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 -------------...

Latin Hypercube Sampling when parameters are defined according to specific probability distributions

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...