[R] Cross build Makefile
Hello, I am trying to use Yan and Rossini's Makefile for cross building Windows versions of R packages in Linux with R 1.9.0. When compiling R with the mingw tools I get an error about expm1 being undeclared when first found at src/main/arithmetic.c:1019 If I fiddle a bit with it later on I also get errors about log1p bein undeclared. Any idea what should I look for? I am using R 1.9.0 in Debian, with R-mathlib avaliable, and gcc 3.3. Thanks, iago __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hidden markov models in R?
Hi Cezar, Download and install the repeated package by Jim Lindsey and type ?hidden bye, ingmar Hi, friends! Has R estimation (library, for example) to do estimation in HMM? Thanks in advance, Cezar Freitas Estatistico - Comissao Permanente para os Vestibulares / UNICAMP Probabilidade e Estatistica Aplicadas - IME / USP | IMECC / UNICAMP Campinas | Sao Paulo, SP - Brasil __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Greater than 1 or less than 1?
> Date: Sun, 20 Jun 2004 18:32:46 -0400 > From: "Zhen Chen" <[EMAIL PROTECTED]> > > I have problem evaluating the expression h = exp(x)/(exp(exp(x))-1) for > large negative x. This expression is actually the probability > that y = 1 when y is a Poisson random variable truncated at 0, hence > must satisfy 0 <= h <= 1. However, when > x < -18, I may get an h value that is larger than 1 while the true > value should be a quantity that is smaller than but very close to 1. > For example when x = -19, h = 1.031174. I tried to use > different form of h and none of > them give me an h value that is less than or equal to 1. I also tried > to find patterns, but discovered none: for some x < -18, h is below 1; > for others > h is greater than 1. Is there any trick that enables me to obtain > theoretically correct results from this expression? > exp(x)/(exp(exp(x)) - 1) is less than 1 for me for x = -18 with R-1.9.0 on a Solaris 9 system, a NetBSD 2.0C system and a Windows XP system. You could try exp(x)/expm1(exp(x)), but if the longer expression doesn't work, then this may not either, though it does give slightly different results on my systems. E.g.: > x = -19 > exp(x)/(exp(exp(x)) - 1) - 1 [1] -2.047911e-09 > exp(x)/(expm1(exp(x))) - 1 [1] -2.801398e-09 log(1 + x) and exp(x) - 1 are often treated specially in math libraries for when x << 0. Ray Brownrigg __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Greater than 1 or less than 1?
On Sun, 20 Jun 2004, Zhen Chen wrote: > I have problem evaluating the expression h = exp(x)/(exp(exp(x))-1) for > large negative x. This expression is actually the probability > that y = 1 when y is a Poisson random variable truncated at 0, hence > must satisfy 0 <= h <= 1. However, when You would be better off using the functions provided for the Poisson distribution. Either dpois(1,exp(x))/ppois(0.5,exp(x),lower.tail=FALSE) or to get 1-h ppois(1.5,exp(x),lower.tail=FALSE)/ppois(0.5,exp(x),lower.tail=FALSE) -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Greater than 1 or less than 1?
"Zhen Chen" <[EMAIL PROTECTED]> writes: > I have problem evaluating the expression h = exp(x)/(exp(exp(x))-1) > for large negative x. This expression is actually the probability > that y = 1 when y is a Poisson random variable truncated at 0, hence > must satisfy 0 <= h <= 1. However, when > x < -18, I may get an h value that is larger than 1 while the true > value should be a quantity that is smaller than but very close to 1. > For example when x = -19, h = 1.031174. I tried to use > different form of h and none of > them give me an h value that is less than or equal to 1. I also tried > to find patterns, but discovered none: for some x < -18, h is below 1; > for others > h is greater than 1. Is there any trick that enables me to obtain > theoretically correct results from this expression? expm1() should help... What platform is this? I don't see it until x=-30: > exp(-30) [1] 9.357623e-14 > exp(exp(-30))-1 [1] 9.348078e-14 which is of course "wrong" since exp(x) > x + 1 mathematically. However, notice that in double precision calculations the latter value is only accurate up to 1e-15 or so. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fw: Evaluating strings as variables
[EMAIL PROTECTED] writes: > > sapply(colors, get) > > > > or? > unlist(mget(colors, envir = as.environment(-1), inherits = TRUE)) Ah, yes, forgot about mget. Doesn't seem to make things much cleaner though... (although get() also needs a bit more care about environments). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Greater than 1 or less than 1?
