Re: [R-sig-eco] biplot with most important species
Do you know how to fix this error? It hapens when I try to get the raster and convert do ASC (because it is a maxent demand) >bio1 <- "D:/biorecortadobrasil/biobio1.tif" >bio1 >stackbios <- stack(bio1) #stackeando os arquivos >rasterstackbios <- raster(stackbios) >agregrasterstackbios <- aggregate(rasterstackbios, fact=2) ## By default aggregates using mean, but see fun= >writeRaster(agregrasterstackbios, "D:/biorecortadobrasil/asc/outfile.asc", format="ascii", overwrite=TRUE) Warning message:In .local(x, filename, ...) : all cell values are NA 2016-10-12 4:44 GMT-06:00 Bjorn: > Hi all, > > there might be a simple solution to do this, but I don't seem to manage to > find it. I have done a PCA using vegan. I now want to create a biplot with > only those species that explain a certain (cumulative) amount of the > variation along the first 2 PC axes (in order to keep things clear). How > could this be done? > > Thanks in advance! > > Kind regards, > > Bjorn > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[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] biplot with most important species
Hi Bjorn, A common practice in simplifying ordinatin plots is to keep species that show the best fit into the ordination space. The position of such species in the ordination diagram really (may) tell something. In linear methods like PCA a linear fit is suitable. This can be computed using vegan::envfit function. For this I have a very simple function reduce.pca, which you can source using this line of code: source(url("http://vitsyrovatka.info/lib/exe/fetch.php?media=zpradat:functions:reduce.pca.r;)) The code and example may be viewed here (skip the Czech introduction): http://vitsyrovatka.info/doku.php?id=zpradat:cs:fun:reducepca Your criterion on species selection is more complicated. You can change the function accordingly. I am not completely sure but a solution might be multiplying species fit by species variance, then ordering species acoording to this fit*variance and add species until the desired variance is achieved. I might be wrong, anybody feel free to correct me, please. Cheers, Vit Dne 2016-10-12 12:44, Bjorn napsal: Hi all, there might be a simple solution to do this, but I don't seem to manage to find it. I have done a PCA using vegan. I now want to create a biplot with only those species that explain a certain (cumulative) amount of the variation along the first 2 PC axes (in order to keep things clear). How could this be done? Thanks in advance! Kind regards, Bjorn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] biplot with most important species
Hi Bjorn, I have done this in the past using ggplot2. I think that I plotted everything, but only labeled those that were above some threshold. In other words, I changed the label in the input data to "". I think that is how I solved this problem. HTH, Stephen On Wed, Oct 12, 2016 at 5:44 AM, Bjornwrote: > Hi all, > > there might be a simple solution to do this, but I don't seem to manage to > find it. I have done a PCA using vegan. I now want to create a biplot with > only those species that explain a certain (cumulative) amount of the > variation along the first 2 PC axes (in order to keep things clear). How > could this be done? > > Thanks in advance! > > Kind regards, > > Bjorn > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis "A big computer, a complex algorithm and a long time does not equal science." -Robert Gentleman [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] biplot with most important species
Hi all, there might be a simple solution to do this, but I don't seem to manage to find it. I have done a PCA using vegan. I now want to create a biplot with only those species that explain a certain (cumulative) amount of the variation along the first 2 PC axes (in order to keep things clear). How could this be done? Thanks in advance! Kind regards, Bjorn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology