[R-sig-eco] Plot map in R - center and move labels: x.coords and y.coords

Hello, I am new in R and I want to plot a map, but I am not able to center and move the label of "y.coords" library (rgdal) p1<-readOGR(".", "WGS") clab = 0.8 cmain = 2 caxis = 0.8 par(mar=c(4,3,1,1), mgp=c(3, 1, 0), las=1) plot(p1,asp=1, main= "A - P", xlab="x.coords",

[R-sig-eco] GAM parameters: Biomod 2

Hello, I am using Biomod 2 to modelling species distribution. I ran some algorithms like GAM, GLM, RF and CTA. I did not change the parameters. How can I known the quadratic terms of GAM? I used the variables with form linear (e.g. precipitation, altimetry, temperature) I did not use

[R-sig-eco] Modelling: opinion of new methods

Hello everyone! I am new in modelling species (plants). However, I used some approaches like ENFA (Biomapper), Maxent, generalized linear and additive models (in R) and Biomod2. I would like to improve my knowledge in this area.Currently, what methods have been used? Any suggestions? Regards,

Re: [R-sig-eco] Calculate AIC, DIC and BIC for models machine learning

Simulation and > Computation, 47, 1382–1396. > > Jane Elith > > On 22/3/19, 10:05 pm, "R-sig-ecology on behalf of > r-sig-ecology-requ...@r-project.org" on behalf of r-sig-ecology-requ...@r-project.org> wrote: > > > Message: 2 > Date: Thu, 21

Re: [R-sig-eco] R-sig-ecology Digest, Vol 132, Issue 10

Prof Dr. Ralf Schäfer thank you for sharing the links. Best regards, Lara Silva <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> Sem vírus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-emai

[R-sig-eco] Calculate AIC, DIC and BIC for models machine learning

Hello everyone! In R, it is possible to calculate AIC, DIC, or BIC for models machine learning, like RF, ANN, GBM, MARS? Are there any functions or specific packages in R? Any suggestion? Thanks Lara

Re: [R-sig-eco] Error in run GAM (Biomod 2)

rue nature is not some ideal that we have to > live up to. It’s who we are right now, and that’s what we can make friends > with and celebrate. > Excerpted from: Awakening Loving-Kindness by Pema Chödrön > > > On 3/18/19, 6:28 AM, "R-sig-ecology on behalf of Lara Silva"

[R-sig-eco] Error in run GAM (Biomod 2)

Hello I am trying to run several algorithms in biomod 2 (GLM, GAM, ANN, SRE) but I received the following menssage. Model=GAM GAM_mgcv algorithm chosen Automatic formula generation... > GAM (mgcv) modelling...Error in smooth.construct.tp.smooth.spec(object, dk$data,

Re: [R-sig-eco] [R-sig-Geo] Error in running Maxent within biomod2

ttps://cran.r-project.org/web/packages/biomod2/index.html > > or you can use the R command: > > maintainer("biomod2") > > David L. Carlson > Department of Anthropology > Texas A University > > -Original Message- > From: R-sig-Geo [mailto:r-sig-geo-bo

[R-sig-eco] Error in running Maxent within biomod2

I got an error when running Maxent within biomod2 Running Maxent...Error in system(command = paste("java ", ifelse(is.null(Options@MAXENT.Phillips$memory_allocated), : What does it means? Thanks [[alternative HTML version deleted]] ___

[R-sig-eco] Doubt_projection map Biomod2

Hello, I am trying to model a species in biomod2 with 4 algorithms. myBiomodModelOut_2 <- BIOMOD_Modeling( myBiomodData_2, models=c('GLM','GAM','ANN', 'SRE'), NbRunEval=10, DataSplit=70, Yweights=NULL, VarImport=10, models.eval.meth=c('ROC','TSS'), # evaluation metrics will be calculated