I have problem evaluating the expression h = exp(x)/(exp(exp(x))-1) for large negative x. This expression is actually the probability that y = 1 when y is a Poisson random variable truncated at 0, hence must satisfy 0 <= h <= 1. However, when x < -18, I may get an h value that is larger than 1 while the true value should be a quantity that is smaller than but very close to 1. For example when x = -19, h = 1.031174. I tried to use different form of h and none of them give me an h value that is less than or equal to 1. I also tried to find patterns, but discovered none: for some x < -18, h is below 1; for others h is greater than 1. Is there any trick that enables me to obtain theoretically correct results from this expression? Thanks. Zhen Chen, Ph.D. Assistant Professor of Biostatistics Department of Biostatistics & Epidemiology University of Pennsylvania School of Medicine 423 Guardian Drive -- 625 Blockley Hall Philadelphia, PA 19104-6021 voice: 215-573-8545 fax: 215-573-4865 email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Another NEWBIE
Dear Frank, First, thank you for your kind remarks about the Rcmdr package. Please note that the Rcmdr package is meant to be a basic statistics GUI for R, to be used, for example, in an introductory statistics course. It covers only a very small fraction of what's available in R. Almost all of the statistical capabilities of the Rcmdr package are from other packages. In particular, since you mention it, the factor-analysis dialog simply calls the factanal() function in the stats package, which is part of the standard R distribution. See ?factanal (or press the Help button in the Rcmdr factor-analysis dialog) for details. As well, you can take a look at the R commands that the Rcmdr generates. Regards, John > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of F.Kalder > Sent: Sunday, June 20, 2004 4:06 PM > To: [EMAIL PROTECTED] > Subject: Re: [R] Another NEWBIE > > Hello, > > And thanks again for your answers, perspectives and more... > > So, as I understood, R can (nearly) do anything. So, also > because it's free, it is worth a try ;-). > > I then next will start with reading some introductory texts. > And, wow, I'm quite 'overloaded', because there is so much > stuff available, I don?t know where to start and get a foot > in the door. I think I take one of the advices and will begin > with the "Notes on the use of R for psychology experiments > and questionnaires" text. > > The hint to the Rcmdr package was nice :-). That was nearly > like SPSS base system. When at last to know, which package to > use and for what kind of problem is another thing of course ... > > Still I have had problems with importing SPSS files. But I > will read on it too. > > The factor analysis tool of Rcmdr I didn?t fully understand. > So, there also will be much work to do. > > I also noticed that my stats abilities aren?t very profound. > I?m so 'drilled' in doing 'standard stuff' and using more the > SPSS output than knowing exactly what I have to do, that I > will have to have a much closer look into a good book on > stats ... well, the Hair et al. is a good book of course, but > any recommendations are welcome :-). > > You all wrote about the graphics in R and those in Rcmdr I > saw are to me mostly the same as in SPSS. Nevertheless, I > even don?t know when and for what to use that whole bunch of > graphics anyway ... still looking sometimes a bit envy on > huge 3D-graphics of multivariate bell curves and stuff on > book covers but can?t do anything with it. > > The data entries by ASCII files are strange to me, because > I?m so used to work with a (the SPSS) spread sheet (mostly > the good old typing in from paper & pencil questionnaires), > that I don?t know how to handle that yet. > Maybe using a SPSS- or at least Excel-like tool would be > helpful for that. > > So, my next move will be reading the mentioned text on > questionnaires and then some basic introduction on R, knowing > then, how it principally works, what?s with the packages, how > to manage the data and so on ... I also think, I have to do > some homework on stats either ... > > Thanks again ... > > Frank > __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and echoing R comments
Charles H. Franklin wrote: Is there any way to echo comments from an R source file into an SWeave->LaTeX document? Example: # Npop is population total # Npoph0..Npoph2 are stratum totals # Npoph is vector of stratum totals Npop<-sum(to2000) Npoph0<-sum(to2000[bg==0]) Npoph1<-sum(to2000[bg==1]) Npoph2<-sum(to2000[bg==2]) Npoph<-c(Npoph0,Npoph1,Npoph2) In the final LaTeX document, I'd like the comments to be echoed so readers other than me have guidance about variable names etc. I suppose advocates of literate programming might argue that if the comment is important it should be in the body of the .snw file, not merely as R comments. Still... it seems easier to use brief comments in the code itself and more explanatory text in the body of the document. Searches of "Sweave" and "comment" in the list and documentation didn't turn up anything about echoing comments in either R or Sweave. Thanks. Charles I agree that it would be nice to see comments in the output. I hope that Fritz Leisch will consider adding a hook that is a user-provided R function that take vectors of character strings representing a chunk of code and generating any desired LaTeX markup for pretty printing of the code. The function would return character vectors in LaTeX format. I like comments to appear in a smaller font, and for certain character translations, such as <- being replaced with a left arrow. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fw: Evaluating strings as variables
> "Robin Gruna" <[EMAIL PROTECTED]> writes:
>
>> I have the following problem: I have a list as follows,
>>
>> > values <- list(red = 1, yellow = 2, blue = 3)
>>
>> > values
>> $red
>> [1] 1
>>
>> $yellow
>> [1] 2
>>
>> $blue
>> [1] 3
>>
>> There is also a vector containing the diffrent "colors" as character
>> strings:
>>
>> > colors <- c("red", "red", "blue", "yellow", "red", "blue")
>> > colors
>> [1] "red""red""blue" "yellow" "red""blue"
>>
>> Now i can attach the list values to R:
>>
>> > attach(values)
>> > red
>> [1] 1
>>
>> etc...
>>
>> Now to my problem: How can I make R in a simple way to evaluate the
>> strings "red", "blue" etc. as variables, returning their numeric
>> values ? As result I want to get a vector containing the values of the
>> colors like this one:
>>
>> > values.colors
>> [1] 1 1 3 2 1 3
>
> Forget about the attach() business, and do
>
> values <- unlist(values) # or values <- c(red = 1, yellow = 2, blue = 3)
> values.colors <- values[colors]
>
> If you insist on going via variables, try
>
> sapply(colors, get)
>
or?
