Package 'novelforestSG'

Download Model Fitted to novelforest_data

Description

Download the brms model fitted to novelforest_data (Lai et al. 2021). The model object is too large (16.5 MB) to be included with the package, so this function downloads the model from the developmental GitHub website. The generalised linear mixed-effect model was fitted via brms::brm so this package is recommended to make full use of the model object.

Usage

download_model(save_to = NULL)

Arguments

save_to

Path and name of the file where the R object is saved to. Defaults to NULL, which does not save the model object locally.

Value

A brms model output of class brmsfit, which is a list containing the input data and other slots that store the model components.

Notably, the data slot contains a data.frame with the following response variables:

SD_N_0

first-order native taxonomic diversity, i.e., species richness

SD_N_2

second-order native taxonomic diversity, i.e., inverse Simpson index

SD_E_0

first-order exotic taxonomic diversity

SD_E_2

second-order exotic taxonomic diversity

FD_N_0

first-order native functional diversity

FD_N_2

second-order native functional diversity

FD_E_0

first-order exotic functional diversity

FD_E_2

second-order exotic functional diversity,

and the following explanatory variables (and measurement units if you backtransform them using backtransform):

dist

Distance to old-growth forests (m)

size

Patch area (km^2)

nitrogen

Total soil nitrogen (mg/kg)

phosphorous

Total extractable soil phosphorous (mg/kg)

potassium

Total extractable soil potassium (mg/kg)

patch

Forest patch ID

#' Note that all explanatory variables were log-transformed and standardised to zero mean and unit standard deviations. Use backtransform to obtain the variables in their original scales. See Lai et al. (2021) for more details on model building and data collection.

References

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

See Also

backtransform, brms::brmsfit, brms::brm

Examples

## Not run: 
novelforest_model <- download_model()

# library(brms)  # recommended
summary(novelforest_model)

# to obtain input data
novelforest_model$data

## End(Not run)

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Novel Forest Raw Dataset

Description

The raw data used in Lai et al. (2021) and Neo et al. (2017).

Usage

novelforest_data

Format

A list of four data.frame:

trees

a table of woody stems measured, with treeID as the unique identifier

pres

a table of presences of vascular plant species in each plot

plots

a table of the environmental measurements or landscape characteristics for each plot, with plotID as the unique identifier

patches

a table of the patches and their characteristics, with patchID as the unique identifier

With the following variables:

patch

Forest patch identifier

plot

Plot identifier

UID

Stem identifier

species

Species name following Chong et al. (2011)

stem

Indicator column denoting whether a stem is the main trunk (=1) of an individual tree, or otherwise (=0)

dbh_2011

Diameter-at-breast-height (cm) measured in year 2011.

canopy

% Canopy cover

litter

Leaf litter depth / cm

nitrogen

Soil total Nitrogen /g^-1 kg^-1

phosphorous

Soil extractable Phosphorous /mg^-1 kg^-1

potassium

Soil extractable Potassium /mg^-1 kg^-1

dist

Distance to nearest old-growth forest /km

type

Type of forest; ABA: abandoned-land forest type, WAS: waste-woodland forest type

size

Size (i.e., area) of forest patch /ha

See Lai et al. (2021) or Neo et al. (2017) for more detail on data collection.

References

Chong, K. Y., Tan, H. T. W. and Corlett, R. T. (2011). A summary of the total vascular plant flora of Singapore. Gardens' Bulletin Singapore, 63, 197-204.

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

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

Examples

# Tree community matrix (by stem counts)
comm_stem <- xtabs(~ plot + species, data = novelforest_data$trees)
comm_stem[1:10, 1:4]

# Species occurrence matrix (of all vascular plants)
comm_all <- xtabs(~ plot + species, data = novelforest_data$pres)
comm_all[1:10, 1:4]

# Reproduce (part of) the summary table (Appendix S2) in the supplementary
# material of Neo et al. (2017)
with(novelforest_data,
    apply(plots[3:8], 2,
        function(x) tapply(x, plots$patch, mean, na.rm = TRUE))
    )

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novelforestSG

Description

Forest community data used in Lai et al. (2021); also comprised part of the raw data used in Neo et al. (2017).

Details

The main component of novelforestSG is the dataset, which can be accessed with novelforest_data. See ?novelforest_data for more details.

Author(s)

Hao Ran Lai, [email protected]
Kwek Yan Chong, [email protected]
Alex Thiam Koon Yee
Maintainer: Hao Ran Lai, [email protected]

References

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

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

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