Data and codes for Lessons learned from a detailed exploration of APEX as a tool to represent corn residue management and cover crops

Code used to generate information used in Arnillas et al. (2025) "Lessons learned from a detailed exploration of APEX as a tool to represent corn residue management and cover crops", the information generated, and the codes to process and visualize it. The codes have not been tested independently, hence, edits will be necessary. For some codes, it may be necessary to download apex_functions_2.R from https://github.com/carlos-arnillas/apex_io/tree/main. apex_functions_2.R is a library of functions developed during this project to support I/O of the several text files used by APEX. winter_crops_test_adj4.R Code that run the simulation as a set of modifications of the input files in run1wc.zip controlled by the scenarios stored in winter_crops_test5b.RData. winter_crops_test_adj4_detailed.R Code that reads the data stored in winter_crops_test5b.RData and generate several figures that support the analyses reported in the manuscript and several otherm figures. run1wc.zip Input file with the descriptors of soil, crops, weather, crop management, and several input parameters required by APEX. winter_crops_test5b.RData File containing all the information generated to test APEX in our study case and the variables describing the scenarios tested and the parameters of the simulation. lres List of results of each simulation. Each simulation is stored as an element of the list. The name of the element correspond to the name column in the scenarios table. The results of each scenario is stored in several tables. The structure and meaning of the following tables correspond to the structure and meaning of the tables as described in the APEX Theoretical Documentation (https://epicapex.tamu.edu/manuals-and-publications/): sao sad dgz dhy dgn msa swn dws asa wss awp dcn acn aws mws mgz The following tables have been added to report complementary information: out_txt: text showing errors and other messages. sad1: same information from than the one stored in SAD, but with crop information listed in long instead of wide format. cvf: table reporting intermediate values necesary to estimate the cover factor (CVF). cvrs: table reporting intermediate values necesary to estimate the above ground crop residue (CVRS). uw: table reporting intermediate values necesary to estimate daily water uptake by soil layer (UW). rwt: table reporting intermediate values necesary to estimate the root weight by soil layer (RWT). scenarios Table describing the conditions used to run each of the scenarios (when relevant, the column names match the correspoing variable being modified in the APEX simulation). Relevant variables used in this simulation are: CPNM: Code of the crop used as cover crop in the simulation. Values: NA means no cover crop, CLVR: Red clover, COAT: Oats, RYE: Rye. ORHI: Values describing the fraction of crop biomass removed from the main crop (corn) after harvesting the grains. weather: Simulation using a repetitive pattern with always the same weather year after year (s, static) or an scenario in which after certain year the weather pattern changes (m, mixed). CNUM: Numeric code representing the crop being used as cover crop. Values: NA means no cover crop, 2397: Red clover, 2363: Oats, 2364: Rye. HU: Heat units of the corresponding cover crop (used to describe the crop growth pattern). SeedDensity: Number seeds added by the model during the planting operation of the cover crop. name: Name of the scenario. The scenario is composed by the soil code (always "O"), and the values from the columns ORHI, CPNM, and weather. CPNMf: A factor (sensu R) created from CPNM to facilitate the presentation of results. ORHIf: