The R object Lai_et_al_2020_JEcol_boral_output.rds contains the data input and the boral model output described in
Lai, H. R., Chong, K. Y., Yee, A. T. K., Tan, H. T. W., & van Breugel, M. (2020). Functional traits that moderate tropical tree recruitment during post-windstorm secondary succession. Journal of Ecology, 108, 1322--1333. doi: 10.1111/1365-2745.13347
We analysed the data using the boral v1.6 package in R (see versions in Lai et al. 2020), therefore you will need to install boral to access most of the data input and model output easily:
install.packages("boral")
library(boral)
and then import our boral object into your R session:
mod <- readRDS("Lai_et_al_2020_JEcol_boral_output.rds")
Next, see help(boral) to access many of its well-documented functions or give Hui (2016) MEE a read (see citation("boral")). As a start, summary(mod) will be most useful for an overview of all our parameter estimates, though we've done our best to show the most informative model summaries in our Supplementary Information.
The data inputs are formatted the way boral likes it and are accessible via:
- Community data a.k.a. site--species matrix:
mod$y - Environmental covariates:
mod$X - Trait data:
mod$traits
Please note that both environmental covariates and traits were centered to zero mean and scaled to unit standard deviation, as described in Lai et al. (2020). For the trait data, only the leaf traits are collected by us in situ, while the other traits are a mixture of our field collection and published datasets, or entirely the latter (see our Supplementary Information). Therefore, these traits from various sources are probably more suitable to be used to scrutinise our analyses (or in a meta-analysis) than to be directly used as raw trait inputs for another analysis. The leaf traits that were collected from our field sites are accessible from the file Lai_et_al_2020_JEcol_leaf_traits.rds, and note that both specific leaf area (SLA) and lamina thickness (Th) are natural log-transformed as described in our paper. If you use these leaf traits, please cite an earlier paper in which they had been used:
Yee, A. T. K., Lai, H. R., Chong, K. Y., Neo, L., Koh, C. Y., Tan, S. Y., … Tan, H. T. W. (2019). Short-term responses in a secondary tropical forest after a severe windstorm event. Journal of Vegetation Science, 30(4), 720--731. https://doi.org/10.1111/jvs.12753
If you use traits other than the leaf traits, please refer to our Supplementary Information for citations and original data sources or, better yet, make a new data request from TRY.
- Because our model was fitted with an older version of
boral(v1.6), you may run into compatibility issue with newer package versions. If so, try using the same version ofboral:
require(devtools)
install_version("boral", version = "1.6")
predict.boral()inboralv1.9 (and potentially future versions) breaks with models fitted withboralv1.7, so I guess it'll also break with our model.
We believe that the sharing of datasets is important for advancing ecology. At the same time, for data sharing to be successful and sustainable, it is important that those individuals whose time and efforts generated the data are acknowledged. Therefore, when you use the data or model output in your original research or meta-analysis, we appreciate if the following papers are cited:
- For leaf trait data: Yee, A. T. K., Lai, H. R., Chong, K. Y., Neo, L., Koh, C. Y., Tan, S. Y., … Tan, H. T. W. (2019). Short-term responses in a secondary tropical forest after a severe windstorm event. Journal of Vegetation Science, 30(4), 720--731. https://doi.org/10.1111/jvs.12753
- For everything else: Lai, H. R., Chong, K. Y., Yee, A. T. K., Tan, H. T. W., & van Breugel, M. (2020). Functional traits that moderate tropical tree recruitment during post-windstorm secondary succession. Journal of Ecology, 108, 1322--1333. doi: 10.1111/1365-2745.13347
If this dataset forms the entirety or >50% of your own dataset used for a publication, we suggest that you might raise the possibility of coauthorship with the corresponding authors of the papers above (depending on the circumstances coauthorship may or may not be appropriate, but let's have a conversation at least).
See the LICENSE file for license rights and limitations (CC-BY-4.0).
Hao Ran Lai hrlai.ecology@gmail.com
Might as well shamelessly advertise our blog post on the Journal of Ecology website.