Re: [R-sig-eco] AIC in Biomod 2

riginal Message- > From: R-sig-ecology [mailto:r-sig-ecology-boun...@r-project.org] On > Behalf Of Lara Silva > Sent: Saturday, March 9, 2019 5:32 PM > To: r-sig-ecology@r-project.org > Subject: [R-sig-eco] AIC in Biomod 2 > > Hello > > Is there a

[R-sig-eco] AIC in Biomod 2

Hello Is there any way to calculate the AIC in Biomod 2? Thanks, Lara [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Vegan_package: Plot PCA

Thank you! Eduard Szöcs escreveu no dia terça, 26/02/2019 à(s) 23:24: > biplot() has a "choices" argument for this. > > Eduard > > Am 27. Feb. 2019, um 01:19, Lara Silva schrieb: >> >> Hello, >> >> I am using the VEGAN package to do PCA of my va

Re: [R-sig-eco] Vegan_package: Plot PCA

gt; The option choices helps you to select the axis. In your case it would be > choices = c(1,3) [axis 1 vs 3] or choices = c(2,3) [axis 2 vs 3] > > Hope this would help you. > > > Abdoul > > > Le mar. 26 févr. 2019 à 19:20, Lara Silva a > écrit : > >> He

[R-sig-eco] Vegan_package: Plot PCA

Hello, I am using the VEGAN package to do PCA of my variables. bio.pca <- rda(variables, scale=TRUE) # Argument scale=TRUE bio.pca summary(bio.pca) # Default scaling 2 summary(bio.pca, scaling=2) sum_bio <-summary(bio.pca) names(sum_bio) sum_bio$species #make basic plot

Re: [R-sig-eco] Select a percentage of combinations

- combinations[,sample(1:ncol(combinations), > floor(ncol(combinations)*0.2))] ## subsets out 20% of the columns from that > object. > ## Note that sample() samples without replacement, by default. > sample > > Hope that helps! > Shane > > On Tue, 26 Feb 2019 at 12:38, La

[R-sig-eco] Select a percentage of combinations

Hello, I want to select sets of combinations, but I do not want use all 1140 combn (20,3) choose (20,3) - total of 1140. [,1091] [,1092] [,1093] [,1094] [,1095] [,1096] [,1097] [,1098] [,1099] [,1100] [1,] 13 13 13 13 13 13 13 13 13 13 [2,]

Re: [R-sig-eco] Use rbind for more than two data frame

Thanks for the advice! Mollie Brooks escreveu no dia quinta, 21/02/2019 à(s) 11:31: > Try changing "bio15_FP" to "bio15" so that the names match. > > > On 21Feb 2019, at 13:29, Lara Silva wrote: > > Hello, > > I am trying to join different data f

[R-sig-eco] Use rbind for more than two data frame

Hello, I am trying to join different data frames using rbind but I have the following mensage: sdmata_global <- rbind(sdmdata_SM,sdmdata_P,sdmdata_T,sdmdata_F,sdmdata_SJ) Error in match.names(clabs, names(xi)) : names do not match previous names > class(sdmdata_SM) [1] "data.frame" >

Re: [R-sig-eco] Problem in generate random samples in r

mber of samples you wanna draw. > > best, > > Henrik > > > On 20. Feb 2019, at 12:20, Lara Silva wrote: > > > > Hello, > > > > I am trying to generate random samples from the following code > > > > ### Setting random seed to always create the

[R-sig-eco] Problem in generate random samples in r

Hello, I am trying to generate random samples from the following code ### Setting random seed to always create the same ### Random set of points set.seed(0) absences_15000<-absences[sample(nrow(absences), 15000),] points(absences_15000, cex=0.1) ## Subsample_1 set.seed(0)

[R-sig-eco] How to manipulatechange the space between the numbers of axes (equal interval)? How to add a legend to a map (plot raster)?

Hello, I´m trying to plot a map in R. Is it possible to change the values of x.axis and y.axis and have the same interval (space between the numbers)? How to add a legend for the map? https://www.dropbox.com/s/60tavy6vez33mw3/Plot_map.tiff?dl=0 >