[R-sig-Geo] Re : Ecological Niche Factor Analysis

[Mathieu Basille]

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 Éluard
---- 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 at data,b2 at data,b3 at 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 graphical parameter "type" is obsolete 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 : graphical parameter "type" is obsolete 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. 
> 
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--

~$ 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 Éluard