plotbiomes

Overview

R package for plotting Whittaker' biomes with ggplot2.

Plotting Whittaker' biomes was also addressed in BIOMEplot package by Georges Kunstler and in ggbiome package by Guillem Bagaria, Victor Granda and Georges Kunstler.

Dataset for the figure

To get the data frame used for plotting, use this:

data(Whittaker_biomes)
Whittaker_biomes

       temp_c precp_cm biome_id  biome precp_mm
1   -10.21600 1.607134        6 Tundra 16.07134
1.1 -10.62857 1.696938        6 Tundra 16.96938
1.2 -11.14116 1.846052        6 Tundra 18.46052
1.3 -11.61776 2.028094        6 Tundra 20.28094
1.4 -12.05961 2.242129        6 Tundra 22.42129
1.5 -12.46799 2.486286        6 Tundra 24.86286

The graph generation was inspired by Figure 5.5 from Ricklefs, R. E. (2008), The economy of nature. W. H. Freeman and Company. (Chapter 5, Biological Communities, The biome concept). While the design and concept of the graph are inspired by the published work, the implementation in this R package is original and created independently to facilitate ecological data visualization and analysis in an R-friendly format for the scientific community. For more details on the dataset implementation, please refer to the accompanying Whittaker_biomes_dataset.html document.

Installation

You can install plotbiomes from GitHub with:

using devtools package:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("valentinitnelav/plotbiomes")

using remotes package:

if (!require(remotes)) install.packages("remotes")
remotes::install_github("valentinitnelav/plotbiomes")

Examples & Vignettes

Check examples at Whittaker_biomes_examples.html and Check_outliers.html vignettess.

Simple example of plotting Whittaker' biomes:

library(plotbiomes)

whittaker_base_plot()

How to cite the package?

I just uploaded this packge on Zenodo after almost 5 years :) I noticed that there are several forks by now and I presume people adapt it to their needs, plus I do not have the time to fully maintain this. Nevertheless, would be nice to cite this package if you make use of it.

You can cite the first release of the package as:

Valentin Ștefan, & Sam Levin. (2018). plotbiomes: R package for plotting Whittaker biomes with ggplot2 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.7145245

Examples of scientific papers using and citing the package can be found here:

Wolf, S., Mahecha, M.D., Sabatini, F.M. et al. Citizen science plant observations encode global trait patterns. Nat Ecol Evol (2022). https://doi.org/10.1038/s41559-022-01904-x

Carmona, C.P., Bueno, C.G., Toussaint, A., Träger, S., Díaz, S., Moora, M., Munson, A.D., Pärtel, M., Zobel, M. and Tamme, R., 2021. Fine-root traits in the global spectrum of plant form and function. Nature, 597(7878), pp.683-687.

Laughlin, D.C., Mommer, L., Sabatini, F.M., Bruelheide, H., Kuyper, T.W., McCormack, M.L., Bergmann, J., Freschet, G.T., Guerrero-Ramírez, N.R., Iversen, C.M. and Kattge, J., 2021. Root traits explain plant species distributions along climatic gradients yet challenge the nature of ecological trade-offs. Nature Ecology & Evolution, 5(8), pp.1123-1134.

Hammond, W.M., Williams, A.P., Abatzoglou, J.T., Adams, H.D., Klein, T., López, R., Sáenz-Romero, C., Hartmann, H., Breshears, D.D. and Allen, C.D., 2022. Global field observations of tree die-off reveal hotter-drought fingerprint for Earth’s forests. Nature communications, 13(1), pp.1-11.

Lembrechts, J.J., Van den Hoogen, J., Aalto, J., Ashcroft, M.B., De Frenne, P., Kemppinen, J., Kopecký, M., Luoto, M., Maclean, I.M., Crowther, T.W. and Bailey, J.J., 2022. Global maps of soil temperature. Global Change Biology, 28(9), pp.3110-3144.

Falster, D., Gallagher, R., Wenk, E.H., Wright, I.J., Indiarto, D., Andrew, S.C., Baxter, C., Lawson, J., Allen, S., Fuchs, A. and Monro, A., 2021. AusTraits, a curated plant trait database for the Australian flora. Scientific Data, 8(1), pp.1-20.

Massante, J.C., Götzenberger, L., Takkis, K., Hallikma, T., Kaasik, A., Laanisto, L., Hutchings, M.J. and Gerhold, P., 2019. Contrasting latitudinal patterns in phylogenetic diversity between woody and herbaceous communities. Scientific reports, 9(1), pp.1-10.

valentinitnelav / plotbiomes

readme