[R] Odp: How to still processing despite bug errors?
Petr PIKAL
petr.pikal at precheza.cz
Tue Jan 18 11:21:21 CET 2011
Hi
Look at function ?try
Regards
Petr
r-help-bounces at r-project.org napsal dne 17.01.2011 21:57:42:
> Hi, everybody.
>
> I am working processing EEG data from 1000 pacients. I have a specific
> syntax to perform the Spectral Analysis and a loop to analyse all
subjects.
> each subject data are in separate folders (P1, P2 P3...)
>
> My question is: in some cases, some errors can appear in one subject. I
want
> to know if is possible to jump to the next subject and perform the same
> syntax , exibiting an error like:
>
> Working on P1
> Error "X" in P1
>
> Working on P2...
>
> The idea is to let the computer processing continuosly all the subjects
and
> at the end only see the problems in the subjects that R could not
perform
> the analysis.
> Each Subject takes 20 minutes to perform the analysis and I don't want
to
> stay days in front of PC, waiting for the next error in order to start
the
> syntax again with the next subject.
>
> Any ideas?
> Thanks in Advance.
>
> Altay Lino de Souza.
>
> On Mon, Jan 17, 2011 at 9:00 AM, <r-help-request at r-project.org> wrote:
>
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> >
> >
> > Today's Topics:
> >
> > 1. Re: Displaying ylab in mfrow (Peter Ehlers)
> > 2. Re: \examples{} in Rd file (Peter Ehlers)
> > 3. Re: data prep question (Bill.Venables at csiro.au)
> > 4. problem installing rgdal (alessandro.sarretta at inwind.it)
> > 5. rootogram for normal distributions (Hugo Mildenberger)
> > 6. Help in Coxme (Nelson Martins)
> > 7. Re: how to add a derived column to a data frame? (Petr Savicky)
> > 8. Re: \examples{} in Rd file (Prof Brian Ripley)
> > 9. Re: Time and xts (Gabor Grothendieck)
> > 10. Re: problem installing rgdal (Prof Brian Ripley)
> > 11. Hausman Test (Holger Steinmetz)
> > 12. Re: fgev_error_matrix_singular (Uwe Ligges)
> > 13. transform a df with a condition (Patrick Hausmann)
> > 14. Re: transform a df with a condition (Patrick Hausmann)
> > 15. Re: rootogram for normal distributions (Achim Zeileis)
> > 16. Re: Hausman Test (Achim Zeileis)
> > 17. Re: rootogram for normal distributions (Hadley Wickham)
> > 18. Re: transform a df with a condition (Henrique Dallazuanna)
> > 19. Re: Hausman Test (Holger Steinmetz)
> > 20. Re: transform a df with a condition (Duncan Murdoch)
> > 21. Re: rootogram for normal distributions (Achim Zeileis)
> > 22. Re: data prep question (Gabor Grothendieck)
> > 23. Re: Hausman Test (Arne Henningsen)
> > 24. Re: Hausman Test (Achim Zeileis)
> > 25. Re: Hausman Test (Achim Zeileis)
> > 26. Re: holding objects in dataframes (Uwe Ligges)
> > 27. Re: Hausman Test (Arne Henningsen)
> > 28. Re: Hausman Test (Holger Steinmetz)
> > 29. ODD ODD ODD stuff!! (Freddy Gamma)
> > 30. xyplot: modify axis tick marks (Kang Min)
> > 31. Getting Synonyms using wordnet (Nick)
> > 32. Re: ODD ODD ODD stuff!! (Sarah Goslee)
> > 33. Re: xyplot: modify axis tick marks (Dennis Murphy)
> > 34. Re: Random Effects Meta Regression (Viechtbauer Wolfgang (STAT))
> > 35. Re: ODD ODD ODD stuff!! (Jim Holtman)
> > 36. Re: data prep question (rstrothe)
> > 37. grid.table with head of two rows (victor)
> > 38. Re: xyplot: modify axis tick marks (Gabor Grothendieck)
> > 39. Re: data prep question (Hadley Wickham)
> > 40. Re: xyplot: modify axis tick marks (Dennis Murphy)
> > 41. Memory issues (Emmanuel Bellity)
> > 42. Re: xyplot: modify axis tick marks (Hugo Mildenberger)
> > 43. Please ask R questions on StackOverflow.com (Prasad Chalasani)
> > 44. Re: Help in Coxme (Nelson Martins)
> > 45. Re: rootogram for normal distributions (Hugo Mildenberger)
> > 46. a remove question (Erin Hodgess)
> > 47. Re: a remove question (David Winsemius)
> > 48. Re: a remove question (Joshua Wiley)
> > 49. Re: a remove question (David Winsemius)
> > 50. Re: a remove question (Hugo Mildenberger)
> > 51. Computing and Finding (ufuk beyaztas)
> > 52. WORK AREA TO SAVE (Barbara.Rogo at uniroma1.it)
> > 53. Re: WORK AREA TO SAVE (Duncan Murdoch)
> > 54. Re: a remove question (Pete Brecknock)
> > 55. Re: Memory issues (Chris Howden)
> > 56. Re: how to calculate the consistency of different clusterings
> > (Michael Bedward)
> > 57. Re: ODD ODD ODD stuff!! (Sarah Goslee)
> > 58. Re: rootogram for normal distributions (Deepayan Sarkar)
> > 59. effects packages for mixed model? (array chip)
> > 60. Using summaryBy with weighted data (Solomon Messing)
> > 61. Re: Using summaryBy with weighted data (Joshua Wiley)
> > 62. Equivalent to Stata egen tag (Denis Kazakevich)
> > 63. data frame column name change (eric)
> > 64. R looks for a folder not specified (l.chhay)
> > 65. Re: Selecting the first occurrence of a value after an
> > occurrence of a different value (surreyj)
> > 66. Re: data frame column name change (Jorge Ivan Velez)
> > 67. Re: R looks for a folder not specified (Jim Lemon)
> > 68. Re: Truetype and Opentype font in pdf device (Prof Brian Ripley)
> > 69. Finding NAs in DF (Johannes Graumann)
> > 70. Re: Finding NAs in DF (Ivan Calandra)
> > 71. Re: median by geometric mean (S Ellison)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 16 Jan 2011 03:40:40 -0800
> > From: Peter Ehlers <ehlers at ucalgary.ca>
> > To: Kumar Mainali <kpmainali at gmail.com>
> > Cc: "r-help at r-project.org" <r-help at r-project.org>
> > Subject: Re: [R] Displaying ylab in mfrow
> > Message-ID: <4D32D938.4080908 at ucalgary.ca>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > On 2011-01-15 18:54, Kumar Mainali wrote:
> > > Dear R users,
> > >
> > > I cannot display ylab with the following code while trying to stack
7
> > rows
> > > of 3 histograms each. Thanks in advance!
> > >
> > > par(mfrow=c(7,3))
> > > par(mar=c(2,2,2,2))
> > > par(oma=c(5,5,0,0))
> > >
> > > with (newdata<- subset(table, Month1 == "1"), hist(newdata$CarapWid,
> > > breaks=5*(0:80), col="gray80", main="All individuals", xlab="", xlim
> > > =c(15,85), ylab="April 2007"))
> >
> > Your code is neither reproducible nor minimal.
> > And it doesn't look as though it would produce
> > anything like what you seem to want.
> >
> > I suspect that you may wish to look at ?title
> > and in particular at the 'ylab' and 'outer'
> > arguments.
> >
> > Or you might consider using lattice or ggplot2.
> >
> > Peter Ehlers
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 16 Jan 2011 03:46:12 -0800
> > From: Peter Ehlers <ehlers at ucalgary.ca>
> > To: Adelchi Azzalini <azzalini at stat.unipd.it>
> > Cc: "r-help at r-project.org" <r-help at r-project.org>
> > Subject: Re: [R] \examples{} in Rd file
> > Message-ID: <4D32DA84.60002 at ucalgary.ca>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Adelchi,
> >
> > Since % is the LaTeX comment character, you may want to
> > try escaping it.
> >
> > Peter Ehlers
> >
> > On 2011-01-16 02:35, Adelchi Azzalini wrote:
> > > [Hope this is the right list where to send...]
> > >
> > > An attempt to update package 'mnormt' involves the addition of a
> > > small new function called 'pd.solve'. When I come to the package
> > > checking stage, an error occurs in parsing pd.solve.Rd.
> > > The full transcript of the outcome is copied below (it includes
details
> > > on my installation) but the critical point is where the \examples{}
> > > section includes a %*%. The relevant portion of the source file is
> > >
> > > \examples{
> > > x<- toeplitz(rev(1:4))
> > > x.inv<- pd.solve(x)
> > > print(x.inv %*% x)
> > > logDet<- attr(x.inv, "log.det")
> > > print(abs(logDet - determinant(x, logarithm=TRUE)$modulus))
> > > }
> > >
> > > which leads to the message
> > >
> > > ### ** Examples
> > > >
> > > > x<- toeplitz(rev(1:4))
> > > > x.inv<- pd.solve(x)
> > > > print(x.inv
> > > + logDet<- attr(x.inv, "log.det")
> > > Error: unexpected symbol in:
> > > " print(x.inv
> > > logDet"
> > >
> > > When I install the package, it works, except that the documentation
> > > portion looks like:
> > >
> > > Examples
> > > x<- toeplitz(rev(1:4))
> > > x.inv<- pd.solve(x)
> > > print(x.inv
> > > logDet<- attr(x.inv, "log.det")
> > > print(abs(logDet - determinant(x, logarithm=TRUE)$modulus))
> > >
> > > It seems that the examples are parsed as ordinary text, not R
commands.
