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rptR

Goal

The goal of rptR is to provide point estimates, confidence intervals and significance tests for the repeatability (intra-class correlation coefficient) of measurements based on generalised linear mixed models (GLMMs). The function ?summary.rpt produces summaries in a detailed format, whereby ?plot.rpt plots the distributions of bootstrap or permutation test estimates.

Citation

When using rptR, please cite our paper:

Stoffel, M. A., Nakagawa, S., & Schielzeth, H. (2017). rptR: Repeatability estimation and variance decomposition by generalized linear mixed-effects models. Methods in Ecology and Evolution, 8(11), 1639-1644.

Installation

You can install the stable version of rptR from CRAN with:

install.packages("rptR")

Or the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("mastoffel/rptR", build_vignettes = TRUE, dependencies = TRUE) 
# manual
browseVignettes("rptR")

If you find a bug, please report a minimal reproducible example in the issues.

Example

Repeatability of beetle body length (BodyL) for both Container and Population while adjusting for Treatment and Sex:

library(rptR)
data(BeetlesBody)

rpts <- rpt(BodyL ~ Treatment + Sex + (1 | Container) + (1 | Population), 
            grname = c("Container", "Population"), data = BeetlesBody, 
            datatype = "Gaussian", nboot = 100, npermut = 100)

summary(rpts)
#> 
#> Repeatability estimation using the lmm method
#> 
#> Call = rpt(formula = BodyL ~ Treatment + Sex + (1 | Container) + (1 | Population), grname = c("Container", "Population"), data = BeetlesBody, datatype = "Gaussian", nboot = 100, npermut = 100)
#> 
#> Data: 960 observations
#> ----------------------------------------
#> 
#> Container (120 groups)
#> 
#> Repeatability estimation overview: 
#>       R     SE   2.5%  97.5% P_permut  LRT_P
#>  0.0834 0.0247 0.0449  0.135     0.01      0
#> 
#> Bootstrapping and Permutation test: 
#>             N    Mean   Median   2.5%  97.5%
#> boot      100 0.08428 0.077960 0.0449 0.1352
#> permut    100 0.00428 0.000315 0.0000 0.0232
#> 
#> Likelihood ratio test: 
#> logLik full model = -1528.553
#> logLik red. model = -1555.264
#> D  = 53.4, df = 1, P = 1.34e-13
#> 
#> ----------------------------------------
#> 
#> 
#> Population (12 groups)
#> 
#> Repeatability estimation overview: 
#>       R     SE   2.5%  97.5% P_permut  LRT_P
#>   0.491  0.107  0.233  0.644     0.02      0
#> 
#> Bootstrapping and Permutation test: 
#>             N   Mean Median   2.5%  97.5%
#> boot      100  0.477  0.491  0.233  0.644
#> permut    100  0.454  0.453  0.422  0.483
#> 
#> Likelihood ratio test: 
#> logLik full model = -1528.553
#> logLik red. model = -1595.399
#> D  = 134, df = 1, P = 3.19e-31
#> 
#> ----------------------------------------

Plotting

rptR estimates uncertainties around repeatability estimates with parametric bootstrapping. The distribution of bootstrap estimates can easily be plotted.

plot(rpts, grname="Container", type="boot", cex.main=0.8, col = "#ECEFF4")
plot(rpts, grname="Population", type="boot", cex.main=0.8, col = "#ECEFF4")