Overview | Download Ameriflux data for Bondville | Convert to PEcAn-CF format | Concatenate years | Load | Plot entire time series | Plot 8-26-1996 to 10-14-1996 | Convert to BioCro Model format

Overview | Connect to BETY database and retrieve appropriate format for AmerifluxLBL datasets [TODO: Update to work with R-OpenSci traits BETY] | Download AmerifluxLBL data for selected site and dates (US-WCr, 2000 to 2005) | Convert downloaded AmerifluxLBL data to CF format | Gapfill CF met drivers | Create MAAT model-specific met drivers

Sources: | Variables | Extracting data | Solar Radiation (PAR) vs Temp | RH vs Temp | Solar Radiation and Precipitation: NARR daily vs 3 hourly | Precipitation v Temperature | Compare Solar Radiation | Max Solar Radiation for June 1-Aug31 2010 | Max Solar Radiation (PAR) Model v OBS | PAR residuals (model - obs) | Correlations of daily max solar radiation | Compare daily and 3hourly downscaled NARR | Multiple variables | Some sanity checks on variables | More diagnostic plots

Subdaily Data | Extract | Downscale | Convert to model-specific format | Daily: what to do with ISIMIP - only daily average RH

Subdaily Training Data | Extract Training Data and Merge All Years Into 1 File | Generate Linear Regression Models From Training Data | Coarse Data to Downscale | Extract Data We Want To Downscale | Predict Subdaily Data Using Statistics From Training Data

Introduction | Installation | Overview of features | Simulating reflectance | Inversion

Fitting priors to data (point estimates, all grass species in GLOPNET). | Example: Specific Leaf Area based on all grasses | MLE Fit to glopnet Specific Leaf Area data | Fitting priors to data with uncertainty estimates (generating posterior predictive distribution of an unobserved C4 grass species based on values collected from many PFTs. | Vcmax data from Wullschleger (1993) | Classify Wullschleger Data into Functional Types | 1. query functional types from BETY | Add data from C4 species | Miscanthus: Wang D, Maughan MW, Sun J, Feng X, Miguez FE, Lee DK, Dietze MC, 2011. Impact of canopy nitrogen allocation on growth and photosynthesis of miscanthus (Miscanthus x giganteus). Oecologia, in press | Muhlenbergia glomerata | Zea Mays (Corn) | take a look at the raw data by functional type: | Add unobserved C4 species so JAGS calculates posterior predictive distribution | Write and Run Meta-analysis | Other Examples / Approaches | Examples | Package rriskDistributions

Overview | MAAT Installation and usage | Installing the R packages | MAAT XML configuration | E.g. Running without met drivers and using user-specified met conditions | E.g. Running with met drivers | Full PEcAn XML configuration with MAAT options | E.g. pecan.xml file with MAAT configuration options. | Simple MAAT run in PEcAn

install package from Github | Define species groups | Run the Bayesian allometry model | Predict for individual trees | Predict for a stand

Reading model output

Map | Plot all maps for BETYdb | Misc additional code

Introduction | Install package from Github | Load library and example data | run QA/QC checks | Merge data into one data frame | Fit FvCB model to composite data | Refit with leaf-level random effects | Fitting the model with covariates | Citations

Meta-analysis: Example of Single.MA

Load Libraries | Select lat and lon points for Champaign County Boundary | Query Elevation points | Define boundary in postGIS | Define PostGIS geom | insert statement | Update geom statement | Insert into BETYdb

PEcAn.DB functions | R dplyr interface | rOpensci traits API

Install package from Github | Parameter Data Assimilation (a.k.a. calibration) in PEcAn | Which one to use? | Adding PDA tags to pecan.xml | Method specific settings | 1. PEcAn data pipeline with emulator | 2. PEcAn data pipeline with BayesianTools | 3. Own data with emulator | 4. Own data with BayesianTools

Multi-Site Hierarchical PDA | Initiate a new run from the web interface | Start with multi-settings | Fill in site-specific input information | Modify ensemble analysis tags | Global SA | Settings for HB-PDA | The workflow for HB-PDA