> > > I am really puzzled. Any explanation?
> > >
> > > Adelchi Azzalini
> > >
> > [... snip ...]
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Sun, 16 Jan 2011 22:48:46 +1100
> > From: <Bill.Venables at csiro.au>
> > To: <rstrothe at gmail.com>, <r-help at r-project.org>
> > Subject: Re: [R] data prep question
> > Message-ID:
> > <
> > 1BDAE2969943D540934EE8B4EF68F95FB27A48C274 at EXNSW-MBX03.nexus.csiro.au>
> >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Here is one way
> >
> > Here is one way:
> >
> > > con <- textConnection("
> > + ID TIME OBS
> > + 001 2200 23
> > + 001 2400 11
> > + 001 3200 10
> > + 001 4500 22
> > + 003 3900 45
> > + 003 5605 32
> > + 005 1800 56
> > + 005 1900 34
> > + 005 2300 23")
> > > dat <- read.table(con, header = TRUE,
> > + colClasses = c("factor", "numeric", "numeric"))
> > > closeAllConnections()
> > >
> > > tmp <- lapply(split(dat, dat$ID),
> > + function(x) within(x, TIME <- TIME - min(TIME)))
> > > split(dat, dat$ID) <- tmp
> > > dat
> > ID TIME OBS
> > 1 001 0 23
> > 2 001 200 11
> > 3 001 1000 10
> > 4 001 2300 22
> > 5 003 0 45
> > 6 003 1705 32
> > 7 005 0 56
> > 8 005 100 34
> > 9 005 500 23
> > >
> >
> >
> > ________________________________________
> > From: r-help-bounces at r-project.org [r-help-bounces at r-project.org] On
> > Behalf Of Matthew Strother [rstrothe at gmail.com]
> > Sent: 16 January 2011 07:26
> > To: r-help at r-project.org
> > Subject: [R] data prep question
> >
> > I have a data set with several thousand observations across time,
grouped
> > by subject (example format below)
> >
> > ID TIME OBS
> > 001 2200 23
> > 001 2400 11
> > 001 3200 10
> > 001 4500 22
> > 003 3900 45
> > 003 5605 32
> > 005 1800 56
> > 005 1900 34
> > 005 2300 23
> > ...
> >
> > I would like to identify the first time for each subject, and then
subtract
> > this value from each subsequent time. However, the number of
observations
> > per subject varies widely (from 1 to 20), and the intervals between
times
> > varies widely. Is there a package that can help do this, or a loop
that
> > can be set up to evaluate ID, then calculate the values? The outcome
I
> > would like is presented below.
> > ID TIME OBS
> > 001 0 23
> > 001 200 11
> > 001 1000 10
> > 001 2300 22
> > 003 0 45
> > 003 1705 32
> > 005 0 56
> > 005 100 34
> > 005 500 23
> > ...
> >
> > Any help appreciated.
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Sun, 16 Jan 2011 11:28:13 +0100 (CET)
> > From: "alessandro.sarretta at inwind.it" <alessandro.sarretta at inwind.it>
> > To: r-help at r-project.org
> > Subject: [R] problem installing rgdal
> > Message-ID:
> > <23477963.3728391295173693963.JavaMail.defaultUser at defaultHost>
> > Content-Type: text/plain;charset="UTF-8"
> >
> > Dear R experts,
> > I'm trying to install rgdal in my R 2.11.1 (Ubuntu 10.10).
> > I have as an ouput the following messages. It seems that there are
problems
> > with libgdal1.7.0 or sqlite3...
> > Could someboby help me?
> > Thanks a lot!
> > Ale
> >
> > > install.packages()
> > Warning in install.packages() :
> > argument 'lib' is missing: using
'/home/ale/R/i686-pc-linux-gnu-library/2.
> > 11'
> > trying URL '
> > http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/RSQLite_0.9-4.
> > tar.gz'
> > Content type 'application/x-gzip' length 1298948 bytes (1.2 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.2 Mb
> >
> > * installing *source* package ?RSQLite? ...
> > checking for gcc... gcc -std=gnu99
> > checking for C compiler default output file name... a.out
> > checking whether the C compiler works... yes
> > checking whether we are cross compiling... no
> > checking for suffix of executables...
> > checking for suffix of object files... o
> > checking whether we are using the GNU C compiler... yes
> > checking whether gcc -std=gnu99 accepts -g... yes
> > checking for gcc -std=gnu99 option to accept ISO C89... none needed
> > checking how to run the C preprocessor... gcc -std=gnu99 -E
> > checking for gcc... (cached) gcc -std=gnu99
> > checking whether we are using the GNU C compiler... (cached) yes
> > checking whether gcc -std=gnu99 accepts -g... (cached) yes
> > checking for gcc -std=gnu99 option to accept ISO C89... (cached) none
> > needed
> > checking for library containing fdatasync... none required
> > configure: creating ./config.status
> > config.status: creating src/Makevars
> > ** libs
> > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
-DSQLITE_ENABLE_FTS3_PARENTHESIS
> > -
> > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-DBI.c -o
RS-DBI.o
> > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
-DSQLITE_ENABLE_FTS3_PARENTHESIS
> > -
> > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-SQLite.c -o
> > RS-SQLite.o
> > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
-DSQLITE_ENABLE_FTS3_PARENTHESIS
> > -
> > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c param_binding.c -o
> > param_binding.o
> > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
-DSQLITE_ENABLE_FTS3_PARENTHESIS
> > -
> > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c sqlite-all.c -o
> > sqlite-all.
> > o
> > sqlite-all.c:1: warning: extra tokens at end of #ifdef directive
> > mkdir -p ../inst/include
> > cp sqlite/sqlite3.h ../inst/include
> > cp sqlite/sqlite3ext.h ../inst/include
> > gcc -std=gnu99 -shared -o RSQLite.so RS-DBI.o RS-SQLite.o
param_binding.o
> > sqlite-all.o -L/usr/lib/R/lib -lR
> > installing to /home/ale/R/i686-pc-linux-gnu-library/2.11/RSQLite/libs
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices ...
> > ** testing if installed package can be loaded
> >
> > * DONE (RSQLite)
> >
> > The downloaded packages are in
> > ?/tmp/RtmprTwixW/downloaded_packages?
> > > install.packages()
> > Warning in install.packages() :
> > argument 'lib' is missing: using
'/home/ale/R/i686-pc-linux-gnu-library/2.
> > 11'
> > trying URL '
> > http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/rgdal_0.6-33.tar.
> > gz'
> > Content type 'application/x-gzip' length 1422992 bytes (1.4 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.4 Mb
> >
> > * installing *source* package ?rgdal? ...
> > gdal-config: gdal-config
> > checking for gcc... gcc -std=gnu99
> > checking for C compiler default output file name... a.out
> > checking whether the C compiler works... yes
> > checking whether we are cross compiling... no
> > checking for suffix of executables...
> > checking for suffix of object files... o
> > checking whether we are using the GNU C compiler... yes
> > checking whether gcc -std=gnu99 accepts -g... yes
> > checking for gcc -std=gnu99 option to accept ANSI C... none needed
> > checking how to run the C preprocessor... gcc -std=gnu99 -E
> > checking for egrep... grep -E
> > checking for ANSI C header files... yes
> > checking for sys/types.h... yes
> > checking for sys/stat.h... yes
> > checking for stdlib.h... yes
> > checking for string.h... yes
> > checking for memory.h... yes
> > checking for strings.h... yes
> > checking for inttypes.h... yes
> > checking for stdint.h... yes
> > checking for unistd.h... yes
> > checking proj_api.h usability... yes
> > checking proj_api.h presence... yes
> > checking for proj_api.h... yes
> > checking for pj_init_plus in -lproj... yes
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_double'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_text'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_double'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free_table'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_bytes'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_blob'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_last_insert_rowid'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_name'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_int'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_count'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_decltype'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_type'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
> > collect2: ld returned 1 exit status
> > ./configure: line 3065: ./proj_conf_test: No such file or directory
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_double'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_text'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_double'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free_table'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_bytes'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_blob'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_last_insert_rowid'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_name'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_int'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_count'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
> > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_decltype'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_type'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
> > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
> > collect2: ld returned 1 exit status
> > ./configure: line 3099: ./proj_conf_test: No such file or directory
> > Package CPP flags: -I/usr/include/gdal
> > Package LIBS: -L/usr/lib -lgdal1.7.0
> > configure: creating ./config.status
> > config.status: creating src/Makevars
> > ** libs
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c OGR_write.cpp -o
> > OGR_write.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c gdal-bindings.cpp -o
gdal-
> > bindings.o
> > gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-
> > pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c local_stubs.c
-o
> > local_stubs.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_geom.cpp -o
ogr_geom.o
> > gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-
> > pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c
ogr_polygons.c -o
> > ogr_polygons.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_proj.cpp -o
ogr_proj.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrdrivers.cpp -o
> > ogrdrivers.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrsource.cpp -o
> > ogrsource.o
> > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > gnu-library/2.11/sp/include" -fpic -g -O2 -c projectit.cpp -o
> > projectit.o
> > g++ -shared -o rgdal.so OGR_write.o gdal-bindings.o local_stubs.o
> > ogr_geom.o
> > ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
-L/usr/lib -
> > lgdal1.7.0 -lproj -L/usr/lib/R/lib -lR
> > installing to /home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal/libs
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices ...
