[R] [R-pkgs] new package 'trackObjs' - mirror objects to files, provide summaries modification times
From ?trackObjs: Overview of trackObjs package Description: The trackObjs package sets up a link between R objects in memory and files on disk so that objects are automatically resaved to files when they are changed. R objects in files are read in on demand and do not consume memory prior to being referenced. The trackObjs package also tracks times when objects are created and modified, and caches some basic characteristics of objects to allow for fast summaries of objects. Each object is stored in a separate RData file using the standard format as used by 'save()', so that objects can be manually picked out of or added to the trackObjs database if needed. Tracking works by replacing a tracked variable by an 'activeBinding', which when accessed looks up information in an associated 'tracking environment' and reads or writes the corresponding RData file and/or gets or assigns the variable in the tracking environment. Details: There are three main reasons to use the 'trackObjs' package: * conveniently handle many moderately-large objects that would collectively exhaust memory or be inconvenient to manage in files by manually using 'save()' and 'load()' * keep track of creation and modification times on objects * get fast summaries of basic characteristics of objects - class, size, dimension, etc. There is an option to control whether tracked objects are cached in memory as well as being stored on disk. By default, objects are not cached. To save time when working with collections of objects that will all fit in memory, turn on caching with 'track.options(cache=TRUE)', or start tracking with 'track.start(..., cache=TRUE)'. Here is a brief example of tracking some variables in the global environment: library(trackObjs) track.start(tmp1) x - 123 # Not yet tracked track(x) # Variable 'x' is now tracked track(y - matrix(1:6, ncol=2)) # 'y' is assigned tracked z1 - list(a, b, c) z2 - Sys.time() track(list=c(z1, z2)) # Track a bunch of variables track.summary(size=F) # See a summary of tracked vars classmode extent lengthmodified TA TW x numeric numeric[1] 1 2007-09-07 08:50:58 0 1 y matrix numeric [3x2] 6 2007-09-07 08:50:58 0 1 z1 listlist [[3]] 3 2007-09-07 08:50:58 0 1 z2 POSIXt,POSIXct numeric[1] 1 2007-09-07 08:50:58 0 1 # (TA=total accesses, TW=total writes) ls(all=TRUE) [1] x y z1 z2 track.stop() # Stop tracking ls(all=TRUE) character(0) # Restart using the tracking dir -- the variables reappear track.start(tmp1) # Start using the tracking dir again ls(all=TRUE) [1] x y z1 z2 track.summary(size=F) classmode extent lengthmodified TA TW x numeric numeric[1] 1 2007-09-07 08:50:58 0 1 y matrix numeric [3x2] 6 2007-09-07 08:50:58 0 1 z1 listlist [[3]] 3 2007-09-07 08:50:58 0 1 z2 POSIXt,POSIXct numeric[1] 1 2007-09-07 08:50:58 0 1 track.stop() # the files in the tracking directory: list.files(tmp1, all=TRUE) [1] ... [3] filemap.txt .trackingSummary.rda [5] x.rday.rda [7] z1.rda z2.rda There are several points to note: * The global environment is the default environment for tracking - it is possible to track variables in other environments, but that environment must be supplied as an argument to the track functions. * Vars must be explicitly 'track()'ed - newly created objects are not tracked. (This is not a feature, but there is currently no way of automatically tracking newly created objects - this is on the wishlist.) Thus, it is possible for variables in a tracked environment to either tracked or untracked. * When tracking is stopped, all tracked variables are saved on disk and will be no longer accessible until tracking is started again. * The objects are stored each in their own file in the tracking dir, in the format used by 'save()'/'load()' (RData files). List of basic functions and common calling patterns: Six functions cover the majority of common usage of the trackObjs package: * 'track.start(dir=...)': start tracking the global environment, with files saved in 'dir' *
[R] [R-pkgs] scuba 1.1-8
Version 1.1-8 of package 'scuba' has been uploaded to CRAN. 'scuba' is a package for scuba diving calculations and decompression models. It supports dive profiles (tables, plotting etc), analysis of dive profiles using decompression models, gas toxicity calculations, and gas usage calculations. New features in version 1.1-8: . support for dive profiles uploaded from a dive computer . new dataset: dive profile from a wreck dive on nitrox . bug fix in oxygen toxicity calculations Adrian Baddeley ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-pkgs] QCA version 0.4-5
QCA implements the Qualitative Comparative Analysis using a boolean minimization algorithm for data coded with presence/absence of the causal conditions that affects a phenomenon of interest. This new release has an experimental function that obtains the same exact solutions as the main minimization function, using a shortcut instead of the classical complete and exhaustive algorithm. This new function is faster and uses significantly less memory (50 MB compared to 1.5 GB for large datasets). It should appear soon on CRAN, feedback is welcome. -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R survey package again
On 7/9/07 11:42 PM, eugen pircalabelu wrote: I have a sample from a survey where household were interviewed. The sample has 4 criteria on which the stratification was based: REGION, SIZE OF HOUSEHOLD, SIZE OF LOCALITY, AGE OF HEAD OF HOUSEHOLD. Since i don't have the whole information in each cell of the cross region*sizehh*sizeloc*age i can't use the postStratify function from Survey package. Is that correct? (I think so but i need a competent answer) The only additional info that i have is the size of a cell from a 2*2 crossing (eg: I know the population size for all the strata defined by region*sizehh, region*sizeloc, sizeloc*age) so i have the behaviour of the population but in a 2 by 2 cross for each of these criteria. You're right, poststratification can't work from two-way marginal distributions, but raking or calibration can. However it seems odd that you only have this much information, since the full joint distribution would have been needed for stratification. Usually these details would be documented as part of the sample design. Can you get this information from those responsible for the sample design? It would also be good to check your understanding of the design. A sampling frame listing details of household size and age of household head would have been needed to do the four-way stratification you mention, but in my experience such frames aren't very common. James -- James Reilly Department of Statistics, University of Auckland Private Bag 92019, Auckland, New Zealand __ R-help@stat.math.ethz.ch 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] R first.id last.id function error
Hi Jim,
Thanks for going to the trouble of writing the function. I'll copy and try it.
