Comparability of Results from Pair and Classical Model Formulations for Different Sexually Transmitted Infections

The “classical model” for sexually transmitted infections treats partnerships as instantaneous events summarized by partner change rates, while individual-based and pair models explicitly account for time within partnerships and gaps between partnerships. We compared predictions from the classical and pair models over a range of partnership and gap combinations. While the former predicted similar or marginally higher prevalence at the shortest partnership lengths, the latter predicted self-sustaining transmission for gonorrhoea (GC) and Chlamydia (CT) over much broader partnership and gap combinations. Predictions on the critical level of condom use (Cc) required to prevent transmission also differed substantially when using the same parameters. When calibrated to give the same disease prevalence as the pair model by adjusting the infectious duration for GC and CT, and by adjusting transmission probabilities for HIV, the classical model then predicted much higher Cc values for GC and CT, while Cc predictions for HIV were fairly close. In conclusion, the two approaches give different predictions over potentially important combinations of partnership and gap lengths. Assuming that it is more correct to explicitly model partnerships and gaps, then pair or individual-based models may be needed for GC and CT since model calibration does not resolve the differences

Total and partitioned soil respiration and below-ground carbon budget in SAFE intensive carbon plots

This dataset contains two parts: 1) 'data' worksheet: measured soil respiration, values of individual measurements across all plots. 2) 'Soil C cycle' worksheet: calculated summaries of the components of the below-ground carbon cycle, including total and component soil respiration (this study), soil carbon pools and flows of organic carbon (previous studies). These data form the basis of the below-ground carbon cycle in Riutta et al 2021 GBC. This sheet contains mean values in each 1 ha carbon plot. This worksheet include two addititional carbon plots from Lambir Hills National Park (see Kho et al. 2013 JGR), which are not part of the SAFE Project. SAFE Intensive Carbon Plots, part of the Global Ecosystem Monitoring (GEM) network, see http://gem.tropicalforests.ox.ac.uk/. Total soil respiration is measured at 25 points per plot, in the middle of each subplot (16 points per plot in OP, in subplot corners), using PVC collars of 10.65 cm internal diameter, inserted into approximately 5 cm depth. Partitioned respiration is measured at four points per plot, a using a cluster of six collars (see below). Disturbance experiment in the plot centre to assess the potential bias on fluxes caused by the collar installation. All the methods and installation is described in detail in the GEM Intensive Carbon Plots manual, available at http://gem.tropicalforests.ox.ac.uk/files/rainfor-gemmanual.v3.0.pdf. The aim is to measure monthly, but in practice the measurement interval is almost always longer (problems with access, staffing and instruments). EGM-4 infrared CO2 analyser and SRC-1 respiration chamber (PP Systems). Chamber closure time is 124 seconds, CO2 concentration inside the chamber is recorded every 5 s. Flux is calculated from the linear change in concentration in the chamber headspace. Conversion from parts per million (ppm) of total gas volume per second per unit collar area to mega grams (1 Mg = 10^6 g) of carbon per hectare per month. Idea gas law: pV=nRT --> n=pV/(RT) Mass-Mole: n=m/M --> m=n*M Combined: m=MpV/(RT) p (constant) 101,325 R (constant) 8.314472 T temperature in Kelvins --> AirT_Use + 273.15 V headspace volume M_carbon 12.01 parts per million to absolute units 10^-6 A collar area, m2 0.008825 m2 to hectare 10^4 grams to megagrams 10^-6 seconds to months 2592000 Flux_MgCha-1month-1 = Slope_ppm_s-1 * M* p* V /(R*T) * 10^-6 / A * 10^4 * 10^-6 * 2592000 Soil collar codes Partitioned respiration C1 All soil respiration components: litter, roots, mycorrhiza, soil organic matter (SOM) C2 Roots excluded (litter, mycorrhiza, SOM) C3 Roots and mycorrhiza excluded (litter, SOM) S1 Litter excluded (roots, mycorrhiza, SOM) S2 Litter and roots excluded (mycorrhiza, SOM) S3 Litter, roots and mycorrhiza excluded (only SOM) D1 Double litter, roots, mycorrhiza, soil organic matter (SOM) D2 Roots