> > ** testing if installed package can be loaded
> > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> > unable to load shared library
'/home/ale/R/i686-pc-linux-gnu-library/2.
> > 11/rgdal/libs/rgdal.so':
> > /usr/lib/libgdal1.7.0.so.1: undefined symbol: sqlite3_bind_int
> > ERROR: loading failed
> > * removing ?/home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal?
> >
> > The downloaded packages are in
> > ?/tmp/RtmprTwixW/downloaded_packages?
> > Warning message:
> > In install.packages() :
> > installation of package 'rgdal' had non-zero exit status
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Sun, 16 Jan 2011 11:45:27 +0100
> > From: Hugo Mildenberger <Hugo.Mildenberger at web.de>
> > To: r-help at r-project.org
> > Subject: [R] rootogram for normal distributions
> > Message-ID: <201101161145.28281.Hugo.Mildenberger at web.de>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Using R-2.12.1 and latticeExtra-0.6-14, I would like to understand
> > why a rootogram displaying samples from the Poisson distribution looks
like
> > I
> > expected it, whereas a rootogram using the normal distribution does
not:
> >
> > library(latticeExtra)
> > rootogram(~rpois(1000, lambda = 50), dfun = function(x) dpois(x,
lambda =
> > 50))
> >
> > rootogram(~rnorm(1000), dfun = function(x) dnorm(x,mean(x),sd(x)))
> >
> > I probably can't attach figures here. Thus a textual description of
what I
> > get may
> > suffice: With increasing sample size, the rootogram using random
samples
> > from the Poisson distribution shows decreasing differences (bars are
> > quickly
> > approaching the zero line), whereas the displayed differences for
random
> > samples of the normal distribution are always large. The differences
even
> > increase
> > with sample size, i.e, the hanging bars tend to vanish for very large
> > samples.
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Sun, 16 Jan 2011 10:07:30 +0000
> > From: Nelson Martins <nelson.e.v.martins at gmail.com>
> > To: r-help at r-project.org
> > Subject: [R] Help in Coxme
> > Message-ID:
> > <AANLkTimQCz9bOm-b5XhgvKSDh7_cz71dVqiRf1mkMT-Z at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > I am a relative newbie to survival analysis and R in general, but
> > would like to use the coxme package to analyse some data I currently
> > have.
> > The data is relative to survival times of drosophila melanogaster
> > populations to infection with pathogens, and has the variables:
> > Time,
> > Status,
> > Treatment (4 treatments + 2 controls)
> > Population
> > Replicate
> > ?and I'm currently using the following call
> > mixed<- coxme(formula = Surv(Time, Status) ~ strata(Treatment) + (1 |
> > Population/Replicate),x=T,y=T)
> >
> > The treatments have very different mortality profiles, that's why I'm
> > using stratification.
> > I have several problems:
> > 1 - I'm able to get the results, and to compare the different
treatments
> > using glht (e.g. - glht(mixed,mcp(Treatment="Tukey"))), only if I
> > don't stratify the treatments
> > 2 - I'm ?unable to plot the results as in other cox models (cph,coxph)
> > using survplot/survfit. The other models don't allow specifying random
> > variables (Populations and Replicates), which is of great importance
> > to me.
> > 3 - One other problem I'm having is in plotting the hazard curves
> > (i.e. the instantaneous risk at each day). Is it possible to do it
> > using
> > these functions, hopefully with the associated standard errors?
> >
> > Thank you for your time and help
> >
> > Best regards
> > Nelson Martins
> >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Sun, 16 Jan 2011 10:59:27 +0100
> > From: Petr Savicky <savicky at praha1.ff.cuni.cz>
> > To: r-help at r-project.org
> > Subject: Re: [R] how to add a derived column to a data frame?
> > Message-ID: <20110116095927.GA6767 at praha1.ff.cuni.cz>
> > Content-Type: text/plain; charset=us-ascii
> >
> > On Sun, Jan 16, 2011 at 03:01:49PM +0800, r-help wrote:
> > > I have a data frame with 10 columns: A:J and I want to have the
output as
> > a data frame with 11 columns, the value of 11th column is??
> > >
> > >
> > > for each row, if any column can be divided by 13, then the 11th
column
> > has a values of 1, otherwise, it has a value of 0. How to do that?
> > >
> > >
> > > input is
> > >
> > > a=matrix(1:10000,1000,10)
> > >
> > > dimnames(a)=list(NULL,LETTERS[1:10])
> >
> > I am sorry for an error in the previous solution for a general
> > matrix. It should be, for example
> >
> > x <- as.numeric(rowSums(a %% 13 == 0) != 0)
> > b <- cbind(a, x)
> >
> > or
> >
> > x <- (rowSums(a %% 13 == 0) != 0) + 0
> >
> > Petr Savicky.
> >
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Sun, 16 Jan 2011 12:51:00 +0000 (GMT)
> > From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> > To: Peter Ehlers <ehlers at ucalgary.ca>
> > Cc: "r-help at r-project.org" <r-help at r-project.org>
> > Subject: Re: [R] \examples{} in Rd file
> > Message-ID:
> > <alpine.LFD.2.00.1101161246530.10278 at gannet.stats.ox.ac.uk>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > On Sun, 16 Jan 2011, Peter Ehlers wrote:
> >
> > > Adelchi,
> > >
> > > Since % is the LaTeX comment character, you may want to
> > > try escaping it.
> >
> > As package 'base' does at
> > https://svn.r-project.org/R/trunk/src/library/base/man/matmult.Rd
> >
> > > Peter Ehlers
> > >
> > > On 2011-01-16 02:35, Adelchi Azzalini wrote:
> > >> [Hope this is the right list where to send...]
> >
> > Either R-devel or this -- I would probably send questions about
> > preparing packages to R-devel as you are more likely to catch the
> > attention of active developers there.
> >
> > >> An attempt to update package 'mnormt' involves the addition of a
> > >> small new function called 'pd.solve'. When I come to the package
> > >> checking stage, an error occurs in parsing pd.solve.Rd.
> > >> The full transcript of the outcome is copied below (it includes
details
> > >> on my installation) but the critical point is where the \examples{}
> > >> section includes a %*%. The relevant portion of the source file is
> > >>
> > >> \examples{
> > >> x<- toeplitz(rev(1:4))
> > >> x.inv<- pd.solve(x)
> > >> print(x.inv %*% x)
> > >> logDet<- attr(x.inv, "log.det")
> > >> print(abs(logDet - determinant(x, logarithm=TRUE)$modulus))
> > >> }
> > >>
> > >> which leads to the message
> > >>
> > >> ### ** Examples
> > >> >
> > >> > x<- toeplitz(rev(1:4))
> > >> > x.inv<- pd.solve(x)
> > >> > print(x.inv
> > >> + logDet<- attr(x.inv, "log.det")
> > >> Error: unexpected symbol in:
> > >> " print(x.inv
> > >> logDet"
> > >>
> > >> When I install the package, it works, except that the documentation
> > >> portion looks like:
> > >>
> > >> Examples
> > >> x<- toeplitz(rev(1:4))
> > >> x.inv<- pd.solve(x)
> > >> print(x.inv
> > >> logDet<- attr(x.inv, "log.det")
> > >> print(abs(logDet - determinant(x, logarithm=TRUE)$modulus))
> > >>
> > >> It seems that the examples are parsed as ordinary text, not R
commands.
> > >> I am really puzzled. Any explanation?
> > >>
> > >> Adelchi Azzalini
> > >>
> > > [... snip ...]
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> > --
> > Brian D. Ripley, ripley at stats.ox.ac.uk
> > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> > University of Oxford, Tel: +44 1865 272861 (self)
> > 1 South Parks Road, +44 1865 272866 (PA)
> > Oxford OX1 3TG, UK Fax: +44 1865 272595
> >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Sun, 16 Jan 2011 08:03:53 -0500
> > From: Gabor Grothendieck <ggrothendieck at gmail.com>
> > To: rnick <nikos.rachmanis at gmail.com>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Time and xts
> > Message-ID:
> > <AANLkTikAdjJ0pXVL-qcZMCWHqx5n3Q-Fs-JRj6MptgVJ at mail.gmail.com>
> > Content-Type: text/plain; charset=windows-1252
> >
> > On Sat, Jan 15, 2011 at 11:20 PM, rnick <nikos.rachmanis at gmail.com>
wrote:
> > >
> > > Hi all,
> > > I have run into a problem and some help would be highly appreciated.
