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microsud / dysbiosisR

The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
https://microsud.github.io/dysbiosisR/
GNU General Public License v3.0
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dysbiosisOBB error #5

Open lxsteiner opened 3 months ago

lxsteiner commented 3 months ago

Hi,

Thank you for providing a nice summary of dysbiosis indexes in one package!

I was trying it out on the test data and then mine as well, unfortunately dysbiosisOBB gives me an error. I was able to calculate all other indexes with me own data.

> dysbiosis.oob <- dysbiosisOBB(fix.rarephi,
+                               group_col = "PhageCode",
+                               case_label = "PHI",
+                               seed_value = 1235,
+                               add_tuneRF_params = list(ntreeTry=100,
+                                                        stepFactor=1.5,
+                                                        improve=0.01,
+                                                        trace=TRUE,
+                                                        dobest=FALSE),
+                               ntree = 100,
+                               plot_roc = TRUE)
The random seed of your session for reproducibility is: 1235
mtry = 61  OOB error = 20% 
Searching left ...
mtry = 41   OOB error = 20% 
0 0.01 
Searching right ...
mtry = 91   OOB error = 20% 
0 0.01 
The mtry used is : 416191
Error in mtry < 1 || mtry > p : 'length = 3' in coercion to 'logical(1)'

Could you please tell if the error says anything to you? I'm not sure where the issue could be, I used a phyloseq object with absolute counts in all other calculations. Transformed it here to relative abundance summed to 1 or 100, made no difference (since in the tutorial you mention multiple times that the test data is relative abundance, summed to 100, so I wasn't sure if that was important).

The error seems rather to be coming from the logical evalution of "||" inside an if() statement (according to Google), so I guess it has to do with https://github.com/microsud/dysbiosisR/blob/292adc8d2f078230c155b2ce0b47d2c6c55f5d12/R/dysbiosisOBB.R#L86 though not really sure 😅

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Thanks.

gutmicrobe commented 3 months ago

Thanks for using the R package and the query. My apologies for late response. I am unable to recreate the error. Is it possible that you have missing info or group column is not a 'factor'? in your sample_data?