Re: [R] Data frame organization
Aaaah finally !!! Thanks a lot !!! Arnaud Le lun. 26 août 2019 18 h 28, Jim Lemon a écrit : > Hi Arnaud, > The reason I wrote the following function is that it always takes me > half a dozen tries with "reshape" before I get the syntax right: > > amdf<-read.table(text="A 10 > B 5 > C 9 > A 5 > B 15 > C 20") > library(prettyR) > stretch_df(amdf,"V1","V2") > V1 V2_1 V2_2 > 1 A 105 > 2 B5 15 > 3 C9 20 > > Jim > > On Tue, Aug 27, 2019 at 4:06 AM Arnaud Mosnier > wrote: > > > > Hi, > > > > I have a really simple question. > > I need to convert a data.frame with the following format > > > > A 10 > > B 5 > > C 9 > > A 5 > > B 15 > > C 20 > > > > in this format > > > > A 10 5 > > B 515 > > C 920 > > > > Thanks !!! > > > > [[alternative HTML version deleted]] > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Data frame organization
Hi, I have a really simple question. I need to convert a data.frame with the following format A 10 B 5 C 9 A 5 B 15 C 20 in this format A 10 5 B 515 C 920 Thanks !!! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] file connection when using parallel
Dear UserRs,
I have a little problem creating a file connection when working in parallel
(see the reproducable script below).
I am sure this is something obvious,
Can you enlighten me ?
Thanks,
Arnaud
# This part works
#
cat("This is a test file" , file={f <- tempfile()})
con <- file(f, "rt")
# Doing what I think is the same thing gives an error message when executed
in parallel
#--
library(parallel)
cl <- makeCluster(2)
## Exporting the object f into the cluster
clusterExport(cl, "f")
clusterEvalQ(cl[1], con <- file(f[[1]], "rt"))
#Error in checkForRemoteErrors(lapply(cl, recvResult)) :
# one node produced an error: cannot open the connection
## Creating the object f into the cluster
clusterEvalQ(cl[1],cat("This is a test file" , file={f <- tempfile()}))
clusterEvalQ(cl[1],con <- file(f, "rt"))
#Error in checkForRemoteErrors(lapply(cl, recvResult)) :
# one node produced an error: cannot open the connection
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[R] Clean method to convert date and time between time zones keeping it in POSIXct format
Dear UseRs,
I know two ways to convert dates and time from on time zone to another but
I am pretty sure that there is a better (cleaner) way to do that.
Here are the methods I know:
## The longest way ...
T1 <- as.POSIXct("2016-05-09 10:00:00", format="%Y-%m-%d %H:%M:%S",
tz="America/New_York")
print(T1)
T2 <- as.POSIXct(format(T1, tz="UTC"), tz="UTC") # format convert it to
character, so I have to convert it back to POSIXct afterward.
print(T2)
## The shortest but probably not the cleanest ...
attributes(T1)$tzone <- "UTC"
print(T1)
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Re: [R] Reading some csv files from different folders and add the name of each files to the first column of files
Hi Lida,
You can try this:
d- choose.dir() # choose the folder with the subdirectories containing the
csv files
f - list.files(d, full.names = TRUE, recursive = TRUE)
# Here the example for the sing files
selsing - grep(sing,f) #Select the files notaining the word sing
allsing - data.frame() #Create an empty data frame
# Loop among the selected files
for (i in 1:length(f[selsing])){
dat - read.csv(file=f[selsing][i]) # suppose that the csv files have a
header
allsing - rbind(allsing,data.frame(FileID =
gsub(EA_sing_|.txt,,basename(f[selsing][i])), dat)) #Combine the file
ID with the other columns and add the result to the all sing object
}
Now, you just have to do it for the other cases and save your final object.
Hope this help !
Arnaud
###
Date: Sat, 25 Jul 2015 15:03:21 -0500
From: Lida Zeighami lid.z...@gmail.com
To: r-help@r-project.org
Subject: [R] Reading some csv files from different folders and add the
name of each files to the first column of files
Message-ID:
CAMqbV1CXN0=r+hxmays40smymgdbhdqk1v+n5bhmbpgbr3m...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
I have 600 folders in which there are 3 csv files. The name of folders are
as follows: EA_aa, EA_bb, EA_cc, EA_dd,
In each folder there are 3 csv files:
in folder EA_aa there are:
EA_sing_aa.csvqwerty
EA_ska_aa.csv
EA_tat_aa.csv
In folder EA_bb:
EA_sing_bb.csv
EA_ska_bb.csv
EA_tat_bb.csv
...
I need to read all the same kind of files (for example sing files) in one
dataframe but before that I should add a column to each files with the name
of file as a row names!
So in output I should have just 3 csv files such as
EA_sing.csv: (rbind all EA_sing_*.csv file)
EA_ska.csv: (rbind all EA_ska_*.csv files)
EA_tat.csv: (rbind all EA_tat_*.csv files)
And in each file the first column should be added as row names which
containing the file name! So the format will be as follow:
EA_sing.csv:
1st column 2nd column 3rd column
aayhhhghj
aa k ki Fyh
bb k ki vgd
bb k gki Fyh
bbk reci Fyh
cc k hcd hyd
dd lmb Fyh
EA_ska.csv:
1st column 2nd column 3rd column
aayhhhghj
aa k ki Fyh
bb k ki Fyh
cc k gki Fyh
cc k reci oki
cc k hcd Fyh
dd lmb dsf
EA_tat.csv:
1st column 2nd column 3rd column
aayhhhghj
aa k ki Fyh
bb k ki Fyh
cc k gki Fyh
cc k reci oki
dd k hcd Fyh
dd lmb dsf
Would you please help me how to can I do that?
Thanks
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[R] Comparing gam models fitted using ti()
Dear R-Help list, I want to compare gam models including interaction with simpler models. For interaction models, I used gam(Y~ti(X1) + ti(X2) + ti(X1,X2)) removing the interaction, the models end as Y~ti(X1) + ti(X2) How those models compare with models with the form Y ~ s(X1) + s(X2) In my case, the former (i.e. ti() ) have a better AIC value than those with s(). Should I keep the ti() form or use only the s() form when I have no interaction ? Thanks for your help ! Arnaud [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Submodel selection using dredge and gam (mgcv)
Hi Kamil, Thanks for your answer. In fact, I already tried something with operators in such a way you advise, but it seems more complicated due to the use of the s() and ti() operators. Can you provide a solution for the following example ? library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) bt - gam(y~s(x0)+s(x1)+ti(x0,x1), data=dat,method=ML) library(MuMIn) # this does not work dredge(bt, subset = (!(x0,x1) | (x0 x1))) dredge(bt, subset = (!ti(x0,x1) | (s(x0) s(x1 Cheers, Arnaud 2014-11-11 4:11 GMT-05:00 Kamil Bartoń kamil.bar...@o2.pl: Hi Arnaud, your question has in fact nothing to do with gam or model selection. What you are asking is: what is the logical expression that yields True when AB is False or both A and B are True. Now replace the words with operators (!AB | (A B)) and voilà. See also: help(Logic, base) fortunes::fortune(350) best, kamil On 2014-11-10 21:26, Arnaud Mosnier wrote: Hi, I want to use dredge to test several gam submodels including interactions. I tried to find a way in order to keep models with interaction only if the single variables occurring in the interaction are also included. i.e.: for y~s(x0)+s(x1)+ti(x0, x1) I want to keep y ~ s(x0) y ~ s(x1) y ~ s(x0) + s(x1) y ~ s(x0) + s(x1) + ti(x0,x1) and I want to remove y ~ s(x0) + ti(x0,x1) y ~ s(x1) + ti(x0,x1) y ~ ti(x0,x1) I know that I should use the subset option of the dredge function. However, I can not find the correct matrix / expression to obtain what I need ! Here a small example. # Create some data (use mgcv example) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) # Create the global gam model # Here a model with interaction. Note the use of ti() bt - gam(y~s(x0)+s(x1)+s(x2)+s(x3)+ti(x1,x2), data=dat,method=ML) # Use dredge to test sub-models library(MuMIn) print(modstab - dredge(bt)) # Here the 11th model include the interaction but do not include the single variables x1 and x2 # ... I want to avoid that kind of model. get.models(modstab, subset = 11) Any help would be appreciated ! Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] Submodel selection using dredge and gam (mgcv)
