novelforest_data {novelforestSG}

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))
    )