Readme

Weed communities in three cropping systems suitable for the Midwestern USA were studied from 2017 through 2020 to examine how diversified cropping systems affected weed community diversity, stand density, and aboveground mass. A baseline 2-year cropping system with corn (*Zea mays* L.) and soybean (*Glycine max* (L.) Merr.) was diversified with cool-season crops, namely oat (*Avena sativa* L.), red clover (*Trifolium pratense* L.), and alfalfa (*Medicago sativa* L.) in 3-year and 4-year systems. Herbicide was not applied in oat, red clover, and alfalfa. The reduction in the mass of herbicide active ingredients applied in the 3-year and 4-year systems was associated with increased weed stand density, aboveground mass, and community diversity, but did not cause crop yield loss. The addition of the cool-season crops into the cropping system did not affect densities of emerged weeds but did affect weed growth. The dominance of aggressive weed species such as common waterhemp (*Amaranthus tuberculatus* (Moq ex DC) J.D. Sauer) and common lambsquarter (*Chenopodium album* L.) tended to be greater in corn and soybean phases of the rotations than in oat, red clover, and alfalfa.


The following folders are populated as the manuscript submission progresses. 

1-Background: motivation to conduct the research and relevant .pdf of the literature   

2-Data: raw and clean data sheets  

3-Picture: graphics for manuscript submission.

4-Data-wrangling: `.R` files with codes to clean the raw data  

5-Analysis: `.Rmd` executable files to analyze the data and render report. Each `.Rmd` file is devoted to address one set of questions.
+ Crop_yields.Rmd: Did rotation and corn herbicide affect crop yield? How are yields at the experiment site compared to Iowa's and Boone County's yields?
+ Community.Rmd: Did crop identity and corn herbicide affect community diversity, evenness, and richness indices? How?  
+ Individual-sp-difference.Rmd: Did crop identity and corn herbicide affect individual density and aboveground mass of 7 most abundant species? How?  

6_Draft: to put everything together in Manuscript_whole.Rmd. 
+ `ecol.bib` (the Zotero generated bibliography)
+ `Introduction.Rmd`
+ `MandM.Rmd` 
+ `Discussion.Rmd`  

7-Extra: AppendixA-model-diagnosis.Rmd - model diagnosis

General workflow:  
1 - Each `.Rmd` file is devoted to address one hypothesis. 
2 - All the pieces are put together under `Manuscript_whole.Rmd`. The execution of `Manuscript_whole.Rmd` will generate: 
  i) a latex-figure folder with all the figures from the `.Rmd` files.
  ii) a `.tex` file and a `.pdf` file.  
3 - The `.tex` file is uploaded to Overleaf for final polishing that are very inconvenient or impossible to do in R. 


I sincerely thank the R user community, `bookdown` authors, Zotero, and ISU Lunchinators for inspiration, coaching, and troubleshooting. 
This current structure works best for me.