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@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@csiro.au)
>   4. problem installing rgdal (alessandro.sarretta@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@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@ucalgary.ca>
> To: Kumar Mainali <kpmainali@gmail.com>
> Cc: "r-help@r-project.org" <r-help@r-project.org>
> Subject: Re: [R] Displaying ylab in mfrow
> Message-ID: <4D32D938.4080908@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$CarapWid,
> > breaks=5*(0:80), col="gray80", main="All individuals", xlab="", xlim
> > =c(15,85), ylab="April 2007"))
>
> Your code is neither reproducible nor minimal.
> And it doesn't look as though it would produce
> anything like what you seem to want.
>
> I suspect that you may wish to look at ?title
> and in particular at the 'ylab' and 'outer'
> arguments.
>
> Or you might consider using lattice or ggplot2.
>
> Peter Ehlers
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 16 Jan 2011 03:46:12 -0800
> From: Peter Ehlers <ehlers@ucalgary.ca>
> To: Adelchi Azzalini <azzalini@stat.unipd.it>
> Cc: "r-help@r-project.org" <r-help@r-project.org>
> Subject: Re: [R] \examples{} in Rd file
> Message-ID: <4D32DA84.60002@ucalgary.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Adelchi,
>
> Since % is the LaTeX comment character, you may want to
> try escaping it.
>
> Peter Ehlers
>
> On 2011-01-16 02:35, Adelchi Azzalini wrote:
> > [Hope this is the right list where to send...]
> >
> > An attempt to update package 'mnormt' involves the addition of a
> > small new function called 'pd.solve'.  When I come to the package
> > checking stage, an error occurs in parsing  pd.solve.Rd.
> > The full transcript of the outcome is copied below (it includes details
> > on my installation) but the critical point is where the \examples{}
> > section includes a %*%. The relevant portion of the source file is
> >
> > \examples{
> >     x<- toeplitz(rev(1:4))
> >     x.inv<- pd.solve(x)
> >     print(x.inv %*% x)
> >     logDet<- attr(x.inv, "log.det")
> >     print(abs(logDet - determinant(x, logarithm=TRUE)$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)$modulus))
> >
> > It seems that the examples are parsed as ordinary text, not R commands.
> > I am really puzzled. Any explanation?
> >
> > Adelchi Azzalini
> >
> [... snip ...]
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 16 Jan 2011 22:48:46 +1100
> From: <Bill.Venables@csiro.au>
> To: <rstrothe@gmail.com>, <r-help@r-project.org>
> Subject: Re: [R] data prep question
> Message-ID:
>        <
> 1BDAE2969943D540934EE8B4EF68F95FB27A48C274@EXNSW-MBX03.nexus.csiro.au>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Here is one way
>
> Here is one way:
>
> > con <- textConnection("
> + ID              TIME    OBS
> + 001             2200    23
> + 001             2400    11
> + 001             3200    10
> + 001             4500    22
> + 003             3900     45
> + 003             5605     32
> + 005             1800    56
> + 005             1900    34
> + 005             2300    23")
> > dat <- read.table(con, header = TRUE,
> + colClasses = c("factor", "numeric", "numeric"))
> > closeAllConnections()
> >
> > tmp <- lapply(split(dat, dat$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@r-project.org [r-help-bounces@r-project.org] On
> Behalf Of Matthew Strother [rstrothe@gmail.com]
> Sent: 16 January 2011 07:26
> To: r-help@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@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@inwind.it" <alessandro.sarretta@inwind.it>
> To: r-help@r-project.org
> Subject: [R] problem installing rgdal
> Message-ID:
>        <23477963.3728391295173693963.JavaMail.defaultUser@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@web.de>
> To: r-help@r-project.org
> Subject: [R] rootogram for normal distributions
> Message-ID: <201101161145.28281.Hugo.Mildenberger@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@gmail.com>
> To: r-help@r-project.org
> Subject: [R] Help in Coxme
> Message-ID:
>        <AANLkTimQCz9bOm-b5XhgvKSDh7_cz71dVqiRf1mkMT-Z@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@praha1.ff.cuni.cz>
> To: r-help@r-project.org
> Subject: Re: [R] how to add a derived column to a data frame?
> Message-ID: <20110116095927.GA6767@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@stats.ox.ac.uk>
> To: Peter Ehlers <ehlers@ucalgary.ca>
> Cc: "r-help@r-project.org" <r-help@r-project.org>
> Subject: Re: [R] \examples{} in Rd file
> Message-ID:
>        <alpine.LFD.2.00.1101161246530.10278@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@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@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@gmail.com>
> To: rnick <nikos.rachmanis@gmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] Time and xts
> Message-ID:
>        <AANLkTikAdjJ0pXVL-qcZMCWHqx5n3Q-Fs-JRj6MptgVJ@mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> On Sat, Jan 15, 2011 at 11:20 PM, rnick <nikos.rachmanis@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@stats.ox.ac.uk>
> To: "alessandro.sarretta@inwind.it" <alessandro.sarretta@inwind.it>
> Cc: r-help@r-project.org, Roger Bivand <Roger.Bivand@nhh.no>
> Subject: Re: [R] problem installing rgdal
> Message-ID:
>        <alpine.LFD.2.00.1101161251370.10278@gannet.stats.ox.ac.uk>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> On Sun, 16 Jan 2011, alessandro.sarretta@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@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@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@web.de>
> To: r-help@r-project.org
> Subject: [R] Hausman Test
> Message-ID: <1295186828415-3220016.post@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@statistik.tu-dortmund.de>
> To: Jinrui Xu <jinruixu@umich.edu>
> Cc: r-help@r-project.org
> Subject: Re: [R] fgev_error_matrix_singular
> Message-ID: <4D32FC61.5070606@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@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@uni-bremen.de>
> To: r-help@r-project.org
> Subject: [R] transform a df with a condition
> Message-ID: <4D32FCFF.7010002@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$A==3, ], B1 = 5, K1 = gsub("f","m", K))
>
> Thanks for any help!
