# search for: probability

Displaying 20 results from an estimated 19612 matches for "probability".

2011 Nov 30
2
Nomogram with stratified cph in rms package, how to get failure probability
Hello, I am using Dr. Harrell''s rms package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability. I couldn?t get hazard rate from Hazard(f1) because I used cph for the model. Here is my code: library(rms) f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11, surv=T, x=T, y=T, time.inc=5) surv<- Survival(f1) haz&...
2012 Feb 08
4
standard error for lda()
Hi, I am wondering if it is possible to get an estimate of standard error of the predicted posterior probability from LDA using lda() from MASS? Logistic regression using glm() would generate a standard error for predicted probability with se.fit=T argument in predict(), so would it make sense to get standard error for posterior probability from lda() and how? Another question about standard error estimate f...
2008 Sep 25
2
levelplot/heatmap question
...ike so: (IV1) (IV2) (IV3) ... p(b0) p(b0) p(b0) p(b1) p(b1) p(b1) p(b2) p(b2) p(b2) ... where p(b1) for independent variable 1 is p(b1 != 0) (given model uncertainty - using the BMA package). i''ve also set it so that if the coefficient is negative, the probability is listed as negative (to be able to distinguish between significant positive and negative effects by color). i''d like to create a plot which is a 10x60 grid of rectangles, where each rectangle is colored according to its probability of being nonzero (preferably white would correspond t...
2010 Nov 03
4
[klaR package] [NaiveBayes] warning message numerical 0 probability
....6-4. I compute a model over a 2 classes dataset (composed of 700 examples). To that aim, I use the function NaiveBayes provided in the package klaR. When I then use the prediction function : predict(my_model, new_data). I get the following warning : "In FUN(1:747[[747L]], ...) : Numerical 0 probability with observation 458" As I did not find any documentation or any discussion concerning this warning message, I looked in the klaR source code and found the following line in predict.NaiveBayes.R : "warning("Numerical 0 probability with observation ", i)" Unfortunately, i...
2009 Aug 19
7
Best performance measure?
Hello, I working on a model to predict probabilities. I don''t really care about binary prediction accuracy. I do really care about the accuracy of my probability predictions. Frank was nice enough to point me to the val.prob function from the Design library. It looks very promising for my needs. I''ve put together some tests and run the val.prob analysis. It produces some very informative graphs along with a bunch of performance measures. Unf...
2006 Oct 18
2
Errors with GRED after upgrading to 2.6.18 kernel
ALL: <<diffserv-gred_10-06>> I have attached the current script that I am using. \$TC qdisc add dev \$EDEV parent 2:20 gred setup DPs 3 default 2 grio \$TC qdisc change dev \$EDEV parent 2:20 gred DP 1 limit \$lim min \$minTh max \$maxTh avpkt \$avgPL burst \$bursty bandwidth \$netBand probability 0.02 prio 2 \$TC qdisc change dev \$EDEV parent 2:20 gred DP 2 limit \$lim min \$minTh max \$maxTh avpkt \$avgPL burst \$bursty bandwidth \$netBand probability 0.04 prio 3 \$TC qdisc change dev \$EDEV parent 2:20 gred DP 3 limit \$lim min \$minTh max \$maxTh avpkt \$avgPL burst \$bursty bandwidth \$netBand probabi...
2010 Feb 23
2
e1071: Cannot predict probabilities
Dear list. I using the SVM-methods from the e1071, but I can''t get the probabilities when predicting. Code: x <- matrix(rbinom(100, 10, 0.3), ncol=2) y <- apply(x, 1, sum) fit <- svm(y ~ x, method = "C-classification", kernel = "radial", probability = TRUE) predict(fit, x, probability=TRUE) Here predict doesn''t containing any probabilities (not as attributes either). Does anybody know what I''m doing wrong or if the package contains any bugs? version.string R version 2.9.2 (2009-08-24) Version of the e1071-package: 1.5-21 C...
2011 Oct 12
8
plot probability density function (pdf)
I have 2 series of variables, I want to plot the probability density function of these 2 variabels (i.e. two curves in one graph), I just want to compare these two variable distribution. what should I do? can I use ggplot2 package? -- View this message in context: http://r.789695.n4.nabble.com/plot-probability-density-function-pdf-tp3897055p3897...
2004 Dec 01
2
chisq.test probabilities method unclear
Hi list, i''ve got a question about the chisq.test function. in the use of the "given probabilities" method (p= ...), normally there should be typed in probabilities in the range of 0 to 1 with the absolute sum of 1.0 (r-help) But it is possible to use probabilities > than 1. or the sum <1.! without any warning message Ok, now the question, what does r calcutate in
2005 Jul 02
2
probability-probability plot
Hi, there. Is there any function in R to plot the probability-probability plot (PP plot)? Suppose I am testing some data against normal. Thanks. Yulei \$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$ Yulei He 1586 Murfin Ave. Apt 37 Ann Arbor, MI 48105-3135 yuleih at umich.edu 734-647-0305(H) 734-763-0421(O) 734-763-0427(O) 734-764-8263(fax) \$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$\$...
