search for: pvalue

Hi R community I have a little problem, and I tried to solve it by myself but I couldn't. I building an if loop, and I want to check a value inside an interval. This would be the case: pvalue=0,2999 if(pvalue>0.05 or pvalue<0.1) as you can see I would like to check in that if loop if my pvalue is inside of that interval(from 0.05 to 0.1), and I tried these options: if(pvalue>0.05 or pvalue<0.1) (not possible because R don't recognise OR as operator) if(pvalue>0.05...

...code. I am trying to get the p-values, R^2s etc for a number of different groups of variables that are all in one dataset. This is the code: #Stand counter st<-1 #Collections stands<-numeric(67) slopes<-numeric(67) intercepts<-numeric(67) mses<-numeric(67) rsquares<-numeric(67) pValues<-numeric(67) #Start lists for X and Y values within each stand xi<-numeric(0) yi<-numeric(0) #Set the first element to the starting X and Y values xi[1]=X[1] yi[1]=Y[1] #Start looping working through your data, record by record for (i in 2:length(X)) { #If you are in the same stand as o...

...t;-lm(y~method + x1 + x2) summary(lm_ref_b) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.24591 0.73770 1.689 0.1037 methoda -0.32389 0.14025 -2.309 0.0295 * methodc -0.65705 0.13248 -4.960 4.14e-05 *** In summary: idea1: a vs b:pvalue=0.0000001 a vs c:pvalue=0.0000002 b vs c:pvalue=0.8578386 idea2: a vs b:pvalue=0.0683 a vs c:pvalue=0.2069 b vs c:pvalue<0.001 idea3: a vs b:pvalue=0.0295 a vs c:pvalue=0.0978 b vs c:pvalue=4.14e-05 So the result of 3 ideas are different,and I don't know which one is correct. Many thanks fo...

...r> ----- From: Martyn Plummer <plummer at iarc.fr> Date: Thu Apr 10 10:07:01 2003 Subject: [R] for loops and counters Peter, You didn't say what goes wrong, but you mind find this version more useful tstat <- (matrix(means, k,k, byrow=TRUE) - matrix(means, k,k,byrow=FALSE))/rms pvalue <- 2*(1-pt(abs(tstat), df=df)) pvalue[upper.tri(pvalue)] S is designed to allow you to work with "whole objects", which means that for loops can (and should) be avoided. Martyn On 05-Oct-99 Peter B. Mandeville wrote: > I am trying to assign values to a vector (pvalue). Similar co...

I have created a list of tables with the same columns but different number of row. Example (actual list has ~200 elements): > temp1<- data.frame(ID=c("Herb","Shrub"),stat=c(4,5),pvalue=c(.03,.04)) > temp2<- data.frame(ID=c("Herb","Shrub", > "Tree"),stat=c(12,15,13),pvalue=c(.2,0.4,.3)) > L<-list(a=temp1,b=temp2) > L $a ID stat pvalue 1 Herb 4 0.03 2 Shrub 5 0.04 $b ID stat pvalue 1 Herb 12 0.2 2 Shrub...

I am trying to assign values to a vector (pvalue). Similar code works in C but not in R. What am I doing wrong? r <- pvalue <- 0 for(i in (1:(k-1))){ for(j in (i+1):k){ r <- r+1 tstat <- (means[i]-means[j])/rms pvalue[r] <- 2*(1-pt(abs(tstat),df)) } } Thank you. Peter B. -- Peter B. Mandeville...

...binomial-logit glm on a large dataset (69000 lines for 145 predictors). After 3 days working, the stepAIC function did not terminate. I do not know if that is normal but i would like to try computing a "homemade" backward with a repeated glm ; at each step, the predictor with the max pvalue would be excluded until reaching a set of 20 predictors for example. My question is about the factor predictors with several levels. R provides only the pvalues for each level whereas i need an overall pvalue for testing the predictor. On internet, the only solution i found suggests to compu...

Dear All, I am trying to combine dependent p-values in R. May you please help me with this? For independent pvalue combination, one of the popular way is fisher's method which I found the R code here (http://r.789695.n4.nabble.com/fisher-s-posthock-test-or-fisher-s-combination-test-td2195964.html#a2305025): fisher.comb <- function (pvalues) { df=length(pvalues) ch2=(-2*sum(log(pvalues))) return pc...

Hi all, I have some microarray data on 40 samples that fall into two groups. I have a value for 480k probes for each of those samples. I performed a t test (rowttests) on each row(giving the indices of the columns for each group) then used p.adjust() to adjust the pvalues for the number of tests performed. I then selected only the probes with adj-p.value<=0.05. I end up with roughly 2000 probes to do the clustering on but using pvclust, and hclust, the samples do no split up into the two groups. I would have imagined that using only those values that are signifi...

