Converting R to JMP script

GraphicalScore9

Hello,

 

I am not familiar with R and have been working with JMP (still beginner).  I have R code that I need to convert to JMP script.  I called JMP and they suggested I post here to see if someone can help me?

 

The R code is contained here abcd_discrimination/demographics_baseline_clean.R at main · barzilab1/abcd_discrimination · GitHub

 

and I have the datasheet in JMP, just no idea how to convert the script.

 

Is there anyone that can assist?

I attached the file in txt

Thank you in advance for your help.

pdem02.txt

mark_anawis

What is occurring in these steps is data cleanup. "demographics_set" is a data table which is similar to a JMP data table. 

R uses the convention: demographics_set[rows,columns]. Therefore, when you have the following line below, it is applied to all the rows since there is nothing inside the brackets to the left of the comma. For the column "sex_br", it assigns a value of 1 for "F" and 0 for "M" (and anything NOT "F"). The logic is that (sex == "F") returns 1 when TRUE and 0 when FALSE. The ":=" is a left assignment operator (infix). R may not recognize this operator at first so you may need to run the line: `:=` <- `<-` before the rest of the code. This assigns the more typical assignment operator ("<-") to ":=".

demographics_set[, sex_br := (sex == "F")*1]

 Here's another example where there is row subsetting below. For the rows where "demo_ethn_v2" is equal to "1", assign a value of 1 to the column "ethnicity_hisp".

 

demographics_set[demo_ethn_v2 == "1", ethnicity_hisp := 1]

 The is.na() function selects the rows which are not NA for the column inside the brackets.

The as.character() and as.numeric() function convert the column to either character or numeric as stated. Sometimes you need to first convert to character and then to numeric, hence the nested functions which occur in the code.

 

After all this data cleaning, the following line drops factor levels that are no longer used due to subsetting the data frame.

 

demographics_set = droplevels(demographics_set)

  That said, I agree with the others in that it would probably be easier for you to embed this R code inside a JMP script and use the R functions to run the R code. Check out the Scripting Index in JMP under Help menu to find the R functions. You'll probably need R Init() to initialize the connection to R, R Send() to wrap around any file or variable you want to input into the R code, R Submit() to wrap around your R code, R Get() to retrieve output from R back into JMP (or R Get Graphics() if you are retrieving a graphical object), and R Term() to terminate the R interface. Sounds more complicated than it is, but probably still easier than re-writing all the R code as JSL (JMP scripting language). The scripting index has some nice examples to help you along.