Gerard
At 06:30 PM 9/7/2007, jim holtman wrote:
This function should do it for you:
file1 - read.table(textConnection( id rx week dv1
+ 1 1 11 1
+ 2 1 12 1
+ 3 1 13 2
+ 4 2 11 3
+ 5 2 12 4
+ 6 2 13 1
+ 7 3 11 2
+ 8 3 12 3
+ 9 3 13 4
+ 10 4 11 2
+ 11 4 12 6
+ 12 4 13 5
+ 13 5 21 7
+ 14 5 22 8
+ 15 5 23 5
+ 16 6 21 2
+ 17 6 22 4
+ 18 6 23 6
+ 19 7 21 7
+ 20 7 22 8
+ 21 8 21 9
+ 22 9 21 4
+ 23 9 22 5), header=TRUE)
mark.function -
+ function(df){
+ df - df[order(df$id, df$week),]
+ # create 'diff' of 'id' to determine where the breaks are
+ breaks - diff(df$id)
+ # the first entry will be TRUE, and then every occurance of
non-zero in breaks
+ df$first.id - c(TRUE, breaks != 0)
+ # the last entry is TRUE and every non-zero breaks
+ df$last.id - c(breaks != 0, TRUE)
+ df
+ }
mark.function(file1)
id rx week dv1 first.id last.id
1 1 11 1 TRUE FALSE
2 1 12 1FALSE FALSE
3 1 13 2FALSETRUE
4 2 11 3 TRUE FALSE
5 2 12 4FALSE FALSE
6 2 13 1FALSETRUE
7 3 11 2 TRUE FALSE
8 3 12 3FALSE FALSE
9 3 13 4FALSETRUE
10 4 11 2 TRUE FALSE
11 4 12 6FALSE FALSE
12 4 13 5FALSETRUE
13 5 21 7 TRUE FALSE
14 5 22 8FALSE FALSE
15 5 23 5FALSETRUE
16 6 21 2 TRUE FALSE
17 6 22 4FALSE FALSE
18 6 23 6FALSETRUE
19 7 21 7 TRUE FALSE
20 7 22 8FALSETRUE
21 8 21 9 TRUETRUE
22 9 21 4 TRUE FALSE
23 9 22 5FALSETRUE
On 9/7/07, Gerard Smits [EMAIL PROTECTED] wrote:
Hi R users,
I have a test dataframe (file1, shown below) for which I am trying
to create a flag for the first and last ID record (equivalent to SAS
first.id and last.id variables.
Dump of file1:
file1
id rx week dv1
1 1 11 1
2 1 12 1
3 1 13 2
4 2 11 3
5 2 12 4
6 2 13 1
7 3 11 2
8 3 12 3
9 3 13 4
10 4 11 2
11 4 12 6
12 4 13 5
13 5 21 7
14 5 22 8
15 5 23 5
16 6 21 2
17 6 22 4
18 6 23 6
19 7 21 7
20 7 22 8
21 8 21 9
22 9 21 4
23 9 22 5
I have written code that correctly assigns the first.id and
last.id variabes:
require(Hmisc) #for Lags
#ascending order to define first dot
file1- file1[order(file1$id, file1$week),]
file1$first.id - (Lag(file1$id) != file1$id)
file1$first.id[1]-TRUE #force NA to TRUE
#descending order to define last dot
file1- file1[order(-file1$id,-file1$week),]
file1$last.id - (Lag(file1$id) != file1$id)
file1$last.id[1]-TRUE #force NA to TRUE
#resort to original order
file1- file1[order(file1$id,file1$week),]
I am now trying to get the above code to work as a function, and am
clearly doing something wrong:
first.last - function (df, idvar, sortvars1, sortvars2)
+ {
+ #sort in ascending order to define first dot
+ df- df[order(sortvars1),]
+ df$first.idvar - (Lag(df$idvar) != df$idvar)
+ #force first record NA to TRUE
+ df$first.idvar[1]-TRUE
+
+ #sort in descending order to define last dot
+ df- df[order(-sortvars2),]
+ df$last.idvar - (Lag(df$idvar) != df$idvar)
+ #force last record NA to TRUE
+ df$last.idvar[1]-TRUE
+
+ #resort to original order
+ df- df[order(sortvars1),]
+ }
Function call:
first.last(df=file1, idvar=file1$id,
sortvars1=c(file1$id,file1$week), sortvars2=c(-file1$id,-file1$week))
R Error:
Error in as.vector(x, mode) : invalid argument 'mode'
I am not sure about the passing of the sort strings. Perhaps this is
were things are off. Any help greatly appreciated.
Thanks,
Gerard
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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
[R] R survey package again
Hi R-users!! I have some trouble with the survey pakage and i would be very glad if you can give me an advice. I have a sample from a survey where household were interviewed. The sample has 4 criteria on which the stratification was based: REGION, SIZE OF HOUSEHOLD, SIZE OF LOCALITY, AGE OF HEAD OF HOUSEHOLD. Since i don't have the whole information in each cell of the cross region*sizehh*sizeloc*age i can't use the postStratify function from Survey package. Is that correct? (I think so but i need a competent answer) The only additional info that i have is the size of a cell from a 2*2 crossing (eg: I know the population size for all the strata defined by region*sizehh, region*sizeloc, sizeloc*age) so i have the behaviour of the population but in a 2 by 2 cross for each of these criteria. Now, i want to use this info but i don't know the proper way: could i use the svydesign function as here d- svydesign (id=~1, data=tabel, strata = c(region*sizehh,region*sizeloc.), nest=T) and then dd- poststratify(d, data.frame (region*size, region*sizeloc, ), population= data.frame(Nh region*sizehh, Nh region*sizeloc..) or raking would be better for this type of joint distribution while specifying in the svydesign strata =~ region+sizehh+sizeloc+agehhh. Thank you! Bye! - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R first.id last.id function error
This function should do it for you:
file1 - read.table(textConnection( id rx week dv1
+ 1 1 11 1
+ 2 1 12 1
+ 3 1 13 2
+ 4 2 11 3
+ 5 2 12 4
+ 6 2 13 1
+ 7 3 11 2
+ 8 3 12 3
+ 9 3 13 4
+ 10 4 11 2
+ 11 4 12 6
+ 12 4 13 5
+ 13 5 21 7
+ 14 5 22 8
+ 15 5 23 5
+ 16 6 21 2
+ 17 6 22 4
+ 18 6 23 6
+ 19 7 21 7
+ 20 7 22 8
+ 21 8 21 9
+ 22 9 21 4
+ 23 9 22 5), header=TRUE)
mark.function -
+ function(df){
+ df - df[order(df$id, df$week),]
+ # create 'diff' of 'id' to determine where the breaks are
+ breaks - diff(df$id)
+ # the first entry will be TRUE, and then every occurance of
non-zero in breaks
+ df$first.id - c(TRUE, breaks != 0)
+ # the last entry is TRUE and every non-zero breaks
+ df$last.id - c(breaks != 0, TRUE)
+ df
+ }
mark.function(file1)
id rx week dv1 first.id last.id
1 1 11 1 TRUE FALSE
2 1 12 1FALSE FALSE
3 1 13 2FALSETRUE
4 2 11 3 TRUE FALSE
5 2 12 4FALSE FALSE
6 2 13 1FALSETRUE
7 3 11 2 TRUE FALSE
8 3 12 3FALSE FALSE
9 3 13 4FALSETRUE
10 4 11 2 TRUE FALSE
11 4 12 6FALSE FALSE
12 4 13 5FALSETRUE
13 5 21 7 TRUE FALSE
14 5 22 8FALSE FALSE
15 5 23 5FALSETRUE
16 6 21 2 TRUE FALSE
17 6 22 4FALSE FALSE
18 6 23 6FALSETRUE
19 7 21 7 TRUE FALSE
20 7 22 8FALSETRUE
21 8 21 9 TRUETRUE
22 9 21 4 TRUE FALSE
23 9 22 5FALSETRUE
On 9/7/07, Gerard Smits [EMAIL PROTECTED] wrote:
Hi R users,
I have a test dataframe (file1, shown below) for which I am trying
to create a flag for the first and last ID record (equivalent to SAS
first.id and last.id variables.
