Last updated on 2014-04-24 09:49:11.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1 | 0.65 | 13.83 | 14.48 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1 | 0.60 | 14.10 | 14.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1 | 28.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1 | 27.24 | OK | |||
| r-devel-osx-x86_64-clang | 1.1 | 29.42 | OK | |||
| r-devel-osx-x86_64-gcc | 1.1 | ERROR | ||||
| r-devel-windows-ix86+x86_64 | 1.1 | 2.00 | 20.00 | 22.00 | OK | |
| r-patched-linux-x86_64 | 1.1 | 0.60 | 13.80 | 14.40 | OK | |
| r-patched-solaris-sparc | 1.1 | 160.70 | OK | |||
| r-patched-solaris-x86 | 1.1 | 39.50 | OK | |||
| r-release-linux-ix86 | 1.1 | 1.00 | 28.00 | 29.00 | OK | |
| r-release-linux-x86_64 | 1.1 | 0.60 | 13.63 | 14.23 | OK | |
| r-release-osx-x86_64-mavericks | 1.1 | WARN | ||||
| r-release-windows-ix86+x86_64 | 1.1 | 2.00 | 21.00 | 23.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 1.1 | 2.00 | 21.00 | 23.00 | OK |
Version: 1.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘rms’
Flavor: r-devel-osx-x86_64-gcc
Version: 1.1
Check: examples
Result: ERROR
Running examples in ‘shrink-Ex.R’ failed
The error most likely occurred in:
> ### Name: shrink
> ### Title: Global, Parameterwise, and Joint Shrinkage of Regression
> ### Coefficients
> ### Aliases: shrink
> ### Keywords: models regression survival nonlinear
>
> ### ** Examples
>
> # Example with mfp (family = cox)
> library("mfp")
Loading required package: survival
Loading required package: splines
> data("GBSG")
> fit1 <- mfp(Surv(rfst, cens) ~ fp(age, df = 4, select = 0.05) +
+ fp(prm, df = 4, select = 0.05), family = cox, data = GBSG)
>
> shrink(fit1, type = "global", method = "dfbeta")
Shrinkage Factors (type=global, method=dfbeta):
[1] 0.9237358
Shrunken Regression Coefficients:
prm.1 age.1 age.2
-0.1986325 0.3759619 -4.5820305
>
> dfbeta.pw <- shrink(fit1, type = "parameterwise", method = "dfbeta")
> dfbeta.pw
Shrinkage Factors (type=parameterwise, method=dfbeta):
prm.1 age.1 age.2
0.9592653 0.7615833 0.7114137
Postfit:
Call:
coxph(formula = Surv(time, status) ~ prm.1 + age.1 + age.2, data = data.frame(modx),
x = TRUE)
coef exp(coef) se(coef) z p
prm.1 -0.206 0.8136 0.0296 -6.97 3.1e-12
age.1 0.310 1.3634 0.1015 3.05 2.3e-03
age.2 -3.529 0.0293 1.4921 -2.37 1.8e-02
Likelihood ratio test=58.9 on 3 df, p=1.04e-12 n= 686, number of events= 299
> cov2cor(dfbeta.pw$vcov.shrinkage)
prm.1 age.1 age.2
prm.1 1.0000000 0.015627 0.0291499
age.1 0.0156270 1.000000 0.9685090
age.2 0.0291499 0.968509 1.0000000
> sqrt(diag(dfbeta.pw$vcov.shrinkage))
prm.1 age.1 age.2
0.1375348 0.2494794 0.3008002
>
> shrink(fit1, type = "parameterwise", method = "dfbeta",
+ join = list(c("age.1", "age.2")))
Shrinkage Factors (type=parameterwise, method=dfbeta):
prm.1 age.1 age.2
0.9639732 0.8318633 0.8318633
Shrunken Regression Coefficients:
prm.1 age.1 age.2
-0.2072848 0.3385696 -4.1263128
>
> #shrink(fit1, type = "global", method = "jackknife")
> #shrink(fit1, type = "parameterwise", method = "jackknife")
> #shrink(fit1, type = "parameterwise", method = "jackknife",
> # join = list(c("age.1", "age.2")))
>
>
> # Example with rcs
> library("rms")
Error in library("rms") : there is no package called ‘rms’
Execution halted
Flavor: r-devel-osx-x86_64-gcc
Version: 1.1
Check: PDF version of manual
Result: WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `upquote.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
2b75dc99/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks