Data Science for Agriculture
How to manage and manipulate data for agricultural research
Dr. Raun has asked you to do some preliminary analysis of some data from a study conducted to investigate the interactions between foliar N application and frost. You decide to put some of your new R skills to use and produce the report using R Markdown.
To do so, open a new R Markdown file within R Studio. Use “Efaw Foliar N Freeze Mitigation Report” for the title and your name for the author. The new file will contain an example template for an R Markdown document. Click on the Knit HTML button to compile your R Markdown document. Compare the resulting output with the R Markdown script. Read through the template R Markdown file and the resulting output for an explanation of how R Markdown works.
Next, create a subdirectory named data and download the data you will use
(Efaw_Freeze2014.xlsx).
Because the data are in an MS Excel spreadsheet, you will want to use the handy
read.xlsx() function to read in the data. To do so, you will need to install
the xlsx R package first.
Within your R Markdown file, create a new R code block with the chunk name
“read_data” that loads the xlsx package using library() and reads in the data
using the read.xlsx() function. (Hint: You will need to use sheetIndex=1.
Also, don’t modify the Excel file to read it in. Use the startRow and
endRow options within read.xlsx() to read in the header row and data.)
Add a line to the code block that changes the variable for the change in NDVI to all positive values.
Add a line to the code block that uses the as.factor() function to convert
the treatment column from a numeric column to a factor column.
Add a line that summarizes your data frame using the summary() function.
The displayed R code and summary output are useful as you were checking that
the data were read in properly, but you probably don’t want them in your final
report. Use the echo=FALSE and include=FALSE options to the code chunk to
keep these from being displayed in your document.
Below your “read_data” code chunk, add a header entitled Introduction
to your document using the ## notation and add a sentence below introducing
the overall purpose of the report.
