randomforest explained variation

Question

I have the following dataset. I would like to know which bacteria contribute more when comparing the location of the bacteria(categorical) and its pH(numeric).

For instance at the end I would like to say for example that a certain bacterial type is more frequently found in a certain location when looking at the temperature.

             Bacillus Lactobacillus Janibacter Brevibacterium Lawsonella     Location temperature
Sample1              2          30    164          8             21         48 bedroom    27
Sample2              0         211      0        996            195        108 bedroom   35
Sample3              1         938      1         21             38         43 pool   45
Sample4              0          95     17          1              4        334 pool   10
Sample5              0         192     91         25           1207       1659 soil    14
Sample6              0          12     33          6             12        119 soil   21
Sample7              0          16      3          0              0        805 soil    12

The idea is to run randomforest to select those features (bacteria) that are more important when looking at both the location and the temperature.

Is a random forest suitable for this? When I run the following command I get the following error:

randomForest(Location+Temperature ~.,data=mydf)
Error in Location + Temperature : non-numeric argument to binary operator. 

From the error it looks that i cannot use a continuous and categorical variable together. How can I fix this?

Is for exemple convert the numeric temperature variable to ranges of temperatures as a categorical variables would be a solution ?

In fact I have tried and it worked by converting the numeric temperature to ranges and pasting the location so that i have a combination of location and temperature.

randomForest(Location_temperature ~.,data=dat)

I get the list of important bacteria which is what I was looking for. Now how can I know which one contributes more to one location or another since my model i was using all sites? For example how to check that your important variables(let´s say Bacillus is the most important from the randomforest model ) is important in the pool location (how much variation it explains in the pool)?

Answer 1

I think the basic problem you're facing is that you are asking your random forest to predict Location + Temperature, i.e. a compound of two variables. This is not a standard random forest; the problem is a multivariate random forest. I don't think the randomForest package can perform those. There is, however, a MultivariateRandomForest package that can do exactly what you're after.

If you want to learn more about multivariate random forests, Segal & Xiao (2011) seems like the place to start.

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Segal, M., & Xiao, Y. (2011). Multivariate random forests. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 1(1), 80-87.