Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found). Both bladder and bladder2 are there. Thanks, Petra
bladder1 dataset in survival library
5 messages · Marc Schwartz, David Winsemius, Petra Buzkova
On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote:
Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/ bladder.html I can not open it (not found).
In the documentation for my installation of survival, version 2.34-1, the help page only lists bladder and bladder2. Furthermore, executing data(bladder2) gives me a "data set'bladder2' not found" warning. Updating from source to 2.35-4 on the Mac does not improve the situation. The link to the help page you are offering is to the r- devel tree so perhaps this question should have gone to Dr. Lumley?
Both bladder and bladder2 are there.
You are luckier than I.
Thanks, Petra
David Winsemius, MD Heritage Laboratories West Hartford, CT > sessionInfo() R version 2.8.1 Patched (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] lattice_0.17-20 Design_2.1-2 survival_2.35-4 Hmisc_3.5-2 gstat_0.9-59 sp_0.9-32 loaded via a namespace (and not attached): [1] cluster_1.11.12 grid_2.8.1 tools_2.8.1
On Apr 20, 2009, at 8:14 PM, David Winsemius wrote:
On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote:
Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found).
In the documentation for my installation of survival, version 2.34-1, the help page only lists bladder and bladder2. Furthermore, executing data(bladder2) gives me a "data set'bladder2' not found" warning. Updating from source to 2.35-4 on the Mac does not improve the situation. The link to the help page you are offering is to the r-devel tree so perhaps this question should have gone to Dr. Lumley?
Both bladder and bladder2 are there.
You are luckier than I.
Thanks, Petra
David Winsemius, MD Heritage Laboratories West Hartford, CT
sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] lattice_0.17-20 Design_2.1-2 survival_2.35-4 Hmisc_3.5-2 gstat_0.9-59 sp_0.9-32 loaded via a namespace (and not attached): [1] cluster_1.11.12 grid_2.8.1 tools_2.8.1
David, You might want to try to exit from your R session and open a new one, or detach(package:survival) and then re-load: > library(survival) Loading required package: splines > str(bladder) 'data.frame': 340 obs. of 7 variables: $ id : int 1 1 1 1 2 2 2 2 3 3 ... $ rx : num 1 1 1 1 1 1 1 1 1 1 ... $ number: int 1 1 1 1 2 2 2 2 1 1 ... $ size : int 3 3 3 3 1 1 1 1 1 1 ... $ stop : int 1 1 1 1 4 4 4 4 7 7 ... $ event : num 0 0 0 0 0 0 0 0 0 0 ... $ enum : int 1 2 3 4 1 2 3 4 1 2 ... > str(bladder1) 'data.frame': 294 obs. of 11 variables: $ id : int 1 2 3 4 5 6 6 7 8 9 ... $ treatment: Factor w/ 3 levels "placebo","pyridoxine",..: 1 1 1 1 1 1 1 1 1 1 ... $ number : int 1 1 2 1 5 4 4 1 1 1 ... $ size : int 1 3 1 1 1 1 1 1 1 3 ... $ recur : int 0 0 0 0 0 1 1 0 0 1 ... $ start : int 0 0 0 0 0 0 6 0 0 0 ... $ stop : int 0 1 4 7 10 6 10 14 18 5 ... $ status : num 3 3 0 0 3 1 3 0 0 1 ... $ rtumor : chr "." "." "." "." ... $ rsize : chr "." "." "." "." ... $ enum : num 1 1 1 1 1 1 2 1 1 1 ... > str(bladder2) 'data.frame': 178 obs. of 8 variables: $ id : int 1 2 3 4 5 5 6 7 8 8 ... $ rx : num 1 1 1 1 1 1 1 1 1 1 ... $ number: int 1 2 1 5 4 4 1 1 1 1 ... $ size : int 3 1 1 1 1 1 1 1 3 3 ... $ start : int 0 0 0 0 0 6 0 0 0 5 ... $ stop : int 1 4 7 10 6 10 14 18 5 18 ... $ event : num 0 0 0 0 1 0 0 0 1 0 ... $ enum : num 1 1 1 1 1 2 1 1 1 2 ... > sessionInfo() R version 2.9.0 Patched (2009-04-18 r48348) i386-apple-darwin9.6.2 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets [7] methods base other attached packages: [1] survival_2.35-4 Based upon the diff for the bladder help page at: http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/survival/man/bladder.Rd?root=survival&rev=11221&r1=11166&r2=11221 it was added in the last two months. Petra, try either running update.packages() or installing R 2.9.0. HTH, Marc Schwartz
On Apr 20, 2009, at 9:43 PM, Marc Schwartz wrote:
On Apr 20, 2009, at 8:14 PM, David Winsemius wrote:
On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote:
Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found).
In the documentation for my installation of survival, version 2.34-1, the help page only lists bladder and bladder2. Furthermore, executing data(bladder2) gives me a "data set'bladder2' not found" warning. Updating from source to 2.35-4 on the Mac does not improve the situation. The link to the help page you are offering is to the r-devel tree so perhaps this question should have gone to Dr. Lumley?
Both bladder and bladder2 are there.
You are luckier than I.
