Data and code from: Cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield in no-till system - V2

[Note 2023-08-14 - Supersedes version 1, https://doi.org/10.15482/USDA.ADC/1528086] This dataset contains all code and data necessary to reproduce the analyses in the manuscript: Mengistu, A., Read, Q. D. Cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield in no-till system. (Citation will be updated upon final acceptance of manuscript) The .zip archive cropping-systems-1.0.zip contains data and code files. Data stem_soil_CFU_by_plant.csv: Soil disease load (SoilCFUg) and stem tissue disease load (StemCFUg) for individual plants in CFU per gram, with columns indicating year, plot ID, replicate, row, plant ID, previous crop treatment, cover crop treatment, and comments. Missing data are indicated with . yield_CFU_by_plot.csv: Yield data (YldKgHa) at the plot level in units of kg/ha, with columns indicating year, plot ID, replicate, and treatments, as well as means of soil and stem disease load at the plot level. Code cropping_system_analysis_v3.0.Rmd: RMarkdown notebook with all data processing, analysis, and visualization code equations.Rmd: RMarkdown notebook with formatted equations formatted_figs_revision.R: R script to produce figures formatted exactly as they appear in the manuscript The Rproject file cropping-systems.Rproj is used to organize the RStudio project. Scripts and notebooks used in older versions of the analysis are found in the testing/ subdirectory. Excel spreadsheets containing raw data from which the cleaned CSV files were created are found in the raw_data subdirectory.[备注 2023-08-14 - 本版本替代第1版，来源：https://doi.org/10.15482/USDA.ADC/1528086] 本数据集包含复现以下学术手稿中分析所需的全部代码与数据：Mengistu, A.、Read, Q. D. 《覆盖作物与轮作对免耕体系下菜豆壳球孢菌（Macrophomina phaseolina）的组织与土壤种群动态及产量的影响》（手稿最终录用后将更新引用格式）。压缩包cropping-systems-1.0.zip内含数据集与代码文件。数据集stem_soil_CFU_by_plant.csv：记录单株植物的土壤病害负荷（SoilCFUg）与茎组织病害负荷（StemCFUg），单位为每克菌落形成单位（Colony Forming Unit, CFU），列字段包含年份、样地编号、重复组、行号、植株编号、前茬作物处理、覆盖作物处理及备注信息。缺失数据以英文句号.标注。数据集yield_CFU_by_plot.csv：包含样地水平的产量数据（YldKgHa），单位为千克每公顷（kg/ha），列字段包含年份、样地编号、重复组、处理方式，以及样地水平的土壤与茎部病害负荷均值。代码文件包括：cropping_system_analysis_v3.0.Rmd——包含所有数据处理、分析与可视化代码的RMarkdown文档；equations.Rmd——带有格式化公式的RMarkdown文档；formatted_figs_revision.R——用于生成与手稿中格式完全一致的插图的R脚本。R项目文件cropping-systems.Rproj用于管理该RStudio项目。旧版分析所用的脚本与文档存放在testing/子目录中。包含原始数据的Excel表格存放在raw_data子目录中，这些原始数据用于生成已清洗的CSV文件。