How to plot a sample tree from Random Forest in Biomod2, R?

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Hamed Sangoony

Dear Kohbalan

Thanks for your answer. Actually I used biomod2 to run RF, and I should be considered as a fresh man with R. I need the code to be able to check the outcome.

Thanks again

Sincerely

Hamed

Philipp Toscani

Dear Hamed,

I am not familiar with the randomForest in Biomod2 package as I usually work with the standard randomForest package, but I think that the core functionality is similar.

Are you interested in a tree plot of you result as the one attached?

Kind regards,

Philipp

Dear Philipp

Thanks for your response.

Yes, I need exactly this kind of plot. I will be more than grateful if you can send me the code. I am having serious problems to run standard RF in R.

I have a set of species presence data and some environmental variable rasters. I want to see the structure of best tree in forest.

Truly yours

Najat Qader Omar

please see Cross Validated site is a question and answer site for people interested in statistics, machine learning, data analysis, data mining, and data visualization. Join them; it only takes a minute:

I´m sorry, I just noticed your answer by now.

I think you will find some help for your problem in the following thread: http://stats.stackexchange.com/questions/41443/how-to-actually-plot-a-sample-tree-from-randomforestgettree . That´s the source where I took the code from.

I attach you an R-Script which I used to generate the above graph with some comments for you.

As far as I understand the biomod2 Package uses the randomForest library, in this case you should definitly be able to use all functions I used.

Best regards,Philipp

Dear all,

I know this topic is more than 2 years old by now, but as I recently noticed by request, there was a little error in my code (Line 100) due to a wrong variable name. I fixed it in the version below.

Thanks alot for your consideration.

I have fixed the problem somehow (actually I don't remember how!) but I will check this code out.

Anyway, I am very grateful.