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 ...

文件列表：
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: ce50ce8a8a282e7ad38ec913c9f948)
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)

数据集说明：
README —— 入门简要说明
SiteAndVegParams.RData —— 包含本文所分析的6个站点专属参数的R数据结构
RunSimulations2014-06-11.R —— 用于导入美国通量网（Ameriflux）与Daymet数据、运行含spinup（模型自旋预热）年份的气候文件模拟的模板代码（需自行修改）
AmerifluxToClimateFile.R —— 用于导入美国通量网（Ameriflux）与Daymet数据并生成气候文件所需的函数集
pnetcn_NewPhenology.R —— 运行本文所用PnET-CN（新物候程序版本）的顶层函数
pnetcn.R —— 运行传统版PnET-CN（旧物候程序版本）的顶层函数
spinup_pnetcn_NewPhenology.R —— 可将输入气候文件的数据重复任意次数以完成spinup（模型自旋预热）过程的PnET-CN顶层函数替代版本（新物候程序版本）
pnetcn_NewPhenology_cont.R —— 用于承接前次spinup运行结果继续模拟的函数（由spinup_pnetcn_NewPhenology.R调用）
spinup_pnetcn.R —— 可将输入气候文件的数据重复任意次数以完成spinup（模型自旋预热）过程的传统版PnET-CN顶层函数替代版本（旧物候程序版本）
run_pnetcn.R —— 用于运行PnET-CN的函数集，输出格式为月度或年度数据框，而非同时包含两种格式的列表
AllocateMo.R —— PnET-CN的月度分配程序
AllocateYr_NewPhenology.R —— PnET-CN的年度分配程序（适配新物候程序）
AllocateYr.R —— PnET-CN的年度分配程序（适配旧物候程序）
AtmEnviron_NewPhenology.R —— PnET-CN的环境计算程序（适配新物候程序）
AtmEnviron_NewPhenologyOLD.R —— PnET-CN的旧版环境计算程序（新物候适配版本），仅将少量数据保存至数据结构
AtmEnviron.R —— PnET-CN的环境计算程序（适配旧物候程序）
CalculateYr_NewPhenology.R —— 用于计算PnET-CN年度输出值的程序（适配新物候程序）
CNTrans.R —— PnET-CN的碳氮转运程序
Decomp.R —— PnET-CN的分解程序
GrowthInit_NewPhenology.R —— PnET-CN中每年年度聚合变量的初始化程序（适配新物候程序）
initvars.R —— PnET-CN内部共享变量结构的初始化程序
Leach.R —— PnET-CN的淋溶程序
PhenologyNew.R —— 用于计算PnET-CN物候的程序（新物候程序版本）
PhenologyNew2.R —— PnET-CN新物候计算函数的骨架代码，可使用替代（如水分驱动）的物候触发机制适配草地（新物候程序版本，未完成）
Phenology.R —— 用于计算PnET-CN物候的程序（旧物候程序版本）
Photosyn.R —— PnET-CN的光合作用程序
SoilResp.R —— PnET-CN的土壤呼吸程序
storeoutput.R —— 将变量值添加至返回的输出结构中，便于用户在运行PnET-CN后于命令行中直接操作或保存这些变量
StoreYrOutput.R —— PnET-CN的年度结果保存至输出文件的程序（未启用）
Waterbal.R —— PnET-CN的生态系统水量平衡程序
YearInit_NewPhenology.R —— PnET-CN的年度初始化程序（适配新物候程序）
YearInit.R —— PnET-CN的年度初始化程序（适配旧物候程序）
……