search for: dismo

Estimados erreros, Estoy intentando entender como calcula el paquete dismo ( https://cran.r-project.org/web/packages/dismo/index.html) un coeficiente de variación. Os pongo un ejemplo: tmin <- c(10,12,14,16,18,20,22,21,19,17,15,12) # temperatura mínima media mensual de un año tmax <- tmin + 5 # temperatura máxima media mensual de un año prec <- c(0,2,10,30,80,160...

...lguno de los art?culos en los que > se describe esta base de datos den raz?n de este sumatorio. > > Saludos, > > Marcelino > > El 19/06/2018 a las 11:43, Jaume Tormo escribi?: > > Estimados erreros, > > > > Estoy intentando entender como calcula el paquete dismo ( > > https://cran.r-project.org/web/packages/dismo/index.html) un coeficiente > > de > > variaci?n. Os pongo un ejemplo: > > tmin <- c(10,12,14,16,18,20,22,21,19,17,15,12) # temperatura m?nima media > > mensual de un a?o > > tmax <- tmin + 5 # temperatura...

Dear R-helpers and Dr. Hijmans, I can not invoke maxent() in GNU Linux. Could you give me any directions on that? There is maxent.jar in version 3.3.3e in the right folder. ######################################## R: > jar <- paste(system.file(package="dismo"), "/java/maxent.jar", sep='') > jar [1] "/ebio/abt6/jmao/rpacks/dismo/java/maxent.jar" Terminal: jmao at upa:~/rpacks/dismo/java$ ls maxent.jar mebridge1.jar mebridge2.jar ######################################## Thank you in advance. Here is my info: #####...

Dear all, when using .jinit() I get the message .jinit() : Cannot create Java virtual machine (-1). The details: I am using the Dismo package.Dismo has a function 'maxent' that communi-cates with this program(MaxEnt).MaxEnt is available as a stand-alone Java program. It is normal when I execute the command : "jar <- paste(system.file(package="dismo"), "/java/maxent.jar", sep='')&quo...

savePngCentredAt <- function(address) { require(dismo) x <- geocode(address) range <- as.numeric(x[4:7]) + c(-0.01, 0.01, -0.01, 0.01) e <- extent(range) g <- gmap(e, type = "roadmap") require(digest) png(path.expand(paste('~/public_html/',digest(address, algo='sha1'),'.png',sep='')))...

Hey, I am having troubles using the 'predict' function with in the Raster package. I am using pm<-predict(mm, predictors) where mm is the mahalanobis distance and the predictors are a stack of 6 raster layers containing environmental variables. When I try to run the prediction I get the following warning message: Warning message: In layerNames(x): the layerNames function is

...6) > sessionInfo() sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US/en_US/en_US/C/en_US/en_US attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] evaluate_0.3 dismo_0.5-14 rJava_0.8-8 raster_1.7-29 sp_0.9-76 loaded via a namespace (and not attached): [1] grid_2.12.1 lattice_0.19-17 plyr_1.4 stringr_0.4 [5] tools_2.12.1 -- Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany,

...LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936 attached base packages:[1] stats graphics grDevices utils datasets methods base other attached packages:[1] maptools_0.8-10 lattice_0.20-0 foreign_0.8-46 rJava_0.9-2 [5] dismo_0.7-11 raster_1.9-41 sp_0.9-91 loaded via a namespace (and not attached):[1] grid_2.14.0> The details: I am using the Dismo package.Dismo has a function 'maxent' that communi-cates with this program(MaxEnt).MaxEnt is available as a stand-alone Java program. It is normal when...

...d multiple ways of doing this but have memory issues with very large datasets. To overcome this problem I am working with lists. I am now stuck on how to randomlly sample the correct elements of a list. Here is an example of my code and an example dataset. rm(list = ls()) #load libraries library(dismo) library(raster) ##example data #load map of land files<-list.files(path=paste(system.file(package="dismo"),"/ex",sep=""),pattern="grd",full.names=TRUE) mask <- raster(files[[9]]) #make point data pts<-randomPoints(mask,100) #extract the unique cell...

