[R] Binary logistic modelling: setting conditions (defining thresholds) in the fitted model (lrm)

Dear Rlist, We are working with library(Design) R 2.2.1// When using the following fitted model: knots - 5 lrm.1- lrm(X8~rcs(X1,5),x=T,y=T) X8 (binary 0/1 vector) X1, X2 explantory variables We would like to set the probability of X8=1 to zero when the X2 variable is

[R] How to use filled.contour(x,y,z) data for levelplot(z)?

Dear all, We used the following function to create a spatial plot of a raster image: filled.contour(xx,yy,zz, color = terrain.colors, nlevels=10, main=naamjaar, plot.axes = { contour(Xcoord/1000,Ycoord/1000,lim.data, nlevels = 4, col=4,drawlabels = T, axes = FALSE, frame.plot = FFALSE, add =

[R] How to visualise spatial raster data?

Dear R help, We are trying to visualise spatial raster data. We have per line, X Y coordinates and Z(data). How could we visualise this type of data? We also would like to add extra data points to this plot based on new X,Y and Z data. We used the following function but would like to use only

[R] diagnostic functions to assess fitted ols() model: Confidence is too narrow?!

Dear all, When fitting an ols.model, the confidence interval at 95% doesn't cover the plotted data points because it is very narrow. Does this mean that the model is 'overfitted' or is there a specific amount of serial correlation in the residuals? Which R functions can be used to evaluate

[R] Change labels of x-axes in Plot of stl() function?

___ Ir. Jan Verbesselt Research Associate Biosystems Department ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

Re: [R] Change labels of x-axes in Plot of stl() function?

PROTECTED] Sent: Wednesday, December 07, 2005 5:07 PM To: Jan Verbesselt Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Change labels of x-axes in Plot of stl() function? If you look through the output of: stats:::plot.stl you see right near the end that time is hard coded in the call to mtext

[R] Howto? plot legend with no line behind the points

legend(topright, legend.txt,col=1,lty=1, pch=c(19,1),bty=n, pt.bg=1) par(new=T) plot(ts.Y, type=b, lty=1, col=1, pch=1, ylab=, xlab=,yaxt=n,ylim=c(0.1,0.7)) axis(4) mtext(side=4, line=3, Y, cex=1) -- Ir. Jan Verbesselt Research Associate Lab of Geomatics, K.U.Leuven Vital

[R] how to optimise cross-correlation plot to study time lag between time-series?

but seasonality remains in the residuals. -max cross-correlation mostly occurs at lag 0. ___ Ir. Jan Verbesselt Research Associate Biosystems Department ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750   Fax

[R] How to add frame (frame.plot=T) to Plot.Design?

, respectively. e.g., plot(1,axes=T,frame.plot=T). How can this be done with plot.Design(lrm.fit) Thanks, Jan ___ Ir. Jan Verbesselt Research Associate Biosystems Department ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven

Re: [R] How to add values on the axes of the 3D bi-variable lrm fit?

Thanks a lot! A great solution! The 3D-perspective plot can be fine-tuned by adding a list to the argument 'perspArgs' of the function plot.Design. Package: Design, Hmisc. fit - lrm(y ~ rcs(x1,knots)+rcs(x2,knots), tol=1e-14,X=T,Y=T) dd - datadist(x1,x2);options(datadist='dd');

[R] How to add values on the axes of the 3D bi-variable lrm fit?

=NA, theta=50,phi=25) How can I add values to the axes of this plot? (axes with the range of values of each of the explanatory variables x1x2) Thanks, Jan ___ Ir. Jan Verbesselt Research Associate Group of Geomatics

[R] How to add legend of plot.Design function ( method=image)?

for prob. ___ Ir. Jan Verbesselt Research Associate Group of Geomatics Engineering Department Biosystems ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

Re: [R] How to add legend of plot.Design function (method=image)? (if (!.R.) )

Message- From: Jan Verbesselt [mailto:[EMAIL PROTECTED] Sent: Monday, August 22, 2005 4:59 PM To: 'r-help@stat.math.ethz.ch' Subject: How to add legend of plot.Design function ( method=image)? Dear Rlist, How can the Legend of the plot.Design() function can be visualized? Following

[R] Penalized likelihood-ratio chi-squared statistic: L.R. model for Goodness of fit?

regards, Jan Ir. Jan Verbesselt Research Associate Group of Geomatics Engineering Department Biosystems ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750 Fax: +32-16-329760 http

[R] HowTo derive a correct likelihood-ratio chi-squared statistic from lrm() with a rsc() ?

- logl + k*edf return(lrmAIC) } Best regards, Jan ___ Ir. Jan Verbesselt Research Associate Group of Geomatics Engineering Department Biosystems ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven

[R] HOW to Create Movies with R with repeated plot()?

