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+3300569-1208751190-212...@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 > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3300569&i=0>mailing > list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Rioja-package-creating-transfer-function-WA-Error-in-FUN-tp3299636p3300569.html > To unsubscribe from Rioja package, creating transfer function, WA, "Error > in FUN", click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3299636&code=bWF0dC5kLmNvZUBnbWFpbC5jb218MzI5OTYzNnwyMDMzMDk2ODg2>. > > -- View this message in context: http://r.789695.n4.nabble.com/Rioja-package-creating-transfer-function-WA-Error-in-FUN-tp3299636p3302063.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
