[R] Problem of data format using function of tmerger()

2019-03-20 Thread wong jane
We want to perform a survival analysis using time-dependent covariates in the Cox regression. In this analysis, ESRD1_END and ESRD1_TIME are the outcome and follow-up time,respectively. AKI_END is a binary time-dependent variable, while AKI_TIME is the time point for AKI_END measurement. The Cox mo

Re: [R] Solving Function using Conjugate Gradient

2019-03-20 Thread Bert Gunter
You should (almost) always also reply to the list, especially in this case, where others my also fail to help because they perceive your query as homework. However, I should warn you that such comprehensive queries are often dismissed as "do my work for me" requests. See the Posting Guide linked b

Re: [R] Solving Function using Conjugate Gradient

2019-03-20 Thread Bert Gunter
This list has a no homework policy. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Mar 20, 2019 at 8:54 AM smart hendsome via R-help < r-help@r-project.or

Re: [R] R-help Digest, Vol 193, Issue 16

2019-03-20 Thread Frank van Berkum
Dear Simon, Thank you for your response! I was not able to provide you with the requested information at an earlier stage since I am not a full time academic / researcher. An example of a bam call that may result in an error is: bam(formula=Di ~ 1 + Gender + I(L_Dis==0) + s(DisPerc, by=as.numer

Re: [R] data frame solution

2019-03-20 Thread Izmirlian, Grant (NIH/NCI) [E] via R-help
Statements like c(rbind(x, xx+yy), max(t)) and rep(0,length(df$b[1])) don't make any sense. You're example will be easier to understand if you show us the nrow(df) ==3 case. Thanks Grant Izmirlian, Ph.D. Mathematical Statistician izmir...@mail.nih.gov Delivery Address: 9609 Medical Center Dr,

Re: [R] plot.xmean.ordinaly vs plot() in package "rms"

2019-03-20 Thread Michael Dewey
Dear Kim See inline On 19/03/2019 22:29, Kim Jacobsen wrote: Mailing list now included (apologies, first time I post anything so not quite sure how it works). You are quite right, it was a typo. I meant to write that plot.xmean.ordinaly(). So please let me correct my last statement: the plot.x

[R] Solving Function using Conjugate Gradient

2019-03-20 Thread smart hendsome via R-help
Hi R-user, I have a problem regarding to estimate lambda[r] by minimizing the convex function using conjugate gradient in R-programming.  The function as below: Hopefully, anybody in this forum can help me. Thanks so much. __ R-help@r-project.org maili

Re: [R] System("source activate condaenv")

2019-03-20 Thread Bert Gunter
R is *not* RStudio. Please go to the RStudio site, not here, for help with that software. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Mar 20, 2019 at

Re: [R] plot.xmean.ordinaly vs plot() in package "rms"

2019-03-20 Thread Bert Gunter
Please study the documentation to which you were referred. This list is not appropriate for comprehensive tutorials, which is what you need, although all help is of course in some sense a tutorial. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking thi

[R] High p-value

2019-03-20 Thread Thomas Subia via R-help
>From previous posting: "This is my function: wilcox.test(A,B, data = data, paired = FALSE) It gives me high p value, though the median of A column is 6900 and B column is 3500. Why it gives p value high if there is a difference in the median?" Let's examine your choice to use the Wilcoxon tes

[R] How To Extracting Summary Stats for Sepwise Regression

2019-03-20 Thread Paul Bernal
Hello dear friends, What I want is to, somehow data.frame the summary of a stepwise regression (the estimated coefficients and p-values) to show them as a report in table format. However I have not been able to do that. Any help and/or guidance will be greatly appreciated, below are all the detai

Re: [R] System("source activate condaenv")

2019-03-20 Thread Ivan Krylov
On Wed, 20 Mar 2019 09:59:21 +0100 Sandra Elisabeth Chaudron wrote: > I am using the server version of RStudio and I have a script where I > want to activate the conda environment that I set up for a > bioinformatic tool called MinVar. > For that I use in my script the command: system("source > /

[R] System("source activate condaenv")

2019-03-20 Thread Sandra Elisabeth Chaudron
Hi, I am using the server version of RStudio and I have a script where I want to activate the conda environment that I set up for a bioinformatic tool called MinVar. For that I use in my script the command: system("source /home/ubuntu/miniconda3/bin/activate minvar"). I provide the path to activate

Re: [R] plot.xmean.ordinaly vs plot() in package "rms"

2019-03-20 Thread Kim Jacobsen
Mailing list now included (apologies, first time I post anything so not quite sure how it works). You are quite right, it was a typo. I meant to write that plot.xmean.ordinaly(). So please let me correct my last statement: the plot.xmean.ordinaly() command and plot() command are interchangeable as

Re: [R] Fw: problem with nlsLM.....

2019-03-20 Thread J C Nash
Of course, you might just try a more powerful approach. Duncan responded to the obvious issue earlier, but the second problem seems to need the analytic derivatives of the nlsr package. Note that nlsLM uses the SAME very simple forward difference derivative approximation for the Jacobian. Optimi

Re: [R] problem with nlsLM.....

2019-03-20 Thread Ivan Krylov
On Wed, 20 Mar 2019 09:43:11 + akshay kulkarni wrote: > But doesn't removing some of the parameters reduce the precision of > the relationship between the response variable and the > predictors(inefficient estimates of the coefficients)? No, it doesn't, since there is already more variables

Re: [R] problem with nlsLM.....

2019-03-20 Thread Ivan Krylov
On Wed, 20 Mar 2019 08:02:45 + akshay kulkarni wrote: > formulaDH5 <- as.formula(HM1 ~ (a + (b * ((HM2 + 0.3)^(1/2 + > (A*sin(w*HM3 + c) + C)) The problem with this formula is simple: the partial derivative with respect to `a` is the same as the partial derivative with respect to `C`. Th

[R] [mgcv] Memory issues with bam() on computer cluster

2019-03-20 Thread Frank van Berkum
Dear Simon, Thank you for your response! I was not able to provide you with the requested information at an earlier stage since I am not a full time academic / researcher. An example of a bam call that may result in an error is: bam(formula=Di ~ 1 + Gender + I(L_Dis==0) + s(DisPerc, by=as.numer