Argh ! Ok ... my fault ... the use of back-ticks was the solution !!! Thanks, Arnaud 2014-11-12 14:19 GMT-05:00 Kamil Bartoń kamil.bar...@o2.pl: Hi Arnaud, please read ?dredge - Details - Subsetting, where this is explained. On 2014-11-12 15:19, Arnaud Mosnier wrote: Hi Kamil, Thanks for your answer. In fact, I already tried something with operators in such a way you advise, but it seems more complicated due to the use of the s() and ti() operators. Can you provide a solution for the following example ? library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) bt - gam(y~s(x0)+s(x1)+ti(x0,x1), data=dat,method=ML) library(MuMIn) # this does not work dredge(bt, subset = (!(x0,x1) | (x0 x1))) dredge(bt, subset = (!ti(x0,x1) | (s(x0) s(x1 Cheers, Arnaud 2014-11-11 4:11 GMT-05:00 Kamil Bartoń kamil.bar...@o2.pl mailto:kamil.bar...@o2.pl: Hi Arnaud, your question has in fact nothing to do with gam or model selection. What you are asking is: what is the logical expression that yields True when AB is False or both A and B are True. Now replace the words with operators (!AB | (A B)) and voilà. See also: help(Logic, base) fortunes::fortune(350) best, kamil On 2014-11-10 21:26, Arnaud Mosnier wrote: Hi, I want to use dredge to test several gam submodels including interactions. I tried to find a way in order to keep models with interaction only if the single variables occurring in the interaction are also included. i.e.: for y~s(x0)+s(x1)+ti(x0, x1) I want to keep y ~ s(x0) y ~ s(x1) y ~ s(x0) + s(x1) y ~ s(x0) + s(x1) + ti(x0,x1) and I want to remove y ~ s(x0) + ti(x0,x1) y ~ s(x1) + ti(x0,x1) y ~ ti(x0,x1) I know that I should use the subset option of the dredge function. However, I can not find the correct matrix / expression to obtain what I need ! Here a small example. # Create some data (use mgcv example) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,__scale=2) # Create the global gam model # Here a model with interaction. Note the use of ti() bt - gam(y~s(x0)+s(x1)+s(x2)+s(x3)+__ti(x1,x2), data=dat,method=ML) # Use dredge to test sub-models library(MuMIn) print(modstab - dredge(bt)) # Here the 11th model include the interaction but do not include the single variables x1 and x2 # ... I want to avoid that kind of model. get.models(modstab, subset = 11) Any help would be appreciated ! Arnaud [[alternative HTML version deleted]] __ 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] Submodel selection using dredge and gam (mgcv)
Hi, I want to use dredge to test several gam submodels including interactions. I tried to find a way in order to keep models with interaction only if the single variables occurring in the interaction are also included. i.e.: for y~s(x0)+s(x1)+ti(x0, x1) I want to keep y ~ s(x0) y ~ s(x1) y ~ s(x0) + s(x1) y ~ s(x0) + s(x1) + ti(x0,x1) and I want to remove y ~ s(x0) + ti(x0,x1) y ~ s(x1) + ti(x0,x1) y ~ ti(x0,x1) I know that I should use the subset option of the dredge function. However, I can not find the correct matrix / expression to obtain what I need ! Here a small example. # Create some data (use mgcv example) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) # Create the global gam model # Here a model with interaction. Note the use of ti() bt - gam(y~s(x0)+s(x1)+s(x2)+s(x3)+ti(x1,x2), data=dat,method=ML) # Use dredge to test sub-models library(MuMIn) print(modstab - dredge(bt)) # Here the 11th model include the interaction but do not include the single variables x1 and x2 # ... I want to avoid that kind of model. get.models(modstab, subset = 11) Any help would be appreciated ! Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] speed of makeCluster (package parallel)
Thanks Brian, I thought that forking clusters was better ... but as you mentioned, it is not available on windows. Unfortunately, you do not always choose the OS used by your company ! Arnaud Date: Mon, 28 Oct 2013 17:59:10 + From: Prof Brian Ripley rip...@stats.ox.ac.uk To: r-help@r-project.org Subject: Re: [R] speed of makeCluster (package parallel) Message-ID: 526ea5ee.9060...@stats.ox.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 28/10/2013 16:19, Arnaud Mosnier wrote: Hi all, I am quite new in the world of parallelization and I wonder if there is a way to increase the speed of creation of a parallel socket cluster. The time spend to include threads increase exponentially with the number of It increases linearly in my tests (or a decent OS). But really if parallel computing is worthwhile you will be doing minutes of work on each worker process and the startup time will not be signifcant. thread considered and I use of computer with two 8 cores CPU and thus showing a total of 32 threads in windows 7. The first way to speed things up: use a decent OS: forking clusters is much faster. Currently, I use the default parameters (type = PSOCK), but is there any fine tuning parameters that I can use to take advantage of this system ? Thanks in advance for your help ! Arnaud R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) [[alternative HTML version deleted]] -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ 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] speed of makeCluster (package parallel)
Hi all, I am quite new in the world of parallelization and I wonder if there is a way to increase the speed of creation of a parallel socket cluster. The time spend to include threads increase exponentially with the number of thread considered and I use of computer with two 8 cores CPU and thus showing a total of 32 threads in windows 7. Currently, I use the default parameters (type = PSOCK), but is there any fine tuning parameters that I can use to take advantage of this system ? Thanks in advance for your help ! Arnaud R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) [[alternative HTML version deleted]] __ 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.
Re: [R] speed of makeCluster (package parallel)
Thanks Simon, I already read the parallel vignette but I did not found what I wanted. May be you can be more specific on a part of the document that can provide me hints ! Arnaud 2013/10/28 Simon Zehnder szehn...@uni-bonn.de See library(help = parallel) On 28 Oct 2013, at 17:19, Arnaud Mosnier a.mosn...@gmail.com wrote: Hi all, I am quite new in the world of parallelization and I wonder if there is a way to increase the speed of creation of a parallel socket cluster. The time spend to include threads increase exponentially with the number of thread considered and I use of computer with two 8 cores CPU and thus showing a total of 32 threads in windows 7. Currently, I use the default parameters (type = PSOCK), but is there any fine tuning parameters that I can use to take advantage of this system ? Thanks in advance for your help ! Arnaud R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
Re: [R] speed of makeCluster (package parallel)
Thanks a lot Simon, that's useful. I will take a look at this process-pinning things. Arnaud 2013/10/28 Simon Zehnder szehn...@uni-bonn.de First, use only the number of cores as a number of thread - i.e. I would not use hyper threading, etc.. Each core has its own caches and it is always fortunate if a process has enough memory; hyper threads use all the same cache on the core they are running on. detectCores() gives me for example 4 - I know I have 2. I would therefore call makeCluster() with nnode = 2. mcaffinity() lets you perform a technique called process-pinning (see process affinity) and is only possible if the OS supports it. It makes sometimes sense to assign certain processes to certain CPUs such that each process has enough memory in caches (e.g. for a 16 Core machine using 8 processes on CPUs 1, 3, 5, 7, 9, 11, 13 and 15; so each process has the cache of two CPUs). A lot of functions though are not available for Windows. At first it comes always the problem you want to solve and then you look how much memory will be used in a process and how much you have (more often the memory bandwidth is the bottleneck and not the computing power). Look at the architecture of your chips (how much L1 Cache, how much L2 cache). Then you decide how many cores to use and if it makes sense to pin processes to certain cores. There are no general recipes for parallel computing - each problem is different. Some problems are even not scalable. Simon On 28 Oct 2013, at 17:51, Arnaud Mosnier a.mosn...@gmail.com wrote: Thanks Simon, I already read the parallel vignette but I did not found what I wanted. May be you can be more specific on a part of the document that can provide me hints ! Arnaud 2013/10/28 Simon Zehnder szehn...@uni-bonn.de See library(help = parallel) On 28 Oct 2013, at 17:19, Arnaud Mosnier a.mosn...@gmail.com wrote: Hi all, I am quite new in the world of parallelization and I wonder if there is a way to increase the speed of creation of a parallel socket cluster. The time spend to include threads increase exponentially with the number of thread considered and I use of computer with two 8 cores CPU and thus showing a total of 32 threads in windows 7. Currently, I use the default parameters (type = PSOCK), but is there any fine tuning parameters that I can use to take advantage of this system ? Thanks in advance for your help ! Arnaud R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
Re: [R] lowercase and uppercase greek letters
You're right! QFMFT! :-) Thanks 2013/9/17 Rolf Turner rolf.tur...@xtra.co.nz On 09/18/13 07:26, Arnaud Mosnier wrote: Hi all, I want to present a figure including the uppercase and lowercase version of the greek letter phi. I know that I can use expression to have the symbol like in: plot(1~1, main = expression(phi)) But, is there somewhere things like upper(phi) or lower(phi) ? Thanks for your help ! RTFM. From ?plotmath: alpha -- omega Greek symbols Alpha -- Omega uppercase Greek symbols cheers, Rolf Turner [[alternative HTML version deleted]] __ 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.
