[R-sig-Geo] Re : Ecological Niche Factor Analysis
alannie
agg18 at pitt.edu
Fri May 30 22:02:24 CEST 2014
Oh, on that last part with the conversion, I actually used
coordsp<-SpatialPoints(corysp, proj4string=CRS"+proj=longlat
+datum=WGS84")) , bbox = NULL)
Sorry for that mistake. Either way, it does not work.
> 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 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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>>>R-sig-Geo mailing list
>>>R-sig-Geo at r-project.org
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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
>>
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