> > > I have a .csv with the following columns:
> > > Date ? ?Time ? ?Open ? ?High ? ?Low ? ? Close
> > > 1/2/2005 ? ? ? ?17:05 ? 1.3546 ?1.3553 ?1.3546 ?1.35495
> > > 1/2/2005 ? ? ? ?17:10 ? 1.3553 ?1.3556 ?1.3549 ?1.35525
> > > 1/2/2005 ? ? ? ?17:15 ? 1.3556 ?1.35565 1.35515 1.3553
> > > 1/2/2005 ? ? ? ?17:25 ? 1.355 ? ? ? ? ? 1.3556 ?1.355 ? ? ? ? ?
1.3555
> > > ?.
> > > ?..
> > > 2/13/2006 ? ? ? 5:20 ? ?1.18895 1.18925 1.18835 1.1885
> > >
> > > 1) ? ? ?Without using zoo, xts or any other time series object, I am
> > trying to
> > > run this code but fails to pass the argument to the function
> > >
> > > #n is the length of the series
> > >
> > > for (t in seq(from=10,to=n,by=1))
> > > {
> > > ? ? ? ?while (time[t]=='02:00:00')
> > > ? ? ? ?{
> > > ? ? ? ? ? ? ? ?entrytrade(t)
> > > ? ? ? ?}
> > > }
> > > Is this possible to do? If yes, any ideas what I am doing wrong?
> >
> > Posted code needs to be self contained and reproducible so that others
> > can copy it from your post, paste it into R and see the same problem
> > you are seeing. See last line to every r-help message.
> >
> > >
> > > 2) ? ? ?I have also tried with xts by creating the object like this
> > > lines<-data.frame(date,time,open,high,low,close)
> > > z <- read.zoo(lines, header = TRUE, index = list(1, 2), FUN =
> > function(d,t)
> > > as.POSIXct(paste(date,time), format = "%m/%d/%Y %H:%M"))
> > > x<-as.xts(z)
> > >
> > > However, I am unable to call just the time and run the above for
loop.
> > any
> > > ideas here?
> >
> > If by "calling" the time is intended to refer to "extracting" the time
> > then time(x) gives a vector of times.
> >
> > --
> > Statistics & Software Consulting
> > GKX Group, GKX Associates Inc.
> > tel: 1-877-GKX-GROUP
> > email: ggrothendieck at gmail.com
> >
> >
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Sun, 16 Jan 2011 13:08:17 +0000 (GMT)
> > From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> > To: "alessandro.sarretta at inwind.it" <alessandro.sarretta at inwind.it>
> > Cc: r-help at r-project.org, Roger Bivand <Roger.Bivand at nhh.no>
> > Subject: Re: [R] problem installing rgdal
> > Message-ID:
> > <alpine.LFD.2.00.1101161251370.10278 at gannet.stats.ox.ac.uk>
> > Content-Type: text/plain; charset="utf-8"; Format="flowed"
> >
> > On Sun, 16 Jan 2011, alessandro.sarretta at inwind.it wrote:
> >
> > > Dear R experts,
> > > I'm trying to install rgdal in my R 2.11.1 (Ubuntu 10.10).
> > > I have as an ouput the following messages. It seems that there are
> > problems
> > > with libgdal1.7.0 or sqlite3...
> > > Could someboby help me?
> >
> > You would do better to ask on R-sig-geo for this particular package,
> > and ask the maintainer or on R-devel more generally about installing
> > source packages (see the posting guide). But
> >
> > - Your R is need of updating (see the posting guide)
> > - GDAL 1.7.0 is really rather old
> > - The bug seems to be in your libgdal installation: if libgdal was
> > compiled with sqlite support, libgdal.so should be linked to
> > libsqlite3. Do you have sqlite3 installed (not the RSQLite package,
> > but the uduntu package)? If not, please install it. You can check
> > for missing dependencies by (in the terminal)
> >
> > ldd /usr/lib/libgdal.so
> >
> > If 'libsqlite3.so.0' is not there, you need to modify rgdal (I know,
> > because you need to do similar things with a static libgdal). On my
> > Mac I need to alter rgdal/src/Makevars.in to be
> >
> > PKG_LIBS=@PKG_LIBS@ -lproj -lsqlite3 -lexpat -ltiff -ljpeg -lpng -lz
-ldl
> > -lcurl -lssl -lcrypto -lz
> >
> > and so I guess you need at least
> >
> > PKG_LIBS=@PKG_LIBS@ -lsqlite3
> >
> > But because GDAL can be installed with lots of optional facilities
> > (one of which is sqlite3), you may need to ask Ubuntu support for
> > exactly what is needed to link against their build. Or compile
> > current GDAL from the sources for yourself.
> >
> >
> > > Thanks a lot!
> > > Ale
> > >
> > >> install.packages()
> > > Warning in install.packages() :
> > > argument 'lib' is missing: using
> > '/home/ale/R/i686-pc-linux-gnu-library/2.
> > > 11'
> > > trying URL '
> > http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/RSQLite_0.9-4.
> > > tar.gz'
> > > Content type 'application/x-gzip' length 1298948 bytes (1.2 Mb)
> > > opened URL
> > > ==================================================
> > > downloaded 1.2 Mb
> > >
> > > * installing *source* package ?RSQLite? ...
> > > checking for gcc... gcc -std=gnu99
> > > checking for C compiler default output file name... a.out
> > > checking whether the C compiler works... yes
> > > checking whether we are cross compiling... no
> > > checking for suffix of executables...
> > > checking for suffix of object files... o
> > > checking whether we are using the GNU C compiler... yes
> > > checking whether gcc -std=gnu99 accepts -g... yes
> > > checking for gcc -std=gnu99 option to accept ISO C89... none needed
> > > checking how to run the C preprocessor... gcc -std=gnu99 -E
> > > checking for gcc... (cached) gcc -std=gnu99
> > > checking whether we are using the GNU C compiler... (cached) yes
> > > checking whether gcc -std=gnu99 accepts -g... (cached) yes
> > > checking for gcc -std=gnu99 option to accept ISO C89... (cached)
none
> > needed
> > > checking for library containing fdatasync... none required
> > > configure: creating ./config.status
> > > config.status: creating src/Makevars
> > > ** libs
> > > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
> > -DSQLITE_ENABLE_FTS3_PARENTHESIS -
> > > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-DBI.c -o
RS-DBI.o
> > > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
> > -DSQLITE_ENABLE_FTS3_PARENTHESIS -
> > > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-SQLite.c -o
> > RS-SQLite.o
> > > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
> > -DSQLITE_ENABLE_FTS3_PARENTHESIS -
> > > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c param_binding.c
-o
> > > param_binding.o
> > > gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
> > > DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3
> > -DSQLITE_ENABLE_FTS3_PARENTHESIS -
> > > DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c sqlite-all.c -o
> > sqlite-all.
> > > o
> > > sqlite-all.c:1: warning: extra tokens at end of #ifdef directive
> > > mkdir -p ../inst/include
> > > cp sqlite/sqlite3.h ../inst/include
> > > cp sqlite/sqlite3ext.h ../inst/include
> > > gcc -std=gnu99 -shared -o RSQLite.so RS-DBI.o RS-SQLite.o
param_binding.o
> > > sqlite-all.o -L/usr/lib/R/lib -lR
> > > installing to
/home/ale/R/i686-pc-linux-gnu-library/2.11/RSQLite/libs
> > > ** R
> > > ** inst
> > > ** preparing package for lazy loading
> > > ** help
> > > *** installing help indices
> > > ** building package indices ...
> > > ** testing if installed package can be loaded
> > >
> > > * DONE (RSQLite)
> > >
> > > The downloaded packages are in
> > > ?/tmp/RtmprTwixW/downloaded_packages?
> > >> install.packages()
> > > Warning in install.packages() :
> > > argument 'lib' is missing: using
> > '/home/ale/R/i686-pc-linux-gnu-library/2.
> > > 11'
> > > trying URL '
> > http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/rgdal_0.6-33.tar.
> > > gz'
> > > Content type 'application/x-gzip' length 1422992 bytes (1.4 Mb)
> > > opened URL
> > > ==================================================
> > > downloaded 1.4 Mb
> > >
> > > * installing *source* package ?rgdal? ...
> > > gdal-config: gdal-config
> > > checking for gcc... gcc -std=gnu99
> > > checking for C compiler default output file name... a.out
> > > checking whether the C compiler works... yes
> > > checking whether we are cross compiling... no
> > > checking for suffix of executables...