A factor (sensu R) created from ORHI to facilitate the presentation of results. responses Table describing the several response variables generated by APEX (including the ones created for this project). var_code: Code name of the variable. Description: Description of the variable. SAD: Is the variable present in the SAD file? ACY: Is the variable present in the ACY file? ASA: Is the variable present in the ASA file? DGN: Is the variable present in the DGN file? DHY: Is the variable present in the DHY file? MSA: Is the variable present in the MSA file? Any: Is the variable present in any of the previous files? Group: Does the variable is important to describe any of these topics (Plant growth, Nitrogen, Phosphorus, Water dynamics, Erosion, or Soil)? Count (not used) units: Unit of the variable. var_number: Does the variable correspond to any of the variables reported in table X of the APEX user manual? Daily: Is the variable reported on a daily time scale? Extension: Extensions of the files in which the variable can be found. PrintID: Codes of the files in which the variable can be found. main_out (not used) Boundary (not used) folders Internal variable describing where to find the information needed to prepare the simulation. opc Table resembling the operation file used APEX to describe the management implemented in any given field. Some values in there are replaced before running the simulation (see file winter_crops_test-adj4.R). run_fd Folder name of the current simulation.本代码用于生成Arnillas等人2025年发表的论文《基于APEX模型（APEX）模拟玉米残茬管理与覆盖作物的详细探索总结的经验教训》中所用的相关数据，同时包含生成该数据的代码，以及用于处理、可视化结果的代码。 本代码未经过独立测试，因此使用前需进行必要的编辑调整。 部分代码需从https://github.com/carlos-arnillas/apex_io/tree/main下载`apex_functions_2.R`文件。该文件为本项目开发的函数库，用于支持APEX模型所用的各类文本文件的输入输出操作。 `winter_crops_test_adj4.R` 该代码基于`winter_crops_test5b.RData`中存储的情景方案，对`run1wc.zip`内的输入文件进行修改，以此运行模拟任务。 `winter_crops_test_adj4_detailed.R` 该代码读取`winter_crops_test5b.RData`中存储的数据，生成支撑论文分析的多幅图表，以及额外的辅助图表。 `run1wc.zip` 该压缩包为APEX模型所需的输入文件合集，包含土壤、作物、气象、作物管理方案的描述信息，以及多项模拟所需的输入参数。 `winter_crops_test5b.RData` 该文件存储了本研究中用于APEX模型测试的全部生成数据，以及描述测试情景与模拟参数的相关变量。 `lres` 该列表存储了各次模拟的结果，每一次模拟的结果作为列表的一个元素，元素名称与情景表中的`name`列取值一一对应。每个情景的结果存储于多张数据表中，以下数据表的结构与含义均遵循《APEX理论文档》（https://epicapex.tamu.edu/manuals-and-publications/）中的定义： `sao`、`sad`、`dgz`、`dhy`、`dgn`、`msa`、`swn`、`dws`、`asa`、`wss`、`awp`、`dcn`、`acn`、`aws`、`mws`、`mgz` 以下数据表为本项目新增的补充信息表： `out_txt`：存储错误信息与其他提示文本的文本文件。 `sad1`：与`SAD`文件存储的信息一致，但作物信息以长格式而非宽格式呈现。 `cvf`：存储覆盖因子（CVF）估算所需的中间计算值的数据表。 `cvrs`：存储地上作物残茬量（CVRS）估算所需的中间计算值的数据表。 `uw`：存储各土层每日水分吸收量（UW）估算所需的中间计算值的数据表。 `rwt`：存储各土层根系生物量（RWT）估算所需的中间计算值的数据表。 `scenarios`（情景表） 该表用于描述各模拟情景的运行条件（若相关，列名与APEX模拟中待修改的变量一一对应），本模拟所用的关键变量如下： `CPNM`：模拟中所用覆盖作物的代码。取值说明：`NA`代表无覆盖作物，`CLVR`代表红三叶，`COAT`代表燕麦，`RYE`代表黑麦。 `ORHI`：描述主作物（玉米）收获籽粒后被移除的生物量占比的参数。 `weather`：气象情景设置，可选值为`s`（静态，即逐年使用重复的固定气象数据）或`m`（混合，即经过特定年份后切换气象模式）。 `CNUM`：覆盖作物的数字代码。取值说明：`NA`代表无覆盖作物，`2397`代表红三叶，`2363`代表燕麦，`2364`代表黑麦。 `HU`：对应覆盖作物的积温值，用于描述作物生长规律。 `SeedDensity`：模型在覆盖作物播种环节所使用的单位面积播种密度。 `name`：情景名称，由土壤代码（固定为`"O"`）以及`ORHI`、`CPNM`、`weather`三列的取值组合而成。 `CPNMf`：基于`CPNM`生成的R语言因子型变量，用于简化结果可视化展示。 `ORHIf`：基于`ORHI`生成的R语言因子型变量，用于简化结果可视化展示。 `responses`（响应变量表） 该表用于描述APEX模型生成的各类响应变量（包含本项目新增的变量）。 `var_code`：变量的代码名称。 `Description`：变量的详细说明。 `SAD`：标识该变量是否存在于`SAD`文件中。 `ACY`：标识该变量是否存在于`ACY`文件中。 `ASA`：标识该变量是否存在于`ASA`文件中。 `DGN`：标识该变量是否存在于`DGN`文件中。 `DHY`：标识该变量是否存在于`DHY`文件中。 `MSA`：标识该变量是否存在于`MSA`文件中。 `Any`：标识该变量是否存在于上述任意一个文件中。 `Group`：标识该变量是否用于描述以下类别中的一类：作物生长、氮循环、磷循环、水动力过程、土壤侵蚀或土壤特性。 `Count`（未使用） `units`：变量的计量单位。 `var_number`：标识该变量是否与APEX用户手册X表中列出的变量一致。 `Daily`：标识该变量是否为逐日尺度的输出结果。 `Extension`：存储该变量的文件扩展名。 `PrintID`：存储该变量的文件代码。 `main_out`（未使用） `Boundary`（未使用） `folders` 内部变量，用于存储模拟所需文件的存放路径。 `opc` 该数据表与APEX模型所用的田块管理操作文件格式一致，部分参数会在模拟运行前被替换（详见`winter_crops_test_adj4.R`文件）。 `run_fd` 当前模拟任务的文件夹名称。