Dump of file1:
file1
id rx week dv1
1 1 11 1
2 1 12 1
3 1 13 2
4 2 11 3
5 2 12 4
6 2 13 1
7 3 11 2
8 3 12 3
9 3 13 4
10 4 11 2
11 4 12 6
12 4 13 5
13 5 21 7
14 5 22 8
15 5 23 5
16 6 21 2
17 6 22 4
18 6 23 6
19 7 21 7
20 7 22 8
21 8 21 9
22 9 21 4
23 9 22 5
I have written code that correctly assigns the first.id and last.id variabes:
require(Hmisc) #for Lags
#ascending order to define first dot
file1- file1[order(file1$id, file1$week),]
file1$first.id - (Lag(file1$id) != file1$id)
file1$first.id[1]-TRUE #force NA to TRUE
#descending order to define last dot
file1- file1[order(-file1$id,-file1$week),]
file1$last.id - (Lag(file1$id) != file1$id)
file1$last.id[1]-TRUE #force NA to TRUE
#resort to original order
file1- file1[order(file1$id,file1$week),]
I am now trying to get the above code to work as a function, and am
clearly doing something wrong:
first.last - function (df, idvar, sortvars1, sortvars2)
+ {
+ #sort in ascending order to define first dot
+ df- df[order(sortvars1),]
+ df$first.idvar - (Lag(df$idvar) != df$idvar)
+ #force first record NA to TRUE
+ df$first.idvar[1]-TRUE
+
+ #sort in descending order to define last dot
+ df- df[order(-sortvars2),]
+ df$last.idvar - (Lag(df$idvar) != df$idvar)
+ #force last record NA to TRUE
+ df$last.idvar[1]-TRUE
+
+ #resort to original order
+ df- df[order(sortvars1),]
+ }
Function call:
first.last(df=file1, idvar=file1$id,
sortvars1=c(file1$id,file1$week), sortvars2=c(-file1$id,-file1$week))
R Error:
Error in as.vector(x, mode) : invalid argument 'mode'
I am not sure about the passing of the sort strings. Perhaps this is
were things are off. Any help greatly appreciated.
Thanks,
Gerard
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@stat.math.ethz.ch 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] R first.id last.id function error
A slightly easier way to construct first and last if the vector x is
sorted (as is assumed in SAS) is:
first - !duplicated(x)
last - !duplicated(x, fromLast = TRUE)
where the fromLast= argument is added in R 2.6.0.
On 9/7/07, Gerard Smits [EMAIL PROTECTED] wrote:
Hi R users,
I have a test dataframe (file1, shown below) for which I am trying
to create a flag for the first and last ID record (equivalent to SAS
first.id and last.id variables.
Dump of file1:
file1
id rx week dv1
1 1 11 1
2 1 12 1
3 1 13 2
4 2 11 3
5 2 12 4
6 2 13 1
7 3 11 2
8 3 12 3
9 3 13 4
10 4 11 2
11 4 12 6
12 4 13 5
13 5 21 7
14 5 22 8
15 5 23 5
16 6 21 2
17 6 22 4
18 6 23 6
19 7 21 7
20 7 22 8
21 8 21 9
22 9 21 4
23 9 22 5
I have written code that correctly assigns the first.id and last.id variabes:
require(Hmisc) #for Lags
#ascending order to define first dot
file1- file1[order(file1$id, file1$week),]
file1$first.id - (Lag(file1$id) != file1$id)
file1$first.id[1]-TRUE #force NA to TRUE
#descending order to define last dot
file1- file1[order(-file1$id,-file1$week),]
file1$last.id - (Lag(file1$id) != file1$id)
file1$last.id[1]-TRUE #force NA to TRUE
#resort to original order
file1- file1[order(file1$id,file1$week),]
I am now trying to get the above code to work as a function, and am
clearly doing something wrong:
first.last - function (df, idvar, sortvars1, sortvars2)
+ {
+ #sort in ascending order to define first dot
+ df- df[order(sortvars1),]
+ df$first.idvar - (Lag(df$idvar) != df$idvar)
+ #force first record NA to TRUE
+ df$first.idvar[1]-TRUE
+
+ #sort in descending order to define last dot
+ df- df[order(-sortvars2),]
+ df$last.idvar - (Lag(df$idvar) != df$idvar)
+ #force last record NA to TRUE
+ df$last.idvar[1]-TRUE
+
+ #resort to original order
+ df- df[order(sortvars1),]
+ }
Function call:
first.last(df=file1, idvar=file1$id,
sortvars1=c(file1$id,file1$week), sortvars2=c(-file1$id,-file1$week))
R Error:
Error in as.vector(x, mode) : invalid argument 'mode'
I am not sure about the passing of the sort strings. Perhaps this is
were things are off. Any help greatly appreciated.
Thanks,
Gerard
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch 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] [R-pkgs] New R package plink for separate calibration IRT linking
The first version of the package plink has been uploaded to CRAN. plink is a package for conducting unidimensional IRT scaling and chain linking for multiple groups for single-format or mixed-format common items. The package supports eight IRT models and four calibration methods. Dichotomous Models: 1PL, 2PL, 3PL Polytomous Models: -Graded response model -Partial credit model -Generalized partial credit model -Nominal response model -Multiple-choice model Calibration Methods: -Mean/Mean -Mean/Sigma -Haebara -Stocking-Lord Any combination of dichotomous and polytomous items can be supplied with intermingled unique and common items for as many items and groups as system memory allows. Linking constants are computed and returned for all the calibration methods, and (if desired) ability and/or item parameters can be rescaled and returned using any of the estimated linking constants. Any of the included groups can be specified as the base scale, the characteristic curve methods can use symmetric or non-symmetric optimization, various scoring functions can be supplied for the Stocking-Lord method, and there is great flexibility in specifying thetas and theta weights to be integrated over in the characteristic curve methods. In addition to computing linking constants and rescaling ability and item parameters, the methods in the package can be used to compute item/category response probabilities and create plots of item/category characteristic curves. The package is designed to allow for a variety of formats for the item parameters including vectors, lists, matrices, and other objects (irt.pars and sep.pars) available in the package. Item parameters and calibration output can be summarized, and descriptive statistics for the item parameters can be displayed as well. Getting Started: Running the separate calibration is typically a two-step process. The first step is to format the item parameters for processing with the function 'plink'. Parameters should be formatted as either an object of class 'irt.pars' with multiple groups, a set of 'irt.pars' objects, or a set of 'sep.pars' objects. Once in this format, response probabilities can be computed using the functions 'drm', 'gpcm', 'grm', 'mcm', or 'nrm' or linking constants can be computed using 'plink'. The functions 'as.irt.pars', 'sep.pars', and 'combine.pars' can be used to create the 'irt.pars' and 'sep.pars' objects. 'summary' can be used to summarize item parameters (including descriptive statistics) and linking constants, and 'plot' can be used to create item/category characteristic curves. I am currently working on a vignette; however, the documentation contains extensive examples. The best documentation to start with is help(as.irt.pars) and help(plink). Although this is the first version of this package, I have gone through extensive debugging and validation, so there should be few, if any bugs. Many of the examples (and the associated output) can be found in published articles or books, and the output from the various calibration methods has been checked against other available linking software. I hope this will be a useful package for those interested in test linking. I invite any comments and suggestions. Take care -- Jonathan Weeks Doctoral Candidate School of Education University of Colorado, Boulder [EMAIL PROTECTED] 303-517-9666 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-pkgs] adehabitat version 1.7