> > > checking for suffix of object files... o
> > > checking whether we are using the GNU C compiler... yes
> > > checking whether gcc -std=gnu99 accepts -g... yes
> > > checking for gcc -std=gnu99 option to accept ANSI C... none needed
> > > checking how to run the C preprocessor... gcc -std=gnu99 -E
> > > checking for egrep... grep -E
> > > checking for ANSI C header files... yes
> > > checking for sys/types.h... yes
> > > checking for sys/stat.h... yes
> > > checking for stdlib.h... yes
> > > checking for string.h... yes
> > > checking for memory.h... yes
> > > checking for strings.h... yes
> > > checking for inttypes.h... yes
> > > checking for stdint.h... yes
> > > checking for unistd.h... yes
> > > checking proj_api.h usability... yes
> > > checking proj_api.h presence... yes
> > > checking for proj_api.h... yes
> > > checking for pj_init_plus in -lproj... yes
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_double'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_text'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_bind_double'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_free_table'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_bytes'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_blob'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_last_insert_rowid'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_name'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_int'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_count'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_column_decltype'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_type'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
> > > collect2: ld returned 1 exit status
> > > ./configure: line 3065: ./proj_conf_test: No such file or directory
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_double'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_text'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_bind_double'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_free_table'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_bytes'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_blob'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_last_insert_rowid'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_name'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_int'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_count'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
> > `sqlite3_column_decltype'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to
`sqlite3_column_type'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
> > > /usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
> > > collect2: ld returned 1 exit status
> > > ./configure: line 3099: ./proj_conf_test: No such file or directory
> > > Package CPP flags: -I/usr/include/gdal
> > > Package LIBS: -L/usr/lib -lgdal1.7.0
> > > configure: creating ./config.status
> > > config.status: creating src/Makevars
> > > ** libs
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c OGR_write.cpp -o
> > OGR_write.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c gdal-bindings.cpp -o
> > gdal-
> > > bindings.o
> > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-
> > > pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c
local_stubs.c -o
> > > local_stubs.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_geom.cpp -o
> > ogr_geom.o
> > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-
> > > pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c
ogr_polygons.c
> > -o
> > > ogr_polygons.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_proj.cpp -o
> > ogr_proj.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrdrivers.cpp -o
> > ogrdrivers.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrsource.cpp -o
> > ogrsource.o
> > > g++ -I/usr/share/R/include -I/usr/include/gdal
> > -I"/home/ale/R/i686-pc-linux-
> > > gnu-library/2.11/sp/include" -fpic -g -O2 -c projectit.cpp -o
> > projectit.o
> > > g++ -shared -o rgdal.so OGR_write.o gdal-bindings.o local_stubs.o
> > ogr_geom.o
> > > ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
-L/usr/lib
> > -
> > > lgdal1.7.0 -lproj -L/usr/lib/R/lib -lR
> > > installing to /home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal/libs
> > > ** R
> > > ** inst
> > > ** preparing package for lazy loading
> > > ** help
> > > *** installing help indices
> > > ** building package indices ...
> > > ** testing if installed package can be loaded
> > > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> > > unable to load shared library
'/home/ale/R/i686-pc-linux-gnu-library/2.
> > > 11/rgdal/libs/rgdal.so':
> > > /usr/lib/libgdal1.7.0.so.1: undefined symbol: sqlite3_bind_int
> > > ERROR: loading failed
> > > * removing ?/home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal?
> > >
> > > The downloaded packages are in
> > > ?/tmp/RtmprTwixW/downloaded_packages?
> > > Warning message:
> > > In install.packages() :
> > > installation of package 'rgdal' had non-zero exit status
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> > --
> > Brian D. Ripley, ripley at stats.ox.ac.uk
> > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> > University of Oxford, Tel: +44 1865 272861 (self)
> > 1 South Parks Road, +44 1865 272866 (PA)
> > Oxford OX1 3TG, UK Fax: +44 1865 272595
> >
> > ------------------------------
> >
> > Message: 11
> > Date: Sun, 16 Jan 2011 06:07:08 -0800 (PST)
> > From: Holger Steinmetz <Holger.steinmetz at web.de>
> > To: r-help at r-project.org
> > Subject: [R] Hausman Test
> > Message-ID: <1295186828415-3220016.post at n4.nabble.com>
> > Content-Type: text/plain; charset=us-ascii
> >
> >
> > Hi,
> >
> > can anybody tell me how the Hausman test for endogenty works?
> >
> > I have a simulated model with three correlated predictors (X1-X3). I
also
> > have an instrument W for X1
> >
> > Now I want to test for endogeneity of X1 (i.e., when I omit X2 and X3
from
> > the equation).
> >
> > My current approach:
> >
> > library(systemfit)
> >
> > fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> > print(hausman.systemfit(fitOLS, fit2sls))
> >
> > This seems to work fine. However, when I include X2 as a furter
predictor,
> > the 2sls-estimation doesn't work.
> >
> > Thanks in advance
> > Holger
> >
> > --
> > View this message in context:
> > http://r.789695.n4.nabble.com/Hausman-Test-tp3220016p3220016.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> >
> >
> > ------------------------------
> >
> > Message: 12
> > Date: Sun, 16 Jan 2011 15:10:41 +0100
> > From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
> > To: Jinrui Xu <jinruixu at umich.edu>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] fgev_error_matrix_singular
> > Message-ID: <4D32FC61.5070606 at statistik.tu-dortmund.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > See ?try in order to get the automated process going and for ignoring
or
> > separately post-processing stuff where the method does not work.
> >
> > Uwe Ligges
> >
> >
> > On 15.01.2011 21:48, Jinrui Xu wrote:
> > >
> > > Hello everyone,
> > >
> > > I am using fgev from evd package to fitting my data with general
extreme
> > > value distribution. The command I used is simple: y <- fgev(x).
> > > The error is "observed information matrix is singular;" How can I
solve
> > > these problem. I tried all methods in optim and it did not work. I
fixed
> > > values for scale, location and shape. This works, but I have lots of
> > > different dataset to fit, so is there any automatic ways to solve
the
> > > error? Thanks!
> > >
> > > jinrui,
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > ------------------------------
> >
> > Message: 13
> > Date: Sun, 16 Jan 2011 15:13:19 +0100
> > From: Patrick Hausmann <patrick.hausmann at uni-bremen.de>
> > To: r-help at r-project.org
> > Subject: [R] transform a df with a condition
> > Message-ID: <4D32FCFF.7010002 at uni-bremen.de>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > Dear all,
> >
> > for each A == 3 in 'df' I would like to change the variables B and K.
> > My result should be the whole df and not the subset (A==3)...
> >
> > df <- data.frame(A = c(1,1,3,2,2,3,3),
> > B = c(2,1,1,2,7,8,7),
> > K = c("a.1", "d.2", "f.3",
> > "a.1", "k.4", "f.9", "f.5"))
> >
> > x1 <- within(df[df$A ==3, ], {
> > B1 <- 5
> > K1 <- gsub("f","m", K)
> > })
> >
> > x2 <- transform(df[df$A==3, ], B1 = 5, K1 = gsub("f","m", K))
> >
> > Thanks for any help!
> > Patrick
> >
> >
> >
> > ------------------------------
> >
> > Message: 14
> > Date: Sun, 16 Jan 2011 15:19:01 +0100
> > From: Patrick Hausmann <patrick.hausmann at uni-bremen.de>
> > To: r-help at r-project.org
> > Subject: Re: [R] transform a df with a condition
> > Message-ID: <4D32FE55.3040204 at uni-bremen.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Arrg, sorry - of course I don't want *new* variables. So this is my
> > correct example:
> >
> > df <- data.frame(A = c(1,1,3,2,2,3,3),
> > B = c(2,1,1,2,7,8,7),
> > K = c("a.1", "d.2", "f.3",
> > "a.1", "k.4", "f.9", "f.5"))
> >
> > x1 <- within(df[df$A ==3, ], {
> > B <- 5
> > K <- gsub("f","m", K)
> > })
> >
> > x2 <- transform(df[df$A==3, ], B = 5, K = gsub("f","m", K))
> >
> > Thanks
> > Patrick
> >
> > Am 16.01.2011 15:13, schrieb Patrick Hausmann:
> > > Dear all,
> > >
> > > for each A == 3 in 'df' I would like to change the variables B and
K.
> > > My result should be the whole df and not the subset (A==3)...
> > >
> > > df <- data.frame(A = c(1,1,3,2,2,3,3),
> > > B = c(2,1,1,2,7,8,7),
> > > K = c("a.1", "d.2", "f.3",
> > > "a.1", "k.4", "f.9", "f.5"))
> > >
> > > x1 <- within(df[df$A ==3, ], {
> > > B1 <- 5
> > > K1 <- gsub("f","m", K)
> > > })
> > >
> > > x2 <- transform(df[df$A==3, ], B1 = 5, K1 = gsub("f","m", K))
> > >
> > > Thanks for any help!