> Patrick
>
>
>
> ------------------------------
>
> Message: 14
> Date: Sun, 16 Jan 2011 15:19:01 +0100
> From: Patrick Hausmann <patrick.hausmann@uni-bremen.de>
> To: r-help@r-project.org
> Subject: Re: [R] transform a df with a condition
> Message-ID: <4D32FE55.3040204@uni-bremen.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Arrg, sorry - of course I don't want *new* variables. So this is my
> correct example:
>
> df <- data.frame(A = c(1,1,3,2,2,3,3),
>                  B = c(2,1,1,2,7,8,7),
>                  K = c("a.1", "d.2", "f.3",
>                        "a.1", "k.4", "f.9", "f.5"))
>
> x1 <- within(df[df$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@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@uibk.ac.at>
> To: Hugo Mildenberger <Hugo.Mildenberger@web.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] rootogram for normal distributions
> Message-ID: <alpine.DEB.2.00.1101161526120.22514@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@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@uibk.ac.at>
> To: Holger Steinmetz <Holger.steinmetz@web.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] Hausman Test
> Message-ID: <alpine.DEB.2.00.1101161534270.22514@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@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@rice.edu>
> To: Achim Zeileis <Achim.Zeileis@uibk.ac.at>
> Cc: r-help@r-project.org
> Subject: Re: [R] rootogram for normal distributions
> Message-ID:
>        <AANLkTik6qAwA+131E4gt-==iSe0Pw=dhvbusMKB71ct7@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@gmail.com>
> To: Patrick Hausmann <patrick.hausmann@uni-bremen.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] transform a df with a condition
> Message-ID:
>        <AANLkTinfkPn_vYTdCdL-3-7=VRjF3Y-z5moFJWCC-MoO@mail.gmail.com>
> Content-Type: text/plain
>
> Try this:
>
> df[df$A == 3, c('B', 'K')] <- with(df[df$A == 3, c('B', 'K')], cbind(5,
> gsub("f", "m", K)))
>
> On Sun, Jan 16, 2011 at 12:19 PM, Patrick Hausmann <
> patrick.hausmann@uni-bremen.de> wrote:
>
> > Arrg, sorry - of course I don't want *new* variables. So this is my
> correct
> > example:
> >
> >
> > df <- data.frame(A = c(1,1,3,2,2,3,3),
> >                 B = c(2,1,1,2,7,8,7),
> >                 K = c("a.1", "d.2", "f.3",
> >                       "a.1", "k.4", "f.9", "f.5"))
> >
> > x1 <- within(df[df$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@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@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@web.de>
> To: r-help@r-project.org
> Subject: Re: [R] Hausman Test
> Message-ID: <1295189597126-3220065.post@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@gmail.com>
> To: Patrick Hausmann <patrick.hausmann@uni-bremen.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] transform a df with a condition
> Message-ID: <4D330682.8000906@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@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@uibk.ac.at>
> To: Hadley Wickham <hadley@rice.edu>
> Cc: r-help@r-project.org
> Subject: Re: [R] rootogram for normal distributions
> Message-ID: <alpine.DEB.2.00.1101161557470.22514@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@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@gmail.com>
> To: Matthew Strother <rstrothe@gmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] data prep question
> Message-ID:
>        <AANLkTimqB4wh9sNJhs1-MSsSvPCVB=c0j1-M8A7XxJQr@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, Jan 15, 2011 at 4:26 PM, Matthew Strother <rstrothe@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@googlemail.com>
> To: Holger Steinmetz <Holger.steinmetz@web.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] Hausman Test
> Message-ID:
>        <AANLkTimL2hvb7sfpJSU4hRjVzUM+m5w0RQcW4ahTzVpa@mail.gmail.com<AANLkTimL2hvb7sfpJSU4hRjVzUM%2Bm5w0RQcW4ahTzVpa@mail.gmail.com>
> >
> Content-Type: text/plain; charset=windows-1252
>
> Hi Holger!
>
> On 16 January 2011 15:53, Holger Steinmetz <Holger.steinmetz@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@uibk.ac.at>
> To: Holger Steinmetz <Holger.steinmetz@web.de>
> Cc: r-help@r-project.org
> Subject: Re: [R] Hausman Test
> Message-ID: <alpine.DEB.2.00.1101161619580.22514@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@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@uibk.ac.at>
> To: Arne Henningsen <arne.henningsen@googlemail.com>
> Cc: r-help@r-project.org, Holger Steinmetz <Holger.steinmetz@web.de>
> Subject: Re: [R] Hausman Test
> Message-ID: <alpine.DEB.2.00.1101161634170.22514@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@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@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@statistik.tu-dortmund.de>
> To: Alexander Shenkin <ashenkin@ufl.edu>
> Cc: r-help@r-project.org
> Subject: Re: [R] holding objects in dataframes
> Message-ID: <4D331377.3050601@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

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