Відео

Thank you Sir but if I run df <- data.frame(species=df$species,coordinates(d)) make error Error: unable to find an inherited method for function ‘coordinates’ for signature ‘obj = "sdmdata"’.

I'm having issues with spatrasters working in the ensemble function. The example code in the help section also runs into the same error. Any ideas on how to fix this? p2 <- ensemble(m, newdata=preds, filename='ens2.img',setting=list(method='weighted', stat='TSS',opt=2)) Error in .canProcessInMemory(.out[[1]], max(nlyr(.out), nlyr(newdata)) * : no slot of name "cpp" for this object of class "SpatRaster"

Really love this thank you

Hi! I'm having a repetitive error related to the 'newdata' part in the prediction. I followed every step in the tutorial, but it gives me: d <- sdmData(species~., spg, predictors = bioc, bg = list(method='gRandom', n=1000)) m <- sdm(species~., data = d, methods = c('brt','maxent','rf'), replication=c('sub','boot'), test.p=30, n=3) p3 <- predict(m, bioc) Error in .local(object, ...) : predict the number of values returned by the predict does not match the number of cells in newdata! I have also transformed the data manually but it doesn't seem to work, I checked the dimensions of the RasterStack and it is the same as the rest of the objects.

By entering the density of occurrence of the species at certain points, I want to predict the density at which they can be seen at other points. Is this possible? Can you suggest any method?

Can’t we used the uncropped predictors in prediction?

Thank you sir for making this useful video. I face error while trying to (raster)extractspg and bioc together

Great!! Video could you please make a video on the Biomod2 package?

Thank you so much for your great video!

Can an r3PG model be included in an sdm model in R?

Thank you for the great tutorial. Have one question, how to calculate the threshold maximizing the TSS/the maximum training sensitivity plus specificity threshold?

I want sdm code quickly pls

Kindly add a new video as we have now CMIP 6 data.

thanks for Sharing, really appreciate for newbie like me

Great video!, I have a question, how can i do a fine tuning and parameter selection for models such as glm, gam, rf and maxent?

Hi, great video! Question - is there anyway to deal with spatial auto correllation (the presence of systematic spatial variation in a variable) with this package? Thank you

How can we get evaluation for ensemble one TSS and ROC vakue ?

Hi Everyone, did anyone tried running this -- m <- sdm(species~., d, methods=c('Maxent'), replication=c('sub'), test.p=40,n=1, parallelSetting=list(ncore=4,method='parallel')) - I am unable to run maxent as my R crashes when using MAXENT, can anyone suggest me what can we be done ?

May someone please help. Does anyone know how to get the rcurve for the ensemble model?

p<-predict(m,biom,filename='pm21W5decPM.grd') Error in m[i] <- .self$whichMethod(m[i]) : replacement has length zero > What can i do sir

Great tutorial ever

Dear Dr. Babak Naimi, Thank you for your very teachable tutorial. please could you get me the scripts you are using on this live tutorial? Thank you.

SIR i need help. Kindly share your suggestion Iam using R 4.1.3 SDM was running properly but now predict function not working. An error appearing p1 <- predict(m, newdata=biom, filename='prs.img') Error in .updateGDAL(object, v, cell, band, setminmax) : no longer supported Sir what can i do

hello sir, this was very helpful for me. The prolem is I am not getting all the ML methods in getmethodNames() like svm,cart,rf. Please help me to add them into mine.

Hello :) I have downloaded occurrence data manually from gbif and stored it in my directory as a .cvs file. I already read the records into r and started cleaning the data. I removed duplicated records and the records without coordinates. Now I wanted to keep only the records that are over the extent of my study area, which is part of south america. Any inputs on how do I do that? Nothing I tryed worked out...