unlist(mget(colors, envir = as.environment(-1), inherits = TRUE))
Matthias
> --
>O__ Peter Dalgaard Blegdamsvej 3
> c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
> ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
>
> __
> [EMAIL PROTECTED] mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Another NEWBIE
Hello, And thanks again for your answers, perspectives and more... So, as I understood, R can (nearly) do anything. So, also because it's free, it is worth a try ;-). I then next will start with reading some introductory texts. And, wow, I'm quite 'overloaded', because there is so much stuff available, I don?t know where to start and get a foot in the door. I think I take one of the advices and will begin with the "Notes on the use of R for psychology experiments and questionnaires" text. The hint to the Rcmdr package was nice :-). That was nearly like SPSS base system. When at last to know, which package to use and for what kind of problem is another thing of course ... Still I have had problems with importing SPSS files. But I will read on it too. The factor analysis tool of Rcmdr I didn?t fully understand. So, there also will be much work to do. I also noticed that my stats abilities aren?t very profound. I?m so 'drilled' in doing 'standard stuff' and using more the SPSS output than knowing exactly what I have to do, that I will have to have a much closer look into a good book on stats ... well, the Hair et al. is a good book of course, but any recommendations are welcome :-). You all wrote about the graphics in R and those in Rcmdr I saw are to me mostly the same as in SPSS. Nevertheless, I even don?t know when and for what to use that whole bunch of graphics anyway ... still looking sometimes a bit envy on huge 3D-graphics of multivariate bell curves and stuff on book covers but can?t do anything with it. The data entries by ASCII files are strange to me, because I?m so used to work with a (the SPSS) spread sheet (mostly the good old typing in from paper & pencil questionnaires), that I don?t know how to handle that yet. Maybe using a SPSS- or at least Excel-like tool would be helpful for that. So, my next move will be reading the mentioned text on questionnaires and then some basic introduction on R, knowing then, how it principally works, what?s with the packages, how to manage the data and so on ... I also think, I have to do some homework on stats either ... Thanks again ... Frank -- +++ Jetzt WLAN-Router für alle DSL-Einsteiger und Wechsler +++ GMX DSL-Powertarife zudem 3 Monate gratis* http://www.gmx.net/dsl __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] regarding saving R graphis images directly to directory
On Sunday 20 June 2004 15:15, SAURIN wrote: > Dear R, > > I am student at University of new haven, CT.I am trying to run my R > scripts where I don't have X11() authentication to my account. I run > those R scripts and when I generate any graphics I get error and it > comes out from system. > > if possible , please let me know how can i run R scripts ...so, that > I just SAVE BOX PLOT or HISTOGRAM jpeg or png files to current > directory without poping up on screen or without using any devices or > make them silent..or something. You could output to postscript (see ?postscript for details). This sounds like a UNIX/Linux system, so you could probably use 'convert' afterwards to get jpeg/png if you want. You can start R with 'R -g none' to make postscript the default device. Hope that helps, Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fw: Evaluating strings as variables
"Robin Gruna" <[EMAIL PROTECTED]> writes:
> I have the following problem: I have a list as follows,
>
> > values <- list(red = 1, yellow = 2, blue = 3)
>
> > values
> $red
> [1] 1
>
> $yellow
> [1] 2
>
> $blue
> [1] 3
>
> There is also a vector containing the diffrent "colors" as character strings:
>
> > colors <- c("red", "red", "blue", "yellow", "red", "blue")
> > colors
> [1] "red""red""blue" "yellow" "red""blue"
>
> Now i can attach the list values to R:
>
> > attach(values)
> > red
> [1] 1
>
> etc...
>
> Now to my problem: How can I make R in a simple way to evaluate the strings "red",
> "blue" etc. as variables, returning their numeric values ?
> As result I want to get a vector containing the values of the colors like this one:
>
> > values.colors
> [1] 1 1 3 2 1 3
Forget about the attach() business, and do
values <- unlist(values) # or values <- c(red = 1, yellow = 2, blue = 3)
values.colors <- values[colors]
If you insist on going via variables, try
sapply(colors, get)
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Fw: Evaluating strings as variables
- Original Message -
From: Robin Gruna
To: [EMAIL PROTECTED]
Sent: Sunday, June 20, 2004 5:42 PM
Subject: Evaluating strings as variables
Hello,
I have the following problem: I have a list as follows,
> values <- list(red = 1, yellow = 2, blue = 3)
> values
$red
[1] 1
$yellow
[1] 2
$blue
[1] 3
There is also a vector containing the diffrent "colors" as character strings:
> colors <- c("red", "red", "blue", "yellow", "red", "blue")
> colors
[1] "red""red""blue" "yellow" "red""blue"
Now i can attach the list values to R:
> attach(values)
> red
[1] 1
etc...
Now to my problem: How can I make R in a simple way to evaluate the strings "red",
"blue" etc. as variables, returning their numeric values ?
As result I want to get a vector containing the values of the colors like this one:
> values.colors
[1] 1 1 3 2 1 3
Thanks a lot,
greetings Robin
[[alternative HTML version deleted]]
__
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[R] regarding saving R graphis images directly to directory
Dear R, I am student at University of new haven, CT.I am trying to run my R scripts where I don't have X11() authentication to my account. I run those R scripts and when I generate any graphics I get error and it comes out from system. if possible , please let me know how can i run R scripts ...so, that I just SAVE BOX PLOT or HISTOGRAM jpeg or png files to current directory without poping up on screen or without using any devices or make them silent..or something. Thakn you, Saurin Jnai __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Html help does not work in Mac OSX 10.3.4
Hello: You are damn right! I haven't noticed because I rarely use the html help. I will be working on. I'll let you know. Regards. On Fri, 18 Jun 2004, Emilio A. Laca wrote: > I recently upgraded from R 1.8 to 1.9. I removed 1.8 following the > instructions. Html help has not worked since. When htmlhelp="TRUE" the > help.start() command results in the "patience" message and nothing else > happens. I am using mac osx 10.3.4. Help worked fine when I was using R 1.8. > > I need help help ;-] Thanks! > -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem locfit
I have a problem with the use of locfit with censured data, when I carry out locfit by: fitbmt<-locfit(~recur,data=BMTAGE11,cens=df.status,family="hazard",alpha=0.5) it does not give me any message, but if I want to obtain the graph or even if I ask for (fitbmt) made it gives me the following message: > fitbmt31 Problem: Object "fitbmt31" not found, while calling subroutine slocfit Use traceback() to see the call stack I have this problem with several dataset ,but I don't know what is the problem thank you for your help - Dialoguez en direct avec vos amis grâce à Yahoo! Messenger ! [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Sweave and echoing R comments
Is there any way to echo comments from an R source file into an SWeave->LaTeX document? Example: # Npop is population total # Npoph0..Npoph2 are stratum totals # Npoph is vector of stratum totals Npop<-sum(to2000) Npoph0<-sum(to2000[bg==0]) Npoph1<-sum(to2000[bg==1]) Npoph2<-sum(to2000[bg==2]) Npoph<-c(Npoph0,Npoph1,Npoph2) In the final LaTeX document, I'd like the comments to be echoed so readers other than me have guidance about variable names etc. I suppose advocates of literate programming might argue that if the comment is important it should be in the body of the .snw file, not merely as R comments. Still... it seems easier to use brief comments in the code itself and more explanatory text in the body of the document. Searches of "Sweave" and "comment" in the list and documentation didn't turn up anything about echoing comments in either R or Sweave. Thanks. Charles -- Charles H. Franklin Professor, Political Science University of Wisconsin, Madison 608-263-2022 [EMAIL PROTECTED] [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] A way to list only variables or functions?