excluded (double litter, mycorrhiza, SOM) D3 Roots and mycorrhiza excluded (double litter, SOM) X Organic layer of the soil removed Disturbance The purpose of the disturbance experiment is to quantify how much disturbance the removal of the roots and mixing the soil causes, compared to just hammering in the deep collar ND1 Roots severed, not removed and soil not mixed at the installation ND2 ND1-ND5 are replicates, same treatmet ND3 ND4 ND5 D1 Roots removed, soil mixed at the installation D2 D1-D5 are replicates D3 D4 D5 Project: This dataset was collected as part of the following SAFE research project: Changing carbon dioxide and water budgets from deforestation and habitat modification Funding: These data were collected as part of research funded by: Sime Darby Foundation (Grant, SAFE Core data) European Research Council Advanced Investigator Grant, GEM-TRAIT (Grant, Grant number 321131) NERC Human-Modified Tropical Forests Programme: Biodiversity And Land-use Impacts on tropical ecosystem function (BALI) Project (Grant, NE/K016369/1) NERC standard grant: The multi-year impacts of the 2015/2016 El Niño on the carbon cycle of tropical forests worldwide (Grant, NE/P001092/1) HSBC Malaysia (Grant) The University of Zurich (Grant) This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs. Permits: These data were collected under permit from the following authorities: Sabah Biodiversity Council (Research licence JKM/MBs.1000-2/2 JLD.6 (76)) XML metadata: GEMINI compliant metadata for this dataset is available here Files: This dataset consists of 2 files: SAFE_SoilRespiration_Data_SAFEdatabase_update_2021-01-11.xlsx, SAFE_soil_DATA.zip SAFE_SoilRespiration_Data_SAFEdatabase_update_2021-01-11.xlsx This file contains dataset metadata and 2 data tables: Soil respiration data (described in worksheet data) Description: Soil respiration data by individual measurements Number of fields: 21 Number of data rows: 20602 Fields: ForestType: Old-growth, Logged or Oil palm (Field type: categorical) SAFEPlotName: SAFE plot name (Field type: location) PlotName: Plot name (Field type: id) ForestPlotsCode: Plot code in the ForestPlots database (this should be used in publications, instead of plot name). OP plot is not in the ForestPlots database (ForestPlotsCode = NA) (Field type: id) Date: Measurement date (dd/mm/yyyy) (Field type: date) Observers: Observers (Field type: comments) Subplot: Subplot number within each plot, 1-25 (in OP, because the total respiration collars are in subplot corners, no subplot numbers are used, but the collars are refered to as SR1 - SR16. Subplot numbers are used for the partitioned respiration) (Field type: id) MeasurementType: Total, Partitioned or Disturbance (Field type: categorical) CollarType: Total; Partitioned: C1, C2, C3, S1, S2, S3, D1, D2, D3, X; Disturbance: ND1, ND2, ND3, ND4, ND5, D1, D2, D3, D4, D5 (see metadata description for codes) (Field type: id) EGM_RecordNumber: Record number in of the raw flux file. (Field type: id) SoilMoisture: Volumetric soil moisture content (% of pore space) next to the collar. measured with Campbell Scientific Hydrosense sensor with 12 cm rods. (Field type: numeric) SoilT: Soil temperature (°C) is measured with a handheld digital thermometer next to the collar, inserted into 10 cm depth (Field type: numeric) AirT: Air temperature (°C) is measured with a handheld digital thermometer outside the chamber, at the chamber height, in a shaded spot (Field type: numeric) Slope: Slope of the linear regression between time (seconds) from the chamber closure and CO2 concentration (parts per million, ppm) in the chamber headspace. (Field type: numeric) Remarks: Any notes in the field or at data entry stage. 0 = no remarks. If the measurement is repeated in the field multiple times, the other flux estimates are sometimes written in the remarks (not consistent). 