similar to: vis.gam() contour plots

I am using the mgcv package to develop vis.gam plots and having trouble figuring out how to relabel the z-axis (image attached). It is currently labeled as "linear predictor," but I would like to change it to a different name. Currently I am using this code: vis.gam(model1,theta=320,ticktype="detailed",color="gray",nCol=12, zlab="BCS") However, when run

Hello List! I asked this before (with no solution), but maybe this time... I'm trying to project a surface to the XY under a 3d cloud using lattice. I can project contour lines following the code for fig 13.7 in Deepayan Sarkar's "Lattice, Multivariate Data Visualization with R", but it fails when I try to "color them in" using panel.levelplot. ?utilities.3d says there

Hello, I'm trying to illustrate the relationships between various trait and environment data gathered from a number of sites. I've created a GAM to do this: gam1=gam(trait~s(env1)+s(env2)+te(env1,env2)) and I know how to create a 3D plot using vis.gam. I want to be able to show points on the 3D plot indicating the sites that the data came from. I can do this on a 2D plot when there is one

Hi everyone, I ran a binomial GAM consisting of a tensor product of two continuous variables, a continuous parametric term and crossed random intercepts on a data set with 13,042 rows. When trying to plot the tensor product with vis.gam(), I get the following error message: Error in persp.default(m1, m2, z, col = col, zlim = c(min.z, max.z), xlab = view[1], : invalid 'z' limits In

Hi, Please see the attached contour plot (I am sorry about the big file). This was created using the vis.gam() function in "mgcv" package. However, my question is somewhat broader. In generating this figure, I first created the contours using vis.gam() and then I plotted the points. These point are plotted on top of the contours so that some of the contour lines are only partially

Hi list, I'm working with gamm models of this sort, using Simon Wood's mgcv library: gm<- gamm(Z~te(x,y),data=DATA,random=list(Group=~1)) gm1<-gamm(Z~te(x,y,by=Factor)+Factor,data=DATA,random=list(Group=~1)) with a dataset of about 70000 rows and 110 levels for Group in order to test whether tensor product smooths vary across factor levels. I was wondering if comparing those two

Hello everyone. I am doing a logistic gam (package mgcv) on a pretty large dataframe (130.000 cases with 100 variables). Because of that, the gam is fitted on a random subset of 10000. Now when I want to predict the values for the rest of the data, I get the following error: > gam.basis_alleakti.1.pr=predict(gam.basis_alleakti.1, +

I'm trying to make a set of contour plots of bivariate kernel density estimates, showing three such plots overlaid, similar to this plot http://euclid.psych.yorku.ca/SCS/Private/Test/ridge-boot2.pdf except that I would like to have the contours *filled* (using transparent colors). To make this reproducible, I've saved the results of KernSmooth::bkde2D() in the following file:

Hi, I'd like to compare SST data for year 2000 with SST for year 2001. I managed to get filled contour plots showing monthly SST for both years (12 plots for each year, 24 plots in total). In order to compare year 2000 and year 2001, however, I'd need to have the same legend scale (same color bar) in both years plots. Thus, my question is: is there a way to set the legend scale in

Hello folks, i'm a R beginner and i want to put in a same plot both contour lines and persp plot. For example, fn<-function(x,y){sin(x)+2*y} #this looks like a corrugated tin roof x<-seq(from=1,to=100,by=1) #generates a list of x values to sample y<-seq(from=1,to=100,by=1) #generates a list of y values to sample z<-outer(x,y,FUN=fn) #applies the funct. across the combos of x

Here is another, perhaps trivial, plotting question. I am making a filled contour plot and have almost everything dialed in the way I want it. The last hurdle (that I can foresee) is adjusting the look of the key. I'm plotting the 25%, 50%, 75%, and 95% quantiles and I want the key to be evenly spaced, e.g., the width of the 25% and the 95% should look the same on the key. They are labeled

The following plot is a first approximation to what I need: *********************************** mu1 <- 0 mu2 <- 5 s <- 1 x <- seq(-2.5, 7.5, length = 41) y <- seq(-2.5, 2.5, length = 41) f <- function(x,y){ term1 <- 1/(2*pi*sqrt(s*s)) term2 <- -1/2 term3 <- (x - mu1)^2/s term4 <- (y - mu1)^2/s term5 <- (x - mu2)^2/s term1*(.5 * exp(term2*(term3 + term4)) + .5 *

Dear R help contributors, I'd like to plot ground temperature with time on X-axis and depth on Y-axis on this datasets ( http://r.789695.n4.nabble.com/file/n3301033/NEdaily.csv NEdaily.csv ), and to do so I use the following commands: library(RSEIS) xNE <- seq(1, as.numeric(as.Date(max(NEdaily[[1]])) - as.Date(min(NEdaily[[1]]))), 1) yNE <- rev(c(-0.3, -0.5, -0.7, -0.9, -1.1,

Hi, I want to draw a figure similar to http://dsarkar.fhcrc.org/lattice/book/images/Figure_13_07_stdBW.png from http://lmdvr.r-forge.r-project.org/figures/figures.html (figure 13.7) . However instead of using a contour plot as a panel for the wireframe I want to use a levelplot. Can somebody help me with this? Thanks in advance for any help, Kind regards, Anton Bossenbroek

Hi everyone, I hope this question is beyond "read the manual". My task is simple, just to plot the following, but the plot in the middle should be a filled.contour plot: http://gallery.r-enthusiasts.com/graph/Scatterplot_with_marginal_histograms_78 Background: I prefer filled.contour rather than hist2d. Because, I could use kernel smooth, so the plot for discrete data won't be too

Hello list, I just started R today and tried something quite simple. I wanted to create a colored plot and eventually after hours of fiddling around got it working. However, my solution seems very suboptimal and I'd really appreciate your hints on how to improve. I believe that R already offers many functions I coded (e.g. distance between two vectors, vector length, vector normalization and

Dear all, As a newbie in R I would like to do the following (simple?) thing: to plot a filled.contour plot over a map showing country boundaries (e.g. for Europe) What i do is: map('worldHires',xlim=c(-10,40),ylim=c(35,70),boundary = TRUE,border=0.1) map.axes() filled.contour(mslp, zlim=c(1000,1020),color.palette = colorRampPalette(c("blue", "white",

Rers: I can't seem to locate the command to suppress what appears to be a faint internal grid when running the following command to make a filled contour plot of some data I have (x,y,z being the inputs):

Hi, I'm working with gamm models of this sort: gm<- gamm(Z~te(x,y),data=DATA,random=list(Group=~1)) gm1<-gamm(Z~te(x,y,by=Factor)+Factor,data=DATA,random=list(Group=~1)) with a dataset of about 70000 rows and 110 levels for Group if I use plot(gm1$gam), I obtain 3 different surface plots, one for each level of my factor but I would like to create more complex contour plots for those 3

Hi, In fitting GAMs to assess environmental preferences, I use the part of the fit where the lower confidence interval is above zero as my criterion for positive association between the environmental variable and species abundance. However I like to plot this on the original scale of species abundance. To do so I extract the fit and SE using predict.gam. Lately I compared more