Here they are again modified to remove that bug: ls.funs <- function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if(is.function(get(x,env=env)))x)) ls.var <- function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if(!is.function(get(x,env=env)))x)) Date: Sun, 20 Jun 2004 17:02:40 +0100 (BST) From: Prof Brian Ripley <[EMAIL PROTECTED]> To: Shin, Daehyok <[EMAIL PROTECTED]> Cc: <[EMAIL PROTECTED]> Subject: RE: [R] A way to list only variables or functions? On Sun, 20 Jun 2004, Shin, Daehyok wrote: > Neat! Thanks. Note that these are not correct, as the get is not done from the correct environment. The function ls.str I pointed you to is correct. > How about incorporating this support into standard commands, ls() or > objects()? Well, there already is ls[f].str. > Daehyok Shin (Peter) > > > -Original Message- > > From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] > > Sent: Sunday, June 20, 2004 AM 10:06 > > To: [EMAIL PROTECTED]; [EMAIL PROTECTED] > > Subject: RE: [R] A way to list only variables or functions? > > > > > > > > > > These two functions will list the functions and variables > > respectively: > > > > ls.funs <- > > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > > (is.function(get(x)))x)) > > > > ls.vars <- > > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > > (!is.function(get(x)))x)) > > > > > > To use: > > > > ls.funs() > > ls.vars() > > > > > > Date: Sat, 19 Jun 2004 22:59:57 -0400 > > From: Shin <[EMAIL PROTECTED]> > > To: R Help <[EMAIL PROTECTED]> > > Subject: [R] A way to list only variables or functions? > > > > > > I am curious if there is any way to list only variables or functions in > > current environment, rather than listing all objects? Thanks. > > > > -- > > Daehyok Shin (Peter) > > Geography Department > > Univ. of North Carolina-Chapel Hill > > > > > > > > ___ > > No banners. No pop-ups. No kidding. > > > > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Another NEWBIE
Charles and Kimberly Maner wrote: Hi Frank. I am (somewhat) new to R as well, but almost a 10 yr SAS veteran. I work for a very large US Bank and have spent a considerable part of my career in Corp Mktg leveraging data for, arguably, data mining, next purchase, attrition, balance diminishment and the like. I am now managing an Operations Research group in their Customer Service and Support (aka Telephone/Call Center Support) within the forecasting and analytics group. What I have found, broadly and personally, regarding R vs. sAS is the following: 1. You simply can't beat the price of R vs. Insightful Corp.'s S-Splus, not to mention SAS. 2. The support folks for R are among the very best, (e.g., most helpful, energetic and enthusiastic to help) 3. R is far, far leaner from what I have seen thus far for modeling, binning/discretizing, graphing, etc. vs. SAS. Thanks for your note. I assume you meant to say 'more capable' rather than 'leaner'. 4. SAS is, per a previous post, (quite debatably) superior for manipulation and handling of fantastically large datasets. I have found that R's strength is not really in merging datasets and dataset manipulation. Although, major caveat here, it greatly depends on what you need done to the data. For lagging, diffing, binning, R is superior. For match merging, at this stage, I vote for SAS. (Again, I stress I've only 6-8 mos of moderate R experience.) You are right, for huge datasets. For others, R is great, even for merging. Many examples are provided in the Alzola and Harrell text on http://biostat.mc.vanderbilt.edu 5. The challenge with R is, perhaps, it's very strength--language density. Once I learn how to do something in R vs. SAS, R's code is fractionally as large as SAS. Literally, it may take 10 lines of code in SAS vs. a one liner in R. That's powerful. However, due to my SAS experience, I've banged out the SAS code and am still looking/hunting for the R equivalent. However, once doing so, it's, borrowing from a popular vegetable drink slogan, "Wow, I could have done that in R." Yes I agree. 6. And, lastly, while R is well documented, I seem to find one of the areas of documentation somewhat lacking is a great big R "recipe" book. (Suggestions, BTW, are welcome here.) Documentation of the R language is in place with more being published, (alongside S-Plus), annually. However, there does not appear to be, for example, an "R Transition Recipes for Experienced SAS Users" book. That, ultimately, is what would help me, (I think.) Again, the issue really is simply learning and using the language. Experienced R users, I'm convinced, could do everything R I'm doing in SAS, (with money left over for a few coffees at Starbuck's). I agree. What I really think is needed is a compendium of examples, especially for data manipulation. I gave a talk about this last week; abstract is at http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/FrankHarrellrmanip with links to other places. A meager attempt at navigating some of the more commonly used R functions is at http://biostat.mc.vanderbilt.edu/s/finder/finder.html In conclusion, I still think that, given one's budget and projects, there's a place for SAS and R to co-exist. But, that paradigm diminishes as (1) the size of the datasets become smaller and, (2) your problems are more academic/researchy/specific in nature. For graphing, esp. w/the Lattice package, R is simply superior (IMHO), period, to SAS. (For some reason, SAS has just not felt the need to improve their graphics, at least the SAS/Graph part of their offering.) And, for the SAS lovers out there, this opinion is mine only as I continue to be primarily a SAS client attempting to transition to R. Frank, while I've probably been too wordy, I've attempted to provide another perspective for you. Good luck. No, well said, Thanks, Frank Thanks, Charles -- Message: 7 Date: Sat, 19 Jun 2004 18:15:19 +0200 (MEST) From: "F.Kalder" <[EMAIL PROTECTED]> Subject: Re: [R] Another NEWBIE To: [EMAIL PROTECTED] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hi, Thank you all who anwered me. I think, I mainly thought to understand the difference between SPSS /SAS and R, but didn't really get the point (what explains the question, wich metods R can't do). Maybe, because I don't have much experience with programming (near to none). My background in stats goes also only back to indroductory classes and an advanced course in multivariate statistics. To this, I'm working with Hair, Anderson, Tatham & Blacks's "Multivariate Data Analysis" (5th Ed.) as my ressource, mainly with questionnaire analysis (Reliability Analysis and Factor Analysis, also MDS, Conjoint etc. plus sometimes standard MANOVA, Multiplke Regression etc.). So, maybe my stats aren't sophisticated enough to use R, I'm just a standard user of applied statistical methods, not an academic researcher or even a statistician. It