Dear all, I have uploaded to CRAN the version 1.7 of the package 'adehabitat'. Significant changes are listed below: * The Brownian bridge kernel estimation algorithm has been greatly improved. It now takes more than 80% less time than the previous version. A new function liker has also been added, which estimates the one of the two smoothing parameters of the bridge kernel using a maximum likelihood approach (recommended in Horn et al., Ecology, in press). Examples of the help page demonstrate the use and interest of this function. Comparison between kernelbb and the Visual basic algorithm provided in the paper of Horn et al. returned consistent results. * The function kernelUD has also been improved. It now takes more than 50% less time than the previous version. In addition the grid argument of this function, now also allows a list of objects of class asc to be passed as grid where the UD should be estimated. Happy testing, Clément Calenge. -- Clément CALENGE LBBE - UMR CNRS 5558 - Université Claude Bernard Lyon 1 - FRANCE tel. (+33) 04.72.43.27.57 fax. (+33) 04.72.43.13.88 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-pkgs] ggplot2 - version 0.5.5
ggplot2 === ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics. Find out more at http://had.co.nz/ggplot2, and check out the over 500 examples of ggplot in use. Changes in version 0.5.5 Improvements: * ggplot now gives rather more helpful errors if you have misspecified a variable name in the aesthetic mapping * changed default hline and vline intercepts to 0 * added count output variable from stat_density for creating stacked/conditional density plots * added parameters to geom_boxplot to control appearance of outlying points * overriding aesthetics with fixed values that have already been set with aesthetics now actually works * slightly better names for xaxis and yaxis grobs * added aes_string function to make it easier to construction aesthetic mapping specifications in functions * continuous scales now have labels argument so that you can manually specify labels if desired * stat_density now calculates densities on a common grid across groups. This means that position_fill and position_stack now work properly * if numeric, legend labels right aligned * polar coordinates much improved, and with better examples Documentation: * fixed argument documentation for qplot * added (very) rudimentary documentation about what functions return * documentation now lists extra variables created by statistics Bug fixes: * coord_flip now works with segment and all interval geoms * geom_errorbar now works in all coordinate systems * derived y axes (eg. on histogram) are now labelled correctly * fixed bug in stat_quantile caused by new output format from predict.rq * fixed bug if x or y are constant * fixed bug in histogram where sometimes lowest bar was omitted * fixed bug in stat_qq which prevent setting aesthetics * fixed bug in qplot(..., geom=density, position=identity) * fixed stat_qq so that unnecessary arguments are no longer passed to the distribution function Subtractions: * removed grid argument from ggsave, replaced by ggtheme(theme_bw) * removed add argument from qplot Regards, Hadley -- http://had.co.nz/ ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R and Windows Vista
Hello group, it is reported (R for Windows FAQ) that R runs under Windows Vista. However, does someone here have experience with R under Vista 64 and large (3 or 4 GB) memory? Greeting - Jan Budczies [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R-help Digest, Vol 54, Issue 30
Ron Crump wrote: Hi, I have a dataframe that contains pedigree information; that is individual, sire and dam identities as separate columns. It also has date of birth. These identifiers are not numeric, or not sequential. Obviously, an identifier can appear in one or two columns, depending on whether it was a parent or not. These should be consistent. Not all identifiers appear in the individual column - it is possible for a parent not to have its own record if its parents were not known. Missing parental (sire and/or dam) identifiers can occur. I need to export the data for use in another program that requires the pedigree to be coded as integers, increasing with date of birth (therefore sire and dam always have lower identifiers than their offspring) and with missing values coded as 0. How would I go about doing this? You might look at http://www.qimr.edu.au/davidD/sib-pair.R, specifically the read.pedigree() and wrlink() functions. The former is not very impressive speedwise -- I usually perform these tasks in the my Sib-pair (Fortran) program, which is on the same webpage. It will order the pedigree by generational position, so a DOB is not required to do the sort. Terry Therneau's kinship package does that ordering, but doesn't include output routines for the Linkage format. David Duffy. | David Duffy (MBBS PhD) ,-_|\ | email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v __ R-help@stat.math.ethz.ch 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] R and Windows Vista
Jan Budczies wrote: Hello group, it is reported (R for Windows FAQ) that R runs under Windows Vista. However, does someone here have experience with R under Vista 64 and large (3 or 4 GB) memory? There is no 64-bit version of R for Windows available now. Mainly because there are no really stable gcc compilers available for that platform yet. You are welcome to contribute patches that make R work under 64-bit Vista with some compilers, of course. Uwe Ligges Greeting - Jan Budczies [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R and Windows Vista
On Thu, 30 Aug 2007, Jan Budczies wrote: Hello group, it is reported (R for Windows FAQ) that R runs under Windows Vista. However, does someone here have experience with R under Vista 64 and large (3 or 4 GB) memory? Yes, the person who wrote the FAQ entry does. Note that the distributed Windows binary of R is a 32-bit executable, so the maximum memory it can address is 4GB (and it can do that in Vista 64 on a 4GB RAM machine, unlike any 32-bit version of Windows). If you want to use R on Vista 64, I suggest you use a current R-devel snapshot, as some changes have been made based on this experience. Greeting - Jan Budczies [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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 __ R-help@stat.math.ethz.ch 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] R 2.5.1 - Rscript through tee
[Dirk Eddelbuettel] [François Pinard] #!/usr/bin/Rscript options(echo=TRUE) a - 1 Sys.sleep(3) a - 2 If I execute ./pp.R at the shell prompt, the output shows the timely progress of the script as expected. If I use ./pp.R | tee OUT instead, the output seems buffered and I see it all at once at the end. [...] So, is there a way to tell R (or Rscript) that standard output should be unbuffered, even if it is not directly connected to a terminal? Use explicit print statements, e.g. print(a - 1) Yes, I noticed that print statements get written. But I wanted the mere echo trace of the execution of the script to be synchronous (as some statements take many seconds to compute, which I symbolically replaced by Sys.sleep above). Littler5D actually won't show anything unless you explicitly call cat() or print(), but then it does [...] It shares the limitation of Rscript, then. Littler is an 'all-in' binary and starts and runs demonstrably faster than Rscript. I'm not familiar with Littler. Speedwise, Rscript is OK for me so far, as most time is spent within R computations, not much in language compilation or script interpretation. [...] the rather petty refusal of Rscript's main author to a least give a reference to littler in Rscript's documentation, let alone credit as 'we were there first', [...] I've long been in academic circles (and elsewhere too), so I'm familiar with the need of recognizing authorship and people's works. However, perusing R mailing list archives, and following actual list contents, I'm sometimes surprised, and even a bit annoyed, by the recurrent starve for credit I observe. Of course, maintainers and contributors much deserve our thanks and, without going into arguments about what is due to whom, I think contributors receive praise on average, would it be only by all the interest shown by the community. However, it gets a bit muddy when maintainers or contributors show bad temper when not receiving the systematic credit they would like to read. Cicero's friends were telling him how upset they felt that there was still no statute of Cicero on the public place. Cicero replied that he much preferred to hear people saying Why no Cicero statute yet? than to hear people saying Why the Cicero statute?. A wise attitude! :-) -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