Re: [R] lowercase and uppercase greek letters
Thanks Murdoch. I tried PHI but not Phi. Arnaud 2013/9/17 Duncan Murdoch murdoch.dun...@gmail.com On 17/09/2013 3:26 PM, Arnaud Mosnier wrote: Hi all, I want to present a figure including the uppercase and lowercase version of the greek letter phi. I know that I can use expression to have the symbol like in: plot(1~1, main = expression(phi)) But, is there somewhere things like upper(phi) or lower(phi) ? No functions for that. You just need to give the letters in lowercase or uppercase: lowercase is phi, uppercase is Phi. Run demo(plotmath) for more hints. Duncan Murdoch [[alternative HTML version deleted]] __ 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] lowercase and uppercase greek letters
Hi all, I want to present a figure including the uppercase and lowercase version of the greek letter phi. I know that I can use expression to have the symbol like in: plot(1~1, main = expression(phi)) But, is there somewhere things like upper(phi) or lower(phi) ? Thanks for your help ! Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] column width in .dbf files using write.dbf ... to be continued
Thanks Bastien,
I completely forgot that I asked this question.
I learned a lot since then ... actually, now I know how to do it, but it
was not the case in 2009 :-)
Arnaud
2013/5/22 bastien.ferland-raym...@mrn.gouv.qc.ca
Hello Arnaud,
You posted this question a long long time ago, however I found your answer
so I decided to post it anyway in case somebody else have the same problem
as you and me.
You were actually very close in finding your solution. The function
DoWritedbf is an internal function from the foreign package. To access it
outside of the package just do:
foreign:::DoWritedbf
so in your line:
invisible(.Call(foreign:::DoWritedbf, as.character(file), dataframe,
as.integer(precision), as.integer(scale), as.character(DataTypes)))
It is explain here:
http://stackoverflow.com/questions/2165342/r-calling-a-function-from-a-namespace
Sorry for the delay in my answer...
Bastien Ferland-Raymond, M.Sc. Stat., M.Sc. Biol.
Division des orientations et projets spéciaux
Direction des inventaires forestiers
Ministère des Ressources naturelles
In reply to :
#
Dear UseRs,
I did not have any answer to my previous message (Is there a way to
define manually columns width when using write.dbf function from the
library foreign ?), so I tried to modify write.dbf function to do what I
want.
Here is my modified version :
write.dbfMODIF - function (dataframe, file, factor2char = TRUE, max_nchar
= 254, width = d)
{
allowed_classes - c(logical, integer, numeric, character,
factor, Date)
if (!is.data.frame(dataframe))
dataframe - as.data.frame(dataframe) if
(any(sapply(dataframe, function(x) !is.null(dim(x)
stop(cannot handle matrix/array columns) cl -
sapply(dataframe, function(x) class(x[1L])) asis - cl == AsIs
cl[asis sapply(dataframe, mode) == character] - character
if (length(cl0 - setdiff(cl, allowed_classes)))
stop(data frame contains columns of unsupported class(es) ,
paste(cl0, collapse = ,))
m - ncol(dataframe)
DataTypes - c(logical = L, integer = N, numeric = F,
character = C, factor = if (factor2char) C else N,
Date = D)[cl]
for (i in seq_len(m)) {
x - dataframe[[i]]
if (is.factor(x))
dataframe[[i]] - if (factor2char)
as.character(x)
else as.integer(x)
else if (inherits(x, Date))
dataframe[[i]] - format(x, %Y%m%d)
}
precision - integer(m)
scale - integer(m)
dfnames - names(dataframe)
for (i in seq_len(m)) {
nlen - nchar(dfnames[i], b)
x - dataframe[, i]
if (is.logical(x)) {
precision[i] - 1L
scale[i] - 0L
}
else if (is.integer(x)) {
rx - range(x, na.rm = TRUE)
rx[!is.finite(rx)] - 0
if (any(rx == 0))
rx - rx + 1
mrx - as.integer(max(ceiling(log10(abs(rx +
3L)
precision[i] - min(max(nlen, mrx), 19L)
scale[i] - 0L
}
else if (is.double(x)) {
precision[i] - 19L
rx - range(x, na.rm = TRUE)
rx[!is.finite(rx)] - 0
mrx - max(ceiling(log10(abs(rx
scale[i] - min(precision[i] - ifelse(mrx 0L, mrx +
3L, 3L), 15L)
}
else if (is.character(x)) {
if (width == d) {
mf - max(nchar(x[!is.na(x)], b))
p - max(nlen, mf)
if (p max_nchar)
warning(gettext(character column %d will be truncated
to %d bytes,
i, max_nchar), domain = NA)
precision[i] - min(p, max_nchar)
scale[i] - 0L
} else {
if (width max_nchar)
warning(gettext(character column %d will be truncated
to %d bytes,
i, max_nchar), domain = NA)
precision[i] - min(width, max_nchar)
}
}
else stop(unknown column type in data frame)
}
if (any(is.na(precision)))
stop(NA in precision)
if (any(is.na(scale)))
stop(NA in scale)
invisible(.Call(DoWritedbf, as.character(file), dataframe,
as.integer(precision), as.integer(scale),
as.character(DataTypes))) }
However, when I wanted to use this function ... it does not find the
DoWritedbf function that is called in the last lines (a function written in
C).
Is there a way to temporally replace the original write.dbf function by
this one in the foreign package ?
Thanks,
Arnaud
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
##
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[R] Pairwise deletion in a linear regression and in a GLM ?
Dear useRs, In a thesis, I found a mention of the use of pairwise deletion in linear regression and GLM (binomial family). The author said that he has used R to do the statistics, but I did not find the option allowing pairwise deletion in both lm and glm functions. Is there somewhere a package allowing that ? Thanks, Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] Pairwise deletion in a linear regression and in a GLM ?
