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eurodist example dataset is malformed
4 messages · Justin Donaldson, Gavin Simpson, Jari Oksanen
On Wed, 2009-08-12 at 20:26 -0400, Justin Donaldson wrote:
The eurodist dataset (my favorite for mds) is malformed. Instead of a
standard distance matrix, it's a data frame. The rownames have gotten
'bumped' to a new anonymous dimension "X". It's possible to fix the data,
but it messes up a lot of example code out there.
X Athens Barcelona Brussels Calais ...
1 Athens 0 3313 2963 3175
2 Barcelona 3313 0 1318 1326
3 Brussels 2963 1318 0 204
4 Calais 3175 1326 204 0
5 Cherbourg 3339 1294 583 460
6 Cologne 2762 1498 206 409
...
Best,
-Justin
What version of R, platform, loaded packages etc? This is not what I see on Linux, 2.9.1-patched r49104.
class(eurodist)
[1] "dist"
sessionInfo()
R version 2.9.1 Patched (2009-08-07 r49104) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8; LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C; LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.1 Have you tried this in a clean session to see if it persists there? If you can reproduce this in a clean session with an up-to-date R or R-Devel then send details of your R back to the list for further investigation. HTH G
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
1 day later
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1 day later
Justin, I suggest you try to remove your malformed eurodist and use the one in R. The svn logs show no changes in eurodist since 2005 when 'r' was added to 'Gibralta' (it still has all the wrong distances which perhaps go back to the poor quality of Cambridge Encyclopaedia). I also installed R 2.9.1 for MacOS to see that there neither is a change in 'eurodist' in the Mac distribution. My virgin eurodist in Mac was clean, with all its errors. All this hints that you have a local copy of malformed eurodist in your computer. Perhaps rm(eurodist) eurodist will help. Cheers, Jari Oksanen
On 15/08/09 06:13 AM, "Justin Donaldson" <jjdonald at indiana.edu> wrote:
Here's my osx data/session info (identical after a re-install):
class(eurodist)
[1] "data.frame"
sessionInfo()
R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base
-Justin On Thu, Aug 13, 2009 at 4:48 AM, Gavin Simpson <gavin.simpson at ucl.ac.uk>wrote:
On Wed, 2009-08-12 at 20:26 -0400, Justin Donaldson wrote:
The eurodist dataset (my favorite for mds) is malformed. Instead of a standard distance matrix, it's a data frame. The rownames have gotten 'bumped' to a new anonymous dimension "X". It's possible to fix the
data,
but it messes up a lot of example code out there.
X Athens Barcelona Brussels Calais ...
1 Athens 0 3313 2963 3175
2 Barcelona 3313 0 1318 1326
3 Brussels 2963 1318 0 204
4 Calais 3175 1326 204 0
5 Cherbourg 3339 1294 583 460
6 Cologne 2762 1498 206 409
...
Best,
-Justin
What version of R, platform, loaded packages etc? This is not what I see on Linux, 2.9.1-patched r49104.
class(eurodist)
[1] "dist"
sessionInfo()
R version 2.9.1 Patched (2009-08-07 r49104) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8; LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C; LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.1 Have you tried this in a clean session to see if it persists there? If you can reproduce this in a clean session with an up-to-date R or R-Devel then send details of your R back to the list for further investigation. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/<http://www.ucl.ac.uk/%7Eucfagls/> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%