Re: [R] [FORGED] Re: SE for all levels (including reference) of a factor atfer a GLM

To give a short answer to the original question: > On 16 Feb 2018, at 05:02 , Rolf Turner wrote: > > In order to ascribe unique values to the parameters, one must apply a > "constraint". With the "treatment contrasts" the constraint is that > beta_1 = 0. ...and

[R] stem - strange leaves

> x [1] 8.0 7.9 7.5 7.0 8.0 7.3 8.0 7.2 7.4 7.3 7.8 8.0 7.7 8.3 7.8 7.8 7.1 7.7 6.9 7.5 7.5 7.3 7.2 7.5 7.2 > stem(x) The decimal point is at the | 6 | 9 7 | 012223334 7 | 778889 8 | 3 > y <- c(x, 8) > stem(y) The decimal point is 1 digit(s) to the left of the | 68 | 0

[R] Problem installing libxml2 under Homebrew

i am trying to install xml2 from CRAN, and it is throwing an error that it cannot find the libxml2 library configuration. The thing is that pkg-config seems to be set up correctly: $ echo $PKG_CONFIG_PATH :/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig $ pkg-config

Re: [R] [FORGED] Re: SE for all levels (including reference) of a factor atfer a GLM

Le 16/02/2018 à 10:24, Peter Dalgaard a écrit : To give a short answer to the original question: On 16 Feb 2018, at 05:02 , Rolf Turner wrote: In order to ascribe unique values to the parameters, one must apply a "constraint". With the "treatment contrasts" the

[R] Competing risks - calibration curve

Dear R users, I am new to R and wanted to apply competing risk methods in my research work. I used the R code given by Zhang et al in his paper 'Nomogram for survival analysis in the presence of competing risks published in Ann Trans Med 2017:5(20):403. I am struggling with getting

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

Hi > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg holly > Sent: Thursday, February 15, 2018 3:58 PM > To: r-help mailing list > Subject: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are > > Hi all; > >

Re: [R] stem - strange leaves

Hi I do not know why does it happen but you can control the behaviour by setting scale to 0.5. Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Leif Ruckman > Sent: Friday, February 16, 2018 9:18 AM > To: r-help@r-project.org > Subject:

Re: [R] Competing risks - calibration curve

Hi, Sorry not to provide R-code in my previous mail. R code is below #install.packages("rms") require(rms) #install.packages("mstate") library(mstate) require(splines) library(ggplot2) library(survival) library(splines) #install.packages("survsim") require(survsim) set.seed(10)

Re: [R] stem - strange leaves

> > From: Leif Ruckman [mailto:leif.ruck...@kau.se] > > Sent: Friday, February 16, 2018 3:27 PM > > To: PIKAL Petr > > Subject: RE: stem - strange leaves > > > > Thank you, I also found that solution but I think it is strange that > > this happens at all. I have tried

Re: [R] weighed Fleming-Harrington log rank test

You are correct that the survreg routine only supports 'rho' of the Fleming-Harrington G-rho tests. This is a function of age -- I wrote the original code back when I was working with Tom (Fleming), and he was only using 1 parameter. Later he and David expanded the test to two parameters.

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

Hi Petr; Thanks. I do save the result in pdf by using the following command. ggsave("z7.pdf", p4, height = 95, width = 8, device=pdf, limitsize = F,dpi=300) I can achieve the y axis with 733 levels. But I need get the plot WITHOUT reordering the names. Regards, Greg On Fri, Feb 16, 2018

Re: [R] stem - strange leaves

In addition to stem() in the graphics package, there are other implementations of stem-and-leaf plots that add additional features such as stem.leaf() in package aplpack which will includes a function to produce back to back stem and leaf plots. David L

Re: [R] stem - strange leaves

Hi R is open source so you could dig into the code. However the actual stem function is probably written in C, so it is beyond my expertise. If you replied to the list there could be experts who are able to provide explanation. > stem function (x, scale = 1, width = 80, atom = 1e-08) { if

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

Hi What do you mean „without reordering the names“. Factor variable is ordered according to its levels and you can freely change the ordering. This is why factors are useful and worth to use in many cases instead of character vectors. See this result > iris$MySpecies<-factor(iris$Species,

Re: [R] weighed Fleming-Harrington log rank test

Thank you Terry. Right now I can use comp() from survMisc package to do the 2-parameter version of F-H weighting. I think both SAS and stata offer the 2-parameter version, so just thought it would be nice if survdiff() can have that option given it's standard package in R.  Thanks! John On

Re: [R] error in loading rgdal package

Hi Loris, Thanks. I tried to update the R software and reinstalled the GDAL library. It works now. On Thu, Feb 15, 2018 at 11:49 PM, Loris Bennett wrote: > Hi Lily, > > lily li writes: > > > Hi R users, > > > > Could you help me to see this

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

Hi Petr; I would like to get a plot with names as they are in the original file. They are chemical names and I have 733 in the my file. For example, let me give to chemical names "*2-hydroxybutyrate/2-hydroxyisobutyrate*" and "*palmitoyl-arachidonoyl-glycerol (16:0/20:4) [1]**" .So, what should I

[R] hurdle model - count and response predictions

Hello, I'm using pscl to run a hurdle model. Everything works great until I get to the point of making predictions. All of my "count" predictions are lower than my actual data, and lower than the "response" predictions, similar to the issue described here (

[R] analysis of covariance and constrained parameters

Consider an analysis of covariance involving age and cohort. The goal is to assess whether the influence of cohort depends upon the age. The simplest case involves data as follows value Age Cohort x1   1   3 x2   1   4 x3   1   5 x4   2   3 x5   2  

Re: [R] hurdle model - count and response predictions

I answered the question on SO. In short the differences come from truncated vs. untruncated models and conditional vs. unconditional expectations. Feel free to follow-up on SO or here on the list... On Fri, 16 Feb 2018, John Wilson wrote: Hello, I'm using pscl to run a hurdle model.