Dear All, I am trying to write my first R script. The code is simply cat(Hello!\n) However, when I run $ R CMD BATCH myscript.R I do not see Hello! on the console. I am using Fedora 7 (Linux) and R-2.5.1. Any ideas? Thanks in advance, Paul __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
Paul Smith wrote: Dear All, I am trying to write my first R script. The code is simply cat(Hello!\n) However, when I run $ R CMD BATCH myscript.R I do not see Hello! on the console. I am using Fedora 7 (Linux) and R-2.5.1. Any ideas? You shouldn't see it on the console! BATCH writes its output to a file. You should find a file called myscript.Rout that does contain the 'Hello!'. Barry __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
Use rscript Rscript myscript.R or Rscript -e 'cat(Hello!\n)' will show Hello! on the console. R CMD BATCH writes its output to the file myscript.Rout Paul Smith wrote: Dear All, I am trying to write my first R script. The code is simply cat(Hello!\n) However, when I run $ R CMD BATCH myscript.R I do not see Hello! on the console. I am using Fedora 7 (Linux) and R-2.5.1. Any ideas? Thanks in advance, Paul -- View this message in context: http://www.nabble.com/R-CMD-BATCH%3A-cat-does-not-print-tf4353572.html#a12405494 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
On 8/30/07, Barry Rowlingson [EMAIL PROTECTED] wrote: I am trying to write my first R script. The code is simply cat(Hello!\n) However, when I run $ R CMD BATCH myscript.R I do not see Hello! on the console. I am using Fedora 7 (Linux) and R-2.5.1. Any ideas? You shouldn't see it on the console! BATCH writes its output to a file. You should find a file called myscript.Rout that does contain the 'Hello!'. Thanks, Barry. Indeed, the file myscript.Rout exists and contains the output of cat. I was expecting a behavior similar to the bash scripts. And by the way, cannot a R script write only on the console and just what one tells it to write, likewise bash scripts? Paul __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
On 8/30/07, Vladimir Eremeev [EMAIL PROTECTED] wrote: Use rscript Rscript myscript.R or Rscript -e 'cat(Hello!\n)' will show Hello! on the console. R CMD BATCH writes its output to the file myscript.Rout Thanks, Vladimir. Rscript is exactly what I was looking for! Paul Paul Smith wrote: Dear All, I am trying to write my first R script. The code is simply cat(Hello!\n) However, when I run $ R CMD BATCH myscript.R I do not see Hello! on the console. I am using Fedora 7 (Linux) and R-2.5.1. Any ideas? Thanks in advance, Paul -- View this message in context: http://www.nabble.com/R-CMD-BATCH%3A-cat-does-not-print-tf4353572.html#a12405494 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R CMD BATCH: cat does not print
Paul Smith wrote: Thanks, Barry. Indeed, the file myscript.Rout exists and contains the output of cat. I was expecting a behavior similar to the bash scripts. And by the way, cannot a R script write only on the console and just what one tells it to write, likewise bash scripts? Not easily, I think. The 'BATCH' command is really intended for long-running or off-line jobs that may be disconnected from a terminal. Barry __ R-help@stat.math.ethz.ch 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] R and Web Applications
Hello, I'm curious to know how people are calling R from web applications (I've been looking for Perl but I'm open to other languages). After doing a search, I came across the R package RSPerl, but I'm having difficulties getting it installed (on Mac OSX). I believe the problem probably has to do with changes in R since the package release. Below you will see where the installation process comes to an end. Does anyone have any suggestions, or perhaps a direction to point me in? Thanks in advance for your insight! Chris * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Versions/2.5/Resources/library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R and Web Applications
The R packages and projects for the web and R are listed here: http://www.lmbe.seu.edu.cn/CRAN/doc/FAQ/R-FAQ.html#R-Web-Interfaces On 8/30/07, Chris Parkin [EMAIL PROTECTED] wrote: Hello, I'm curious to know how people are calling R from web applications (I've been looking for Perl but I'm open to other languages). After doing a search, I came across the R package RSPerl, but I'm having difficulties getting it installed (on Mac OSX). I believe the problem probably has to do with changes in R since the package release. Below you will see where the installation process comes to an end. Does anyone have any suggestions, or perhaps a direction to point me in? Thanks in advance for your insight! Chris * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Versions/2.5/Resources/library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R and Web Applications
Hi Chris -- RWebServices provides a way to expose R functionality as (SOAP-based) web services. http://bioconductor.org/packages/2.0/bioc/html/RWebServices.html This might be more than you are looking for, and has not been tested on MacOS (which seems to be your platform). Martin Chris Parkin [EMAIL PROTECTED] writes: Hello, I'm curious to know how people are calling R from web applications (I've been looking for Perl but I'm open to other languages). After doing a search, I came across the R package RSPerl, but I'm having difficulties getting it installed (on Mac OSX). I believe the problem probably has to do with changes in R since the package release. Below you will see where the installation process comes to an end. Does anyone have any suggestions, or perhaps a direction to point me in? Thanks in advance for your insight! Chris * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Versions/2.5/Resources/library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-help@stat.math.ethz.ch 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] R and Web Applications
Dear Chris, I use Python (http://www.python.org) in combination with Rpy (http://rpy.sourceforge.net/). Rpy enables you to use R commands inside Python, not the other way around. Works quite well, also for different R versions (I currently run R 2.5.1 under Linux). cheers, Paul Chris Parkin schreef: Hello, I'm curious to know how people are calling R from web applications (I've been looking for Perl but I'm open to other languages). After doing a search, I came across the R package RSPerl, but I'm having difficulties getting it installed (on Mac OSX). I believe the problem probably has to do with changes in R since the package release. Below you will see where the installation process comes to an end. Does anyone have any suggestions, or perhaps a direction to point me in? Thanks in advance for your insight! Chris * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Versions/2.5/Resources/library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax:+31302531145 http://intamap.geo.uu.nl/~paul __ R-help@stat.math.ethz.ch 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] R Help
I got the Warning message below when I tried to load Locfit. What is wrong?
Regards
Ola Asteman
--
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(foreign)
library(mgcv)
This is mgcv 1.3-19
library(locfit)
Loading required package: akima
Error: package 'akima' could not be loaded
In addition: Warning message:
there is no package called 'akima' in: library(pkg, character.only = TRUE,
logical = TRUE, lib.loc = lib.loc)
--
This e-mail and any attachment may be confidential and may a...{{dropped}}
__
R-help@stat.math.ethz.ch 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] R Help
You don't have installed the akima pakage.
install.packages(akima, dep=T)
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/08/07, Ola Asteman [EMAIL PROTECTED] wrote:
I got the Warning message below when I tried to load Locfit. What is
wrong?