_ Ir. Jan Verbesselt Research Associate Group of Geomatics Engineering Department Biosystems ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

[R] DEV2bitmap: jpeg with res=400 not enough for CORELDRAW poster A0

save pictures (colors/resolution) optimally for import into CorelDraw for an A0 poster? Pdf?/tiff?/bmp?/ Thanks, Jan ___ ir. Jan Verbesselt Research Associate Lab of Geomatics Engineering K.U. Leuven Vital Decosterstraat 102. B

[R] Restricted cubic spline function ERROR?: glm(Y~rcs(x,5))

Dear all, Is the restricted cubic spline function working properly in the glm model? We used glm(y~rcs(x,5), family=binomial) but it seems that for some theoretical reasons the rcs, restricted cubic spline function can not be fitted by a glm function. Is this correct? Regards, Jan

[R] derive an AIC value of an lrm model similar to the AIC of a glm model?

the rcs, restricted cubic spline fun. can not be fitted by a glm function. With pentrace(), depending on the penalty, AIC values are derived but which penalty setting should we use? Thanks in advance, Regards, Jan ___ ir. Jan

RE: [R] Re: HOWTO compare univariate binomial glm lrm models which are not nested

Dear all, Thanks a lot for the input. I will take the considerations into account. Referring to; 2 or 3 completely pre-chosen models or you will invalidate inference and estimates if you use these comparisons to build a final model The aim is not use the comparisons to build a final model but

[R] HOWTO compare univariate binomial glm lrm models which are not nested

models. Thanks in advance, Regards, Jan- ___ ir. Jan Verbesselt Research Associate Lab of Geomatics Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel: +32-16-329750 Fax: +32-16-329760 http

[R] Range in probabilities of a fitted lrm model (Y~X)

, Jan ___ ir. Jan Verbesselt Research Associate Lab of Geomatics Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

[R] negetative AIC values: How to compare models with negative AIC's

AIC: -167.7 A negative AIC occurs! How can the negative AIC from different models be compared with each other? Is this result logical? Is the lowest AIC still correct? Thanks, Jan ___ ir. Jan Verbesselt Research Associate

[R] Confidence interval for Tau-a or c-index to compare logistic lrm (binary) models with each other.

___ ir. Jan Verbesselt Research Associate Lab of Geomatics Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be/ __ R-help

[R] ERROR NaNs produced; when comparing two logistic regression models with the ANOVA CHI test

___ ir. Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be/ __ R-help@stat.math.ethz.ch mailing

[R] Plotting: Plot several axis at right hand side of the plot

___ ir. Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

[R] ts to irts

___ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

[R] ARIMA() fitting with XREG

___ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be

[R] correlation coefficient of ARIMA() or GLS() ?

are still auto correlated...?! Tips, advice or examples are mostly welcome. Many thanks in advance, Regards, Jan _ Jan Verbesselt Research Associate Lab of Geomatics and Forest

[R] cor.test() - p-values may be incorrect due to tie

Hi R specialists, When testing the association between two time series the cor.test gives the following message...- p-values may be incorrect due to tie What does it mean? (it is not described in the help) Thankx, Jan cor.test(Origi[,1],Origi[,2], alternative = c(two.sided),method =

[R] Test Relation between Time Series? = Cross Correlation Analysis with ccf()

to test the relationship between to time series vs dependence of results? (max. correlation coefficient, lag) Thanks a lot, Jan ___ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital

[R] High/low level: Plot 2 time series with different axis (left and right)

Dear R specialists, I have two time series in a data.frame and want to plot them in the same plot(), with the left axis scaled to time series 1 (-700,0) and the right axis scaled to time series 2 (-0.2, 0.4). plot(timeserie1) lines(timeserie2, col=c(2)) = this one should be scaled differently

Re: [R] Internal NA removal out of Time Series with na.omit.ts()

Thanks for the tips and advice! I found out how the NA's came into the time series. By a threshold mechanism, extreme values (outliers) are removed from the time series (environmental data, remote sensing data) and set as NA. A solution could be to detect an outlier and replace it by the

[R] Internal NA removal out of Time Series with na.omit.ts()

(ts.Lin, type=c(correlation), na.action=na.omit) Error in na.omit.ts(as.ts(x)) : time series contains internal NAs ((ts.Lin contains two time series, where one contains internal NAs (--an NA not a the end/beginning of a time serie))) Thanks a lot! Jan Verbesselt

[R] Diagnostic tool for s.window in the STL method for Time seriesAnalysis

the STL method take n(p), the number of observations in each cycle of the seasonal component, automatically from the FREQUENCY of the ts (Timeseries) object? Thanks a lot, Jan __ Jan Verbesselt Research Associate Lab

[R] readcsvIts() to create irregular time series

__ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=janv http

[R] Read date for timeserie object

__ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=janv http://gloveg.kuleuven.ac.be

[R] tsdiag and tsStructure for np,ns,nt and nl determination

) __ Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=janv http

[R] Filtering Time Series / apply STL method

(Timeserie) - NULL was the solution. The aim is to apply the STL function on these results because at the moment STL runs but results are not logical. *** Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital

[R] STL- TimeSeries Decomposition

*** Jan Verbesselt Research Associate Lab of Geomatics and Forest Engineering K.U. Leuven Vital Decosterstraat 102. B-3000 Leuven Belgium Tel:+32-16-329750 Fax: +32-16-329760 http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=janv