David, You might want to try to exit from your R session and open a new one, or detach(package:survival) and then re-load:
Restarting R and loading only survival does not change the warning from data(bladder2) for me, but using str (for the first time) gives the same results as you offered: > str(bladder2) 'data.frame': 178 obs. of 8 variables: $ id : int 1 2 3 4 5 5 6 7 8 8 ... $ rx : num 1 1 1 1 1 1 1 1 1 1 ... $ number: int 1 2 1 5 4 4 1 1 1 1 ... $ size : int 3 1 1 1 1 1 1 1 3 3 ... $ start : int 0 0 0 0 0 6 0 0 0 5 ... $ stop : int 1 4 7 10 6 10 14 18 5 18 ... $ event : num 0 0 0 0 1 0 0 0 1 0 ... $ enum : num 1 1 1 1 1 2 1 1 1 2 ... > data(bladder2) Warning message: In data(bladder2) : data set 'bladder2' not found So I ask myself, why would data(bladder2) fail? It appears that I do not completely understand the data() function. A snippet from the output of data(): Data sets in package ?survival?: aml (leukemia) Acute Myelogenous Leukemia survival data bladder Bladder Cancer Recurrences bladder1 (bladder) Bladder Cancer Recurrences bladder2 (bladder) Bladder Cancer Recurrences So bladder1 and bladder2 are part of bladder? It appears so. From the help page: "Where the datasets have a different name from the argument that should be used to retrieve them the index will have an entry like beaver1 (beavers)which tells us that dataset beaver1 can be retrieved by the call data(beaver)." David Winsemius, MD Heritage Laboratories West Hartford, CT
1 day later
Petra, try either running update.packages() or installing R 2.9.0.
Thanks Mark, I got it now. Thanks, Petra ________________________________________ Petra Buzkova, PhD Department of Biostatistics University of Washington 206-897-1962 (phone) 206-616-4075 (fax)
Marc Schwartz wrote:
On Apr 20, 2009, at 8:14 PM, David Winsemius wrote:
On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote:
Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found).
In the documentation for my installation of survival, version 2.34-1, the help page only lists bladder and bladder2. Furthermore, executing data(bladder2) gives me a "data set'bladder2' not found" warning. Updating from source to 2.35-4 on the Mac does not improve the situation. The link to the help page you are offering is to the r-devel tree so perhaps this question should have gone to Dr. Lumley?
Both bladder and bladder2 are there.
You are luckier than I.
Thanks, Petra
David Winsemius, MD Heritage Laboratories West Hartford, CT
sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] lattice_0.17-20 Design_2.1-2 survival_2.35-4 Hmisc_3.5-2 gstat_0.9-59 sp_0.9-32 loaded via a namespace (and not attached): [1] cluster_1.11.12 grid_2.8.1 tools_2.8.1
David, You might want to try to exit from your R session and open a new one, or detach(package:survival) and then re-load:
library(survival)
Loading required package: splines
str(bladder)
'data.frame': 340 obs. of 7 variables: $ id : int 1 1 1 1 2 2 2 2 3 3 ... $ rx : num 1 1 1 1 1 1 1 1 1 1 ... $ number: int 1 1 1 1 2 2 2 2 1 1 ... $ size : int 3 3 3 3 1 1 1 1 1 1 ... $ stop : int 1 1 1 1 4 4 4 4 7 7 ... $ event : num 0 0 0 0 0 0 0 0 0 0 ... $ enum : int 1 2 3 4 1 2 3 4 1 2 ...
str(bladder1)
'data.frame': 294 obs. of 11 variables: $ id : int 1 2 3 4 5 6 6 7 8 9 ... $ treatment: Factor w/ 3 levels "placebo","pyridoxine",..: 1 1 1 1 1 1 1 1 1 1 ... $ number : int 1 1 2 1 5 4 4 1 1 1 ... $ size : int 1 3 1 1 1 1 1 1 1 3 ... $ recur : int 0 0 0 0 0 1 1 0 0 1 ... $ start : int 0 0 0 0 0 0 6 0 0 0 ... $ stop : int 0 1 4 7 10 6 10 14 18 5 ... $ status : num 3 3 0 0 3 1 3 0 0 1 ... $ rtumor : chr "." "." "." "." ... $ rsize : chr "." "." "." "." ... $ enum : num 1 1 1 1 1 1 2 1 1 1 ...
str(bladder2)
'data.frame': 178 obs. of 8 variables: $ id : int 1 2 3 4 5 5 6 7 8 8 ... $ rx : num 1 1 1 1 1 1 1 1 1 1 ... $ number: int 1 2 1 5 4 4 1 1 1 1 ... $ size : int 3 1 1 1 1 1 1 1 3 3 ... $ start : int 0 0 0 0 0 6 0 0 0 5 ... $ stop : int 1 4 7 10 6 10 14 18 5 18 ... $ event : num 0 0 0 0 1 0 0 0 1 0 ... $ enum : num 1 1 1 1 1 2 1 1 1 2 ...
sessionInfo()
R version 2.9.0 Patched (2009-04-18 r48348) i386-apple-darwin9.6.2 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets [7] methods base other attached packages: [1] survival_2.35-4 Based upon the diff for the bladder help page at: http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/survival/man/bladder.Rd?root=survival&rev=11221&r1=11166&r2=11221 it was added in the last two months. Petra, try either running update.packages() or installing R 2.9.0. HTH, Marc Schwartz