Hi Jose, To my perception na.omit is different from a pairwise deletion. With na.omit, you omit totally that case if there is a missing value for one of the variable you consider in the model. In the pairwise deletion, the case with some missing value is kept and values that are not missing are used in the statistics calculations. However, I agree that pairwise deletion is not good practice (so it would be surprising that it is the default in lm !!). I just when to be able to recalculate the statistics given in this thesis. Arnaud 2012/12/13 Jose Iparraguirre jose.iparragui...@ageuk.org.uk Hi Arnaud, A quick help search of lm or glm tells you that 'the factory-fresh default is na.omit'. If you then look up 'na.omit', you'll read that it 'returns the object with incomplete cases removed'. So, pairwise deletion is the default option in both lm and glm. On a related note, it goes without saying that pairwise deletion is not good practice in most cases, and that R has ways to impute these missing cases depending on assumptions regarding the cause or nature of their missingness. Regards, José José Iparraguirre Chief Economist Age UK -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Arnaud Mosnier Sent: 13 December 2012 15:40 To: r-help@r-project.org Subject: [R] Pairwise deletion in a linear regression and in a GLM ? Dear useRs, In a thesis, I found a mention of the use of pairwise deletion in linear regression and GLM (binomial family). The author said that he has used R to do the statistics, but I did not find the option allowing pairwise deletion in both lm and glm functions. Is there somewhere a package allowing that ? Thanks, Arnaud [[alternative HTML version deleted]] __ 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. Wrap Up and Run 10k is back! Also, new for 2013 2km intergenerational walks at selected venues. So recruit a buddy, dust off the trainers and beat the winter blues by signing up now: http://www.ageuk.org.uk/10k Milton Keynes | Oxford | Sheffield | Crystal Palace | Exeter | Harewood House, Leeds | Tatton Park, Cheshire | Southampton | Coventry Age UK Improving later life http://www.ageuk.org.uk --- Age UK is a registered charity and company limited by guarantee, (registered charity number 1128267, registered company number 6825798). Registered office: Tavis House, 1-6 Tavistock Square, London WC1H 9NA. For the purposes of promoting Age UK Insurance, Age UK is an Appointed Representative of Age UK Enterprises Limited, Age UK is an Introducer Appointed Representative of JLT Benefit Solutions Limited and Simplyhealth Access for the purposes of introducing potential annuity and health cash plans customers respectively. Age UK Enterprises Limited, JLT Benefit Solutions Limited and Simplyhealth Access are all authorised and regulated by the Financial Services Authority. -- This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you receive a message in error, please advise the sender and delete immediately. Except where this email is sent in the usual course of our business, any opinions expressed in this email are those of the author and do not necessarily reflect the opinions of Age UK or its subsidiaries and associated companies. Age UK monitors all e-mail transmissions passing through its network and may block or modify mails which are deemed to be unsuitable. Age Concern England (charity number 261794) and Help the Aged (charity number 272786) and their trading and other associated companies merged on 1st April 2009. Together they have formed the Age UK Group, dedicated to improving the lives of people in later life. The three national Age Concerns in Scotland, Northern Ireland and Wales have also merged with Help the Aged in these nations to form three registered charities: Age Scotland, Age NI, Age Cymru. [[alternative HTML version deleted]] __ 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.
Re: [R] Pairwise deletion in a linear regression and in a GLM ?
Thanks Jose, but I doubt that the author of these analysis used such a complex approach. Arnaud 2012/12/13 Jose Iparraguirre jose.iparragui...@ageuk.org.uk Sorry, Arnaud, I misinterpreted the question. There isnt a built-in option in lm or glm to run pairwise deletion, but in the psych package you can run regressions on covariance matrices rather than on raw data. So, first, you can obtain a covariance matrix by cov() with the option use=pairwise.complete.obs or within psych, set.cor( ,use=pairwise), which will give you the correlations pairwise, and then you use the function mat.regress using the pairwise matrix. Hope this helps, ** ** José ** ** ** ** *From:* Arnaud Mosnier [mailto:a.mosn...@gmail.com] *Sent:* 13 December 2012 16:13 *To:* Jose Iparraguirre *Cc:* r-help@r-project.org *Subject:* Re: [R] Pairwise deletion in a linear regression and in a GLM ? ** ** Hi Jose, To my perception na.omit is different from a pairwise deletion. With na.omit, you omit totally that case if there is a missing value for one of the variable you consider in the model. In the pairwise deletion, the case with some missing value is kept and values that are not missing are used in the statistics calculations. However, I agree that pairwise deletion is not good practice (so it would be surprising that it is the default in lm !!). I just when to be able to recalculate the statistics given in this thesis. Arnaud ** ** 2012/12/13 Jose Iparraguirre jose.iparragui...@ageuk.org.uk Hi Arnaud, A quick help search of lm or glm tells you that 'the factory-fresh default is na.omit'. If you then look up 'na.omit', you'll read that it 'returns the object with incomplete cases removed'. So, pairwise deletion is the default option in both lm and glm. On a related note, it goes without saying that pairwise deletion is not good practice in most cases, and that R has ways to impute these missing cases depending on assumptions regarding the cause or nature of their missingness. Regards, José José Iparraguirre Chief Economist Age UK -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Arnaud Mosnier Sent: 13 December 2012 15:40 To: r-help@r-project.org Subject: [R] Pairwise deletion in a linear regression and in a GLM ? Dear useRs, In a thesis, I found a mention of the use of pairwise deletion in linear regression and GLM (binomial family). The author said that he has used R to do the statistics, but I did not find the option allowing pairwise deletion in both lm and glm functions. Is there somewhere a package allowing that ? Thanks, Arnaud [[alternative HTML version deleted]] __ 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. Wrap Up and Run 10k is back! Also, new for 2013 2km intergenerational walks at selected venues. So recruit a buddy, dust off the trainers and beat the winter blues by signing up now: http://www.ageuk.org.uk/10k Milton Keynes | Oxford | Sheffield | Crystal Palace | Exeter | Harewood House, Leeds | Tatton Park, Cheshire | Southampton | Coventry Age UK Improving later life http://www.ageuk.org.uk --- Age UK is a registered charity and company limited by guarantee, (registered charity number 1128267, registered company number 6825798). Registered office: Tavis House, 1-6 Tavistock Square, London WC1H 9NA. For the purposes of promoting Age UK Insurance, Age UK is an Appointed Representative of Age UK Enterprises Limited, Age UK is an Introducer Appointed Representative of JLT Benefit Solutions Limited and Simplyhealth Access for the purposes of introducing potential annuity and health cash plans customers respectively. Age UK Enterprises Limited, JLT Benefit Solutions Limited and Simplyhealth Access are all authorised and regulated by the Financial Services Authority. -- This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you receive a message in error, please advise the sender and delete immediately. Except where this email is sent in the usual course of our business, any opinions expressed in this email are those of the author and do not necessarily reflect the opinions of Age UK or its subsidiaries and associated companies. Age UK monitors all e-mail transmissions passing through its network and may block or modify mails which are deemed to be unsuitable. Age Concern England (charity number 261794) and Help the Aged (charity number
Re: [R] increase the usage of CPU and Memory
Hi Xi, Maybe you should try to parallelize your calculations. See package parallel. http://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf Arnaud On Mon, Jun 25, 2012 at 8:07 PM, Xi amzhan...@gmail.com wrote: Dear All, I have been searching online for help increasing my R code more efficiently for almost a whole day, however, there is no solution to my case. So if anyone could give any clue to solve my problem, I would be very appreciate for you help. Thanks in advance. Here is my issue: My desktop is with i7-950 Quad-core CPU with 24Gb memory, and a ?NVIDIA GTX 480 ?graphic card, and I am using a 64-bit version of R under 64-bit Windows . I am running a for loop to generate a 461*5 matrix data, which is coming from the coefficients of 5 models. The loop would produce 5 values one time, and it will run 461 times in total. I have tried to run the code inside the loop just once, it will cost almost 10 seconds, so if we intuitively calculate the time of the whole loop will cost, it would be 4610 seconds, equal to almost one and a half hours, which is exactly the whole loop taking indeed. But I have to run this kinda loop for 30 data-sets! Although I thought I am using a not-bad at all desktop, I checked the usage of CPU and memory during my running R code, and found out the whole code just used 15% of CPU and 10% of memory. Does anyone have the same issue with me? or Does anyone know some methods to shorten the running time and increase the usage of CPU and memory? Many thanks, Xi [[alternative HTML version deleted]] __ 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.
Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method
Thanks for this good idea ! Arnaud 2012/5/1 Ted Harding ted.hard...@wlandres.net On 01-May-2012 19:58:41 Arnaud Mosnier wrote: Dear UseRs, Is there a way to define the lower-upper bounds for parameters fitted by optim using the Nelder-Mead method ? Thanks, Arnaud The Nelder-Mead method does not provide built-in capability to set bounds on the range of paramaters. However, you can achieve it by hand by re-defining the function being minimised, so that it tests whether an out-of-range parameter parameter value is being used. If not out-of-range, then return the standard value of the function. If out-of range, then return a very large value. Nelder-Mead will very happily bounce off high walls of this kind, and if the minimum of the function is at the wall will happily converge as close to it as you please. Hoping this helps, Ted. - E-Mail: (Ted Harding) ted.hard...@wlandres.net Date: 01-May-2012 Time: 22:39:15 This message was sent by XFMail - [[alternative HTML version deleted]] __ 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] Define lower-upper bound for parameters in Optim using Nelder-Mead method
Dear UseRs, Is there a way to define the lower-upper bounds for parameters fitted by optim using the Nelder-Mead method ? Thanks, Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] Use of optim to fit two curves at the same time ?