Regards
Ola Asteman
--
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(foreign)
library(mgcv)
This is mgcv 1.3-19
library(locfit)
Loading required package: akima
Error: package 'akima' could not be loaded
In addition: Warning message:
there is no package called 'akima' in: library(pkg, character.only = TRUE,
logical = TRUE, lib.loc = lib.loc)
--
This e-mail and any attachment may be confidential and may a...{{dropped}}
__
R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] R Help
[EMAIL PROTECTED] napsal dne 28.08.2007 13:33:13:
You don't have installed the akima pakage.
install.packages(akima, dep=T)
And wait about two months and update your R version to 2.6.0. Or update
now to 2.5.1
Regards
Petr
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/08/07, Ola Asteman [EMAIL PROTECTED] wrote:
I got the Warning message below when I tried to load Locfit. What is
wrong?
Regards
Ola Asteman
--
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(foreign)
library(mgcv)
This is mgcv 1.3-19
library(locfit)
Loading required package: akima
Error: package 'akima' could not be loaded
In addition: Warning message:
there is no package called 'akima' in: library(pkg, character.only =
TRUE,
logical = TRUE, lib.loc = lib.loc)
--
This e-mail and any attachment may be confidential and m...{{dropped}}
__
R-help@stat.math.ethz.ch 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] [R-pkgs] proftools package now available from CRAN
PROFILE OUTPUT PROCESSING TOOLS FOR R = This package provides some simple tools for examining Rprof output and, in particular, extracting and viewing call graph information. Call graph information, including which direct calls where observed and how much time was spent in these calls, can be very useful in identifying performance bottlenecks. One important caution: because of lazy evaluation a nested call f(g(x)) will appear on the profile call stack as if g had been called by f or one of f's callees, because it is the point at which the value of g(x) is first needed that triggers the evaluation. EXPORTED FUNCTIONS The package exports five functions: readProfileData reads the data in the file produced by Rprof into a data structure used by the other functions in the package. The format of the data structure is subject to change. flatProfile is similar to summaryRprof. It returns either a matrix with output analogous to gprof's flat profile or a matrix like the by.total component returned by summaryRprof; which is returned depends on the value of an optional second argument. printProfileCallGraph produces a printed representation of the call graph. It is analogous to the call graph produced by gprof with a few minor changes. Reading the gprof manual section on the call graph should help understanding this output. The output is similar enough to gprof output for the cgprof (http://mvertes.free.fr/) script to be able to produce a call graph via Graphviz. profileCallGraph2Dot prints out a Graphviz .dot file representing the profile graph. Times spent in calls can be mapped to node and edge colors. The resulting files can then be viewed with the Graphviz command line tools. plotProfileCallGraph uses the graph and Rgraphviz packages to produce call graph visualizations within R. You will need to install these packages to use this function. A SIMPLE EXAMPLE Collect profile information for the examples for glm: Rprof(glm.out) example(glm) Rprof() pd - readProfileData(glm.out) Obtain flat profile information: flatProfile(pd) flatProfile(pd, FALSE) Obtain a printed call graph on the standard output: printProfileCallGraph(pd) If you have the cgprof script and the Graphviz command line tools available on a UNIX-like system, then you can save the printed graph to a file, printProfileCallGraph(pd, glm.graph) and either use cgprof -TX glm.graph to display the graph in the interactive graph viewer dotty, or use cgprof -Tps glm.graph glm.ps gv glm.ps to create a PostScript version of the call graph and display it with gv. Instead of using the printed graph and cgprof you can use create a Graphviz .dot file representation of the call graph with profileCallGraph2Dot(pd, filename = glm.dot, score = total) and view the graph interactively with dotty using dotty glm.dot or as a postscript file with dot -Tps glm.dot glm.ps gv glm.ps Finally, if you have the graph package from CRAN and the Rgraphviz package from Bioconductor installed, then you can view the call graph within R using plotProfileCallGraph(pd, score = total) The default settings for this version need some work.] OPEN ISSUES My intention was to handle cycles roughly the same way that gprof does. I am not completely sure that I have managed to do this; I am also not completely sure this is the best approach. The graphs produced by cgprof and by plotProfileGraph and friends when mergeEdges is false differ a bit. I think this is due to the heuristics of cgprof not handling cycle entries ideally and that the plotProfileGraph graphs are actually closer to what is wanted. When mergeEdges is true the resulting graphs are DAGs, which simplifies interpretation, but at the cost of lumping all cycle members together. gprof provides options for pruning graph printouts by omitting specified nodes. It may be useful to allow this here as well. Probably more use should be made of the graph package. IMPLEMENTATION NOTES The implementation is extremely crude (a real mess would be more accurate) and will hopefully be improved over time--at this point it is more of an existence proof than a final product. Performance is less than ideal, though using these tools it was possible to identify some problem points and speed up computing the profile data by a factor of two (in other words, it may be bad now but it used to be worse). More careful design of the data structures and memoizing calculations that are now repeated is likely to improve performance substantially. -- Luke Tierney Chair, Statistics and
Re: [R] R 2.5.1 - Rscript through tee
On 26 August 2007 at 22:47, François Pinard wrote: | I met a little problem for which someone might have a solution. Let's | say I have an executable file (named pp.R) with this contents: | |#!/usr/bin/Rscript |options(echo=TRUE) |a - 1 |Sys.sleep(3) |a - 2 | | If I execute ./pp.R at the shell prompt, the output shows the timely | progress of the script as expected. If I use ./pp.R | tee OUT | instead, the output seems buffered and I see it all at once at the end. | | The problem does not come from the tee program, as if I use this | command: | |(echo a; sleep 5; echo b) | tee OUT | | the output is timely, not batched. | | So, is there a way to tell R (or Rscript) that standard output should be | unbuffered, even if it is not directly connected to a terminal? Use explicit print statements, e.g. print(a - 1) Also, you still have little as an alternate, at least on Unix [1]. Littler5D actually won't show anything unless you explicitly call cat() or print(), but then it does: qa-v40z1:~/svn/hancock/app/aggposview cat /tmp/fp2.r #!/usr/bin/env r options(echo=TRUE) cat(a - 1, \n) Sys.sleep(3) cat(a - 2, \n) foo:~ /tmp/fp2.r | tee /tmp/fp2.r.out 1 2 foo:~ Littler is an 'all-in' binary and starts and runs demonstrably faster than Rscript. Hth, Dirk [1] And despite the rather petty refusal of Rscript's main author to a least give a reference to littler in Rscript's documentation, let alone credit as 'we were there first', the fact remains that littler became available in Sep 2006 whereas Rscript was not released until R 2.5.0 a good six month later. Oh well. | In case useful, here is local R information: | | Version: | platform = x86_64-unknown-linux-gnu | arch = x86_64 | os = linux-gnu | system = x86_64, linux-gnu | status = | major = 2 | minor = 5.1 | year = 2007 | month = 06 | day = 27 | svn rev = 42083 | language = R | version.string = R version 2.5.1 (2007-06-27) | | Locale: | LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA.UTF-8;LC_MONETARY=fr_CA.UTF-8;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTIFICATION=C | | Search Path: | .GlobalEnv, package:stats, package:utils, package:datasets, fp.etc, package:graphics, package:grDevices, package:methods, Autoloads, package:base | | -- | François Pinard http://pinard.progiciels-bpi.ca | | __ | R-help@stat.math.ethz.ch 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. -- Three out of two people have difficulties with fractions. __ R-help@stat.math.ethz.ch 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] R-2.5.1 RedHat EL5 compilation failed