> > > Patrick
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > ------------------------------
> >
> > Message: 15
> > Date: Sun, 16 Jan 2011 15:28:58 +0100 (CET)
> > From: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > To: Hugo Mildenberger <Hugo.Mildenberger at web.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] rootogram for normal distributions
> > Message-ID: <alpine.DEB.2.00.1101161526120.22514 at paninaro.uibk.ac.at>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > On Sun, 16 Jan 2011, Hugo Mildenberger wrote:
> >
> > > Using R-2.12.1 and latticeExtra-0.6-14, I would like to understand
> > > why a rootogram displaying samples from the Poisson distribution
looks
> > like I
> > > expected it, whereas a rootogram using the normal distribution does
not:
> > >
> > > library(latticeExtra)
> > > rootogram(~rpois(1000, lambda = 50), dfun = function(x) dpois(x,
lambda =
> > 50))
> > >
> > > rootogram(~rnorm(1000), dfun = function(x) dnorm(x,mean(x),sd(x)))
> > >
> > > I probably can't attach figures here. Thus a textual description of
what
> > > I get may suffice: With increasing sample size, the rootogram using
> > > random samples from the Poisson distribution shows decreasing
> > > differences (bars are quickly approaching the zero line), whereas
the
> > > displayed differences for random samples of the normal distribution
are
> > > always large. The differences even increase with sample size, i.e,
the
> > > hanging bars tend to vanish for very large samples.
> >
> > The normal distribution is a continuous distribution, i.e., the
frequency
> > for each observed value will essentially be 1/n and not converge to
the
> > density function. Hence, you would need to look at histogram or
smoothed
> > densities. Rootograms, on the other hand, are intended for discrete
> > distributions.
> > Z
> >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > ------------------------------
> >
> > Message: 16
> > Date: Sun, 16 Jan 2011 15:39:16 +0100 (CET)
> > From: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > To: Holger Steinmetz <Holger.steinmetz at web.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Hausman Test
> > Message-ID: <alpine.DEB.2.00.1101161534270.22514 at paninaro.uibk.ac.at>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > On Sun, 16 Jan 2011, Holger Steinmetz wrote:
> >
> > >
> > > Hi,
> > >
> > > can anybody tell me how the Hausman test for endogenty works?
> > >
> > > I have a simulated model with three correlated predictors (X1-X3). I
also
> > > have an instrument W for X1
> > >
> > > Now I want to test for endogeneity of X1 (i.e., when I omit X2 and
X3
> > from
> > > the equation).
> > >
> > > My current approach:
> > >
> > > library(systemfit)
> > >
> > > fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > > fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> > > print(hausman.systemfit(fitOLS, fit2sls))
> > >
> > > This seems to work fine. However, when I include X2 as a furter
> > predictor,
> > > the 2sls-estimation doesn't work.
> >
> > When you don't need any instruments for X2, then you should employ
> >
> > Y ~ X1 + X2, inst = ~ W + X2
> >
> > Then, regressor X2 is unaltered in the second stage of the regression
> > (after projection onto the instruments).
> >
> > hth,
> > Z
> >
> > > Thanks in advance
> > > Holger
> > >
> > > --
> > > View this message in context:
> > http://r.789695.n4.nabble.com/Hausman-Test-tp3220016p3220016.html
> > > Sent from the R help mailing list archive at Nabble.com.
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > ------------------------------
> >
> > Message: 17
> > Date: Sun, 16 Jan 2011 08:44:14 -0600
> > From: Hadley Wickham <hadley at rice.edu>
> > To: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] rootogram for normal distributions
> > Message-ID:
> > <AANLkTik6qAwA+131E4gt-==iSe0Pw=dhvbusMKB71ct7 at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > > The normal distribution is a continuous distribution, i.e., the
frequency
> > > for each observed value will essentially be 1/n and not converge to
the
> > > density function. Hence, you would need to look at histogram or
smoothed
> > > densities. Rootograms, on the other hand, are intended for discrete
> > > distributions.
> >
> > I don't think that's true - rootograms are useful for both continuous
> > and discrete distributions. See (e.g.) p 314 at
> > http://www.edwardtufte.com/tufte/tukey, where Tukey himself uses a
> > rootogram with a normal distribution.
> >
> > Hadley
> >
> > --
> > Assistant Professor / Dobelman Family Junior Chair
> > Department of Statistics / Rice University
> > http://had.co.nz/
> >
> >
> >
> > ------------------------------
> >
> > Message: 18
> > Date: Sun, 16 Jan 2011 12:52:31 -0200
> > From: Henrique Dallazuanna <wwwhsd at gmail.com>
> > To: Patrick Hausmann <patrick.hausmann at uni-bremen.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] transform a df with a condition
> > Message-ID:
> > <AANLkTinfkPn_vYTdCdL-3-7=VRjF3Y-z5moFJWCC-MoO at mail.gmail.com>
> > Content-Type: text/plain
> >
> > Try this:
> >
> > df[df$A == 3, c('B', 'K')] <- with(df[df$A == 3, c('B', 'K')],
cbind(5,
> > gsub("f", "m", K)))
> >
> > On Sun, Jan 16, 2011 at 12:19 PM, Patrick Hausmann <
> > patrick.hausmann at uni-bremen.de> wrote:
> >
> > > Arrg, sorry - of course I don't want *new* variables. So this is my
> > correct
> > > example:
> > >
> > >
> > > df <- data.frame(A = c(1,1,3,2,2,3,3),
> > > B = c(2,1,1,2,7,8,7),
> > > K = c("a.1", "d.2", "f.3",
> > > "a.1", "k.4", "f.9", "f.5"))
> > >
> > > x1 <- within(df[df$A ==3, ], {
> > > B <- 5
> > >
> > > K <- gsub("f","m", K)
> > > })
> > >
> > > x2 <- transform(df[df$A==3, ], B = 5, K = gsub("f","m", K))
> > >
> > > Thanks
> > > Patrick
> > >
> > > Am 16.01.2011 15:13, schrieb Patrick Hausmann:
> > >
> > > Dear all,
> > >>
> > >> for each A == 3 in 'df' I would like to change the variables B and
K.
> > >> My result should be the whole df and not the subset (A==3)...
> > >>
> > >> df <- data.frame(A = c(1,1,3,2,2,3,3),
> > >> B = c(2,1,1,2,7,8,7),
> > >> K = c("a.1", "d.2", "f.3",
> > >> "a.1", "k.4", "f.9", "f.5"))
> > >>
> > >> x1 <- within(df[df$A ==3, ], {
> > >> B1 <- 5
> > >> K1 <- gsub("f","m", K)
> > >> })
> > >>
> > >> x2 <- transform(df[df$A==3, ], B1 = 5, K1 = gsub("f","m", K))
> > >>
> > >> Thanks for any help!
> > >> Patrick
> > >>
> > >> ______________________________________________
> > >> R-help at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > >> PLEASE do read the posting guide
> > >> http://www.R-project.org/posting-guide.html
> > >> and provide commented, minimal, self-contained, reproducible code.
> > >>
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > --
> > Henrique Dallazuanna
> > Curitiba-Paraná-Brasil
> > 25° 25' 40" S 49° 16' 22" O
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> > ------------------------------
> >
> > Message: 19
> > Date: Sun, 16 Jan 2011 06:53:17 -0800 (PST)
> > From: Holger Steinmetz <Holger.steinmetz at web.de>
> > To: r-help at r-project.org
> > Subject: Re: [R] Hausman Test
> > Message-ID: <1295189597126-3220065.post at n4.nabble.com>
> > Content-Type: text/plain; charset=us-ascii
> >
> >
> > Dear Achim,
> >
> > thank you very much.
> >
> > One follow up question. The Hausman-test always gives me a p-value of
1 -
> > no
> > matter
> > how small the statistic is.
> >
> > I now generated orthogonal regressors (X1-X3) and the test gives me
> >
> >
> > Hausman specification test for consistency of the 3SLS
estimation
> >
> > data: data
> > Hausman = -0.0138, df = 2, p-value = 1
> >
> > What is confusing to me is the "3SLS". I am just beginning to learn
about
> > instrumental variables (I am a psychologist ;) Perhaps that's a
problem?
> >
> > As a background, here's the complete simulation:
> >
> > W = rnorm(1000)
> > X2 = rnorm(1000)
> > X3 = rnorm(1000)
> > X1 = .5*W + rnorm(1000)
> > Y = .4*X1 + .5*X2 + .6*X3 + rnorm(1000)
> > data = as.data.frame(cbind(X1,X2,X3,Y,W))
> >
> > fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> >
> > print(hausman.systemfit(fitOLS, fit2sls))
> >
> > Best,
> > Holger
> > --
> > View this message in context:
> > http://r.789695.n4.nabble.com/Hausman-Test-tp3220016p3220065.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> >
> >
> > ------------------------------
> >
> > Message: 20
> > Date: Sun, 16 Jan 2011 09:53:54 -0500
> > From: Duncan Murdoch <murdoch.duncan at gmail.com>
> > To: Patrick Hausmann <patrick.hausmann at uni-bremen.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] transform a df with a condition
> > Message-ID: <4D330682.8000906 at gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > On 16/01/2011 9:13 AM, Patrick Hausmann wrote:
> > > Dear all,
> > >
> > > for each A == 3 in 'df' I would like to change the variables B and
K.
> > > My result should be the whole df and not the subset (A==3)...