Hi all, Just a minor issue that I am not sure whether this is considered a "bug." It is about the help page. In the help page of printCoefmat(), for the argument 'eps.Pvalue', the description is as below: number, .. I have to read the source to figure out that this argument is to be used by format.pval(). Maybe the description of 'eps.Pvalue' can be revised to refer users to the help page of format.pval()? Regards, Shu Fai

On 29/10/2023 3:48 a.m., Shu Fai Cheung wrote: > Hi all, > > Just a minor issue that I am not sure whether this is considered a > "bug." It is about the help page. > > In the help page of printCoefmat(), for the argument 'eps.Pvalue', the > description is as below: > > number, .. > > I have to read the source to figure out that this argument is to be > used by format.pval(). > > Maybe the description of 'eps.Pvalue' can be revised to refer users to > the help page of format.pval()? Th...

Hello, I have some discrete pvalues and I would like to sort them. Then add random noise so that they are ordered the same way as the original pvalues. Off course I don't want any pvalues less than 0 or greater than 1. Any ideas on how to do this in R? -- Thanks, Jim. [[alternative HTML version deleted]]

Hello R-List I use DClusters package (I work in a cancer regestry). I have 2 questions about it: 1-how is it possible to get back the bootstrap pValue? I mean the pValue of the calculated statistic with respect of the distribution of this statistic under the null hypothesis. 2-how is it possible to test an overdispersion in the poisson model? for choosing a best model I need this mesure of dispersion. Should I build a glm(cases~expected,family=q...

It might help if you provided the code you used. It's possible that you didn't use direction="backward" in stepAIC(). Or if you did, it was still running, so whatever else you try will still be slow. The statement "R provides only the pvalues for each level" is wrong: look at the anova() function. Bob On 29 June 2017 at 11:13, Beno?t PELE <benoit.pele at acoss.fr> wrote: > Hello, > > i am a newby on R and i am trying to make a backward selection on a > binomial-logit glm on a large dataset (69000 lines for 145...

...All, I am using wilcox.test to test two samples, data_a and data_b, earch sample has 3 replicates, suppose data_a and data_b are 20*3 matrix. Then I used the following to test the null hypothesis (they are from same distribution.): wilcox.test(x=data_a, y=data_b, alternative="g") I got pvalue = 1.90806170863311e-09. When I switched data_a and data_b by doing the following: wilcox.test(x=data_b, y=data_a, alternative="g") I got pvalue = 0.999999998111886. I suppose because I am test them with same null hypothesis, I should get same result (pvalue). Since I am not a savy stati...

...Critical Z etc. were added by hand. I need an example of how I can mix alphanumeric and numeric data on output. Can you assist? R is proving to be a really fine computational language that is easy to use. Thank you. Sincerely, Mary A. Marion u xbar alpha zcrit zcrit2 zstat pvalue 140 150 .05 1.6449 1.96 4 6.334248e-05 LB95 UB95 LB90 UB90 145.1 154.9 145.888 154.112 Beta Power 0.021 0.979 Critical Z = 1.645 Zstatistic = 4 Empirical Mean 150 [ 135.1, 144.9 ) = Ao(?o) Population Mean 140 [ 145.1, 154.9 ] = C(x...

...ssion from: (NULL) (137.122.144.35) Dear R group, I have noticed a strange anomaly with the shapiro.test() function. Unfortunately I do not know how to calculate the shapiro test P values manually so I don't know if this is an actual bug. So, to produce the results, run the following code: pvalues = 0; for (i in 1:17) { j = 1:(i+3); pvalues[i]=shapiro.test(j)$p; } plot(pvalues); print(pvalues); Now I just made the graph to illustrate that the p-values are strictly decreasing. To me this makes intuitive sense: we are using the Shapiro test to test normality of (1,2,3,4),(1,2,3,4,5), and...

Full_Name: David Sterling Version: 2.4.0 OS: OS X Submission from: (NULL) (64.81.102.199) lillie.test() dies without grace producing the error message: 'Error in if (pvalue > 0.1) { : missing value where TRUE/FALSE needed' when passed a vector of identical values. Examples: > lillie.test(c(0,0,0,0,0,0,0,0,0,0)) Error in if (pvalue > 0.1) { : missing value where TRUE/FALSE needed > lillie.test(c(1,1,1,1,1,1,1,1,1,1)) Error in if (pvalue > 0.1) { : m...

Dear all, I observer a strange behavior of the pvalues of the t-test under the null hypothesis. Specifically, I obtain 2 samples of 3 individuals each from a normal distribution of mean 0 and variance 1. Then, I calculate the pvalue using the t-test (var.equal=TRUE, samples are independent). When I make a histogram of pvalues I see that consistently t...

I made an ANOVA with repeated mesures (aov(Mesure~Distance*Genre*Correct+Error(Sujet/(Distance*Genre*Correct)), data)) and I would like to extract the pvalues. The output is: ----------------------------------------------------------- Error: Sujet Df Sum Sq Mean Sq F value Pr(>F) Residuals 21 97.082 4.623 Error: Sujet:Distance Df Sum Sq Mean Sq F value Pr(>F) Distance 1 0.043 0.043 0.0162 0.9 Residuals 21 56.283...