Data from: Quantifying and reducing uncertainties in estimated soil CO2 fluxes with hierarchical data-model integration

Ogle K, Ryan E, Dijkstra FA, Pendall E

Date Published: November 16, 2016

DOI: http://dx.doi.org/10.5061/dryad.mb605

 

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Title Dataset1_HBD
Downloaded 10 times
Description Dataset1_HBD contains individual observations of CO2 and time, along with categorical or integer identifiers for day, vegetation type, plot, session (group). DayN = day since 1/1/2006; Datecode = unique integer ID for each measurement date; Min = minutes after chamber closure; Veg = vegetation treatment ID (1 = vegetated; 2 = herbicide); Plot = plot ID; Group = chamber session ID; CorrCO2 = corrected CO2 concentration (ppm); SoilT = soil temperature (celcius) in/near temperature in surface layer.
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Title Dataset2a_HBD
Downloaded 72 times
Description Dataset2a_HBD contains the integer identifiers for date, vegetation type, and plot associated with each chamber session; dateID, vegID, and PlotID are the same as Datecode, Veg, and Plot in Dataset1_HBD, but each row in Dataset2a_HBD corresponds to the chamber session ID (i.e., Group in Dataset1_HBD).
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Title Dataset2b_HBD
Downloaded 18 times
Description Dataset2b_HBD contains various constants and sample size information required for the the HBD (hierarchical Bayesian diffusion model). This includes Tmtcode, which is a list of 30 values giving the treatment ID associated with each of the 30 plots (ordered by plot #), where 1 = ct, 2 = cT, 3 = Ct, 4 = CT, 5 = ctd, and 6 = cts, for c = ambient CO2, C = elevated CO2, t = ambient temperature, T= warmed, d = deep irritation, and s = shallow irrigation. This dataset also contains Ctrt, denoting the CO2 treatment level associated with each of the 6 treatments; 1 = ambient CO2 and 2 = elevated CO2.
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Title Dataset3_HBD
Downloaded 23 times
Description Dataset3_HBD contains soil water content data for every plot and date. SWC_DSM1[r,c] is the soil water content associated with day = r and plot ID = c. Plot ID (columns) correspond to Plot in Dataset1_HBD; r = 1 (row #1) corresponds to 12/21/2006 or day 355 from 1/1/2006, with rows ordered by date (no missing days).
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Title Dataset4_HBD
Downloaded 28 times
Description Dataset4_HBD contains atmospheric pressure data for every date, with row #1 corresponding to 3/1/2007 (i.e., day 425 since 1/1/2006). Rows are ordered by day (no missing dates).
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Title ModelCode_HBD_SI
Downloaded 19 times
Description OpenBUGS / JAGS model code that uses Dataset1_HBD.txt, Dataset2a_HBD.txt, Dataset2b_HBD.txt, Dataset3_HBD.txt, and Dataset4_HBD.txt
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Title Initials_HBDa_SI
Downloaded 44 times
Description Initials (starting) values for first MCMC chain, to be used with the OpenBUGS / JAGS model code (ModelCode_HBD_SI.txt).
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Title Initials_HBDb_SI
Downloaded 6 times
Description Initials (starting) values for second MCMC chain, to be used with the OpenBUGS / JAGS model code (ModelCode_HBD_SI.txt).
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Title Initials_HBDc_SI
Downloaded 60 times
Description Initials (starting) values for third MCMC chain, to be used with the OpenBUGS / JAGS model code (ModelCode_HBD_SI.txt).
Download Initials_HBDc_SI.txt (139.8 Kb)
Download Read_me_HBD.pdf (37.05 Kb)
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Title ModelScript_HBD_SI
Downloaded 26 times
Description OpenBUGS script file for running the model (ModelCode_HBD_SI.txt) and calling the corresponding datasets (Dataset1_HBD.txt, Dataset2a_HBD.txt, Dataset2b_HBD.txt, Dataset3_HBD.txt, and Dataset4_HBD.txt) and initial / starting values (Initials_HBDa_S1.txt, Initials_HBDb_S1.txt, Initials_HBDc_S1.txt).
Download ModelScript_HBD_SI.txt (3.055 Kb)
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Title Dataset2b_SI
Downloaded 13 times
Description Dataset2b_SI.txt is very similar to Dataset2b_HBD.txt and contains various constants, sample size information, and treatment codes required to run the HBL model. See Dataset2b_HBD.txt description for additional details.
Download Dataset2b_SI.txt (228 bytes)
Download Read_me_HBL.pdf (38.92 Kb)
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Title ModelScript_HBL_SI
Downloaded 8 times
Description ModelScript_HBL_SI.txt is the OpenBUGS script file for running the HBL model (ModelCode_HBL_SI.txt), reading the correct data files, and loading the initial values for three MCMC chains (Initials_a … b_S1.txt). Note that the script calls Dataset1_SI.txt and Dataset2a_SI.txt, which are not provided because they are exactly the same as the data files called Dataset1_HBD.txt and Dataset2a_HBD.txt, respectively. In particular, Dataset1_SI.txt can be created by grabbing for following columns (variables) from Dataset1_HBD.txt: Datecode, Min, Veg, Plot, Group, and CorrCO2. Dataset2a_SI.txt can be created by simply making a copy of Dataset2a_HBD.txt.
Download ModelScript_HBL_SI.txt (3.14 Kb)
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Title ModelCode_HBL_SI
Downloaded 6 times
Description ModelCode_HBL_SI.txt is the OpenBUGS model code for implementing the HBL model.
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Title Initials_a_SI
Downloaded 7 times
Description Initials_a_S1.txt contains initial (starting) values for parameters in the HBL model, for chain 1.
Download Initials_a_SI.txt (141.8 Kb)
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Title Initials_b_SI
Downloaded 54 times
Description Initials_b_S1.txt contains initial (starting) values for parameters in the HBL model, for chain 2.
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Title Initials_c_SI
Downloaded 11 times
Description Initials_c_S1.txt contains initial (starting) values for parameters in the HBL model, for chain 3.
Download Initials_c_SI.txt (141.4 Kb)
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When using this data, please cite the original publication:

Ogle K, Ryan E, Dijkstra FA, Pendall E (2016) Quantifying and reducing uncertainties in estimated soil CO2 fluxes with hierarchical data-model integration. Journal of Geophysical Research: Biogeosciences 121(12): 2935-2948. http://dx.doi.org/10.1002/2016jg003385

Additionally, please cite the Dryad data package:

Ogle K, Ryan E, Dijkstra FA, Pendall E (2016) Data from: Quantifying and reducing uncertainties in estimated soil CO2 fluxes with hierarchical data-model integration. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mb605
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