About

Welcome to the R package novelforestSG! It contains the data input and downloadable brms model output described in

Lai, H. R., Tan, G. S. Y., Neo, L., Kee, C. Y., Yee, A. T. K., Tan, H. T. W., & Chong, K. Y. (2021). Decoupled responses of native and exotic tree diversities to distance from old-growth forest and soil phosphorus in novel secondary forests. Applied Vegetation Science, 24, e12548. https://doi.org/10.1111/avsc.12548

Using the data

To install the novelforestSG package:

install.packages("novelforestSG")

Or install the development version:

install.packages("devtools")  # prerequisite
devtools::install_github("hrlai/novelforestSG")

To access our dataset:

library(novelforestSG)
novelforest_data

For more information, see ?novelforest_data.

Because the predictor variables were log-transformed and then scale to zero mean and unit SD prior to modelling, you may wish to backtransform them to their original scales, simply by:

backtransform()

Using the model

The model object is too large (16.5 MB) to come with the package, but the download_model function can download the model from our GitHub development website for you: see ?download_model for a worked example.

Because we analysed the data using the brms v2.10.0 package in R, it is highly recommended that you install brms to squeeze the most out of the model output:

install.packages("brms")

You may also need RTools or Xcode, depending on your operating system; see the brms homepage. This will take a few minutes so have a cup of hot beverage handy.

Issues

Please feel free to report any issues to our GitHub Issue page.

Citation

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 paper is cited:

Lai, H. R., Tan, G. S. Y., Neo, L., Kee, C. Y., Yee, A. T. K., Tan, H. T. W., & Chong, K. Y. (2021). Decoupled responses of native and exotic tree diversities to distance from old-growth forest and soil phosphorus in novel secondary forests. Applied Vegetation Science, 24, e12548. https://doi.org/10.1111/avsc.12548

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.

You may also be interested in a companion not-just-trees paper:

Neo, L., Yee, A. T. K., Chong, K. Y., Kee, C. Y., & Tan, H. T. W. (2017). Vascular plant species richness and composition in two types of post-cultivation tropical secondary forest. Applied Vegetation Science, 20(4), 692–701. doi: 10.1111/avsc.12322

Contacts

Hao Ran Lai
Kwek Yan Chong