I am using the {sdm} package to do the species distribution modelling of invasive species. The {vifcor} was done succesfully and the variables(rasters) with high correlation were excluded. I am unable to compile my rasters(bioclim variables, elevation , ndvi) , occurance data into the {sdmData} object. Below is my code and error. d<-sdmData(formula=occurrence~., train=sp, predictors=biom1) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘sdmData’ for signature ‘"formula", "data.frame", "missing", "RasterStack"’ > sp <- as(sp, 'Spatial') Error in as(sp, "Spatial") : no method or default for coercing “data.frame” to “Spatial” please help me to solve this sir

Thank you for this video. May someone kindy assist, i am get this error trying to get slot "presence" from an object of a basic class ("NULL") with no slots in the modelling step

Hi! Does someone know why I have such an error after trying to use predict function? Error in .updateGDAL(object, v, cell, band, setminmax) : no longer supported

Hi, I have a problem in coding as "sp" is my occurrence, vars are selected bioclimatic variables after the collinearity check. data <- sdmData(species~., train = sp, predictors = vars, + bg = list(n=1000)) ORR data <- sdmData(species~., sp, predictors = vars) In both cases, I'm having the error below. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘sdmData’ for signature ‘"formula", "data.frame", "missing", "RasterStack"’ any advise are more than welcom! thans

Hi Babak - great video! I am struggling to get maxent to work with this sdm package. The maxent model completes training but when I apply predictions, I get the following error message: "Error in .local(object, ...) : Error in prediction....!" Any idea why that error is occurring?

Hello sir, First of all thank you so much for uploading this tutorial. it was very helpful. Sir i have a doubt sir here we are using CMIP5 DATA instead for uploading CMIP6 future climate data what should we do .

How do you incorporate other form of measurements outside presence/absence like abundance or any measurement like species density in this model?. Wondering if its the same or there are major changes to follow?

please help me, how can i fix "Error: cannot allocate vector of size 12.0 Gb"

SIR I HAVING THE ISSUE IN THE CROPING STEP spg <- crop(spg, e) where the error appears tobe like this Error in (function(classes, fdef, mtable): unable to find an inherited method for function crop for signature 'NULL' . Sir can you please help me with this

Error in loadNamespace(x) : there is no package called ‘devtools’ ............ how can I install Babknaimi sdm to my r studio

Thanks a lot for this tutorial. It really helped me to publish my first SDM using R, well appreciated. One question: Is there any code that I can use to split the response curve?. For example, instead of having 9 curves in one row, is it possible to have 3 rows (every 3 curves in one row). Thanks a lot.

Thanks for the great tutorial. Have one question, how do I evaluate the ensemble model outcome(en)?, AUC, TSS and other stuffs.

Thanks for the great tutorial. Have one question, how do I evaluate the ensemble model outcome(en)?, AUC, TSS and other stuffs.

I am working to model species distribution using R with HP pc, Cori 7, 8th generation, RAM 8GB, processor 1.99 GB , while my PC does not give results. What is the minimum capacity of PC to run SDM?

thank you very much I was very lost in the part of quantifying the importance of bioclimatic variables and your video helped me a lot

Anyone else having trouble using predict function for maxent algorithm?

thank you for sharing this video, I wonder whether raster::getData()function downloading the present data?

brilliant tutorial! Apologies if I missed this, but do where can I find the code used in this tutorial? Thanks so much

Hi! thank you so much for the great video!^^ Is that possible to create a background points radius (buffer) around the presence data?

And the Maxent? How we can implement Maxent in sdm package?

thank you very much for this.. a little confusion with the gui(m) code though.. Which package needs to be installed for this code to work? I got lost at that point..

Hello! I've been trying to figure out if you can plot the randomly generated background pseudo-absences from the sdmData object, but have yet to find or figure it out. Can someone help me, if it is indeed possible? Would be cool to see how the function is generating the new data. Thanks in advance.

Thanks for sharing. Wonderful

Thank you Babak. very helpful video here. Exactly what I was looking for!

Thanks a lot for such a wonderful package. I have few questions, would be great if you can guide me a little. 1. How to create a null model (Raes & ter Steeges, 2007) and then use it to compare with the actual generated model (which is generated using sdm package)? 2. I would like to generate MaxEnt model, but there are few setting which I need to specifically use while generating the model through sdm r package. These settings are generated through ENMeval R package. How do we use those settings (arguments) while using sdm r package, can you please give an example, arguments like jackknife, regularisation multiplier etc.. I am relatively new in R. <appendix: maxent parameters github.com/shandongfx/workshop_maxent_R/blob/master/code/Appendix3_maxentParameters_v2.pdf> 3. Is SDM supports background similarity test like ENMtools? I would like to use the functionality for comparing two models.