Matt Coe
2011-Feb-22 20:06 UTC
[R] Transfer function observed vs predicted values graph problem
Hi, I am trying to make a palaeoenvironmental transfer function using the R package rioja that predicts the water-table (measured as depth to the water table) of an area given the testate amoebae that are found there. I've carried out weighted averaging of the data and am trying to produce a graph that shows the observed water-table versues the model's predicted values. Following the instructions in the rioja help booklet (see below), I end up with a graph where the origin is not at the bottom left of the diagram, i.e. the graph is showing some values that suggest that the water table is, say, 1m above ground. I've tried entering the water-tables as negative values but the same thing happens. Does anybody know if there something I'm missing out? Or is there a way that, if the values returned are less than 0, then they can automatically be put just as 0? Any help would be most appreciated, Thank you, Matthew My environmental matrix (x) is: SampleId WTD Moisture pH EC 1 "1" "20" "91.72700" "3.496674" " 85.02688" 2 "2" " 2" "93.88913" "3.550794" " 85.69465" 3 "3" "26" "90.30269" "3.948559" "113.19206" 4 "4" " 5" "94.14427" "3.697213" " 48.56375" 5 "5" "30" "90.04269" "3.745020" "108.57278" .... 90 "GAL_15" "70" "94.07849" "3.777932" " 66.77673" The species matrix (y) contains the abundance of 32 species over 90 sites, set out like this F1 AmpFlav AmpWri ArcCat ArcDis 1 1 22.2929936 0.0000000 0.0000000 0.0000000 2 2 30.9677419 0.0000000 0.0000000 3.2258065 fit <- WA(y, x, tolDW = FALSE, use.N2=TRUE, check.data=TRUE, lean=FALSE) # plot predicted vs. observed plot(fit) plot(fit, resid=TRUE) # Water-table reconstruction pred <- predict(fit, y) #plot the reconstruction plot(sites, pred$fit[, 1], type="b") # cross-validation model using bootstrapping fit.xv <- crossval(fit, cv.method="boot", nboot=1000) par(mfrow=c(1,2)) plot(fit) plot(fit, resid=TRUE) plot(fit.xv, xval=TRUE) plot(fit.xv, xval=TRUE, resid=TRUE) [[alternative HTML version deleted]]
mdc
2011-Feb-23 08:30 UTC
[R] Transfer function observed vs predicted values graph problem
Hi, I am trying to make a palaeoenvironmental transfer function using the R package rioja that predicts the water-table (measured as depth to the water table) of an area given the testate amoebae that are found there. I've carried out weighted averaging of the data and am trying to produce a graph that shows the observed water-table versues the model's predicted values. Following the instructions in the rioja help booklet (see below), I end up with a graph where the origin is not at the bottom left of the diagram, i.e. the graph is showing some values that suggest that the water table is, say, 1m above ground. I've tried entering the water-tables as negative values but the same thing happens. Does anybody know if there something I'm missing out? Or is there a way that, if the values returned are less than 0, then they can automatically be put just as 0? Any help would be most appreciated, Thank you, Matthew My environmental matrix (x) is: SampleId WTD Moisture pH EC 1 "1" "20" "91.72700" "3.496674" " 85.02688" 2 "2" " 2" "93.88913" "3.550794" " 85.69465" 3 "3" "26" "90.30269" "3.948559" "113.19206" 4 "4" " 5" "94.14427" "3.697213" " 48.56375" 5 "5" "30" "90.04269" "3.745020" "108.57278" .... 90 "GAL_15" "70" "94.07849" "3.777932" " 66.77673" The species matrix (y) contains the abundance of 32 species over 90 sites, set out like this F1 AmpFlav AmpWri ArcCat ArcDis 1 1 22.2929936 0.0000000 0.0000000 0.0000000 2 2 30.9677419 0.0000000 0.0000000 3.2258065 fit <- WA(y, x, tolDW = FALSE, use.N2=TRUE, check.data=TRUE, lean=FALSE) # plot predicted vs. observed plot(fit) plot(fit, resid=TRUE) # Water-table reconstruction pred <- predict(fit, y) #plot the reconstruction plot(sites, pred$fit[, 1], type="b") # cross-validation model using bootstrapping fit.xv <- crossval(fit, cv.method="boot", nboot=1000) par(mfrow=c(1,2)) plot(fit) plot(fit, resid=TRUE) plot(fit.xv, xval=TRUE) plot(fit.xv, xval=TRUE, resid=TRUE) -- View this message in context: http://r.789695.n4.nabble.com/Transfer-function-observed-vs-predicted-values-graph-problem-tp3320663p3320663.html Sent from the R help mailing list archive at Nabble.com.