Thanks Mathieu! This has gone very well so far, but I cannot seem to get the XY location data and the bioclim maps in the same proj4string. CODE: pr <- slot(count.points(corysp, bio), "data")[,1] Error in count.points(corysp, bio) : different proj4string in w and xy
This seems strange since everything in the same coordinate system WGS 1984 from previous analysis. class(corysp) [1] "SpatialPointsDataFrame" attr(,"package") [1] "sp" summary(corysp) Object of class SpatialPointsDataFrame Coordinates: min max coords.x1 -124.1643 -119.7514 coords.x2 37.0000 40.8030 Is projected: NA proj4string : [NA] Number of points: 44 Data attributes: taxon_name Y_latitude X_longitud Collinsia corymbosa:44 Min. :37.00 Min. :-124.2 1st Qu.:37.98 1st Qu.:-123.8 Median :39.46 Median :-123.8 Mean :38.99 Mean :-123.3 3rd Qu.:39.50 3rd Qu.:-122.6 Max. :40.80 Max. :-119.8 I have tried to change the coordinate system using CODE: coordsp<-SpatialPoints(corysp, proj4string=CRS(as.character(NA)), bbox = NULL) But get the same issue: pr <- slot(count.points(coordsp, bio), "data")[,1] Error in count.points(coordsp, bio) : different proj4string in w and xy Also, I still cannot may histograms using the bioclim map data. Thanks so much for your assistance! You have helped me so much! Alannie > > > Dear Alannie, > > I think your problem comes from the handling of rasters as sp classes, not > from the actual ENFA methods. You should try to import the rasters > properly first, and check that they are actually valid > 'SpatialPixelsDataFrame's. For instance, using rgdal: > > library(rgdal) > bio1 <- readGDAL("bio1.asc") > bio2 <- readGDAL("bio2.asc") > bio3 <- readGDAL("bio3.asc") > bio <- cbind(bio1, bio2, bio3) > names(bio) <- c("bio1", "bio2", "bio3") > summary(bio) > image(bio) > spplot(bio) > ... > > The rest of the analysis should work as expected. > Mathieu. > > > -- > > ~$ whoami > Mathieu Basille, PhD > > ~$ locate --details > University of Florida \\ > Fort Lauderdale Research and Education Center > (+1) 954-577-6314 > http://ase-research.org/basille > > ~$ fortune > « Le tout est de tout dire, et je manque de mots > Et je manque de temps, et je manque d'audace. » > -- Paul Ãluard > ---- Le mar., 27 mai 2014 21:56:19 -0400 alannie a écrit ---- > >>Hi, >> >>I have been using ENFA in R to perform some analyses. >> >>I have gotten the procedure to work before, however I can't seem to >>replicate the code. This is very important since I would like to do this >>analysis for a wide range of species. >> >>Please advise of best practice for implementing the procedure. >> >>Going from the very beginnings of the procedure: >> >>1) read in .csv formatted locations data for the interested species >> >> /code/ species1<-read.csv("species1.csv",head=T, sep=",") >> species1coords<-SpatialPoints(species1) >> >>2) read in raster files (I am using the bioclim variables converted into >>ASCII) >> >> /code/ b1<-read.asc("bio1.asc") >> b2<-read.asc("bio2.asc") >> b3<-read.asc("bio3.asc") >> >>3) combine the maps into a single data frame and add slots to the >> individual >>maps >> /code/ map<-cbind(b1@data,b2@data,b3@data) *this form does not allow me >>to visualize the maps using image(map) >> map2<-cbind(b1,b2,b3) *this form, with out the slots, >>does allow me to visualize the maps using image(map2) >> >>4) following this step is making a histogram: hist(map, type = "l") I >>usually cannot make one, but when I am able to make a histogram, the >>variables show up on a single graph with the warning: >> >>Warning messages: >>1: In title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) : >> graphical parameter "type" is obsolete >>2: In axis(1, ...) : graphical parameter "type" is obsolete >>3: In axis(2, ...) : graphical parameter "type" is obsolete >> >>4) The tab: >> /code/ tab <- slot(map, "data"), I get this warning: >>Error in slot(map, "data") : >> cannot get a slot ("data") from an object of type "double" >> >>Sometimes I get other warnings such as 'x is not numeric' or something >> about >>NA values. >> >>I will spare the rest of the issues I face. >> >>I believe the origins of these issues are the starting data inputs. I >> would >>appreciate any assistance in modifying the data inputs. I have tried to >> look >>through other resources, however I have not found anything to help with >> my >>specific issues. >> >>If I can get this worked out, I also hope to post some code somewhere to >>aide others in their SDM adventures. >> >>Thank you for reading! >> >>A >> >> >> >> >> >> >> >> >> >> >>-- >>View this message in context: >> http://r-sig-geo.2731867.n2.nabble.com/Ecological-Niche-Factor-Analysis-tp7586516.html >>Sent from the R-sig-geo mailing list archive at Nabble.com. >> >>_______________________________________________ >>R-sig-Geo mailing list >>R-sig-Geo@r-project.org >>https://stat.ethz.ch/mailman/listinfo/r-sig-geo >> > > -- > > ~$ whoami > Mathieu Basille, PhD > > ~$ locate --details > University of Florida \\ > Fort Lauderdale Research and Education Center > (+1) 954-577-6314 > http://ase-research.org/basille > > ~$ fortune > « Le tout est de tout dire, et je manque de mots > Et je manque de temps, et je manque d'audace. » > -- Paul Ãluard > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > > > > _______________________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://r-sig-geo.2731867.n2.nabble.com/Ecological-Niche-Factor-Analysis-tp7586516p7586523.html > To start a new topic under R-sig-geo, email > ml-node+s2731867n2731867...@n2.nabble.com > To unsubscribe from Ecological Niche Factor Analysis, visit > http://r-sig-geo.2731867.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7586516&code=YWdnMThAcGl0dC5lZHV8NzU4NjUxNnwtMjAxOTYzNDk0MQ== -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Re-ReA-Ecological-Niche-Factor-Analysis-tp7586535.html Sent from the R-sig-geo mailing list archive at Nabble.com. _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo