[R-sig-Geo] Ecological Niche Factor Analysis

Wed Jun 18 19:49:06 CEST 2014

Dear Alannie, 

Sorry for the very late answer. Sometimes even projections that should be the same are not, I guess due to the way R stores them. 'count.points' actually checks for 

identical(proj4string(corysp), proj4string(bio))

So you can simply check:

proj4string(corysp)

and 

proj4string(bio)

There might be a tiny difference that prevents the function to work. If this is the case, but you are sure that the two data sets are properly projected in the same projection, you can simply use (you'll get a warning):

proj4string(corysp) <- proj4string(bio)

and run 'count.points' again.

As for the histograms, I think you're trying to use 'hist.kasc' from the legacy adehabitat. And, as its name suggests, this only works --

~$ 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 Éluardfor kascs, not SpatialPixelsDataFrames (the function is actually not available anymore in the new adehabitatMA). Try to use any column of the SPDF as a regular data frame column, with 'hist' and 'density' if that's what you're looking for.

Hope this helps,
Mathieu.

---- Le ven., 30 mai 2014 16:02:24 -0400 alannie  a écrit ---- 

>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
>>> Â« Le tout est de tout dire, et je manque de mots
>>> Et je manque de temps, et je manque d'audace. Â»
>>> -- Paul Ã‰luard
>>> ---- Le mar., 27 mai 2014 21:56:19 -0400 alannie a Ã©crit ----
>>>
>>>>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.
>>>>
>>>>_______________________________________________
>>>>R-sig-Geo mailing list
>>>>R-sig-Geo at 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
>>> Â« Le tout est de tout dire, et je manque de mots
>>> Et je manque de temps, et je manque d'audace. Â»
>>> -- Paul Ã‰luard
>>>
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>>
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>--
>View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Re-ReA-Ecological-Niche-Factor-Analysis-tp7586536.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