R help - Feb 2011 - Rioja package, creating transfer function, WA, "Error in FUN"

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


Any help would be most appreciated, 
Best wishes, 
Matthew
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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

On Thu, 2011-02-10 at 09:40 -0800, 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"
That's your problem, the odbc stuff has read the data in as characters.
CSV would be a lot simpler, just save your excel sheets as CSV files and
read them in with:

Env <- read.csv("my_excel_sheet.csv", row.names = 1)

etc... where my_excel_sheet.csv is the name of your saved csv file or
just use:

Env <- read.csv(file.choose(), row.names = 1)

if finding files via the GUI is helpful to you.

It is odd that the species data set has been read in OK though - I say
OK, but you still need to get the F1 column out of the species data and
set it as the row names of your data.

Sorry I'm coming to this late; I've been away and not really following
the list for a few weeks.

If you can't get things working, contact me off list and send the Excel
files and I'll send back a script that will load the files and do the WA
for you to look at.

HTH

G
> 
> > 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
> 
> 
> Any help would be most appreciated, 
> Best wishes, 
> Matthew
-- 
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