R code to reproduce analyses of aboveground carbon stocks and associated plant diversity in fragmented and continuous forest sites in Sabah, Malaysian Borneo, 2017
Creators: name: Fleiss, S.
Publisher: name: NERC Environmental Information Data Centre
publisherIdentifier: https://ror.org/04xw4m193
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Borneo
subject: Agriculture
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/1
subject: Biodiversity
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/2
subject: Climate and climate change
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/4
subject: Ecosystem services
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/6
subject: Land use
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/12
subject: Soil
valueUri: http://onto.nerc.ac.uk/CEHMD/topic/17
subject: Forest fragmentation
subject: Oil palm
subject: Tropical rainforest
subject: Conservation set-aside
subject: Sustainable agriculture
subject: Agricultural landscapes
subject: Plant biodiversity
subject: Flora
subject: Carbon storage
subject: Roundtable on Sustainable Palm Oil
subject: Planta
subject: climate change mitigation
valueUri: http://www.eionet.europa.eu/gemet/concept/15032
subject: flora (biology)
valueUri: http://www.eionet.europa.eu/gemet/concept/3305
subject: biodiversity
valueUri: http://www.eionet.europa.eu/gemet/concept/827
subject: agricultural ecology
valueUri: http://www.eionet.europa.eu/gemet/concept/191
subject: environmental impact of agriculture
valueUri: http://www.eionet.europa.eu/gemet/concept/2831
subject: agriculture
valueUri: http://www.eionet.europa.eu/gemet/concept/232
subject: tropical forest
valueUri: http://www.eionet.europa.eu/gemet/concept/8687

description: The R code "carbon_stock_calculations.R" estimates aboveground carbon stocks for 49 plots in 14 fragmented forest sites and 4 continuous forest sites in Sabah, Malaysian Borneo, using the vegetation dataset 'Vegetation and habitat data for fragmented and continuous forest sites in Sabah, Malaysian Borneo, 2017'. The 14 fragmented sites were all in Roundtable on Sustainable Palm Oil-certified oil palm plantations, and are hereafter termed 'conservation set-asides'. The code also estimates the aboveground carbon stocks of oil palm plantations for comparison.
The R code "analyses_and_figures.R" runs analyses and makes figures of aboveground carbon stocks and associated plant diversity for these sites, as presented in Fleiss et al. (2020)
This R code was created in order to investigate the following: (1) to establish the value of conservation set-asides for increasing oil palm plantation aboveground carbon stocks; (2) to establish whether set-asides with high aboveground carbon stocks can have co-benefits for plant diversity; (3) to compare the carbon stocks and vegetation structure of conservation set-asides with that of continuous forest, including assessing tree regeneration potential by examining variation in seedling density; (4) to examine potential drivers of variation in aboveground carbon stocks of conservation set-asides (topography, degree of fragmentation, and soil parameters); (5) to scale-up the estimates of the aboveground carbon stocks of conservation set-asides, in order to predict average carbon stocks of oil palm plantations with and without set-asides, and for varying coverage of set-asides across the plantation.
description: The data used in these analyses were collected in July - October 2017. The 14 fragmented sites were all in Roundtable on Sustainable Palm Oil-certified oil palm plantations; and they varied from isolated forest fragments to sites connected to forest reserves outside the oil palm plantation. The four continuous forest sites were located in Danum Valley and Malua Forest Reserves, and include both primary and logged forest sites.
At each site, vegetation was surveyed in 2-3 circular plots spaced 100 m apart along a transect (the smallest fragmented sites had only 2 plots and all other sites had 3). In each plot, living trees and palms, saplings, seedlings, deadwood, and lianas on trees were surveyed in a nested plot design. All living trees, saplings and seedlings were identified to genus, and to species where possible. Field data were collected in collaboration with experienced local botanists. In addition, eight soil parameters were measured from topsoil samples in each plot. Metrics relating to the degree of forest fragmentation in the surrounding landscape were calculated for each plot, using drone (UAV) imagery from an oil palm company. Note that additional measurements (e.g. ground vegetation) are available in the full dataset, which were not included in these analyses (see https://doi.org/10.5285/c67b06b7-c3f6-49a3-baf2-9fc3a72cb98a ).