Original Message Subject: [R] R-2.5.1 RedHat EL5 compilation failed From: Wang Chengbin [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: 26.08.2007 15:22 I can't get R-2.5.1 compiled under RedHat EL5 with gcc 4.1.1. Configure failed at the following: You don't need to compile, you could also use the Fedora Core 6 Extras repository package(s) of R (current: is R-2.5.1-2.fc6.i386.rpm) to install the necessary rpm packages from there. (Best is to use the smart package manager, there you can easily activate channels which are repositories.) As far as I understood FC6 is the base of RHEL 5. Stefan -=-=- ... Time is an illusion, lunchtime doubly so. (Ford Prefect) __ R-help@stat.math.ethz.ch 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] R-2.5.1 RedHat EL5 compilation failed
I can't get R-2.5.1 compiled under RedHat EL5 with gcc 4.1.1. Configure failed at the following: checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... no checking for main in -ltermcap... no checking for main in -ltermlib... no checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R-2.5.1 RedHat EL5 compilation failed
Well, the INSTALL file said The main source of information on installation is the `R Installation and Administration Manual', an HTML copy of which is available as file `doc/html/R-admin.html'. Please read that before installing R. But if you are impatient, read on but please refer to the manual to resolve any problems. (If you obtained R using Subversion, the manual is at doc/manual/R-admin.texi.) and this _is_ discussed there. Hint: is readline-devel installed? On Sun, 26 Aug 2007, Wang Chengbin wrote: I can't get R-2.5.1 compiled under RedHat EL5 with gcc 4.1.1. Configure failed at the following: checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... no checking for main in -ltermcap... no checking for main in -ltermlib... no checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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 __ R-help@stat.math.ethz.ch 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] R 2.5.1 - Rscript through tee
Hi, people. I met a little problem for which someone might have a solution. Let's say I have an executable file (named pp.R) with this contents: #!/usr/bin/Rscript options(echo=TRUE) a - 1 Sys.sleep(3) a - 2 If I execute ./pp.R at the shell prompt, the output shows the timely progress of the script as expected. If I use ./pp.R | tee OUT instead, the output seems buffered and I see it all at once at the end. The problem does not come from the tee program, as if I use this command: (echo a; sleep 5; echo b) | tee OUT the output is timely, not batched. So, is there a way to tell R (or Rscript) that standard output should be unbuffered, even if it is not directly connected to a terminal? In case useful, here is local R information: Version: platform = x86_64-unknown-linux-gnu arch = x86_64 os = linux-gnu system = x86_64, linux-gnu status = major = 2 minor = 5.1 year = 2007 month = 06 day = 27 svn rev = 42083 language = R version.string = R version 2.5.1 (2007-06-27) Locale: LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA.UTF-8;LC_MONETARY=fr_CA.UTF-8;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:stats, package:utils, package:datasets, fp.etc, package:graphics, package:grDevices, package:methods, Autoloads, package:base -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch 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] R old versions archive anywhere?
Hi Folks, Does anyone know if (apparently not on CRAN) there is any archive of older versions of R packages? Or is it the case that not only are old versions on CRAN humanesly destoyed, but all older versions out in the wild are hunted down and shot? (I can find older versions of the R core, but not of other packages). With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 23-Aug-07 Time: 19:37:30 -- XFMail -- __ R-help@stat.math.ethz.ch 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] R old versions archive anywhere?
On Thu, 23 Aug 2007, [EMAIL PROTECTED] wrote: Hi Folks, Does anyone know if (apparently not on CRAN) there is any archive of older versions of R packages? Yes. On CRAN. At the bottom of the page listing all the packages there is a section - Related Directories Archive Previous versions of the packages listed above. - linking to [CRAN]/src/contrib/Archive -thomas __ R-help@stat.math.ethz.ch 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] R old versions archive anywhere?
On 23 August 2007 at 19:37, (Ted Harding) wrote: | Does anyone know if (apparently not on CRAN) there is | any archive of older versions of R packages? See $CRAN/src/contrib/Archive/ which has further subdirectories A to Z each of which contain all known versions of all packages starting with that letter. BTW, I used these file listing (directly parsed from R via a call to 'links -dump' and a trivial awk filter) to construct a rough `CRAN growth curve' to motivate my talk at UseR! about our efforts of turning all of CRAN and BioC into .deb packages. Dirk -- Three out of two people have difficulties with fractions. __ R-help@stat.math.ethz.ch 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] [R-pkgs] brew 1.0-1
brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module. brew is written in R with no package dependencies, and it's not just for the web. It can be used as an alternative to Sweave in a limited context. See the brew-test-1.brew file in the distribution for some salient differences between the two. brew can also complement Sweave since it can be written to do conditional inclusion of or loop over Sweave code chunks. The 1.0-1 version should show up on the CRAN mirrors shortly, but in the mean time it can be got from: http://www.rforge.net/brew/ Best, Jeff -- http://biostat.mc.vanderbilt.edu/JeffreyHorner ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R mailinglist ETH website now with trusted certificate
Some of you, notably I think users of MS Internet Explorer, may be happy to learn that since yesterday, the web server of the R mailing lists https://stat.ethz.ch/ now runs an ``official'' / trusted certificate as opposed to the inofficial one (Math deparment ETH) that we have had for years instead. In particular, this should make access to the (first but by far not only) mailing list archives more convenient to you, e.g. for this month, for R-help, https://stat.ethz.ch/pipermail/r-help/2007-August/thread.html In parallel, the R Foundation is getting (buying) certificates for several R-project.org servers, notably also the subversion (R source) server, and these will hopefully be put in place as well with the next few weeks. Martin Maechler, ETH Zurich R core __ R-help@stat.math.ethz.ch 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] R on a flash drive
I often run R via a Ceedo virtualisation on a USB drive (http://www.ceedo.com/) with XP. It costs a few dollars to it this way, but is a very low stress installation and has worked flawlessly, albeit a little slower (barely noticeable). Very handy if you are often working on various machines without administrator rights (as I do in clinic) - just plug in your USB and go directly back to your project. It then removes any trace of you (so they say) when you log out. And you can use it for other software (within limits though) you might want to carry around. Hope that helps. Scott Scott Williams MD Peter MacCallum Cancer Centre Melbourne Australia -Original Message- From: John Kane [mailto:[EMAIL PROTECTED] Sent: Tuesday, 21 August 2007 12:28 AM To: John Kane; Erin Hodgess; r-help@stat.math.ethz.ch Subject: Re: [R] R on a flash drive Oops meant to send this to the list. --- John Kane [EMAIL PROTECTED] wrote: --- Erin Hodgess [EMAIL PROTECTED] wrote: Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Yes I run R, occasionally, on a USB with no problem on WindowsXP. It works well, albeit a bit more slowly than from the hard drive which is as you would expect. The last time I upgraded the USB (to 2.5.0 ?) I simply downloaded R and installed it on the USB drive rather than the C: drive and then installed all my usual optional packages using the normal Rgui interface. I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca __ R-help@stat.math.ethz.ch 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] R on a flash drive