> > >
> > > df<- data.frame(A = c(1,1,3,2,2,3,3),
> > > B = c(2,1,1,2,7,8,7),
> > > K = c("a.1", "d.2", "f.3",
> > > "a.1", "k.4", "f.9", "f.5"))
> > >
> > > x1<- within(df[df$A ==3, ], {
> >
> > This is the problem: you've subsetted the dataset here, and lost all
> > the other lines. You want something like this:
> >
> > x3 <- within(df, {
> > B <- ifelse(A == 3, 5, B)
> > K <- ifelse(A == 3, gsub("f", "m", K), as.character(K))
}
> > )
> >
> > You need the "as.character" as by default K will be a factor, not a
> > character vector, and ifelse will take the factor level instead of the
> > label.
> >
> > If the condition was more complicated than A == 3, you might want to
> > calculate it first and use the calculated value each time:
> >
> >
> > x3 <- within(df, {
> > changes <- A == 3
> > B <- ifelse(changes, 5, B)
> > K <- ifelse(changes, gsub("f", "m", K),
as.character(K))
> > rm(changes)
> > }
> > )
> >
> > > B1<- 5
> > > K1<- gsub("f","m", K)
> > > })
> > >
> > > x2<- transform(df[df$A==3, ], B1 = 5, K1 = gsub("f","m", K))
> > >
> > > Thanks for any help!
> > > Patrick
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > ------------------------------
> >
> > Message: 21
> > Date: Sun, 16 Jan 2011 15:59:58 +0100 (CET)
> > From: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > To: Hadley Wickham <hadley at rice.edu>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] rootogram for normal distributions
> > Message-ID: <alpine.DEB.2.00.1101161557470.22514 at paninaro.uibk.ac.at>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > On Sun, 16 Jan 2011, Hadley Wickham wrote:
> >
> > >> The normal distribution is a continuous distribution, i.e., the
> > frequency
> > >> for each observed value will essentially be 1/n and not converge to
the
> > >> density function. Hence, you would need to look at histogram or
smoothed
> > >> densities. Rootograms, on the other hand, are intended for discrete
> > >> distributions.
> > >
> > > I don't think that's true - rootograms are useful for both
continuous
> > > and discrete distributions. See (e.g.) p 314 at
> > > http://www.edwardtufte.com/tufte/tukey, where Tukey himself uses a
> > > rootogram with a normal distribution.
> >
> > OK, let me rephrase: Rootograms as implemented in rootogram() are
intended
> > for discrete distributions. At least that's my reading. But maybe I've
> > missed a trick that you can point us to.
> > Z
> >
> > > Hadley
> > >
> > > --
> > > Assistant Professor / Dobelman Family Junior Chair
> > > Department of Statistics / Rice University
> > > http://had.co.nz/
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > ------------------------------
> >
> > Message: 22
> > Date: Sun, 16 Jan 2011 10:04:07 -0500
> > From: Gabor Grothendieck <ggrothendieck at gmail.com>
> > To: Matthew Strother <rstrothe at gmail.com>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] data prep question
> > Message-ID:
> > <AANLkTimqB4wh9sNJhs1-MSsSvPCVB=c0j1-M8A7XxJQr at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Sat, Jan 15, 2011 at 4:26 PM, Matthew Strother <rstrothe at gmail.com>
> > wrote:
> > > I have a data set with several thousand observations across time,
grouped
> > by subject (example format below)
> > >
> > > ID ? ? ? ? ? ? ?TIME ? ?OBS
> > > 001 ? ? ? ? ? ? 2200 ? ?23
> > > 001 ? ? ? ? ? ? 2400 ? ?11
> > > 001 ? ? ? ? ? ? 3200 ? ?10
> > > 001 ? ? ? ? ? ? 4500 ? ?22
> > > 003 ? ? ? ? ? ? 3900 ? ?45
> > > 003 ? ? ? ? ? ? 5605 ? ?32
> > > 005 ? ? ? ? ? ? 1800 ? ?56
> > > 005 ? ? ? ? ? ? 1900 ? ?34
> > > 005 ? ? ? ? ? ? 2300 ? ?23
> > > ...
> > >
> > > I would like to identify the first time for each subject, and then
> > subtract this value from each subsequent time. ?However, the number of
> > observations per subject varies widely (from 1 to 20), and the
intervals
> > between times varies widely. ? Is there a package that can help do
this, or
> > a loop that can be set up to evaluate ID, then calculate the values?
?The
> > outcome I would like is presented below.
> > > ID ? ? ? ? ? ? ?TIME ? ?OBS
> > > 001 ? ? ? ? ? ? 0 ? ? ? ? ? ? ? 23
> > > 001 ? ? ? ? ? ? 200 ? ? ? ? ? ? 11
> > > 001 ? ? ? ? ? ? 1000 ? ?10
> > > 001 ? ? ? ? ? ? 2300 ? ?22
> > > 003 ? ? ? ? ? ? 0 ? ? ? ? ? ? ? 45
> > > 003 ? ? ? ? ? ? 1705 ? ?32
> > > 005 ? ? ? ? ? ? 0 ? ? ? ? ? ? ? 56
> > > 005 ? ? ? ? ? ? 100 ? ? ? ? ? ? 34
> > > 005 ? ? ? ? ? ? 500 ? ? ? ? ? ? 23
> >
> > Since the data frame appears to be already sorted by time within ID we
> > can do this:
> >
> > > transform(DF, OBS = ave(OBS, ID, FUN = function(x) x - x[1]))
> > ID TIME OBS
> > 1 1 2200 0
> > 2 1 2400 -12
> > 3 1 3200 -13
> > 4 1 4500 -1
> > 5 3 3900 0
> > 6 3 5605 -13
> > 7 5 1800 0
> > 8 5 1900 -22
> > 9 5 2300 -33
> >
> > --
> > Statistics & Software Consulting
> > GKX Group, GKX Associates Inc.
> > tel: 1-877-GKX-GROUP
> > email: ggrothendieck at gmail.com
> >
> >
> >
> > ------------------------------
> >
> > Message: 23
> > Date: Sun, 16 Jan 2011 16:28:15 +0100
> > From: Arne Henningsen <arne.henningsen at googlemail.com>
> > To: Holger Steinmetz <Holger.steinmetz at web.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Hausman Test
> > Message-ID:
> > <AANLkTimL2hvb7sfpJSU4hRjVzUM
> +m5w0RQcW4ahTzVpa at mail.gmail.com<AANLkTimL2hvb7sfpJSU4hRjVzUM%
> 2Bm5w0RQcW4ahTzVpa at mail.gmail.com>
> > >
> > Content-Type: text/plain; charset=windows-1252
> >
> > Hi Holger!
> >
> > On 16 January 2011 15:53, Holger Steinmetz <Holger.steinmetz at web.de>
> > wrote:
> > > One follow up question. The Hausman-test always gives me a p-value
of 1 -
> > no
> > > matter how small the statistic is.
> > >
> > > I now generated orthogonal regressors (X1-X3) and the test gives me
> > >
> > >
> > > ? ? ? ?Hausman specification test for consistency of the 3SLS
estimation
> > >
> > > data: ?data
> > > Hausman = -0.0138, df = 2, p-value = 1
> > >
> > > What is confusing to me is the "3SLS". I am just beginning to learn
about
> > > instrumental variables (I am a psychologist ;) Perhaps that's a
problem?
> > >
> > > As a background, here's the complete simulation:
> > >
> > > W = rnorm(1000)
> > > X2 = rnorm(1000)
> > > X3 = rnorm(1000)
> > > X1 = .5*W ?+ rnorm(1000)
> > > Y = .4*X1 + .5*X2 + .6*X3 + rnorm(1000)
> > > data = as.data.frame(cbind(X1,X2,X3,Y,W))
> > >
> > > fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > > fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> > >
> > > print(hausman.systemfit(fitOLS, fit2sls))
> >
> > Please do read the documentation of hausman.systemfit(). I regret that
> > comparing 2SLS with OLS results has not been implemented yet:
> >
> > ====== part of documentation of hausman.systemfit() =================
> > Usage:
> >
> > hausman.systemfit( results2sls, results3sls )
> >
> > Arguments:
> >
> > results2sls : result of a _2SLS_ (limited information) estimation
> > returned by ?systemfit?.
> >
> > results3sls : result of a _3SLS_ (full information) estimation
> > returned by ?systemfit?.
> >
> > Details:
> >
> > The null hypotheses of the test is that all exogenous variables
> > are uncorrelated with all disturbance terms. Under this
> > hypothesis both the 2SLS and the 3SLS estimator are consistent but
> > only the 3SLS estimator is (asymptotically) efficient. Under the
> > alternative hypothesis the 2SLS estimator is consistent but the
> > 3SLS estimator is inconsistent.
> >
> > The Hausman test statistic is
> >
> > m = ( b_2 - b_3 )' ( V_2 - V_3 ) ( b_2 - b_3 )
> >
> > where $b_2$ and $V_2$ are the estimated coefficients and their
> > variance covariance matrix of a _2SLS_ estimation and $b_3$ and
> > $V_3$ are the estimated coefficients and their variance covariance
> > matrix of a _3SLS_ estimation.
