[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., Sykes, V. R., Kelly, H. M., Kharel, T., & Bellaloui, N. (2023). Cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield under no-till system. Plant Disease. https://doi.org/10.1094/pdis-03-23-0443-re

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.