Supplement 1. R code for running PnET-CN simulations for AmeriFlux sites, as in text.

File List README (MD5: c3c7b6e8b8c2e42f967dff8c15b6d9e6) SiteAndVegParams.RData (MD5: 86dcf70da2c1e4766cde4a222b78f80b) RunSimulations2014-06-11.R (MD5: a7ad23be70e82619e104dbe42746820b) AmerifluxToClimateFile.R (MD5: 093dfe9d2ff6e61fd2e1b92615d60a70) pnetcn_NewPhenology.R (MD5: 7e069c490ec0321a0572c7f73943e96a) pnetcn_NewPhenology_cont.R (MD5: 44d4689a457b964f48e497f9b4d3d0df) pnetcn.R (MD5: d4168f06879c698f46b12d4dfb748d74) spinup_pnetcn_NewPhenology.R (MD5: a64a22fd94e06389292c8c417d2d75d8) spinup_pnetcn.R (MD5: 1dc1a10f75c4e14e8108919e0a2d31a3) run_pnetcn.R (MD5: 204dcd9176dfe57b83474fc4677253d0) AllocateMo.R (MD5: 7bd2c8e7c2573b64fddef23878be7be6) AllocateYr_NewPhenology.R (MD5: 68c4686f579ae19453fbdd73fdaca927) AllocateYr.R (MD5: 17e49c1aaf9d3d045af11344683eaa45) AtmEnviron_NewPhenologyOLD.R (MD5: f9f9ce07b2d1d29b719f58c0c2bf5eec) AtmEnviron_NewPhenology.R (MD5: 6d11dce44856009c05af514b8960cbf5) AtmEnviron.R (MD5: 6a352d22899c3fe1c10cecd2f2bae41d) CalculateYr_NewPhenology.R (MD5: b0d9d700ba3c9503c8d280a6bd50b0f4) CNTrans.R (MD5: 15f7ea8951957fe0b5714d3164bcb739) Decomp.R (MD5: 6f851eea37ba654a2434a3a9df4f7160) GrowthInit_NewPhenology.R (MD5: ce50ce5fa8a8282e7ad38ec913c9f948) initvars.R (MD5: 8503263de5d593fde793622256556209) Leach.R (MD5: 49667570a1eae670cb4121f7ca9bfd64) PhenologyNew.R (MD5: 088b2c1b406fab16c4bc55c27c85a5c6) PhenologyNew2.R (MD5: 6d881331616e178c4b79d0bda723a934) Phenology.R (MD5: 07f72b99a8e981d76100548247d948f2) Photosyn.R (MD5: 44755415a892bedc86b0f6bad0f50853) SoilResp.R (MD5: 018dc6e0d4eb5a5f66bb46179099f74b) storeoutput.R (MD5: f527f8a285c169bdb53aa518f15880c5) StoreYrOutput.R (MD5: 984cbf2a2f518b5795c319e48bac1ac4) Waterbal.R (MD5: c3d9d4516e009b9fad7d08ac488f2abc) YearInit_NewPhenology.R (MD5: 0e9957a828f64f25495bdca9c409d070) YearInit.R (MD5: ceb4bab739a52b78cfcf7ca411939174) Ameriflux/ Daymet/ FluxDataFunctions.R (MD5: ae89d6b9cf4e01ba501941ce12690e4b) Description README - Brief notes to get started SiteAndVegParams.RData – R data structures containing site-specific parameters for the six sites analyzed in the paper RunSimulations2014-06-11.R – Template code for importing AmeriFlux and Daymet data and running simulations with climate files including spinup years (must be modified) AmerifluxToClimateFile.R – Functions needed to import Ameriflux and Daymet data and generate climate files pnetcn_NewPhenology.R - Top level function to run the version of PnET-CN used in the paper (new phenology routine) pnetcn.R - Top level function to run traditional version of PnET-CN (old phenology routine) spinup_pnetcn_NewPhenology.R – Alternative version of top-level function that repeats the climate data from the input climate file an arbitrary number of times for spinup (new phenology routine) pnetcn_NewPhenology_cont.R – Function to continue a simulation starting with spinup data from a previous run (called by spinup_pnetcn_NewPhenology.R) spinup_pnetcn.R - Alternative version of top-level function for traditional version of PnET-CN that repeats the climate data from the input climate file an arbitrary number of times for spinup (old phenology routine) run_pnetcn.R - Functions to run PnET-CN with output as data frames of monthly or annual data instead of as a list containing both formats AllocateMo.R - Monthly allocation routine for PnET-CN AllocateYr_NewPhenology.R - Yearly allocation routine for PnET-CN (with new phenology routine) AllocateYr.R - Yearly allocation routine for PnET-CN (with old phenology routine) AtmEnviron_NewPhenology.R - Environmental calculations for PnET-CN (for new phenology routine) AtmEnviron_NewPhenologyOLD.R – Older version of environmental calculations for PnET-CN, with less data saved to data structure (for new phenology routine) AtmEnviron.R - Environmental calculations for PnET-CN (for old phenology routine) CalculateYr_NewPhenology.R - Calculate yearly output values for PnET-CN (for new phenology routine) CNTrans.R - Carbon and nitrogen translocation routine for PnET-CN Decomp.R - Decompositin routine for PnET-CN GrowthInit_NewPhenology.R – Initialize annual aggregation variables for each year in PnET-CN initvars.R - Initialize internal shared variable structures for PnET-CN Leach.R - Leaching routine for PnET-CN PhenologyNew.R - Functions to calculate phenology for PnET-CN (new phenology routine) PhenologyNew2.R - Skeleton code for new functions to calculate phenology for PnET-CN that would use alternative (e.g., water-driven) phenology cues for grasslands (new phenology routine - INCOMPLETE) Phenology.R - Functions to calculate phenology for PnET-CN (old phenology routine) Photosyn.R - Photosynthesis routine for PnET-CN SoilResp.R - Soil respiration routine for PnET-CN storeoutput.R - Adds variable values to the returned output structure so that the user may work with them (or save them) at the command line after running PnET-CN StoreYrOutput.R - Routine to save annual results to an output file for PnET-CN (not used) Waterbal.R - Ecosystem water balance routine for PnET-CN ...