Nice, thank you !
I particularly appreciated the list of possible explanations for it does
not work ! :-)
Arnaud
Le 26 avril 2012 13:49, Greg Snow 538...@gmail.com a écrit :
The phrase does not work is not very helpful, it can mean quit a few
things including:
* Your computer exploded.
* No explosion, but smoke is pouring out the back and microsoft's
NoSmoke utility is not compatible with your power supply.
* The computer stopped working.
* The computer sits around on the couch all day eating chips and
watching talk shows.
* The computer has started picketing your house shouting catchy
slogans and demanding better working conditions and an increase in
memory.
* Everything went dark and you cannot check the cables on the back of
the computer because the lights are off due to the power outage.
* R crashed, but the other programs are still working.
* R gave an error message and stopped processing your code after
running for a while.
* R gave an error message without running any of your code (and is
waiting for your next command).
* R is still running your code and the time has exceeded your patience
so you think it has hung.
* R completed and returned a result, but also gave warnings.
* R completed your command, but gave an incorrect answer.
* R completed your command but the answer is different from what you
expect (but is correct according to the documentation)
There are probably others.
Running your code I think the answer is the last one. The criteria
for optim finishing is a small improvement relative to previous
improvements, not a guarantee of an exactly correct answer. Since
your starting points were very different from the True values this
means that what appears to be a good improvement can still be far from
the answer that you know to be true. There are various arguments that
you can give to optim to improve the fitting process, but sometimes
the easiest thing to do is to just run optim again using the previous
results as the new starting values. Try running the following:
out4 - optim( par=out3$par, fn=function(x){optfunc3(x,dfxy,dfxy2)})
(out4 - optim( par=out4$par, fn=function(x){optfunc3(x,dfxy,dfxy2)}))
and see if it works. Run the last line a couple more times to see
how well it works (at least it worked for me, if this does not work
for you, tell us what does not work means).
On Wed, Apr 25, 2012 at 6:57 AM, Arnaud Mosnier a.mosn...@gmail.com
wrote:
Dear list,
In order to find a solution to my problem, I created a third objective
function including both calculations done in the previous cases. This
function return a value (i.e. the value to be minimize by optim) equal to
the sum of the two sum of squares, but it does not work (see the code
added
at the end of my previous script).
Any suggestion ?
Arnaud
Dear list,
Here is a small example code that use optim and optimize in order to fit
two functions.
Is it possible to fit two functions (like those two for example) at the
same time using optim ... or another function in R ?
Thanks
Arnaud
##
## function 1
x1 - 1:100
y1 - 5.468 * x + 3 # + rnorm(100,0, 10)
dfxy - cbind(x1,y1)
# Objective function
optfunc - function(x, dfxy){
a - x[1]
b - x[2]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - a*xtest + b
sum((ysim - yobs)^2)
}
out- optim(par=c(0.2,5), fn=function(x){optfunc(x, dfxy)}, method =
Nelder-Mead, hessian = F)
## function 2
x2 - seq(0.01, 0.1, length=100)
y2 - exp(30*x2)
dfxy2 - cbind(x2,y2)
# objective function
optfunc2 - function(x, dfxy){
a - x[1]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - exp(a*xtest)
sum((ysim - yobs)^2)
}
out- optimize(f=function(x){optfunc2(x, dfxy2)}, interval=c(0,500))
##
optfunc3 - function(x, dfxy, dfxy2){
a - x[1]
b - x[2]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - a*xtest + b
obj1 - sum((ysim - yobs)^2)
c - x[3]
xtest2 - dfxy2[,1]
yobs2 - dfxy2[,2]
ysim2 - exp(c*xtest2)
obj2 - sum((ysim2 - yobs2)^2)
obj1 + obj2
}
out3- optim(par=c(0.2,5, 500), fn=function(x){optfunc3(x, dfxy, dfxy2)},
method = Nelder-Mead, hessian = F)
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and provide commented, minimal, self-contained, reproducible code.
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com
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Re: [R] Use of optim to fit two curves at the same time ?
I second the proposition ! Thanks to let me discover that absolutely essential library !! :-) Arnaud Le 26 avril 2012 15:30, Marc Schwartz marc_schwa...@me.com a écrit : On Apr 26, 2012, at 12:49 PM, Greg Snow wrote: The phrase does not work is not very helpful, it can mean quit a few things including: * Your computer exploded. * No explosion, but smoke is pouring out the back and microsoft's NoSmoke utility is not compatible with your power supply. * The computer stopped working. * The computer sits around on the couch all day eating chips and watching talk shows. * The computer has started picketing your house shouting catchy slogans and demanding better working conditions and an increase in memory. * Everything went dark and you cannot check the cables on the back of the computer because the lights are off due to the power outage. * R crashed, but the other programs are still working. * R gave an error message and stopped processing your code after running for a while. * R gave an error message without running any of your code (and is waiting for your next command). * R is still running your code and the time has exceeded your patience so you think it has hung. * R completed and returned a result, but also gave warnings. * R completed your command, but gave an incorrect answer. * R completed your command but the answer is different from what you expect (but is correct according to the documentation) There are probably others. snip Since Greg has kindly raised the fortunes package today, I propose that the above be captured as an R Classic. Regards, Marc Schwartz [[alternative HTML version deleted]] __ 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.
Re: [R] Use of optim to fit two curves at the same time ?
Dear list,
In order to find a solution to my problem, I created a third objective
function including both calculations done in the previous cases. This
function return a value (i.e. the value to be minimize by optim) equal to
the sum of the two sum of squares, but it does not work (see the code added
at the end of my previous script).
Any suggestion ?
Arnaud
Dear list,
Here is a small example code that use optim and optimize in order to fit
two functions.
Is it possible to fit two functions (like those two for example) at the
same time using optim ... or another function in R ?
Thanks
Arnaud
##
## function 1
x1 - 1:100
y1 - 5.468 * x + 3 # + rnorm(100,0, 10)
dfxy - cbind(x1,y1)
# Objective function
optfunc - function(x, dfxy){
a - x[1]
b - x[2]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - a*xtest + b
sum((ysim - yobs)^2)
}
out- optim(par=c(0.2,5), fn=function(x){optfunc(x, dfxy)}, method =
Nelder-Mead, hessian = F)
## function 2
x2 - seq(0.01, 0.1, length=100)
y2 - exp(30*x2)
dfxy2 - cbind(x2,y2)
# objective function
optfunc2 - function(x, dfxy){
a - x[1]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - exp(a*xtest)
sum((ysim - yobs)^2)
}
out- optimize(f=function(x){optfunc2(x, dfxy2)}, interval=c(0,500))
##
optfunc3 - function(x, dfxy, dfxy2){
a - x[1]
b - x[2]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - a*xtest + b
obj1 - sum((ysim - yobs)^2)
c - x[3]
xtest2 - dfxy2[,1]
yobs2 - dfxy2[,2]
ysim2 - exp(c*xtest2)
obj2 - sum((ysim2 - yobs2)^2)
obj1 + obj2
}
out3- optim(par=c(0.2,5, 500), fn=function(x){optfunc3(x, dfxy, dfxy2)},
method = Nelder-Mead, hessian = F)
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Use of optim to fit two curves at the same time ?
Dear list,
Here is a small example code that use optim and optimize in order to fit
two functions.
Is it possible to fit two functions (like those two for example) at the
same time using optim ... or another function in R ?
Thanks
Arnaud
##
## function 1
x1 - 1:100
y1 - 5.468 * x + 3 # + rnorm(100,0, 10)
dfxy - cbind(x1,y1)
# Objective function
optfunc - function(x, dfxy){
a - x[1]
b - x[2]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - a*xtest + b
sum((ysim - yobs)^2)
}
out- optim(par=c(0.2,5), fn=function(x){optfunc(x, dfxy)}, method =
Nelder-Mead, hessian = F)
## function 2
x2 - seq(0.01, 0.1, length=100)
y2 - exp(30*x2)
dfxy2 - cbind(x2,y2)
# objective function
optfunc2 - function(x, dfxy){
a - x[1]
xtest - dfxy[,1]
yobs - dfxy[,2]
ysim - exp(a*xtest)
sum((ysim - yobs)^2)
}
out- optimize(f=function(x){optfunc2(x, dfxy2)}, interval=c(0,500))
##
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] GAM (mgcv) warning: matrix not positive definite
Thanks for the explanation !
