similar to: The argument 'eps.Pvalue' of `printCoefmat()`

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

>>>>> Shu Fai Cheung >>>>> on Thu, 6 Jul 2023 17:14:27 +0800 writes: > Hi All, > I would like to ask two questions about printCoefmat(). Good... this function, originally named print.coefmat(), is 25 years old (in R) now: -------------------------------------------------------------------- r1902 | maechler | 1998-08-14 19:19:05 +0200 (Fri,

Hi All, I would like to ask two questions about printCoefmat(). First, I found a behavior of printCoefmat() that looks strange to me, but I am not sure whether this is an intended behavior: ``` r set.seed(5689417) n <- 10000 x1 <- rnorm(n) x2 <- rnorm(n) y <- .5 * x1 + .6 * x2 + rnorm(n, -0.0002366, .2) dat <- data.frame(x1, x2, y) out <- lm(y ~ x1 + x2, dat) out_summary <-

Hi List, My goal is to force R not to print in scientific notation in the sixth column (rel_diff - for the p-value) of my data frame (not a matrix). I have used the format.pval () and printCoefmat () functions on the data frame. The R script is appended below. This issue is that use of the format.pval () and printCoefmat () functions on the data frame gives me the desired results, but coerces

On 15/10/2023 12:05 p.m., Shu Fai Cheung wrote: > Let me clarify my question: > > plot.new() > polygon(c(.5, .5, .75, .8), c(.25, .3, .4, .5)) > > If the device is an on-screen device, can I check whether a particular area > has anything drawn on it, or, to be precise, whether the color of a > particular area has all pixels equal to the background color. That is, if >

Hi All, I want to inspect the content of a plot generated by another function. For example: plot.new() polygon(c(.5, .5, .75, .8), c(.25, .3, .4, .5)) A polygon will be drawn. If I do not know what has been done to generate the plot, is it possible to query the content in the active device? Regards, Shu Fai [[alternative HTML version deleted]]

printCoefmat(signif.legend =FALSE) does not work properly. The option "signif.legend = FALSE" is ignored as shown in the example below. cmat <- cbind(rnorm(3, 10), sqrt(rchisq(3, 12))) cmat <- cbind(cmat, cmat[,1]/cmat[,2]) cmat <- cbind(cmat, 2*pnorm(-cmat[,3])) colnames(cmat) <- c("Estimate", "Std.Err", "Z value", "Pr(>z)") #

I am working with some survival data with missing values. I am using the mice package to do multiple imputation. I have found code in this thread which handles pooling of the MI results: https://stat.ethz.ch/pipermail/r-help/2007-May/132180.html Now I would like to plot a survival curve using the pooled results. Here is a reproducible example: require(survival) require(mice) set.seed(2) dt

Hi You could also look at dev.capture(), depending on which screen device you are using. Paul On 16/10/23 05:24, Duncan Murdoch wrote: > On 15/10/2023 12:05 p.m., Shu Fai Cheung wrote: > > Let me clarify my question: > > > > plot.new() > > polygon(c(.5, .5, .75, .8), c(.25, .3, .4, .5)) > > > > If the device is an on-screen device, can I check

Dear useRs, I would like to summarize results of several tests in groups of two columns - statistic, p-value, statistic, p-value etc. There would be nice to add significance stars, but printCoefmat allows to do it only to last column. Is there any way to do format such table without writing my own complicated function? Thank you in advance, -- Lukasz Komsta Department of Medicinal

Dear editor: I'm writing this letter to enquire where can I download the package of "lmtest". Can you send me this package? THanks a lot. Best regards, Shu-Fei Wu

I want to use something like printCoefmat() in a print.summary method to print a more nicely formatted version of the result from a summary method, but where the estimates may be cross-classified by one or more factors. However, printCoefmat() assumes that the labels for the parameters are the rownames of the object, and prints factors as integers. With one factor, I could just assign that as

Dear R users, I have a data frame in the form below, on which I would like to make normality tests on the values in the ExpressionLevel column. > head(df) ID Plant Tissue Gene ExpressionLevel 1 1 p1 t1 g1 366.53 2 2 p1 t1 g2 0.57 3 3 p1 t1 g3 11.81 4 4 p1 t2 g1 498.43 5 5 p1 t2 g2 2.14 6 6 p1 t2 g3 7.85 I

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

inputfille snpid indid genotype gvariable probeid gene geneexpression rs1040480 CHB_NA18524 C/T 2 GI_19743926-I PTPRT 5.850586 rs1040480 CHB_NA18526 C/C 1 GI_19743926-I PTPRT 6.028641 rs1040480 CHB_NA18529 C/C 3 GI_19743926-I PTPRT 5.944392 rs1040481 CHB_NA18532 C/C 1 GI_19743926-I PTPRT 5.938578 rs1040481 CHB_NA18537 C/C 2 GI_19743926-I PTPRT 5.874439 rs1040481 CHB_NA18540 C/C 3 GI_19743926-I

I want to print the coefficient estimates of a model in a way as consistent with other output in R as possible. stats provides the printCoefmat function for doing this, but there is one problem. I have an additional piece of textual information I want to put on the line with the other info on each coefficient. The documentation for printCoefmat says the first argument must be numeric, which

** I am using the following way to get p-values from fiser exact test. However, I do need to print for each pair the values "n00, n01, n10, n11". How can I print that as a table and not a matrix as below along with the p-value? Any help will be greatly appreciated fish <- function(y, x) {n00 = sum((1-x)*(1-y)); n01 = sum((1-x)*y); n10 = sum(x*(1-y)); n11 = sum(x*y); a =

I'm trying to understand how R prints summary.lm objects and trying to change it slightly for a summary function that calculates standard errors using an alternative method. I've found that I can modify a summary.lm object and then it prints the modified way but I want to change a few things in the print method that I think I might just be able to do. One is that I want the coefficients

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

Dear R people, I have a naive question: after fitting "lm" to a data, I can't extract the pvalue corresponding to a specific covariate in a direct way. Could anyone give me a hint? Thank you very much. Frank