similar to: binomial GLM quasi separation

Dear List, Apologies for this off-topic post but it is R-related in the sense that I am trying to understand what R is telling me with the data to hand. ROC curves have recently been used to determine a dissimilarity threshold for identifying whether two samples are from the same "type" or not. Given the bashing that ROC curves get whenever anyone asks about them on this list (and

Dear List, With regard to the question I previously raised, here is the result I obtained right now, brglm() does help, but there are two situations: 1) Classifiers with extremely high AIC (over 200), no perfect separation, coefficients converge. in this case, using brglm() does help! It stabilize the AIC, and the classification power is better. Code and output: (need to install package:

Dear all, I am encountering some issues with my data and need some help. I am trying to run glm analysis with a presence/absence variable as response variable and several explanatory variable (time, location, presence/absence data, abundance data). First I tried to use the glm() function, however I was having 2 warnings concerning glm.fit () : # 1: glm.fit: algorithm did not converge # 2:

I''m running brglm with binomial loguistic regression. The perhaps multicollinearity-related feature(s) are: (1) the k IVs are all binary categorical, coded as 0 or 1; (2) each row of the IVs contains exactly C (< k) 1''s; (3) k IVs, there are n * k unique rows; (4) when brglm is run, at least 1 IV is reported as involving a singularity. I''ve tried recoding the n

Hi. I'm a big user of level plots. Because filled.contour() didn't do exactly what I wanted, I hacked at it a bit to add these options: (*) Even spacing in the key, even if the contours are not evenly spaced. (*) Horizontal key (*) options to not use layout() and to plot only the level plot _or_ only the key. This means you can use layout yourself to (e.g.) have several

Full_Name: Hugh C. Pumphrey Version: 1.4.1 OS: Linux (Debian Woody) Submission from: (NULL) (129.215.133.170) The function readChar() appears to have some type of problem with memory allocation. I don't know if "memory leak" is the correct term but if one uses readChar() many times, the R binary grows in size until it eats all your memory and swap space. The code enclosed below

Hi everybody, If I am correct, you can compare a model with random effect with the same model without the random effect by using the nlme function, like this: no.random.model <- gls(Richness ~ NAP * fExp, method = "REML", data = RIKZ) random.model <- lme(Richness ~NAP * fExp, data = RIKZ, random = ~1 | fBeach, method = "REML")

Dear All, No-one seemed to know about this on r-help, so I'm trying here.... I'm having problems at the configure stage when trying to build R on Solaris 5.8. configure finds everything it needs but when it runs config.status to make all the Makefiles and headers, I get a huge slew of errors like this: config.status: creating src/extra/zlib/Makefile sed: -e expression #1, char 329:

Hi, there. Suppose I already have sensitivities and specificities. What is the quick R-function to calculate AUC for the ROC plot? There seem to be many R functions to calculate AUC. Thanks. Yulei [[alternative HTML version deleted]]

If you select an option that's not listed during ipv4/ipv6 setup it will accept it without verification. This corrects that behavior and forces a valid option to be picked. --- scripts/ovirt-config-networking | 106 +++++++++++++++++++++------------------ 1 files changed, 58 insertions(+), 48 deletions(-) diff --git a/scripts/ovirt-config-networking b/scripts/ovirt-config-networking index

>> Doesn't work. Apparently the Dell UEFI PXE firmware doesn't know HTTP. > > There's a lot of variation. Do you have a shell option > in your boot selections? None of Dell OptiPlex 990 (firmware A19), 9010 (firmware A22), nor 9020 (firmware A16) seem have a built-in EFI shell option, but in all three cases I had success running the external EFI shell from

Hi there, I have a Java process that writes HDF5 files with the following approximate structure: group "xxx" { group "yyy" { dataset {} dataset {} } group "zzz" { dataset {} dataset {} } } where dataset is a rank one dataspace having a compound datatype defined as: H5T_UNIX_TIME, float, float, float, float I

> > Is syslinux.efi supposed to be able to handle HTTP URLs? > > If the underlying firmware can. Try just specifying an HTTP URL in the > config or on the command line instead of the path-prefix option. Doesn't work. Apparently the Dell UEFI PXE firmware doesn't know HTTP. Somehow I was under the impression improvements from pxelinux variants like lpxelinux were

Hi all, As you can see from below, the result is strange... I would imagined that the bb result should be much higher and close to 1, any way to improve the fit? Any other classification methods? Thank you! data=data.frame(y=rep(c(0, 1), times=100), x=1:200) aa=glm(y~x, data=data, family=binomial(link="logit")) newdata=data.frame(x=6, y=100) bb=predict(aa, newdata=newdata,

I have done a cluster analysis doing: 1-clusNorth <-hclust(dist(Artorious)^2, method="ward") 2-clusNorth$labels <-Artorious$Name ## to show the case names and not numbers 3-dend1 <- as.dendrogram(clusNorth) 4-plot(dend1) My Dendrogram is now showing the names of my cases in the dataframe on the x axis 1 OMNICELL INC COM 2 GETTY IMAGES INC

Hi, there: Suppose I want create variables with indexes in their names, e.g., X_1_1, X_1_2, X_1_3, ..., X_1_10, X_2_1, X_2_2, X_2_3, .. X_2_10,..., X_10_1, X_10_2, ... X_10_10. It looks like I need to use 2 indexes I and J so I is looped from 1 to 10, and J is looped from 1 to 10. But I don't know how to automatically produce X with these combination of indexes. Should I use paste function?

Dear R Users, How do we read netcdf / hdf format files in R ? Also, can we convert netcdf to hdf format in R? Great Thanks, Best Regards, Yogesh [[alternative HTML version deleted]]

Hi, there: Does anyone know how to specify the ranges in the axises when I make scatter plots using pairs()? In the general plot function, I can use xlim and ylim option. But how can I do this if I use pairs()? Thanks. Yulei [[alternative HTML version deleted]]

Hi, there. Does anyone know the R function for calculating the cdf of bivariate normal distribution function? Thanks. Yulei [[alternative HTML version deleted]]

Hi, there: Could someone tell me a simple function of plot ROC curve and calculate AUC in R? My setting is very simple, a column of the true binary response and another column of predicted probabilities. Thanks! Yulei [[alternative HTML version deleted]]