2x, 3x etc. indicate multiple repeats. (Field type: comments) CollarHeight: Height from the top of the soil to the top of the collar, mm. This is used for calculating the total headspapce volume (chamber volume + collar volume above the soil surface). (Field type: numeric) HeadspaceVolume: Total headspace volume, sum of the chamber volume (0.001229 m3) and collar volume (d=0.106 m, h=CollarHeight_mm/1000) (Field type: numeric) AirT_Use: Gap filled air temperature data, missing air temperatures replaced with average temperature in logged (27.1), old-growth forest (26.2) and OP (28.7). This is needed for calculating the flux, but should not be used in response functions etc. (Field type: numeric) Flux: Flux corverted from ppm s-1 to Mg carbon per hectare per month. See conversion below. (Field type: numeric) Quality: 1 - good flux; 0 - missing data or bad measurement; 2 - outlier (Field type: numeric) Girdling_0_1: In Tower Plot (SAF-05), subplots 14-25, all trees were girdled in late January - early February 2016. Post-girdling data = 1, if no girdling = 0. (Field type: numeric) Soil carbon cycle (described in worksheet Soil C cycle) Description: Estimates of soil carbon pools (fine and coarse root biomass, root and litter necromass, soil organic carbon); fluxes of organic carbon into and respiration out of the different pools. Values are means for each intensive carbon plot. Number of fields: 41 Number of data rows: 11 Fields: ForestType: Old-growth, Logged or Oil palm (Field type: categorical) SAFEPlotName: SAFE plot name, as in the SAFE Gazetteer (Field type: location) PlotName: Plot name (used in field work) (Field type: id) ForestPlotsCode: Plot code, as in the ForestPlots database (this should be used in publications, instead of plot name) (Field type: id) SOC_0to100cm: Soil carbon stock, 0-100 cm layer (Field type: numeric) CanopyStock: Biomass stock of the canopy (Field type: numeric) LitterStock: Necromass stock of the litter layer (leaf, branch and reproductive litter) (Field type: numeric) NPP_Canopy: Canopy net primary productivity (Field type: numeric) CanopyHerbivory: Canopy herbivory (Field type: numeric) Litterfall: Canopy litterfall (leaves, reproductive parts, twigs < 2 cm diameter) (Field type: numeric) Frassfall1: Frassfall, 1st literature estimate (Field type: numeric) Frassfall2: Frassfall, 2nd literature estimate (Field type: numeric) Frassfall_Mean: Frassfall, mean of the Frassfall 1 and Frassfall 2 (Field type: numeric) FineRootStock: Fine root biomass stock (Field type: numeric) CoarseRootStock: Coarse root biomass stock (Field type: numeric) Delta_FRstock: Change in fine root biomass stock in logged forest (old-growth forest stock assumed to be in quasi-equilibrium) (Field type: numeric) Delta_CRstock: Change in coarse root biomass stock in logged forest (old-growth forest stock assumed to be in quasi-equilibrium) (Field type: numeric) NPP_FR: Fine root net primary productivity (Field type: numeric) NPP_CR: Coarse root net primary productivity (Field type: numeric) Mortality_FR: Fine root mortality (Field type: numeric) Mortality_CR: Coarse root mortality (Field type: numeric) R_Tot: Total soil respiration (litter, roots, mycorrhiza, soil organic matter) (Field type: numeric) R_SOM: Soil organic matter respiration (Field type: numeric) R_Litter: Litter layer respiration (Field type: numeric) R_Root: Root and priming respiration (Field type: numeric) R_Myc: Mycorrhizal respiration (Field type: numeric) R_Rhizosphere: Rhizosphere respiration (Field type: numeric) R_FRdebris: Fine root debris (recently dead, < 1 year) respiration (Field type: numeric) R_CRdebris: Coarse root debris (recently dead, < 1 year) respiration (Field type: numeric) R_RootTurnover: Root turnover respiration (sum of fine and coarse root debris respiration) (Field type: numeric) R_Het: Heterotrophic respiration (Field type: numeric) Exudation1: Root exudation, 1st literature estimate (Field type: numeric) Exudation2: Root exudation, 2nd literature estimate (Field type: numeric) Exudation3: Root exudation, 3rd literature estimate (Field type: numeric) Exudation4: Root exudation, 4th literature estimate (Field type: numeric) Exudation5: Root exudation, 5th literature estimate (Field type: numeric) Exudation_Mean: Root exudation, mean of the five literature-based estimates (Field type: numeric) LitterToSOM: Litter inputs (> 1 year old material) to soil organic matter (Field type: numeric) FRdebrisToSOM: Fine root debris inputs (> 1 year old material) to soil organic matter (Field type: numeric) CRdebrisToSOM: Coarse root debris inputs (> 1 year old material) to soil organic matter (Field type: numeric) OrgInputsToSOM: Total labile organic inputs (> 1 year old material) to soil organic matter (Field type: numeric) SAFE_soil_DATA.zip Description: Raw EGM files and a ReadMe doc explaining how to interpret Date range: 2011-08-25 to 2018-07-17 Latitudinal extent: 4.1830 to 5.0700 Longitudinal extent: 114.0190 to 117.820