Re: [R] if syntax
On Sun, Jun 20, 2004 at 09:00:39AM -0700, [EMAIL PROTECTED] wrote: > I wanted to look up the internal R documentation for if via "?if", but > this does not work. making the latter work would be a good idea. FYI, it also works inside of (X)Emacs where the (highly recommend) ESS mode is kind enough to translate ?if into ?"if" so that the desired help is in fact shown. Hth, Dirk -- FEATURE: VW Beetle license plate in California __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Another NEWBIE
Hi Frank. I am (somewhat) new to R as well, but almost a 10 yr SAS veteran. I work for a very large US Bank and have spent a considerable part of my career in Corp Mktg leveraging data for, arguably, data mining, next purchase, attrition, balance diminishment and the like. I am now managing an Operations Research group in their Customer Service and Support (aka Telephone/Call Center Support) within the forecasting and analytics group. What I have found, broadly and personally, regarding R vs. sAS is the following: 1. You simply can't beat the price of R vs. Insightful Corp.'s S-Splus, not to mention SAS. 2. The support folks for R are among the very best, (e.g., most helpful, energetic and enthusiastic to help) 3. R is far, far leaner from what I have seen thus far for modeling, binning/discretizing, graphing, etc. vs. SAS. 4. SAS is, per a previous post, (quite debatably) superior for manipulation and handling of fantastically large datasets. I have found that R's strength is not really in merging datasets and dataset manipulation. Although, major caveat here, it greatly depends on what you need done to the data. For lagging, diffing, binning, R is superior. For match merging, at this stage, I vote for SAS. (Again, I stress I've only 6-8 mos of moderate R experience.) 5. The challenge with R is, perhaps, it's very strength--language density. Once I learn how to do something in R vs. SAS, R's code is fractionally as large as SAS. Literally, it may take 10 lines of code in SAS vs. a one liner in R. That's powerful. However, due to my SAS experience, I've banged out the SAS code and am still looking/hunting for the R equivalent. However, once doing so, it's, borrowing from a popular vegetable drink slogan, "Wow, I could have done that in R." 6. And, lastly, while R is well documented, I seem to find one of the areas of documentation somewhat lacking is a great big R "recipe" book. (Suggestions, BTW, are welcome here.) Documentation of the R language is in place with more being published, (alongside S-Plus), annually. However, there does not appear to be, for example, an "R Transition Recipes for Experienced SAS Users" book. That, ultimately, is what would help me, (I think.) Again, the issue really is simply learning and using the language. Experienced R users, I'm convinced, could do everything R I'm doing in SAS, (with money left over for a few coffees at Starbuck's). In conclusion, I still think that, given one's budget and projects, there's a place for SAS and R to co-exist. But, that paradigm diminishes as (1) the size of the datasets become smaller and, (2) your problems are more academic/researchy/specific in nature. For graphing, esp. w/the Lattice package, R is simply superior (IMHO), period, to SAS. (For some reason, SAS has just not felt the need to improve their graphics, at least the SAS/Graph part of their offering.) And, for the SAS lovers out there, this opinion is mine only as I continue to be primarily a SAS client attempting to transition to R. Frank, while I've probably been too wordy, I've attempted to provide another perspective for you. Good luck. Thanks, Charles -- Message: 7 Date: Sat, 19 Jun 2004 18:15:19 +0200 (MEST) From: "F.Kalder" <[EMAIL PROTECTED]> Subject: Re: [R] Another NEWBIE To: [EMAIL PROTECTED] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hi, Thank you all who anwered me. I think, I mainly thought to understand the difference between SPSS /SAS and R, but didn't really get the point (what explains the question, wich metods R can't do). Maybe, because I don't have much experience with programming (near to none). My background in stats goes also only back to indroductory classes and an advanced course in multivariate statistics. To this, I'm working with Hair, Anderson, Tatham & Blacks's "Multivariate Data Analysis" (5th Ed.) as my ressource, mainly with questionnaire analysis (Reliability Analysis and Factor Analysis, also MDS, Conjoint etc. plus sometimes standard MANOVA, Multiplke Regression etc.). So, maybe my stats aren't sophisticated enough to use R, I'm just a standard user of applied statistical methods, not an academic researcher or even a statistician. It was mainly a descision by costs, because R is free software. With the concept, I completely mistook the R concept as a programming environment more as a kind of advanced SPSS Syntax (because I also would call it "programming" when using it), which I now know, is completely wrong. So, I again thank for your help. Cheers, Frank. -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] hidden markov models in R?