Buenas días me gustaria saber cual es la libreria mas actual que contiene al algoritmo de maxima entropia que permite modelar nichos ecologicos; a su vez que libreria presenta mejor temática en la representacion de mapas. Saludos¡ [[alternative HTML version deleted]]

Hi, I am looking for a way to save the result of a function, e.g the lm()-function to a file and reload it afterwards again. I'd like to do that in order to minimize the used memory when running the function in a loop. The actual function I want to store is the evaluate() from the dismo package. I tried it with save() and load() but I am not sure if that is the way I should do it as I don't get the result I desire... ls <- list("A","B","C") for(i in ls){ x <- lm(c(1,2,3)~c(2,5,6)) save(x, file = paste("/path/to/file_",i,sep=&quo...

Dear all, I am currently running an ENFA in R using Adehabitat pkg to assess species distribution and I am really stuck and need some help to finalize my project. I run the ENFA in both original location data and pseudo-absence points (the latter randomly generated using dismo pkg), and now I would like to assess the performance of the ENFA, however, I am not sure about how to tackle this. I did not understand how to extract the prediction values from each output to generate the AUC/ROC. Please, could anyone give me a hand with that? Thank you very much, Leandro...

Hi R user, Could you please give me some hints on how I can convert text in table format in R? I was doing model assessment using dismo package for example: bg <- randomPoints(current, 500) pvtest <- data.frame(extract(current, occtest)) avtest <- data.frame(extract(current, bg)) e2 = evaluate(model, p=pvtest, a=avtest) > e2 class : ModelEvaluation n presences : 10 n absences : 1000 AUC :...

...sted regression trees (GBM). The program gives the fitted values but I wanted to calculate the fitted value by hand to understand in depth. Would you give moe some hints on what is the final model for this example? Thanks KG ------- The following script I used #----------------------- library(dismo) data(Anguilla_train) head(Anguilla_train) angaus.tc5.lr01 <- gbm.step(data=Anguilla_train, gbm.x = 3:13, gbm.y = 2, + family = "bernoulli", tree.complexity = 5, + learning.rate = 0.01, bag.fraction = 0.5) names(angaus.tc5.lr01) [1] &qu...

Hello, I want to use a for loop for repeadely calculating a maxent model (package dismo, function maxent()) which creates an object of the class maxent (S4). I want to collect all the resulting object in a list. I tried to simplify my for loop to explain what I want. There are two problems/questions: 1) How can I create the new variables in the loop (using paste) and assign the objec...

Hola de nuevo. Se me olvidaba la principal razón para utilizar gbm.step del paquete dismo. Como sabéis, los boosted si sobreajustan (a diferencia de los random forest o cualquier otro bootstrap) pero gbm.step hace validación cruzada para determinar el nº óptimo de árboles y evitarlo. Es fundamental. La opción que me queda, Carlos, es hacerlo con gbm, pero muchas veces, y usar...

Hi, I am trying to use the "gbif" function in the "dismo" package and it does not seem to work. I get the same error message every time: Error in if (sp) geo <- TRUE : argument is not interpretable as logical It does not matter whether I query for my species of interest or if I copy and paste those included in the help for the function or the...

Hi all, I run R 2.11.1 under ubuntu 10.10 and caret version 2.88. I use the caret package to compare different models on a dataset. In order to compare their different performances I would like to use the same data partitions for every models. I understand that using a LGOCV or a boot type re-sampling method along with the "index" argument of the trainControl function, one is able to

Gracias Carlos. Hasta donde yo entiendo si las hay: El argumento family puede ser: "gaussian" (for minimizing squared error); por lo que tiene que ser numérica "bernoulli" (logistic regression for 0-1 out-comes); binaria por narices "poisson" (count outcomes; requires the response to be a positive integer); numérica también, pues. La única podría ser

...gt; > Content-Type: text/plain; charset="utf-8"; Format="flowed"; > DelSp="Yes" > > > Bueno, primero te comento que si no le indico la family me hace > Bernuilli y da error por no ser binaria. > > La razón de aplicar gbm.step del paquete dismo es que da una > información fundamental, como la interacción entre las variables o los > partial plots. La interacción te la representa en 3D y es super > explicativo. > > El paquete randomforest también me da los partialplots y sale muy > bien, pero me gustaría probar también con...