Happy to know there is no problem with my models.
Have a good day,
Arnaud
2012/2/3 Simon Wood s.w...@bath.ac.uk
It is completely safe to ignore this. Here is what is going on...
mgcv routine 'mroot' is calling R routine 'chol' to find the *pivoted*
Choleski factor of a positive semi definite matrix. This is deliberate, and
completely ok to do, but 'chol' issues a warning when a matrix is only
positive semi-definite (as opposed to strictly +ve def), even if pivoting
has been requested. 'mroot' therefore suppresses the warning.
best,
Simon
On 03/02/12 20:38, Arnaud Mosnier wrote:
Dear list,
I fitted the same GAM model using directly the function gam(mgcv) ...
then as a parameter of another function that capture the warnings
messages (see below).
In the first case, there is no warning message printed, but in the last
one, the function find two warning messages stating matrix not positive
definite
So my question is: Do I have to worry about those warnings and then why
are they not printed in the simple use of the gam function.
##**###
Here is some further description:
## Simple use of gam
gam(USE ~ X1 + s(X2) + s(X3), family = binomial, data = data,
method=REML) # print no warning message.
## Using a function that capture warnings
Model_n_Warnings - function(expr) {
localWarnings - list()
outModel - withCallingHandlers(expr,
warning = function(w) {
localWarnings[[length(**localWarnings)+1]] - w$message #
store warning message
invokeRestart(muffleWarning) # avoid printing warning
message to console
})
list(outModel=outModel, warnings=localWarnings)
}
out - Model_n_Warnings (gam(USE ~ X1 + s(X2) + s(X3), family =
binomial, data = data, method=REML))
out$warnings
[[1]]
[1] matrix not positive definite
[[2]]
[1] matrix not positive definite
Thanks,
Arnaud
--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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[R] GAM (mgcv) warning: matrix not positive definite
Dear list,
I fitted the same GAM model using directly the function gam(mgcv) ... then
as a parameter of another function that capture the warnings messages (see
below).
In the first case, there is no warning message printed, but in the last
one, the function find two warning messages stating matrix not positive
definite
So my question is: Do I have to worry about those warnings and then why are
they not printed in the simple use of the gam function.
#
Here is some further description:
## Simple use of gam
gam(USE ~ X1 + s(X2) + s(X3), family = binomial, data = data,
method=REML) # print no warning message.
## Using a function that capture warnings
Model_n_Warnings - function(expr) {
localWarnings - list()
outModel - withCallingHandlers(expr,
warning = function(w) {
localWarnings[[length(localWarnings)+1]] - w$message # store
warning message
invokeRestart(muffleWarning) # avoid printing warning message
to console
})
list(outModel=outModel, warnings=localWarnings)
}
out - Model_n_Warnings (gam(USE ~ X1 + s(X2) + s(X3), family = binomial,
data = data, method=REML))
out$warnings
[[1]]
[1] matrix not positive definite
[[2]]
[1] matrix not positive definite
Thanks,
Arnaud
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[R] Model selection and model efficiency - Search for opinions
Hi, In order to find the best models I use AIC, more specifically I calculate Akaike weights then Evidence Ratio (ER) and consider that models with a ER 2 are equally likely. But the same problem remain each time I do that. I selected the best models from a set of them, but I don't know if those models are efficient to predict (or at least represent) my data. I can have selected the best element(s) of the list of the worst models. Do you find it is correct to calculate R2 or pseudo-R2 for the best set of models in order to have an idea of the representativeness of those models and use this value to select the more efficient model ? I would be glad to hear your opinions about this ! Thanks, Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] How to find the likelihood of a null model in R
Try the logLik function with your model ! Arnaud Date: Mon, 25 Jul 2011 12:16:37 +0100 From: Partha Pratim PATTNAIK p.pattn...@sms.ed.ac.uk To: r-help@R-project.org Subject: [R] How to find the likelihood of a null model in R Message-ID: 20110725121637.jo1u2ctuxy8kw...@www.sms.ed.ac.uk Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Dear All, I am working on a dataset having the dependent variable as ordinal data(discrete data) and multiple independent variables. I need to find the likelihood for the NULL model.i.e the model with only the dependent variable and all other independent variables as zero. Kindly let me know how to find the likelihood for a NULL model in R. Is there any specific function in R that can do this task? Please share if anyone has any information on this. Thanks and Regards Partha Pattnaik -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. [[alternative HTML version deleted]] __ 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] GLS models and variance explained
Dear list, Inspecting residuals of my linear models, I detected spatial autocorrelation. In order to take this into account, I decided to use the GLS method with the correlation = corGaus ( ~ X + Y). Then, I can sort my GLS models based on their AIC. But ... how to know the proportion of the variance explained by the best one (it can be best of the worst models) ? R-squared value has not the same meaning for OLS and GLS ... - Could the R2 value calculated with the OLS model (using lm) constitute a potential proxy of the variance explained by the GLS model ? (the answer is probably no) - Is a R-squared based on sqrt(cor(obs, predicted)) a better approach ? - What about pseudo R-squared like Nagelkerke's ? Suggestions for any better approach are welcome ! Thanks in advance, Arnaud __ 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.
Re: [R] Still have problems with tcltk in R 64 bit
I agree that this is a really outdated source but I did not find the
way to tell R using correctly the tcl version included (at least for
the 64 bit version).
If I remove the environment variables, things work for R 32 bit (it
uses the tcl version included), but it does not work in R 64 bit.
Where are the configuration files used to define the path to each tcl version ?
Arnaud
2011/6/14 Uwe Ligges lig...@statistik.tu-dortmund.de:
On 14.06.2011 22:01, Arnaud Mosnier wrote:
I achieve to make tcltk work on R 64 installing Active tcltk8.5 64bit
version then setting windows environment variables as in
http://www.sciviews.org/_rgui/tcltk/InstallRTclTk.html.
Don't read outdated sources but the manuals.
The R binary distribution comes with tcltk under Windows (in ${R_HOME}/tcl)
for both 32-bit and 64-bit and will user a different tcl if you set
environment variables.
Hence the easiest thing is just to tell R not to use your otehrwise set
environment variabes and use its own tcl version.
Uwe Ligges
But now, it uses only this 64 bit version and thus do not work anymore
in R 32 bit !
In my case, it solves my problem as I will probably use only R 64bit
but I do not like to end with an half solution.
Arnaud
2011/6/14 Peter Langfelderpeter.langfel...@gmail.com:
On Tue, Jun 14, 2011 at 12:47 PM, Adrienne Woottenamwoo...@ncsu.edu
wrote:
Taking a quick look for it, it seems that they have replaced it with
tcltk2. I just did the installation with the same version in windows
and it auto loaded the tcltk package and I never installed that
package to begin with. I would try it with tcltk2 and see if you get
the package to install appropriately. I'm not sure why tcltk isn't on
CRAN anymore, it makes no sense not to have both tcltk and tcltk2, but
here's hoping this helps you out.
A
FWIF, tcltk still exists but is now part of the standard R
distribution (core packages is the term I think?) and as such is
installed automatically when you install R. Therefore it is not
available from CRAN.
Peter
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Re: [R] Still have problems with tcltk in R 64 bit
I was pretty sure to have installed tcltk files for 64 bit from the
installer, but to be sure ...
- I removed previously created Environment variables (MY_TCLTK)
- I reinstalled R one more time ... this time with the full
installation option
and ... it does not work (still works with R 32bit) !
- I also tried to define directly the path to the tcl version included
with R ... as the code you provided does ... thus MY_TCLTK =
C:\Program Files\R\R-2.13.0\Tcl\bin64
... still the same error in R 64 bit, and if I want to load tcltk in R
32, it gives me the following error (normal ... it tried to load a 64
bit application in a 32 bit environment).
Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace()
for 'tcltk', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Program
Files/R/R-2.13.0/library/tcltk/libs/i386/tcltk.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: package/namespace load failed for 'tcltk'
I believe that the problem may come from the tcltk.dll file but I do
not understand how it can be broken each time when I installed other
versions ...
Arnaud
2011/6/15 Uwe Ligges lig...@statistik.tu-dortmund.de:
Well, the R code in package tcltk for startup under Windows is, as you could
have found out yourself easily:
.onLoad - function(lib, pkg)
{
packageStartupMessage(Loading Tcl/Tk interface ...,
domain = R-tcltk, appendLF = FALSE)
if(!nzchar(tclbin - Sys.getenv(MY_TCLTK))) {
tclbin - file.path(R.home(), Tcl,
if(.Machine$sizeof.pointer == 8) bin64 else
bin)
if(!file.exists(tclbin))
stop(Tcl/Tk support files were not installed, call.=FALSE)
if(.Machine$sizeof.pointer == 8) {
lib64 - gsub(\\, /, file.path(R.home(), Tcl, lib64),
fixed=TRUE)
Sys.setenv(TCLLIBPATH = lib64)
}
}
library.dynam(tcltk, pkg, lib, DLLpath = tclbin)
.C(tcltk_start, PACKAGE=tcltk)
addTclPath(system.file(exec, package = tcltk))
packageStartupMessage( , done, domain = R-tcltk)
invisible()
}
This tells us that if you do not have MY_TCLTK defined on startup of R,
you probably forgot to select the tcltk files for 64 bit from the installer
when installing your version of R.
Uwe Ligges
On 15.06.2011 14:28, Arnaud Mosnier wrote:
I agree that this is a really outdated source but I did not find the
way to tell R using correctly the tcl version included (at least for
the 64 bit version).
If I remove the environment variables, things work for R 32 bit (it
uses the tcl version included), but it does not work in R 64 bit.
Where are the configuration files used to define the path to each tcl
version ?
Arnaud
2011/6/14 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 14.06.2011 22:01, Arnaud Mosnier wrote:
I achieve to make tcltk work on R 64 installing Active tcltk8.5 64bit
version then setting windows environment variables as in
http://www.sciviews.org/_rgui/tcltk/InstallRTclTk.html.
Don't read outdated sources but the manuals.
The R binary distribution comes with tcltk under Windows (in
${R_HOME}/tcl)
for both 32-bit and 64-bit and will user a different tcl if you set
environment variables.
Hence the easiest thing is just to tell R not to use your otehrwise set
environment variabes and use its own tcl version.
Uwe Ligges
But now, it uses only this 64 bit version and thus do not work anymore
in R 32 bit !
In my case, it solves my problem as I will probably use only R 64bit
but I do not like to end with an half solution.
Arnaud
2011/6/14 Peter Langfelderpeter.langfel...@gmail.com:
On Tue, Jun 14, 2011 at 12:47 PM, Adrienne Woottenamwoo...@ncsu.edu
wrote:
Taking a quick look for it, it seems that they have replaced it with
tcltk2. I just did the installation with the same version in windows
and it auto loaded the tcltk package and I never installed that
package to begin with. I would try it with tcltk2 and see if you get
the package to install appropriately. I'm not sure why tcltk isn't on
CRAN anymore, it makes no sense not to have both tcltk and tcltk2, but
here's hoping this helps you out.
A
FWIF, tcltk still exists but is now part of the standard R
distribution (core packages is the term I think?) and as such is
installed automatically when you install R. Therefore it is not
available from CRAN.
Peter
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[R] Still have problems with tcltk in R 64 bit
Dear R users, Since a long time now, I have the following error when I want to load the tcltk library in R 64 bit. Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'C:/Program Files/R/R-2.13.0/library/tcltk/libs/x64/tcltk.dll': LoadLibrary failure: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. Error: package/namespace load failed for 'tcltk' sessionInfo() gives R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 The problem does not occur with the 32 bit version of R, thus, it is probably linked to the 64 version of Tcltk... I already tried: - to uninstall then reinstall R (changing version too...) - install ActiveTcl8.5.9.2.294317-win32-x86_64-threaded.exe (I also tried installing previous version of ActiveTcl) ... without results ! Reinstalling the application may fix this problem ... I agree, but what should I reinstall ? Any suggestions ? Arnaud __ 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.
Re: [R] Still have problems with tcltk in R 64 bit
I achieve to make tcltk work on R 64 installing Active tcltk8.5 64bit version then setting windows environment variables as in http://www.sciviews.org/_rgui/tcltk/InstallRTclTk.html. But now, it uses only this 64 bit version and thus do not work anymore in R 32 bit ! In my case, it solves my problem as I will probably use only R 64bit but I do not like to end with an half solution. Arnaud 2011/6/14 Peter Langfelder peter.langfel...@gmail.com: On Tue, Jun 14, 2011 at 12:47 PM, Adrienne Wootten amwoo...@ncsu.edu wrote: Taking a quick look for it, it seems that they have replaced it with tcltk2. I just did the installation with the same version in windows and it auto loaded the tcltk package and I never installed that package to begin with. I would try it with tcltk2 and see if you get the package to install appropriately. I'm not sure why tcltk isn't on CRAN anymore, it makes no sense not to have both tcltk and tcltk2, but here's hoping this helps you out. A FWIF, tcltk still exists but is now part of the standard R distribution (core packages is the term I think?) and as such is installed automatically when you install R. Therefore it is not available from CRAN. Peter __ 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] Problems with tcltk
Dear R-helpers, I am using R x64 and when I want to load the tcltk library, it gives me the following error: Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'C:/Program Files/R/R-2.13.0/library/tcltk/libs/x64/tcltk.dll': LoadLibrary failure: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. I tried to reinstall tcltk (ActiveTcl8.5.9.2.294317-win32-x86_64-threaded.exe) but it does not solve my problem. Here is my sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Arnaud __ 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] Problem with tcltk
Dear all, Since I installed the x64 version of R (v2.12.1), I got a problem with tcltk that I did not achieve to resolve. When loading the library, it gives me the following error message: Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'C:/PROGRA~1/R/R-212~1.1/ library/tcltk/libs/x64/tcltk.dll': LoadLibrary failure: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. Error: package/namespace load failed for 'tcltk' The same occur with a freshly installed R 2.12.2 Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'C:/PROGRA~1/R/R-212~1.2/library/tcltk/libs/x64/tcltk.dll': LoadLibrary failure: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem. Error: package/namespace load failed for 'tcltk' Any suggestions ? Arnaud [[alternative HTML version deleted]] __ 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] Variogram (nlme) of a lme object - corSpatial element question
Dear Users, From previous analysis (semi-variograms using package gstat), I found spatial autocorrelation in my dataset. The best fitted model to this spatial correlation structure is the Gaussian model (Spherical, Exponential, Linear tested and comparison done by Sum of Square errors). So I used corGaus function to define this spatial autocorrelation in my lme model using the option correlation. The Variogram function (package nlme) used on a lme object calculates the semi-variogram for the within-group residuals and add the semi-variogram of the corSpatial element (corGaus in my case) included in my model ... so far no problem. I was surprised, however, to see on the plot of the semi-variogram issued from the Variogram function, (see figure at http://imm.io/3OLe) the low range value (~1600 meters) used in the corGaus structure included in the lme object. When I fitted the same corGaus structure manually or using the fit.variogram function (package gstat) on the data of each group defined in lme, it gaves me ranges between 2050 and 2700 meters (mean 2350 meters). Can anyone explain me those differences ? Note: As I mentioned in a previous message ( http://markmail.org/message/gjgag4ohjopevgax), I tried to define a different range in the corGaus function directly in the lme function, but it is not taken into account. Arnaud [[alternative HTML version deleted]] __ 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] Bug in the function Variogram (package nlme) ?
Dears UseRs, In Zuur's book (Mixed effects models and extensions in ecology with R), p 167, it is mentionned that the Variogram function (package nlme) scale the sill to 1. Here is the plot of the semi-variogram given by the Variogram function on my lme object. (http://imm.io/3OLe) Note that the semi-variance exceed 1 !! It can probably explain why the Gaussian correlation structure fitted in my lme model is strange (curve is probably fitted to the data above 1). See my previous message a few minutes ago untitled Variogram (nlme) of a lme object - corSpatial element question. I don't know if it is a bug, but Implications could be important for model fitted with a spatial correlation structure. Arnaud [[alternative HTML version deleted]] __ 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] Potential problem with subset !!!
