Re: [R] how to add a child to a child in XML

Hi, XML doesn't use the `$` to access child nodes. Instead use either `[name]` to get a list of children of that name or `[[name]]` to get the just the first child of that name encountered in the genealogy. Thus for your example... > root$child1 NULL > root[['child1']] On the other hand,

Re: [R] R 3.4.4, internet access fails on Windows XP

To solve similar problem, I just install Lubuntu 17.10 on an old PC (i686) and I am astonished by the reactivity of the computer... it has a second life. The main problem is that Rstudio Desktop 32 bits is no more supported for Ubuntu 32bits computers but the solution using Rstudio Server 32

Re: [R] Plotting Notched Box Plots Log Scale - Losing bottom portion of box plot

Note that: > plot(Iron~Location,data=MyDataIron,log="y",notch=FALSE) > plot(10+Iron~Location,data=MyDataIron,log="y",notch=TRUE) Warning message: In bxp(list(stats = c(10.66, 13.9, 24.9, 39, 60, 10.05, 10.07515, : some notches went outside hinges ('box'): maybe set notch=FALSE ## Both work,

[R] how to add a child to a child in XML

I am trying to add a child to a child using XML package in R. the following fails library(XML) node1 <- c("val1","val2","val3") names(node1) <- c("att1","att2","att3") root <- xmlNode("root", attrs=node1) node2 <- LETTERS[1:3] names(node2) <- paste("name",1:3,sep="") root <-

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

"I see: consistency with additive identity. " Ummm, well: > 1+NULL numeric(0) > sum(1,NULL) [1] 1 Of course, there could well be something here I don't get, but that doesn't look very consistent to me. However, as I said privately, so long as the corner case behavior is documented, which it

[R] Plotting Notched Box Plots Log Scale - Losing bottom portion of box plot

Hello, I'm using the code below to generate some notched box plots. The issue is whenever I use log scale, the sides of the bottom part of the box plots don't plot. I've tried it in RStudio Ver 1.1.419 and R version 3.4.3 and I get the same result. The code and link to my data is below. Thank

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

> On Mar 21, 2018, at 9:58 AM, Jeff Newmiller wrote: > > What do you mean by "should not"? > > NULL means "missing object" in R. The result of the sum function is always > expected to be numeric... so NA_real or NA_integer could make sense as > possible return

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

Use rowSums(is.na(d))==ncol(d) to pick out the rows will no good values. E.g., > d <- data.frame(x1=c(NA,2:4), x2=c(NA,NA,13:14), x3=c(NA,NA,NA,44)) > d x1 x2 x3 1 NA NA NA 2 2 NA NA 3 3 13 NA 4 4 14 44 > s <- rowSums(d, na.rm=TRUE) > s [1] 0 2 16 62 > s[ rowSums(is.na(d))==ncol(d) ] <- NA

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

I see: consistency with additive identity. That makes sense. Thanks. B. > On Mar 21, 2018, at 1:22 PM, peter dalgaard wrote: > > No. The empty sum is zero. Adding it to another sum should not change it. > Nothing audacious about that. This is consistent; other definitions

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

No. The empty sum is zero. Adding it to another sum should not change it. Nothing audacious about that. This is consistent; other definitions just cause trouble. -pd > On 21 Mar 2018, at 18:05 , Boris Steipe wrote: > > Surely the result of summation of non-existent

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

Surely the result of summation of non-existent values is not defined, is it not? And since the NA values have been _removed_, there's nothing left to sum over. In fact, pretending the the result in that case is zero would appear audacious, no? Cheers, Boris > On Mar 21, 2018, at 12:58

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

What do you mean by "should not"? NULL means "missing object" in R. The result of the sum function is always expected to be numeric... so NA_real or NA_integer could make sense as possible return values. But you cannot compute on NULL so no, that doesn't work. See the note under the "Value"