2011 Nov 29
2
Nomogram with stratified cph in Design package-- failure probability
Hello, I am using Dr. Harrell''s design package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability. I couldn?t get hazard rate from Hazard(f1) because I used cph for the model. Here is my code: f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11, surv=T, x=T, y=T, time.inc=5) surv<- Survival(f1) haz<- Hazard...
2016 Apr 12
1
ggplot2
Hi James, If you want to specify the y-values, you need to use stat="identity" as below: ggplot(probability, aes(x=Fertilizer, y=prob)) + geom_bar(stat="identity", aes(fill=Treatment)) best, huzefa On Tue, Apr 12, 2016 at 1:02 PM, James Henson <jfhenson1 at gmail.com> wrote: > Dear R Community, > > Below is a problem with a simple ggplot2 graph. The code returns the error >...
2010 Nov 06
4
calculate probability
Dear All I have 2 value assume 2.4 and 2.9 and mean = 2 variance = with n = 10 I want to find probability = 2.4 and 2.9. How I can do this. Many Thanks. Jumlong -- Jumlong Vongprasert Assist, Prof. Institute of Research and Development Ubon Ratchathani Rajabhat University Ubon Ratchathani THAILAND 34000 [[alternative HTML version deleted]]
2016 Apr 12
1
ggplot2
...ear R Community, Below is a problem with a simple ggplot2 graph. The code returns the error message below. Error: stat_count() must not be used with a y aesthetic. My code is below and the data is attached as a ?text? file. # Graph of the probabilities library(digest) library(DT) datatable(probability) str(probability) probability\$Fertilizer <- as.factor(probability\$Fertilizer) str(probability) library(ggplot2) plot1 <- ggplot(probability, aes(x=Fertilizer, y=prob)) + geom_bar(aes(fill=Treatment)) plot1 Thanks. Best regards, James F. Henson -------------- next part -------------...
2017 Jun 01
1
Latin Hypercube Sampling when parameters are defined according to specific probability distributions
Thank you very much Rob for your answer. I have some difficulties to understand how to apply my agent-based model to each parameter combination generated by the LHS, in particular when parameters are defined by probability distributions. Indeed, I have multiple parameters in my model: parameters which are defined by a single value (like ?temperature", "pressure?) and parameters which are defined by probability distributions (like ?dispersal distance?). It?s correct for me to treat distance as a class. When...
2010 Mar 22
5
calculate response probabilities using sem-analysis
Hi everyone, I just conducted a structural equation model for estimating a response model. This model should predict the probability that someone is responding to a direct mailing. I used the sem package for this. When I have my coefficients I want to know how well my model predicts the probability of response. How can I calculate these probabilities? I tried to use the unstandardized coefficients, just like a regression coeffic...
2012 Feb 07
2
predict.naiveBayes() bug in e1071 package
Hi, I''m currently using the R package e1071 to train naive bayes classifiers and came across a bug: When the posterior probabilities of all classes are small, the result from the predict.naiveBayes function become NaNs. This is an issue with the treatment of the log-transformed probabilities inside the predict.naiveBayes function. Here is an example to demonstrate the problem (you might
2010 Dec 15
2
pmnorm: probabilites don't sum up to 1
...st member, I struggle with the problem, why the probabilities of choosing one of three mutually exclusive alternatives don?t sum up to 1! Let?s assume we have three alternatives X, Y, and Z. Let?s further assume we know their respective utilities: uX, uY, uZ. I?m interested in calculating the probability of choosing X, Y, and Z. Since I assume that the alternatives are mutually exclusive, the probabilities p(X), p(Y), and p(Z) have to sum up to one. The utilities of the 3 alternatives can be expressed in 2 utility differences and, hence, the multivariate case reduces to a bivariate norma...
2012 Nov 15
6
Can't see what i did wrong..
with pred.pca<-predict(splits[[i]]\$pca,trainingData at samples)[,1:nPCs] dframe<-as.data.frame(cbind(pred.pca,class=isExplosive(trainingData,2))); results[[i]]\$classifier<-ksvm(class~.,data=dframe,scaled=T,kernel="polydot",type="C-svc", C=C,kpar=list(degree=degree,scale=scale,offset=offset),prob.model=T) and a degree of 5 i get an error of 0 reported by the ksvm
2007 Feb 20
1
Mahalanobis distance and probability of group membership using Hotelling''s T2 distribution
I want to calculate the probability that a group will include a particular point using the squared Mahalanobis distance to the centroid. I understand that the squared Mahalanobis distance is distributed as chi-squared but that for a small number of random samples from a multivariate normal population the Hotellings T2 (T squared) dis...