> >
> > =========================================
> >
> > Please don't hesitate to write a new version of hausman.systemfit()
> > that can also compare 2SLS with OLS results.
> >
> > Best regards from Copenhagen,
> > Arne
> >
> > --
> > Arne Henningsen
> > http://www.arne-henningsen.name
> >
> >
> >
> > ------------------------------
> >
> > Message: 24
> > Date: Sun, 16 Jan 2011 16:29:03 +0100 (CET)
> > From: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > To: Holger Steinmetz <Holger.steinmetz at web.de>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Hausman Test
> > Message-ID: <alpine.DEB.2.00.1101161619580.22514 at paninaro.uibk.ac.at>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > On Sun, 16 Jan 2011, Holger Steinmetz wrote:
> >
> > >
> > > Dear Achim,
> > >
> > > thank you very much.
> > >
> > > One follow up question. The Hausman-test always gives me a p-value
of 1
> > > - no matter how small the statistic is.
> > >
> > > I now generated orthogonal regressors (X1-X3) and the test gives me
> > >
> > >
> > > Hausman specification test for consistency of the 3SLS
estimation
> > >
> > > data: data
> > > Hausman = -0.0138, df = 2, p-value = 1
> > >
> > > What is confusing to me is the "3SLS".
> >
> > Hausman tests can be used for comparisons of various models. The
> > implementation in systemfit is intended for comparison of 2SLS and
3SLS
> > but can also be (ab)used for comparison of 2SLS and OLS. You just have
to
> > enter the models in the reverse order, i.e.,
hausman.systemfit(fit2sls,
> > fitOLS).
> >
> > A worked example that computes the test statistic "by hand" is also
> > included in
> >
> > help("Baltagi2002", package = "AER")
> >
> > in the section about the US consumption data, Chapter 11.
> >
> > An adaptation is also shown below:
> >
> > ## data
> > library("AER")
> > data("USConsump1993", package = "AER")
> > usc <- as.data.frame(USConsump1993)
> > usc$investment <- usc$income - usc$expenditure
> >
> > ## 2SLS via ivreg(), Hausman by hand
> > fm_ols <- lm(expenditure ~ income, data = usc)
> > fm_iv <- ivreg(expenditure ~ income | investment, data = usc)
> > cf_diff <- coef(fm_iv) - coef(fm_ols)
> > vc_diff <- vcov(fm_iv) - vcov(fm_ols)
> > x2_diff <- as.vector(t(cf_diff) %*% solve(vc_diff) %*% cf_diff)
> > pchisq(x2_diff, df = 2, lower.tail = FALSE)
> >
> > ## 2SLS via systemfit(), Hausman via hausman.systemfit()
> > library("systemfit")
> > sm_ols <- systemfit(expenditure ~ income, data = usc, method =
"OLS")
> > sm_iv <- systemfit(expenditure ~ income, data = usc, method =
"2SLS",
> > inst = ~ investment)
> > hausman.systemfit(sm_iv, sm_ols)
> >
> > hth,
> > Z
> >
> > > I am just beginning to learn about
> > > instrumental variables (I am a psychologist ;) Perhaps that's a
problem?
> > >
> > > As a background, here's the complete simulation:
> > >
> > > W = rnorm(1000)
> > > X2 = rnorm(1000)
> > > X3 = rnorm(1000)
> > > X1 = .5*W + rnorm(1000)
> > > Y = .4*X1 + .5*X2 + .6*X3 + rnorm(1000)
> > > data = as.data.frame(cbind(X1,X2,X3,Y,W))
> > >
> > > fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > > fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> > >
> > > print(hausman.systemfit(fitOLS, fit2sls))
> > >
> > > Best,
> > > Holger
> > > --
> > > View this message in context:
> > http://r.789695.n4.nabble.com/Hausman-Test-tp3220016p3220065.html
> > > Sent from the R help mailing list archive at Nabble.com.
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > ------------------------------
> >
> > Message: 25
> > Date: Sun, 16 Jan 2011 16:37:55 +0100 (CET)
> > From: Achim Zeileis <Achim.Zeileis at uibk.ac.at>
> > To: Arne Henningsen <arne.henningsen at googlemail.com>
> > Cc: r-help at r-project.org, Holger Steinmetz <Holger.steinmetz at web.de>
> > Subject: Re: [R] Hausman Test
> > Message-ID: <alpine.DEB.2.00.1101161634170.22514 at paninaro.uibk.ac.at>
> > Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> >
> > On Sun, 16 Jan 2011, Arne Henningsen wrote:
> >
> > > Hi Holger!
> > >
> > > On 16 January 2011 15:53, Holger Steinmetz <Holger.steinmetz at web.de>
> > wrote:
> > >> One follow up question. The Hausman-test always gives me a p-value
of 1
> > - no
> > >> matter how small the statistic is.
> > >>
> > >> I now generated orthogonal regressors (X1-X3) and the test gives me
> > >>
> > >>
> > >> ? ? ? ?Hausman specification test for consistency of the 3SLS
estimation
> > >>
> > >> data: ?data
> > >> Hausman = -0.0138, df = 2, p-value = 1
> > >>
> > >> What is confusing to me is the "3SLS". I am just beginning to learn
> > about
> > >> instrumental variables (I am a psychologist ;) Perhaps that's a
problem?
> > >>
> > >> As a background, here's the complete simulation:
> > >>
> > >> W = rnorm(1000)
> > >> X2 = rnorm(1000)
> > >> X3 = rnorm(1000)
> > >> X1 = .5*W ?+ rnorm(1000)
> > >> Y = .4*X1 + .5*X2 + .6*X3 + rnorm(1000)
> > >> data = as.data.frame(cbind(X1,X2,X3,Y,W))
> > >>
> > >> fit2sls <- systemfit(Y~X1,data=data,method="2SLS",inst=~W)
> > >> fitOLS <- systemfit(Y~X1,data=data,method="OLS")
> > >>
> > >> print(hausman.systemfit(fitOLS, fit2sls))
> > >
> > > Please do read the documentation of hausman.systemfit(). I regret
that
> > > comparing 2SLS with OLS results has not been implemented yet:
> > >
> > > ====== part of documentation of hausman.systemfit()
=================
> > > Usage:
> > >
> > > hausman.systemfit( results2sls, results3sls )
> > >
> > > Arguments:
> > >
> > > results2sls : result of a _2SLS_ (limited information) estimation
> > > returned by ?systemfit?.
> > >
> > > results3sls : result of a _3SLS_ (full information) estimation
> > > returned by ?systemfit?.
> > >
> > > Details:
> > >
> > > The null hypotheses of the test is that all exogenous variables
> > > are uncorrelated with all disturbance terms. Under this
> > > hypothesis both the 2SLS and the 3SLS estimator are consistent
but
> > > only the 3SLS estimator is (asymptotically) efficient. Under
the
> > > alternative hypothesis the 2SLS estimator is consistent but the
> > > 3SLS estimator is inconsistent.
> > >
> > > The Hausman test statistic is
> > >
> > > m = ( b_2 - b_3 )' ( V_2 - V_3 ) ( b_2 - b_3 )
> > >
> > > where $b_2$ and $V_2$ are the estimated coefficients and their
> > > variance covariance matrix of a _2SLS_ estimation and $b_3$ and
> > > $V_3$ are the estimated coefficients and their variance
covariance
> > > matrix of a _3SLS_ estimation.
> > >
> > > =========================================
> > >
> > > Please don't hesitate to write a new version of hausman.systemfit()
> > > that can also compare 2SLS with OLS results.
> >
> > Arne: Unless I'm missing something, hausman.systemfit() essentially
does
> > the right thing and computes the right statistic and p-value (see my
other
> > mail to Holger). Maybe some preliminary check on the input objects
could
> > be used for determining the right order of models.
> >
> > Best,
> > Z
> >
> > > Best regards from Copenhagen,
> > > Arne
> > >
> > > --
> > > Arne Henningsen
> > > http://www.arne-henningsen.name
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> > ------------------------------
> >
> > Message: 26
> > Date: Sun, 16 Jan 2011 16:49:11 +0100
> > From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
> > To: Alexander Shenkin <ashenkin at ufl.edu>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] holding objects in dataframes
> > Message-ID: <4D331377.3050601 at statistik.tu-dortmund.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > I haven't seen an answer so far, hence I try:
> >
> > As far as I can see, everything is correct here, since you have an
> > element polygons in you data.frame that is a valid vector of mode
list.
> >
> > Nevertheless, since printing /plotting etc. on the dataframe won't
give
> > desired results now, it would be more natural to introduce a new class
> > for your kind of object and write some nice methods for it.
> >
> > Best,
> > Uwe Ligges
> >
> >
> >
> >
> >
> > On 14.01.2011 21:59, Alexander Shenkin wrote:
> > > Hello list,
> > >
> > > I need to keep track of objects that are related to particular
> > > observations. In this case, I
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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