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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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R Dismo package: Difference of test AUC of maxent results and evaluate() function

I would like to ask a more theoretical question about the methods in the dismo package in R: why is the resulting area under the curve characteristics (AUC) so different between the evaluate() function and the AUC of the test data in the maxent()…
Merijn Moens
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Is there a better way for handling SpatialPolygons that cross the antimeridian (date line)?

TL;DR What is the best way in R to handle SpatialPolygons intersecting/overlapping the anti meridian at +/-180° of latitude and cut them into two sections along that meridian? Preface This is going to be a long one, but only because I'm going to…
Where's my towel
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Voronoi approach to buffering polygons while preserving topological integrity

As I understand it R lacks a methods to buffer polygons in a spatially exclusive way that preserves the topology of adjacent polygons. So I'm experimenting with an approach that generates voronoi polygons of the original polygon vertices. Results…
geotheory
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Customize tm_compass() background

In the code below, how do I set background color and transparency fortm_compass()as I can do for map title? library(tmap) library(dismo) ny.map <- gmap(x = "New York", zoom = 13, type = "satellite") print(tm_shape(shp = ny.map) + tm_raster()…
Manojit
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Extracting non-object values from ecocrop in R

I'm working on crop-climate modelling using Robert Hijmans' package 'dismo' and more specifically the function 'ecocrop'. Ecocrop calls a series of 'hidden' functions including, .doEcocrop (ecocrop and .doEcocrop pasted below), which calculate the…
Arferion
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Selecting subsets of each dataset in a list in R

After using kfold from the dismo package, I am attempting to select a subset of the groups that this function makes from different datasets in a list in R. In an individual datset, this is easy: #With an individual dataset: library(dismo) data_car…
Cameron
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How to obtain standard error maps for boosted regression tree model?

I am using the R gbm and dismo libraries to create boosted regression trees (BRTs) of landscape CO2 emissions. I am obtaining maps of CO2 estimates using the raster predict function. For example, if Stacked is my raster stack of input predictor…
sky53
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Return value of gbm.step function in "dismo" package using cross validation

I'm trying the gbm.step function from dismo package to fit a gbm model using cross-validation. According to the dismo document(https://cran.r-project.org/web/packages/dismo/dismo.pdf, page 32), the return value of gbm.step is a gbm object. The gbm…
hiyu
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Using a test sample file with MaxEnt in R

I worked a lot with MaxEnt in R recently (dismo-package), but only using a crossvalidation to validate my model of bird-habitats (only a single species). Now I want to use a self-created test sample file. I had to pick this points for validation by…
S. Gey
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Is there a package for plotting random points with a specific condition from a raster?

I have a few raster files, on which I should plot some random points for pseudoabsence. The condition, or buffer would be 2 random points in every 4x4 pixel area. I found the dismo package, which contains a randomPoints function, which would be…
PickleRick
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Creating Land Mask with randomPoints Error

I am trying to create a background land mask for my data. All of the questions I've seen are for CDO, which I cannot get to load into my R Studio (package ‘cdo’ is not available (for R version 4.0.2)). I am looking at shellfish data where the points…
amerray
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issue with gbm.step() function in R

I'm trying to execute the Cross-Validation for the boosting regression/classification trees using the function gbm.step() from the R package dismo, but it returns a empty output and I can't figure out why. This is the code I'm using: ColIndexCov <-…
G0904B
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Simplifying the data in a raster - R

I have a raster file, which I created from data downloaded from DIVA-GIS: http://www.diva-gis.org/datadown nz_map<-raster("NZL1_msk_cov.grd") Using plot() on this object works great, so there are no issues importing it. The raster object contains a…
clinaaeus
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Species distribution model to produce psuedo-absence data using the randomPoints() function in the Dismo package in R: Error Message

Aim: My aim is to build a species distribution prediction model using the function randomPoints() in the Dismo package with the utlimate aim of generating pseudo-absence points and plotting them on a map. These points will be converted into a rastor…
Alice Hobbs
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R issue with coding in dismo package

I am trying to create a BRT model using the dismo package. When I simplify my model following the cran tutorial, and then try to respecify it I get an error saying: "Error in data[, gbm.x, drop = FALSE] : incorrect number of dimensions". I am not…
Tyler Harrow-Lyle
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