Hi, friends! Has R estimation (library, for example) to do estimation in HMM? Thanks in advance, Cezar Freitas Estatistico - Comissao Permanente para os Vestibulares / UNICAMP Probabilidade e Estatistica Aplicadas - IME / USP | IMECC / UNICAMP Campinas | Sao Paulo, SP - Brasil __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] if syntax
[EMAIL PROTECTED] wrote:
I ran into an interesting oddity of R,
if (0) { print(1); }
else { print(2); }
In both cases the ";" is superflously .
If if(){}else{} is within an expression (e.g. a function's body), both
ways work.
Do you really want to use it outside a function's body? If so, I suggest
to write:
if(...){
...
} else{
...
}
is a syntax error, while
if (0) { print(1); } else { print(2); }
or
if (0) { print(1);
} else { print(2); }
is not. I presume it has to do with the duality of the newline
functioning as an end of command (;) character, though it still seems a
bit odd, and it took me a while to figure out what was wrong. I
eventually figured out that to resolve this ambiguity, I would guess
that ifelse() would be a preferred function.
No. ifelse() is for the vectorized conditions. if(){} else{} is more
efficient for length 1 conditions. Please read help("if") and
help("ifelse").
I wanted to look up the internal R documentation for if via "?if", but
this does not work. making the latter work would be a good idea.
?"if" or help("if") do work perfectly.
Uwe Ligges
regards, /iaw
---
ivo welch
professor of finance and economics
brown / nber / yale
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Re: [R] if syntax
try
?"if"
Best,
Matthias
[EMAIL PROTECTED] wrote:
I ran into an interesting oddity of R,
if (0) { print(1); }
else { print(2); }
is a syntax error, while
if (0) { print(1); } else { print(2); }
or
if (0) { print(1);
} else { print(2); }
is not. I presume it has to do with the duality of the newline
functioning as an end of command (;) character, though it still seems a
bit odd, and it took me a while to figure out what was wrong. I
eventually figured out that to resolve this ambiguity, I would guess
that ifelse() would be a preferred function.
I wanted to look up the internal R documentation for if via "?if", but
this does not work. making the latter work would be a good idea.
regards, /iaw
---
ivo welch
professor of finance and economics
brown / nber / yale
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
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--
Matthias Burger
Bioinformatics R&D
Epigenomics AG www.epigenomics.com
Kleine Präsidentenstraße 1 fax: +49-30-24345-555
10178 Berlin Germanyphone: +49-30-24345-0
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Re: [R] if syntax
This has been discussed several times on this list. Note that line 2 of
paragraph 2 of help("if") says the following :
" In particular, you should not have a newline between '}' and 'else' to
avoid a syntax error in entering a 'if ... else' construct at the
keyboard or via 'source'. "
On Sun, 2004-06-20 at 17:00, [EMAIL PROTECTED] wrote:
> I ran into an interesting oddity of R,
> if (0) { print(1); }
> else { print(2); }
> is a syntax error, while
> if (0) { print(1); } else { print(2); }
> or
> if (0) { print(1);
> } else { print(2); }
> is not. I presume it has to do with the duality of the newline
> functioning as an end of command (;) character, though it still seems a
> bit odd, and it took me a while to figure out what was wrong. I
> eventually figured out that to resolve this ambiguity, I would guess
> that ifelse() would be a preferred function.
>
> I wanted to look up the internal R documentation for if via "?if", but
> this does not work. making the latter work would be a good idea.
>
> regards, /iaw
> ---
> ivo welch
> professor of finance and economics
> brown / nber / yale
>
> __
> [EMAIL PROTECTED] mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
__
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RE: [R] A way to list only variables or functions?
On Sun, 20 Jun 2004, Shin, Daehyok wrote: > Neat! Thanks. Note that these are not correct, as the get is not done from the correct environment. The function ls.str I pointed you to is correct. > How about incorporating this support into standard commands, ls() or > objects()? Well, there already is ls[f].str. > Daehyok Shin (Peter) > > > -Original Message- > > From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] > > Sent: Sunday, June 20, 2004 AM 10:06 > > To: [EMAIL PROTECTED]; [EMAIL PROTECTED] > > Subject: RE: [R] A way to list only variables or functions? > > > > > > > > > > These two functions will list the functions and variables > > respectively: > > > > ls.funs <- > > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > > (is.function(get(x)))x)) > > > > ls.vars <- > > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > > (!is.function(get(x)))x)) > > > > > > To use: > > > > ls.funs() > > ls.vars() > > > > > > Date: Sat, 19 Jun 2004 22:59:57 -0400 > > From: Shin <[EMAIL PROTECTED]> > > To: R Help <[EMAIL PROTECTED]> > > Subject: [R] A way to list only variables or functions? > > > > > > I am curious if there is any way to list only variables or functions in > > current environment, rather than listing all objects? Thanks. > > > > -- > > Daehyok Shin (Peter) > > Geography Department > > Univ. of North Carolina-Chapel Hill > > > > > > > > ___ > > No banners. No pop-ups. No kidding. > > > > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- Brian D. Ripley, [EMAIL PROTECTED] 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] if syntax
I ran into an interesting oddity of R,
if (0) { print(1); }
else { print(2); }
is a syntax error, while
if (0) { print(1); } else { print(2); }
or
if (0) { print(1);
} else { print(2); }
is not. I presume it has to do with the duality of the newline
functioning as an end of command (;) character, though it still seems a
bit odd, and it took me a while to figure out what was wrong. I
eventually figured out that to resolve this ambiguity, I would guess
that ifelse() would be a preferred function.
