Hmsc

Build Status

Description

Hierarchical Modelling of Species Communities (Hmsc) is a flexible framework for Joint Species Distribution Modelling (JSDMs). The framework can be used to relate species occurrences or abundances to environmental covariates, species traits and phylogenetic relationships. JSDMs are a special case of species distribution models (SDMs) that take into account the multivariate nature of communities which allows us to estimate community level responses as well capture biotic interactions and the influence of missing covariates in residual species associations.

The Hmsc package contains functions to fit JSDMs, analyze the output and to generate predictions with these JSDMs. The obligatory data for a HMSC analysis includes a matrix of species occurrences or abundances and a matrix of environmental covariates. Optionally, the user can include information species traits, phylogenetic relationships and information on the spatiotemporal context of the sampling design to account for dependencies among the sampling units.

Installation notes

The latest version othe Hmsc package can be installed from GitHub using install_github function from the devtools package, available from CRAN. The following lines should sucessfully install Hmsc to your R in most cases:

install.packages("devtools") # if not yet installed
library(devtools)
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))

To install a specific tagged version of Hmsc, you must add a ref argument. For instance, to install version 3.0-0, modify the GitHub installation line to:

install_github("hmsc-r/HMSC", ref = "v3.0-0")

Getting started

To get started with the package, we recommend to start with reading the package documentation which can be found by typing help('Hmsc-package'), following the vignettes and reading the help pages for the Hmsc, HmscRandomLevel and sampleMcmc functions. The vignettes are available in the ‘vignette’ folder, or can be accessed from within R by typing e.g. vignette(topic = "vignette_1_univariate", package = "Hmsc"). To see a list of vignettes, type vignette(package = "Hmsc").

Documentation

A good place to start for those interested in using the Hmsc package are the following papers:

Ovaskainen, O., Tikhonov, G., Norberg, A., Blanchet, F. G., Duan, L., Dunson, D., Roslin, T. and Abrego, N. 2017. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology Letters 20, 561-576 https://doi.org/10.1111/ele.12757

During the development of Hmsc several papers have been published describing the different components of the model. To learn more about these different components and Joint Species Distribution Modelling in general we recommend to read these articles.

For spatial latent factors:

Ovaskainen, O., Roy, D. B., Fox, R., and Anderson, B. J. 2017. Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models. Methods in Ecology and Evolution, 7, 428-436. https://doi.org/10.1111/2041-210X.12502

For analysis of time series data:

Ovaskainen, O., Tikhonov, G., Dunson, D., Grøtan, V., Engen, S., Sæther, B.-E. and Abrego, N. 2017. How are species interactions structured in species rich communities? A new method for analysing time-series data. Proceedings of the Royal Society B: Biological Sciences, 284, 20170768. https://doi.org/10.1098/rspb.2017.0768

For covariate dependent species associations:

Tikhonov, G., Abrego, N., Dunson, D. and Ovaskainen, O. 2017. Using joint species distribution models for evaluating how species-to-species associations depend on the environmental context. Methods in Ecology and Evolution 8, 443-452. https://doi.org/10.1111/2041-210X.12723