Displaying 20 results from an estimated 3000 matches similar to: ""Missing links": Hmisc and Design docs"
2013 Apr 19
2
NAMESPACE and imports
I am cleaning up the rms package to not export functions not to be called
directly by users. rms uses generic functions defined in other packages.
For example there is a latex method in the Hmisc package, and rms has a
latex method for objects of class "anova.rms" so there are anova.rms and
latex.anova.rms functions in rms. I use:
2013 Jul 11
0
[R-pkgs] Major Update to rms package
The rms ("Regression Modeling Strategies") package has undergone a
massive update. The entire list of updates is at the bottom of this
note. CRAN has the update for linux and will soon have it for Windows
and Mac - check http://cran.r-project.org/web/packages/rms/ for
availability. This rms update relies on a major update of the Hmisc
package.
The most user-visible changes are:
2011 Mar 01
0
Major update to rms package
A new version of rms is now available on CRAN for Linux and Windows (Mac
will probably be available very soon). Largest changes include latex
methods for validate.* and adding the capability to force a subset of
variables to be included in all backwards stepdown models (single model or
validation by resampling).
Recent updates:
* In survplot.rms, fixed bug (curves were undefined if
2011 Mar 01
0
Major update to rms package
A new version of rms is now available on CRAN for Linux and Windows (Mac
will probably be available very soon). Largest changes include latex
methods for validate.* and adding the capability to force a subset of
variables to be included in all backwards stepdown models (single model or
validation by resampling).
Recent updates:
* In survplot.rms, fixed bug (curves were undefined if
2004 Sep 09
2
Rd syntax error detected in CRAN daily checks
Please forgive me if you already received this. I had an e-mail sending
glitch this morning.
http://cran.r-project.org/src/contrib/checkSummary.html reported an
error in Design.trans.Rd
* checking Rd files ... ERROR
Rd files with syntax errors:
/var/mnt/hda3/R.check/r-devel/PKGS/Design/man/Design.trans.Rd:
unterminated section 'alias'
The .Rd file is attached. It begins
2010 Oct 13
1
Building rpm package for Hmisc on Fedora 12
Hi, I'm trying to get the 'xts' library from CRAN packaged for Fedora 12, and
one of its dependencies is 'Hmisc'. I have created a spec file for that using
R2spec, but building it fails with something in building the manual pages:
Warning: ./man/escapeRegex.Rd:22: unknown macro '\backslash'
[similar warnings snipped]
Warning: newline within quoted string at
2007 Nov 21
0
survest and survfit.coxph returned different confidence intervals on estimation of survival probability at 5 year
I wonder if anyone know why survest (a function in Design package) and
standard survfit.coxph (survival) returned different confidence
intervals on survival probability estimation (say 5 year).
I am trying to estimate the 5-year survival probability on a continuous
predictor (e.g. Age in this case). Here is what I did based on an
example in "help cph". The 95% confidence intervals
2009 Apr 14
1
Function call error in cph/survest (package Design)
Dear UseR,
I do not know if this a problem with me, my data or cph/survest in package
design. The example below works with a standard data set, but not with my
data, but I cannot locate the problem.
Note that I am using an older package of survival to avoid a problem with
the newly renamed function in survival meeting Design.
Dieter
# First, check standard example to make sure
library(Design)
2016 Nov 04
0
Major Update to rms package: 5.0-0
A major new version of the rms package is now on CRAN. The most
user-visible changes are:
- interactive plotly graphic methods for model fits. The best example of
this is survplot for npsurv (Kaplan-Meier) estimates where the number of
risk pop up as you hover over the curves, and you can click to bring up
confidence bands for differences in survival curves
- html methods for model fit
2016 Nov 04
0
Major Update to rms package: 5.0-0
A major new version of the rms package is now on CRAN. The most
user-visible changes are:
- interactive plotly graphic methods for model fits. The best example of
this is survplot for npsurv (Kaplan-Meier) estimates where the number of
risk pop up as you hover over the curves, and you can click to bring up
confidence bands for differences in survival curves
- html methods for model fit
2009 May 20
1
turning off specific types of warnings
Dear R users,
I have a long function that among other things uses the "survest" function from the Design package. This function generates the warning:
In survest.cph (...)