I wanted to look up the internal R documentation for if via "?if", but
this does not work. making the latter work would be a good idea.
regards, /iaw
---
ivo welch
professor of finance and economics
brown / nber / yale
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] A way to list only variables or functions?
Interesting, but it seems too complex.
In my opinion, just listing functions or non-functions meets my need.
Anyway, thanks.
Daehyok Shin (Peter)
> -Original Message-
> From: S?en Merser [mailto:[EMAIL PROTECTED]
> Sent: Sunday, June 20, 2004 AM 10:51
> To: Shin
> Subject: Re: [R] A way to list only variables or functions?
>
>
> hi
> forgot who actualy wrote this code but it works nicely
> use:
> ls.objects(type='function')
>
> regards soren
>
> ls.objects<-function (pos = 1, pattern, mode = "any", type = "any"){
> Object.Name <- ls(pos = pos, envir = as.environment(pos), pattern =
> pattern)
> Object.Mode <- rep("",length(Object.Name))
> Object.Type <- rep("",length(Object.Name))
> Variables <- rep("-",length(Object.Name))
> Observations <- rep("-",length(Object.Name))
> for (i in 1:length(Object.Name)){
> Object.Mode[[i]] <- mode(get(Object.Name[[i]]))
> if(is.list(get(Object.Name[[i]]))){
> if(is.null(class(get(Object.Name[[i]]
> Object.Type[[i]] <- c("unknown")
> else {
> Object.Attrib <- attributes(get(Object.Name[[i]]))
> if(length(Object.Attrib$class) == 1) {
> Object.Type[[i]] <- Object.Attrib$class
> if(Object.Type[[i]]=="data.frame"){
> Variables[[i]] <- as.character(length(Object.Attrib$names))
> Observations[[i]] <- as.character(length(Object.Attrib$row.names))
> }
> }
> else {
> if("data.frame" %in% Object.Attrib$class){
> Object.Type[[i]] <- "data.frame"
> Variables[[i]] <- as.character(length(Object.Attrib$names))
> Observations[[i]] <- as.character(length(Object.Attrib$row.names))
> }
> else {
> if("aov" %in% Object.Attrib$class) Object.Type[[i]] <- "aov"
> }
> }
> }
> }
> if(is.matrix(get(Object.Name[[i]]))){
> Object.Attrib <- dim(get(Object.Name[[i]]))
> Object.Type[[i]] <- c("matrix")
> Variables[[i]] <- as.character(Object.Attrib[2])
> Observations[[i]] <- as.character(Object.Attrib[1])
> }
> if(is.vector(get(Object.Name[[i]])) && (Object.Mode[[i]]=="character" ||
> Object.Mode[[i]]=="numeric")){
> Object.Type[[i]] <- c("vector")
> Variables[[i]] <- c("1")
> Observations[[i]] <- as.character(length(get(Object.Name[[i]])))
> }
> if(is.factor(get(Object.Name[[i]]))){
> Object.Type[[i]] <- c("factor")
> Variables[[i]] <- c("1")
> Observations[[i]] <- as.character(length(get(Object.Name[[i]])))
> }
> if(is.function(get(Object.Name[[i]]))) Object.Type[[i]] <- c("function")
> }
> objList <-
> data.frame(Object.Name,Object.Mode,Object.Type,Observations,Variables)
> if(mode != "any") objList <- objList[objList[["Object.Mode"]]
> == mode,]
> if(type != "any") objList <- objList[objList[["Object.Type"]]
> == type,]
> return(objList)
> }
> - Original Message -
> From: "Shin" <[EMAIL PROTECTED]>
> To: "R Help" <[EMAIL PROTECTED]>
> Sent: Sunday, June 20, 2004 4:59 AM
> Subject: [R] A way to list only variables or functions?
>
>
> > I am curious if there is any way to list only variables or functions in
> > current environment, rather than listing all objects? Thanks.
> >
> > --
> > Daehyok Shin (Peter)
> > Geography Department
> > Univ. of North Carolina-Chapel Hill
> >
> > __
> > [EMAIL PROTECTED] mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> >
>
>
>
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RE: [R] A way to list only variables or functions?
Neat! Thanks. How about incorporating this support into standard commands, ls() or objects()? Daehyok Shin (Peter) > -Original Message- > From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] > Sent: Sunday, June 20, 2004 AM 10:06 > To: [EMAIL PROTECTED]; [EMAIL PROTECTED] > Subject: RE: [R] A way to list only variables or functions? > > > > > These two functions will list the functions and variables > respectively: > > ls.funs <- > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > (is.function(get(x)))x)) > > ls.vars <- > function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if > (!is.function(get(x)))x)) > > > To use: > > ls.funs() > ls.vars() > > > Date: Sat, 19 Jun 2004 22:59:57 -0400 > From: Shin <[EMAIL PROTECTED]> > To: R Help <[EMAIL PROTECTED]> > Subject: [R] A way to list only variables or functions? > > > I am curious if there is any way to list only variables or functions in > current environment, rather than listing all objects? Thanks. > > -- > Daehyok Shin (Peter) > Geography Department > Univ. of North Carolina-Chapel Hill > > > > ___ > No banners. No pop-ups. No kidding. > __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Anyone out there have the XLF Fortran compiler for OS X?
I have code that will crash R every time on an OS X machine, but runs fine on other platforms. The developer I've been working with suspects it's a compiler issue, but I only have the same ones he does (g77). Obviously, the way to test this would be to compile R using another compiler. XLF is the (by IBM, distributed by Absoft) is the only other one I know of. It's pretty expensive on its own, so if somebody has a license and would be willing to help out, please drop me a line. Thanks! __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [MailServer Notification] To External Sender: a virus was found a nd action taken.
