and number of offsprings |
o_o_adj | on the correlation between offspring size and number of offsprings adjusted for maternal size |
Objects m_o_size_tree
, m_o_fecundity_tree
, o_o_unadj_tree
, and o_o_adj_tree
are the corresponding phylogenetic trees for the species included in each of these datasets.
ecology, evolution, correlation coefficients, multilevel models, phylogeny
Wolfgang Viechtbauer, wvb@metafor-project.org, https://www.metafor-project.org
Lim, J. N., Senior, A. M., & Nakagawa, S. (2014). Heterogeneity in individual quality and reproductive trade-offs within species. Evolution, 68(8), 2306–2318. https://doi.org/10.1111/evo.12446
Cinar, O., Nakagawa, S., & Viechtbauer, W. (in press). Phylogenetic multilevel meta-analysis: A simulation study on the importance of modelling the phylogeny. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13760
Hadfield, J. D., & Nakagawa, S. (2010). General quantitative genetic methods for comparative biology: Phylogenies, taxonomies and multi-trait models for continuous and categorical characters. Journal of Evolutionary Biology, 23(3), 494–508. https://doi.org/10.1111/j.1420-9101.2009.01915.x
Nakagawa, S., & Santos, E. S. A. (2012). Methodological issues and advances in biological meta-analysis. Evolutionary Ecology, 26(5), 1253–1274. https://doi.org/10.1007/s10682-012-9555-5
### copy data into 'dat' and examine data
dat <- dat.lim2014$o_o_unadj
dat[1:14, -c(2:3)]
## Not run:
### load metafor package
library(metafor)
### load ape package
library(ape, warn.conflicts=FALSE)
### calculate r-to-z transformed correlations and corresponding sampling variances
dat <- escalc(measure="ZCOR", ri=ri, ni=ni, data=dat)
### copy tree to 'tree'
tree <- dat.lim2014$o_o_unadj_tree
### compute branch lengths
tree <- compute.brlen(tree)
### compute phylogenetic correlation matrix
A <- vcv(tree, corr=TRUE)
### make copy of the species variable
dat$species.phy <- dat$species
### create effect size id variable
dat$esid <- 1:nrow(dat)
### fit multilevel phylogenetic meta-analytic model
res <- rma.mv(yi, vi,
random = list(~ 1 | article, ~ 1 | esid, ~ 1 | species, ~ 1 | species.phy),
R=list(species.phy=A), data=dat)
res
## End(Not run)
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