Dear useRs, Just a little post to provide the answer of a problem that took me some time to resolve ! Hope that reading this will permit the others to avoid that error. When using the subset function, writing subset (data, data$columnname == X) or subset (data, columnname == X) do the same thing. thus, the function consider that argument name given after the coma (like columnname) is the name of a column of the data frame considered. A problem occur when other arguments such as X are the names of both a column of the data frame and an object ! Here is an example: df - data.frame(ID = c(a,b,c,b,e), Other = 1:5) ID - unique (df$ID) ID ## Now the potential problem !! subset (df, df$ID == ID[4]) ## BE CAREFUL subset function use the column ID of the data.frame ## and NOT the object ID containing unique value Sorry if it seems obvious for some of you, but hope that others find it useful !! Arnaud __ 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] Create a function with multiple object as an output
Dear useRs,
I want to make a function that return several object (from a loop).
I know, I can put them in a list, then the function return the list,
but is it possible that it returns several independent object.
I used the assign function to create several object, it works when I
use it outside the function, but not inside.
Any suggestion ?
Here is a piece of code that do something similar to my situation.
testfunc - function ( listobj, valueX) {
for (i in 1:length(listobj)) {
objtemp - get (listobj[i])
objtemp - objtemp * valueX
assign(paste(listobj[i], _, valueX, sep=), objtemp)
}
return (??)
}
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and provide commented, minimal, self-contained, reproducible code.
[R] Column width in dbf file ... again ...
Hello, First please excuse me for reposting the same question I sent a few weeks ago, but I did not have any answer ! I am trying to manually choose the width (i.e. number of character allowed) of columns containing text when creating dbf. files using write.dbf (library foreign). In particular, I want to define this width when the column have to contain text but is empty. In that case, by default, write.dbf give a warning message then choose the width equal to the number of character in the column title. Example: df-data.frame(INDEX=1:10, TEXT=NA_character_) write.dbf(df, paste(choose.dir(), //test.dbf,sep=)) # Give a warning message but create the dbf file. The width of the column TEXT is 4 as the number of character in the word TEXT ! Thanks for your help, P.S. : complementary info. R version 2.10.1 (2009-12-14) i386-pc-mingw32 __ 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] Write.dbf ... problem
Hello, I am trying to manually choose the width (i.e. number of character allowed) of columns containing text when creating dbf. files using write.dbf (library foreign). In particular, I want to define this width when the column have to contain text but is empty. By default, write.dbf give a warning message then choose the width equal to the number of character in the column title. Example: df-data.frame(INDEX=1:10, TEXT=NA_character_) write.dbf(df, paste(choose.dir(), //test.dbf,sep=)) # Give a warning message but create the dbf file. The width of the column TEXT is 4 as the number of character in the word TEXT ! Thanks for your help, Arnaud [[alternative HTML version deleted]] __ 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.
Re: [R] How can I store the results
If you absolutely need a single file for each iteration, you can also
include the iteration number into your output filename.
for(i in 1:dim(your input data)[1]) {
results- your calculation
write.csv(results, paste(filename, _, i, sep=))
}
Arnaud
Date: Wed, 13 Jan 2010 15:59:37 +0100
From: Alex Roy alexroy2...@gmail.com
To: r-help@r-project.org
Subject: [R] How can I store the results
Message-ID:
8bdeb1b51001130659n6341b0e6oe42a029efb7a1...@mail.gmail.com
Content-Type: text/plain
Dear R users,
I am running a R code which gives me 10 columns and
160 rows. I need to run the code for 100 times and each time I need to store
the results in a single file.
I do not know how can I store them in a single file without over writting
the results?
Thanks
Alex
[[alternative HTML version deleted]]
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[R] column width in .dbf files using write.dbf ... to be continued
Dear UseRs,
I did not have any answer to my previous message (Is there a way to define
manually columns width when using write.dbf function from the library
foreign ?), so I tried to modify write.dbf function to do what I want.
Here is my modified version :
write.dbfMODIF - function (dataframe, file, factor2char = TRUE, max_nchar =
254, width = d)
{
allowed_classes - c(logical, integer, numeric, character,
factor, Date)
if (!is.data.frame(dataframe))
dataframe - as.data.frame(dataframe)
if (any(sapply(dataframe, function(x) !is.null(dim(x)
stop(cannot handle matrix/array columns)
cl - sapply(dataframe, function(x) class(x[1L]))
asis - cl == AsIs
cl[asis sapply(dataframe, mode) == character] - character
if (length(cl0 - setdiff(cl, allowed_classes)))
stop(data frame contains columns of unsupported class(es) ,
paste(cl0, collapse = ,))
m - ncol(dataframe)
DataTypes - c(logical = L, integer = N, numeric = F,
character = C, factor = if (factor2char) C else N,
Date = D)[cl]
for (i in seq_len(m)) {
x - dataframe[[i]]
if (is.factor(x))
dataframe[[i]] - if (factor2char)
as.character(x)
else as.integer(x)
else if (inherits(x, Date))
dataframe[[i]] - format(x, %Y%m%d)
}
precision - integer(m)
scale - integer(m)
dfnames - names(dataframe)
for (i in seq_len(m)) {
nlen - nchar(dfnames[i], b)
x - dataframe[, i]
if (is.logical(x)) {
precision[i] - 1L
scale[i] - 0L
}
else if (is.integer(x)) {
rx - range(x, na.rm = TRUE)
rx[!is.finite(rx)] - 0
if (any(rx == 0))
rx - rx + 1
mrx - as.integer(max(ceiling(log10(abs(rx +
3L)
precision[i] - min(max(nlen, mrx), 19L)
scale[i] - 0L
}
else if (is.double(x)) {
precision[i] - 19L
rx - range(x, na.rm = TRUE)
rx[!is.finite(rx)] - 0
mrx - max(ceiling(log10(abs(rx
scale[i] - min(precision[i] - ifelse(mrx 0L, mrx +
3L, 3L), 15L)
}
else if (is.character(x)) {
if (width == d) {
mf - max(nchar(x[!is.na(x)], b))
p - max(nlen, mf)
if (p max_nchar)
warning(gettext(character column %d will be truncated
to %d bytes,
i, max_nchar), domain = NA)
precision[i] - min(p, max_nchar)
scale[i] - 0L
} else {
if (width max_nchar)
warning(gettext(character column %d will be truncated
to %d bytes,
i, max_nchar), domain = NA)
precision[i] - min(width, max_nchar)
}
}
else stop(unknown column type in data frame)
}
if (any(is.na(precision)))
stop(NA in precision)
if (any(is.na(scale)))
stop(NA in scale)
invisible(.Call(DoWritedbf, as.character(file), dataframe,
as.integer(precision), as.integer(scale), as.character(DataTypes)))
}
However, when I wanted to use this function ... it does not find the
DoWritedbf function that is called in the last lines (a function written in
C).
Is there a way to temporally replace the original write.dbf function by this
one in the foreign package ?
Thanks,
Arnaud
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
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[R] column width in .dbf files using write.dbf
Dear useRs, Is there a way to define manually columns width when using write.dbf function from the library foreign ? Thanks, Arnaud R version 2.10.0 (2009-10-26) i386-pc-mingw32 [[alternative HTML version deleted]] __ 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] Strange characters that block import
Dear useRs, I try to import a text file that contain some strange characters coming from the misinterpretation of foreign language characters by another software (see below). Here is an example of text with a line containing characters that bug the import name;number zdsfbg;2 ;3 dtryjh;4 R do not want to import lines after those strange characters (i.e. import only the first two lines, one is the header, the second the first line of data). I already try to import using other encoding such as latin1 or UTF-8 but it does not solve the problem. Replacing those character in a text editor before importing solve the solution, but I want that the user of my script do not have to edit the text before the analysis in R. Any hint ?? Thanks [[alternative HTML version deleted]] __ 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.
