Stack Overflow
Stack Overflow

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.

47 questions
0
votes
1 answer

Can dismo::evaluate() be used for a model fit with glmnet() or cv.glmnet()?

I'm using the glmnet package to create a species distribution model (SDM) based on a lasso regression. I've succesfully fit models using glmnet::cv.glmnet(), and I can use the predict() function to generate predicted probabilities for a given lambda…
erz
  • 1
0
votes
1 answer

How to find extent for mapping (dismo R)?

I am trying to do species distribution mapping in R for invasive oyster species (marine). With the code that I am using, it will plot points only on land (ext= geographic.extent). I cannot find other "extent" options for example marine.extent or a…
amerray
  • 11
  • 1
0
votes
1 answer

java.awt.HeadlessException error running maxent in "dismo" through rJava

I am trying to run the maxent function in the dismo package on macOS through rJava and keep getting this error message. Error in rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", : java.awt.HeadlessException Has anyone seen it before and…
ggbees44
  • 1
0
votes
2 answers

How to subset SpatialPointsDataframe with coordinates stored in matrix using R?

I want to subset a SpatialPointsDataframe with coordinates stored in a matrix. What I have tried so far is following: pts_subset <- pts[pts@coords == mtx, ] # variable holds the coordinates in two columns, and , just like in the…
ExploreR
  • 313
  • 4
  • 15
0
votes
1 answer

Cumulative output format resulting in NAs when using dismo::predict function in R

I have run a maxent model using the dismo package in R. I am able to use the predict function to view the output format as "raw" or "cloglog" but when I try the "cumulative" format I get "NA" values and a blank output. In summary, this code works…
Kate Dey
  • 1
  • 2
0
votes
0 answers

R: MaxEnt species distribution modeling with lapply -> args implicate different number of rows

) I want to apply dismo::maxent to a list of multiple datasets with lapply. But I get the error message that the arguments have a different number of rows, which is very strange because I created one dataset from the other one and they should have…
Denny
  • 47
  • 1
  • 4
0
votes
0 answers

Error: in points2grid(points, tolerance, round) : dimension 1: coordinate intervals are not constant

I'm new working in programming languages at all, but here I'm using R language and I need some help, I'm trying to learn how to make a consensus in SDM. The idea is create a raster and then, use the stack() function. But when I try to apply this on…
Mariana Vilela
  • 19
  • 3
0
votes
2 answers

How are MESS maps calculated in the dismo package?

Elith et al. [1] describe a method of measuring the dissimilarity between the values used in model fitting and the values used in making predictions. In the context of species distribution modelling (ecological niche modelling) that prediction is a…
Tristan
  • 51
  • 1
  • 3
0
votes
0 answers

How to choose the "family" on gbm.step?

my dependent variable is continuous and not normal but I'm not sure which family to choose ... when I run the analysis, this message appears: restart model with a smaller learning rate or smaller step size ... it is the first time that I do this…
ina
  • 13
  • 4
0
votes
1 answer

Species Distribution modelling incorporating climate data in R

I am trying to use data from GBIF to get an idea of Vachellia species disturbution across Africa and overlay this with annual rainfall in R. Any package advice, online resources or tutorials would be greatly appreciated? Thanks in advance
Elizabeth
  • 13
  • 2
0
votes
1 answer

How to replicate a model 10 times and extract several objects (test results) from it, and then make a mean?

excuse me my long question but I really hope that somebody could try to help me improve my code. Basically that's what I would like to do: reiterate the same model (as example random forests) 10 times with different inputs. As a result of each…
Kamil
  • 23
  • 4
0
votes
1 answer

How can I include the temporal aspect when generating pseudo-absence data?

I have 608 observations of satellite-tagged turtles. I want to model these with environmental data which includes sea surface temperature, current speed, wind speed etc. Of course, both the tagging and environmental data vary spatially and…
Jo Harris
  • 98
  • 9
0
votes
1 answer

Unable to fetch maps with dismo gmap()

I am trying to follow a tutorial found here: https://data.cdrc.ac.uk/tutorial/aa5491c9-cbac-4026-97c9-f9168462f4ac/4b026153-2953-4173-ab44-b24b2fb559fd Note: the tutorial requires a free login to access The step I am stuck at in the tutorial is this…
David
  • 195
  • 1
  • 1
  • 10
0
votes
0 answers

problem executing bioclim method in dismo package in R

I'm trying to run species distribution modelling using bioclim method in "dismo" package in R. after installing the necessary package and then load it, everything seems normal. and the "dismo" package appears in the package box of Rstudio, it's…
Ilyas Nursyamsi
  • 3
  • 1
  • 3
0
votes
1 answer

Download the subspecies data using R packages (dismo)

I would like to use dismo (R packages) to download gbif species occurrence data for species distribution analysis. I have read the guideline and successfully proceeded our analysis in most cases. I used the code here. gbif("genus","species",…
Bing-Hong Huang
  • 125
  • 1
  • 9
1 2
3
4