ScanMail for Microsoft Exchange took action on the message. The message details were: Sender = [EMAIL PROTECTED] Recipient(s) = [EMAIL PROTECTED]; Subject = i know your document! Scanning time = 06/20/2004 16:35:42 Engine/Pattern = 7.000-1004/1.909.00 Action taken on message: The attachment more.zip contained WORM_NETSKY.C virus. ScanMail took the action: Deleted. ScanMail has detected a virus in an email you [EMAIL PROTECTED]; __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] A way to list only variables or functions?
These two functions will list the functions and variables respectively: ls.funs <- function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if(is.function(get(x)))x)) ls.vars <- function(env=sys.frame(-1))unlist(lapply(ls(env=env),function(x)if(!is.function(get(x)))x)) To use: ls.funs() ls.vars() Date: Sat, 19 Jun 2004 22:59:57 -0400 From: Shin <[EMAIL PROTECTED]> To: R Help <[EMAIL PROTECTED]> Subject: [R] A way to list only variables or functions? I am curious if there is any way to list only variables or functions in current environment, rather than listing all objects? Thanks. -- Daehyok Shin (Peter) Geography Department Univ. of North Carolina-Chapel Hill __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Constrained non-linear mixed models
WHY THIS FUNCTIONAL FORM?
If this were my problem, I would first want to know why we needed
this particular functional form and why (b*var3+a) and (b*var4+a) had to
be between 0 and 1. When I see things like this, my first impulse is
that these may only be approximations to something else, and then I
would seek a different approximation that might plausibly be better and
was not subject to the constraints.
CREATIVE PLOTS?
What kind(s) of random model(s) are you considering? What
kinds of plots have you made? Before I did heavy modeling, I'd compute
correlations and make plots designed to explore the chosen relationship
from different perspectives, e.g., using lattice graphics, contour and
perspective / wireframe plots, etc. Such plots might suggest
alternative functional forms.
PENALIZING "nlme"?
If I still needed to fit the model you suggested, I might first
rewrite it something like the following:
nlme(log(response)~z+y*log(var1)+x*log(var2)+log01(b*var3+a,
xlim)-x*log01(b*var4+a, xlim), ...
where log01 is something like the following [***UNTESTED***]:
log01 <- function(zz, xlim){
# log(zz) if xlim[1]
# else something that goes balistic othis range
# with rate controlled by xlim[3];
# log01 must be continuous and monotonic.
zz.sm <- (zz
zz.lg <- (zz>xlim[2])
log.zz <- rep(NA, length(zz))
log.zz[zz.sm] <- (log(xlim[1])-
(exp(xlim[3]*(xlim[1]-zz[zz.sm]))-1))
log.zz[zz.lg] <- (log(xlim[2])+
(exp(xlim[3]*(zz[zz.lg]-xlim[2]))-1))
zz.gd <- !(zz.sm | zz.lg)
log.zz[zz.gd] <- log(zz[zz.gd])
log.zz
}
I would first run it with xlim something like c(0.1, 0.9, 0.01).
I'd then look at the cases for which I got log01 outside xlim[1:2] and
(gradually) adjust xlim to get something close to what I wanted, e.g.,
like c(0.01, 0.99, 100). If this didn't work well, I might also try to
modify log01 so it was also differentiable in zz.
FITTING SUBSETS?
I might also try fitting the same model to different subsets of
the data, perhaps suggested by the most plausible random effects models,
then use the parameter estimates as data for a second stage analysis,
following Box and Hunter, "A Useful Method for Model Building" paper;
you should be able to find a complete citation on the web.
MARKOV CHAIN MONTE CARLO (MCMC)?
I think the "gold standard" for this type of problem is MCMC.
There is software available for that, but I haven't used it and
therefore can't comment. However, before I got to that point, I would
make lots of plots and try to several alternative, simpler models to
convince myself that this was both appropriate and necessary.
hope this helps. spencer graves
Hwange Project wrote:
Dear r-helpers,
does anyone knows how to constrain the value of parameters in a non-linear
mixed model:
I've got something like that:
nlme(log(response)~z+y*log(var1)+x*log(var2)+log((b*var3+a)/(b*var4+a)^x)
where 0
and another one :
What means ?
Error in chol((value + t(value))/2) : the leading minor of order 1 is not
positive definite
(my statical books do not go far enough in the detail.
It must be about the Cholesky something if I remember well what I read
long-time ago).
I'm sorry to bother you with this kind of things, but I'm in a remote place
(~18°45'S,26°45'E)
(even if e-mails are working at the incredible speed of 4.8 kbits/sec...)
without a lot of statistical or computer ressources. Thanks,
simon
-
Simon Chamaillé
Hwange Project
CIRAD-CNRS
Hwange Main Camp Research
P. Bag 5776, Dete
(+00 263) 18-647
[EMAIL PROTECTED]
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[R] Constrained non-linear mixed models
Dear r-helpers, does anyone knows how to constrain the value of parameters in a non-linear mixed model: I've got something like that: nlme(log(response)~z+y*log(var1)+x*log(var2)+log((b*var3+a)/(b*var4+a)^x) where 0mailto:[EMAIL PROTECTED]> __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A way to list only variables or functions?
On Sat, 19 Jun 2004, Shin wrote: > I am curious if there is any way to list only variables or functions in > current environment, rather than listing all objects? Thanks. Not really. What you can do is list the objects and then get the objects and look at the modes, as ls.str does. That could easily be modified to just list, but you may find what it gives helpful anyway. -- Brian D. Ripley, [EMAIL PROTECTED] 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