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

Should not the result be NULL if you have removed the NA with na.rm=TRUE ? B. > On Mar 21, 2018, at 11:44 AM, Stefano Sofia > wrote: > > Dear list users, > let me ask you this trivial question. I worked on that for a long time, by > now. > Suppose to have a

Re: [R] Sum of columns of a data frame equal to NA when all the elements are NA

On 21/03/2018 11:44 AM, Stefano Sofia wrote: Dear list users, let me ask you this trivial question. I worked on that for a long time, by now. Suppose to have a data frame with NAs and to sum some columns with rowSums: df <- data.frame(A = runif(10), B = runif(10), C = rnorm(10)) df[1, ] <- NA

Re: [R] R 3.4.4, internet access fails on Windows XP

On 21/03/2018 8:27 AM, Holger Taschenberger wrote: I can install and run R 3.4.4 on Windows XP (32bit). However, calling "Update Packages..." or "Html help" from the RGui.exe main menu fails with a Windows MessageBox saying: "The procedure entry point IdnToAscii could not be located in the

[R] Sum of columns of a data frame equal to NA when all the elements are NA

Dear list users, let me ask you this trivial question. I worked on that for a long time, by now. Suppose to have a data frame with NAs and to sum some columns with rowSums: df <- data.frame(A = runif(10), B = runif(10), C = rnorm(10)) df[1, ] <- NA rowSums(df[ , which(names(df) %in% c("A","B"))],

[R] Confidence intervals for the Instrumental Variable estimators of TWO causal effects

Dear all, I am using the Instrumental Variable approach to estimate the causal effects of TWO endogenous variables in a Mendelian Randomization study. As long as point estimation is concerned, I have no problem: both "ivreg" in library "AER" and "tsls" in library "sem" do the job perfectly. The

[R] R 3.4.4, internet access fails on Windows XP

I can install and run R 3.4.4 on Windows XP (32bit). However, calling "Update Packages..." or "Html help" from the RGui.exe main menu fails with a Windows MessageBox saying: "The procedure entry point IdnToAscii could not be located in the dynamic link library KERNEL32.dll" and the following

Re: [R] Vary an equation using values from a sequence

It depends a bit on what you plan to do with the results. A loop would be easy and straightforward: > k <- 1:5 > for(k in 1:5) print(Data - min(Data) + k) [1] 1 2 3 4 5 6 7 8 9 10 [1] 2 3 4 5 6 7 8 9 10 11 [1] 3 4 5 6 7 8 9 10 11 12 [1] 4 5 6 7 8 9 10 11 12 13

Re: [R] Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository

> On Mar 20, 2018, at 11:49 PM, Persian Irani wrote: > > Hi all! > > While I am trying to read .cel files with oligo package: > > afbatch=read.celfiles(list.celfiles()) > > I get an error: > Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository

[R] selectFGR vs weighted coxph for internal validation and calibration curve- competing risks model

Dear Geskus, I want to develop a prediction model. I followed your paper and analysed thro' weighted coxph approach. I can develop nomogram based on the final model also. But I do not know how to do internal validation of the model and subsequently obtain calibration plot. Is it possible

[R] A new version (1.1.0) of the “spm” package for spatial predictive modelling reelased on CRAN [SEC=UNCLASSIFIED]

Dear R users, A new version (1.1.0) of the “spm” package for spatial predictive modelling is now available on CRAN. The introductory vignette is available here: https://cran.rstudio.com/web/packages/spm/vignettes/spm.html There are several new enhancements to the package including a

[R] Error in GDCprepare step of TCGAbiolinks

Dear Sir/ma'am, I'm using R-3.4.4 and TCGAbiolinks package for the analysis of GDC data. Till today i have reintalled R and R studio for 5 times but one error comes when i analyze the GDC data at the step GDCprepare. the data i am using is not a legacy data of GDC data portal. I think the

[R] Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository

Hi all! While I am trying to read .cel files with oligo package: afbatch=read.celfiles(list.celfiles()) I get an error: Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository How can I overcome this? Thank you in advance __