Odp: How to still processing despite bug errors?

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 

each subject data are in separate folders (P1, P2 P3...)

My question is: in some cases, some errors can appear in one subject. I 

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 

at the end only see the problems in the subjects that R could not 

the analysis.
Each Subject takes 20 minutes to perform the analysis and I don't want 

stay days in front of PC, waiting for the next error in order to start 

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:

Send R-help mailing list submissions to
       r-help at r-project.org

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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 

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 

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

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 

this value from each subsequent time.  However, the number of 

per subject varies widely (from 1 to 20), and the intervals between 

varies widely.   Is there a package that can help do this, or a loop 

can be set up to evaluate ID, then calculate the values?  The outcome 

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.

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 

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_SOUNDEX -DTHREADSAFE=0     -fpic  -g -O2 -c RS-DBI.c -o 

gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 

-
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_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_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 

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 

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 

/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 

/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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

/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 

/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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

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 

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 

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.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 

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 

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 

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 

I
expected it, whereas a rootogram using the normal distribution does 

library(latticeExtra)
rootogram(~rpois(1000, lambda = 50), dfun = function(x) dpois(x, 

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 

get may
suffice: With increasing sample size, the rootogram using random 

from the Poisson distribution shows decreasing differences (bars are
quickly
approaching the zero line), whereas the displayed differences for 

samples of the normal distribution are always large. The differences 

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 

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 

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 

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 

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 

I am really puzzled. Any explanation?

Adelchi Azzalini

[... snip ...]

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 ? ? ? ? ? 

?.
?..
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 

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 

-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) 

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 

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 

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 

sqlite-all.o -L/usr/lib/R/lib -lR
installing to 

** 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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to

`sqlite3_last_insert_rowid'

/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

/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 

/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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to

`sqlite3_last_insert_rowid'

/usr/lib/libgdal1.7.0.so: undefined reference to 

/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
/usr/lib/libgdal1.7.0.so: undefined reference to 

/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 

/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 

/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.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 

-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 

-

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 

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

have an instrument W for X1

Now I want to test for endogeneity of X1 (i.e., when I omit X2 and X3 

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 

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 

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 

value distribution. The command I used is simple: y <- fgev(x).
The error is "observed information matrix is singular;" How can I 

these problem. I tried all methods in optim and it did not work. I 

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 

error? Thanks!

jinrui,

------------------------------

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 

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: 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 

like I

expected it, whereas a rootogram using the normal distribution does 

library(latticeExtra)
rootogram(~rpois(1000, lambda = 50), dfun = function(x) dpois(x, 

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 

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 

displayed differences for random samples of the normal distribution 

always large. The differences even increase with sample size, i.e, 

hanging bars tend to vanish for very large samples.

The normal distribution is a continuous distribution, i.e., the 

for each observed value will essentially be 1/n and not converge to 

density function. Hence, you would need to look at histogram or 

densities. Rootograms, on the other hand, are intended for discrete
distributions.
Z

have an instrument W for X1

Now I want to test for endogeneity of X1 (i.e., when I omit X2 and 

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.

for each observed value will essentially be 1/n and not converge to 

density function. Hence, you would need to look at histogram or 

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')], 

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 

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

--
Henrique Dallazuanna
Curitiba-Paran?-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 

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 

data:  data
Hausman = -0.0138, df = 2, p-value = 1

What is confusing to me is the "3SLS". I am just beginning to learn 

instrumental variables (I am a psychologist ;) Perhaps that's a 

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 

 > 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), 

               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

density function. Hence, you would need to look at histogram or 

densities. Rootograms, on the other hand, are intended for discrete
distributions.

I don't think that's true - rootograms are useful for both 

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 

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/

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 

between times varies widely. ? Is there a package that can help do 

a loop that can be set up to evaluate ID, then calculate the values? 

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 

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 

data: ?data
Hausman = -0.0138, df = 2, p-value = 1

What is confusing to me is the "3SLS". I am just beginning to learn 

instrumental variables (I am a psychologist ;) Perhaps that's a 

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 

- 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 

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 

but can also be (ab)used for comparison of 2SLS and OLS. You just have 

enter the models in the reverse order, i.e., 

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 = 

  sm_iv <- systemfit(expenditure ~ income, data = usc, method = 

    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 

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.

- 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 

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 

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 

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 

    only the 3SLS estimator is (asymptotically) efficient.  Under 

    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 

    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 

the right thing and computes the right statistic and p-value (see my 

mail to Holger). Maybe some preliminary check on the input objects 

be used for determining the right order of models.

Best,
Z

Best regards from Copenhagen,
Arne

--
Arne Henningsen
http://www.arne-henningsen.name

Nevertheless, since printing /plotting etc. on the dataframe won't 

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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