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Questions tagged [dismo]

dismo is an R package for species distribution modeling, focusing on predicting entire geographic distributions form species occurrence data and environmental data.

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Residuals' spatial autocorrelation in Boosted Regression Trees after correcting for it

I am running boosted regression trees (BRT) in R, with the package dismo and I have included a predictor (residual autocovariate) that, in theory, correct for spatial autocorrelation, following a paper from Crase et al (2012). My data units are…
E.Polaina
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Using evaluate function for MaxEntReplicates

I am using Maxent function in dismo package to create some species distribution models. Normally this works: single_model <- maxent(predictors, presence, args=c('jackknife=TRUE', 'randomseed=FALSE',"randomtestpoints=25"), path=output) evaluate.model…
fire_ecologist
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gbm.interactions for gbm.fixed

How can I get interaction assessment for gbm calculated with fixed n.trees? I tried: data(Anguilla_train) angaus.fixed <- gbm.fixed(data=Anguilla_train, gbm.x = 3:13, gbm.y = 2,family = "bernoulli", tree.complexity = 5, learning.rate = 0.01, …
F.Johann
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Exporting plot data from R to Excel

I am using packages gbm and dismo to create regression tree models in R. I first create the model: gen_1 <- gbm.step(data = cray_data, gbm.x = 14:23, gbm.y = 11, family = "bernoulli", tree.complexity = 3, learning.rate = 0.01, bag.fraction =…
SPF_6
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GLM returning negative value for threshold (cut-off)(in R)

I am working with species distribution modeling with GLM. I have (South America) data for Caiman crocodilus species from GBIF (http://www.gbif.org/species/5846514) and bioclimatic data from Worldclim (http://worldclim.org/current). I trying to run…
user3369932
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Biovars (dismo package) with data from DWD

I am new to R and I tried to calculate the bioclimatic variables with the biovars function from the dismo package for weather data from the DWD (Deutscher Wetterdienst). I need those variables for specific inventory plots, and so my first idea was…
I.Klein
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SDM extra value from MODIS

I am trying to extract monthly sea surface temperature, monthly chlorophyll concentration, depth, salintity via R. My tibble consist of 10000 presence-only data with columns of year, month, data, latitude and longitude. How can I extract the value…
treeandcoffee
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dismo MaxEnt does not run with categorical variables

I am trying to build a MaxEnt model in dismo, using a data frame. I already have presence-absence data and extracting the covariates for each point, so the only data I need is this one data frame. I have no issues running the model with continuous…
Sara
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Using dismo::randompoints in a loop

I have an SF object consisting of 81 polygons. What I would like to do, is generate 460 random points within each polygon. compared to st_sample, dismo::randomPoints has a few features I like to make use of; such as not having any created points be…
Beardedant
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How do you save the model output for a class "MaxEnt" object or “BRT”, or “ randomForest” from package ‘dismo’?

How do you save the model output for a class "MaxEnt" object or "BRT", or "randomForest" from Package 'enmSdmX' ---object of S3 class gbm-- Package 'dismo'. The enmSdmX uses the functions in the dismo package. I can’t save it using the vector it is…
Cybil Nicole Cavalieri
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Dismo gbif. Error when downloading gbif data for a particular species that has a huge number of occurrence points

I am using the following code to download data using the gbif function in the dismo package. This code has worked well for other species, but gives an error for Poa pratensis. I have tried to use the rgbif package instead, and that works but the…
Sarah
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How do I customise the colour bar maximum and minimum values on my maps?

I have plotted 3 maps, I need them to have the same scale on the colour bar so that the colours are comparable between the 3 maps. the 3 maps This is the code I have been using to make my maps. ssl.mod.ph <- bioclim(phCurrent, ssl.1900) #suitability…
Em27
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How to centre a raster at -180,180 longitude display, from 0,360 display

I have produced a map from the raster, but the longitude axis is not in the same format as my other maps. I need to have 0 longitude centred. I am predicting the future distribution of various species. My current pH maps have 0 longitude centred but…
Em27
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How to fix the object for Bioclim predict function on raster datasets

I am using the dismo predict function to predict the niche available to marine vertebrates in 2050. I have got a current and future oceanic pH dataset, my future dataset won't work within the predict function. I downloaded the data from noaa…
Em27
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Errors: incorrect number of dimensions when using BIOMOD_Modeling()

I recently start learning how to use biomod2 package, with latest version, 4.2-3. I try to fit a model using the GBM algorithm in BIOMOD_Modeling() from the package biomod2. I've checked the help file and googled for the error. However, the error…
HsunHung Chu
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