S.E. and confidence intervals are approximate except at predictor means.
Use cph(...,x=T,y=T) (and don't use linear.predictors=) for better estimates.
I would like to turn this specific warning off, as it
2009 Sep 30
1
rcs fits in design package
Hi all,
I have a vector of proportions (post_op_prw) such that
>summary(amb$post_op_prw)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.3985 0.9134 0.9962 1.0000
> summary(cut2(amb$post_op_prw,0.0001))
[0.0000,0.0001) [0.0001,0.9962] NA's
1904 1672 1
2009 Feb 18
1
Age as time-scale in a cox model-How to calculate x-time risk?
Dear R users,
My question is more methodology related rather than specific to R usage. Using time on study as time in a cox model, eg:
library(Design)
stanf.cph1=cph(Surv(time, status) ~ t5+id+age, data=stanford2, surv=T)
#In this case the 1000-day survival probability would be:
stanf.surv1=survest(stanf.cph1, times=1000)
#Age in this case is a covariate.
#I now want to compare the above
2008 Nov 03
0
NaN causes "error in fitter" with cph.calibrate from pkg Design
I have been attempting to use cph models to get better calibration
of my models for which I had originally used logistic regression. I
tried running with 40 repetitions and got an error. I then tried 500
repetitions (thinking that the NaNs in the output below might be
caused by that choice) and then let my computer crunch for several
hours and got only the same error message and
2011 Mar 07
0
survest() for cph() in Design package
Hi, I am trying to run a conditional logistic model on a nested case-control
study using cph() and then estimate survival based on the model. The data came
from Prof Bryan Langholz website where he also has the SAS code to this, so I am
trying to replicate the SAS results.
The data attached. Basically, the variables are:
rstime: risk set age
rsentry: fake entry time, just before rstime
setno:
2004 Mar 30
0
koq.q ---- Kent O' Quigley R2
Dear R-users,
I apply to your kind attention to know if someone have used the Splus software
koq.q (Kent & O'Quigley's measure of dependence for censored data) in R and
kindly can help me.
I have tried several times to contact the authors Andrej Blejec
(andrej.blejec at uni-lj.si) or Janez Stare (janez.stare at mf.uni-lj.si) but
unfortunately no one answered me.
Following
2011 Sep 12
1
coxreg vs coxph: time-dependent treatment
Dear List,
After including cluster() option the coxreg (from eha package)
produces results slightly different than that of coxph (from survival)
in the following time-dependent treatment effect calculation (example
is used just to make the point). Will appreciate any explaination /
comment.
cheers,
Ehsan
############################
require(survival)
require(eha)
data(heart)
# create weights
2009 Mar 26
2
R 2.8.1 and 2.9 alpha crash when running survest of Design package
Dear Prof Harrell and everyone,
My PC: Window XP service pack 3 and service pack 2
R version 2.8.1 and 2.9 alpha
For the last 3 days, after updating R, my two computers have been facing
problems when running existing and runable R commands that involves with
Design package
I attempt to use 'survest', but I failed all the times with R (both 2.8.1
and 2.9 alpha) being shut down
2013 Nov 23
0
Hmisc package 3.13-0
A significant update to the Hmisc package is now available on CRAN for
all platforms. Hmisc source is now on github at
https://github.com/harrelfe/Hmisc and the full change log may be found
at https://github.com/harrelfe/Hmisc/commits/master
The most important updates are additions of new graphics functions for
summarizing and displaying data with an aim of replacing tables. There
is also
2003 Jan 01
0
Updates to Hmisc and Design Libraries
The Hmisc and Design libraries have been updated respectively to versions 1.4-2 and 1.1-1. New versions for Linux/Unix/Windows may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/r . Web sites for the libraries are http://hesweb1.med.virginia.edu/biostat/s/Hmisc.html and http://hesweb1.med.virginia.edu/biostat/s/Design.html .
Thanks to Xiao Gang Fan for porting the libraries