This package fits growth models to capture-recapture data of individual sizes. Growth from one time to the next is modeled as a Markov process. Covariates such as environmental variables or individual variables can affect both the intercept and autoregressive parts of the model. Models can include random effects of individual, time, and birth cohort. Time must be in discrete steps. Observations of individual sizes can be missing, but covariates cannot be missing. Individual could represent an individual organism, population, or other unit of replication.
Estimation is done in a state-space framework using maximum marginal likelihood estimation via Template Model Builder.
This package is part of a publication, M E Brooks, C Clements, J Pemberton, and A Ozgul, "Estimation of Individual Growth Trajectories When Repeated Measures Are Missing," The American Naturalist 190, no. 3 (September 2017): 377-388. https://doi.org/10.1086/692797
To install growmod, first install TMB from CRAN, then install growmod via
devtools::install_github("mebrooks/growmod/growmod", build_vignettes = TRUE)
You may need to install the devtools package, compiler tools, and other dependencies first. To install TMB, it may be necessary to install the version of Rtools that matches your version of R.
See vignette("growmod") for an example.
Before publishing results from models fit with growmod, we recommend that you check for potential bias using simulations as described in vignette("sim_growmod").