
Dear Peter,
Thank you very much for your suggestion, I went through the matrices and
removed the headings for pH, WTD etc and did the same for the site names,
which I made purely numerical, and now the WA function is working,
Thanks again!
Matthew

On Fri, Feb 11, 2011 at 12:44 AM, Peter Ehlers [via R] <
ml-node+3300569-1208751190-212946@n4.nabble.com> wrote:

> On 2011-02-10 09:40, mdc wrote:
>
> >
> > Hi, I am a new R user and am trying to construct a palaeoenvironmental
> > transfer function (weighted averaging method) using the package rioja.
> > I've managed to insert the two matrices (the species abundance and the
> > environmental data) and have assigned them to the y and x values
> > respectively. When I try and enter the 'WA' function though, I get an
> 'Error
> > in FUN' message (see below for full values). Alas, I do not know what
> this
> > means and have struggled to find similar problems to this online. Is
> there a
> > step I've missed out between assigning the matrices and the WA function?
> >
> >> SWED=odbcConnectExcel(file.choose())       (SWED is the environmental
> data
> >> file)
> >> sqlTables(SWED)
> >> Env=sqlFetch(SWED, "Sheet1")
> >> odbcClose(SWED)
> >> Env
> >
> >     SampleId WTD  Moisture   pH         EC
> > 1  "N1_1"   "20" "91.72700" "3.496674" " 85.02688"
> > 2  "N1_2"   " 2" "93.88913" "3.550794" " 85.69465"
> > 3  "N1_3"   "26" "90.30269" "3.948559" "113.19206"
> > 4  "N1_4"   " 5" "94.14427" "3.697213" " 48.56375"
> > 5  "N1_5"   "30" "90.04269" "3.745020" "108.57278"
> > ....
> > 90 "GAL_15" "70" "94.07849" "3.777932" " 66.77673"
> >
> >
> >> STEST=odbcConnectExcel(file.choose())
> >> sqlTables(STEST)                                      (STEST is the
> >> species abundance file)
> >> Spe=sqlFetch(STEST, "Sheet8")
> >> odbcClose(STEST)
> >> Spe
> >
> > (The species data contains the abundance of 32 species over 90 sites, set
>
> > out like this)
> >         F1    AmpFlav    AmpWri      ArcCat       ArcDis
> > 1    N1_1 22.2929936 0.0000000  0.0000000  0.0000000
> > 2    N1_2 30.9677419 0.0000000  0.0000000  3.2258065
> >
> >> library(rioja)
> >> y<-as.matrix(Spe)
> >> x<-as.matrix(Env)
> >
> >> WA(y, x, tolDW = FALSE, use.N2=TRUE, check.data=TRUE, lean=FALSE)
>  (the
> >> command from the WA section of the rioja booklet)
> > Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument
>
> Well, the error message is fairly clear: you're feeding in
> something of type 'character' where something else (presumably)
> numeric is wanted.
>
> I don't use rioja, but a quick glance at the documentation
> for WA shows that x should be 'a vector of environmental
> values to be modelled'. The example uses pH which is almost
> surely not a character vector.
>
> Your x is a *matrix* of *character* values. Possibly, you
> want to pull, say, pH out of your Env, convert to numeric
> and try that. Ditto for the other variables.
>
> If the above is total nonsense, please forgive my rioja
> ignorance and wait for more cogent advice from
> someone more knowledgeable than I.
>
> Peter Ehlers
>
> >
> >
> > Any help would be most appreciated,
> > Best wishes,
> > Matthew
>
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