On Wed, 22 Aug 2007, Williams Scott wrote: I often run R via a Ceedo virtualisation on a USB drive (http://www.ceedo.com/) with XP. It costs a few dollars to it this way, but is a very low stress installation and has worked flawlessly, albeit It is not necessary though, as R does not need 'virtualisation'. For Windows this is covered in the rw-FAQ Q2.6. a little slower (barely noticeable). Perhaps the overhead of Credo? Once R starts up (which does take longer on a slow drive) I found no time-able difference in 2.1.x (all the files frequently used from disc are cached on startup). It would be nice to give the R developers the credit for writing R in such a way that it works well from slow media, instead of it being credited to an unnecessary commercial product. Very handy if you are often working on various machines without administrator rights (as I do in clinic) - just plug in your USB and go directly back to your project. It then removes any trace of you (so they say) when you log out. And you can use it for other software (within limits though) you might want to carry around. Many sites would not allow programs to be run from a USB drive or make it a breach of usage conditions to do so. Hope that helps. Scott Scott Williams MD Peter MacCallum Cancer Centre Melbourne Australia -Original Message- From: John Kane [mailto:[EMAIL PROTECTED] Sent: Tuesday, 21 August 2007 12:28 AM To: John Kane; Erin Hodgess; r-help@stat.math.ethz.ch Subject: Re: [R] R on a flash drive Oops meant to send this to the list. --- John Kane [EMAIL PROTECTED] wrote: --- Erin Hodgess [EMAIL PROTECTED] wrote: Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Yes I run R, occasionally, on a USB with no problem on WindowsXP. It works well, albeit a bit more slowly than from the hard drive which is as you would expect. The last time I upgraded the USB (to 2.5.0 ?) I simply downloaded R and installed it on the USB drive rather than the C: drive and then installed all my usual optional packages using the normal Rgui interface. I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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 __ R-help@stat.math.ethz.ch 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] R on a flash drive
Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] R on a flash drive
This is a FAQ. http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-run-R-from-a-CD-or-USB-drive_003f Erin Hodgess wrote: Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Thanks in advance! -- View this message in context: http://www.nabble.com/R-on-a-flash-drive-tf4299172.html#a12236850 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] R on a flash drive
--- Erin Hodgess [EMAIL PROTECTED] wrote: Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Yes I run R, occasionally, on a USB with no problem on WindowsXP. It works well, albeit a bit more slowly than from the hard drive which is as you would expect. The last time I upgraded the USB (to 2.5.0 ?) I simply downloaded R and installed it on the USB drive rather than the C: drive and then installed all my usual optional packages using the normal Rgui interface. I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. __ R-help@stat.math.ethz.ch 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] R on a flash drive
Oops meant to send this to the list. --- John Kane [EMAIL PROTECTED] wrote: --- Erin Hodgess [EMAIL PROTECTED] wrote: Dear R People: Has anyone run R from a flash drive, please? If so, how did it work, please? Yes I run R, occasionally, on a USB with no problem on WindowsXP. It works well, albeit a bit more slowly than from the hard drive which is as you would expect. The last time I upgraded the USB (to 2.5.0 ?) I simply downloaded R and installed it on the USB drive rather than the C: drive and then installed all my usual optional packages using the normal Rgui interface. I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca __ R-help@stat.math.ethz.ch 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] R on a flash drive
John Kane jrkrideau at yahoo.ca writes: I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. Tinn-R works well as a portable editor on a USB flash drive. Likewise, by following the instructions here: http://at-aka.blogspot.com/2006/06/portable- emacs-22050-on-usb.html you can run emacs for windows from your USB flash drive. Michael __ R-help@stat.math.ethz.ch 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] R graphics display window
Hi all: How can the R graphics window be customized programmatically? Either minimized,maximized or change the size of the default that ships with R. Thanks Felipe D. Carrillo Fishery Biologist US Fish Wildlife Service Red Bluff, California 96080 __ R-help@stat.math.ethz.ch 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] R graphics display window
Felipe Carrillo mazatlanmexico at yahoo.com writes: How can the R graphics window be customized programmatically? Either minimized,maximized or change the size of the default that ships with R. Assuming Windows as OS (which you forgot to mention) windows(width = 2, height = 2, pointsize = 12) Dieter __ R-help@stat.math.ethz.ch 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] R graphics display window
On 16/08/2007 7:35 PM, Felipe Carrillo wrote: Hi all: How can the R graphics window be customized programmatically? Either minimized,maximized or change the size of the default that ships with R. Which device are you working with? Most of them allow the size to be selected in the initial call to open the window, e.g. windows(2,2) for a very small window. (The sizes are in inches, assuming your monitor reports the size of its pixels correctly.) options(device) allows you to choose a new default; e.g. options(device=function() windows(2,2)) to always get very small windows. I don't know if any of the devices support programmatic changes from R code, but in Windows you could do most changes by sending Windows messages to the window or doing Windows API calls. You can get the handle using getWindowsHandle(), and then you'll need to write C code to do the work. Duncan Murdoch Thanks Felipe D. Carrillo Fishery Biologist US Fish Wildlife Service Red Bluff, California 96080 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R 2.5.1 configure problem
Hi, I have follwoing problem: I will install R-2.5.1 on a Linux Maschine (64Bit) and I will use the R-GUI JGR (Jaguar) SO I make following steps: ./configure --with-gnu-ld --enable-R-shlib VAR=fPIC VAR=TCLTK_LIBS make I become following error messages: . Entering directory `/root/R-2.5.1/tests' make[2]: Entering directory `/root/R-2.5.1/tests' make[3]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: *** No rule to make target `../../lib/libR.so', needed by `base-Ex.Rout'. Stop. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/root/R-2.5.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/root/R-2.5.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/root/R-2.5.1/tests' make: *** [check] Error 2 Make check all - I become following messages: Entering directory `/root/R-2.5.1/tests' make[2]: Entering directory `/root/R-2.5.1/tests' make[3]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: *** No rule to make target `../../lib/libR.so', needed by `base-Ex.Rout'. Stop. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/root/R-2.5.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/root/R-2.5.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/root/R-2.5.1/tests' make: *** [check] Error 2 Can you help me? With best regards Andreas Hey _ Tel:030/2093-1463 Email: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R 2.5.1 configure problem
Andreas Hey wrote: Hi, I have follwoing problem: I will install R-2.5.1 on a Linux Maschine (64Bit) Which? (CPU and OS, please. There are about four likely possibilities, half a dozen less likely ones...) and I will use the R-GUI JGR (Jaguar) SO I make following steps: ./configure --with-gnu-ld --enable-R-shlib VAR=fPIC VAR=TCLTK_LIBS What are those options supposed to be good for??? You appear to be setting VAR twice, and I don't recall VAR as anything used by configure. And it is unlikely that a Linux system would use anything but GNU ld by default. Did configure terminate succesfully??? What did the output summary say? make I become following error messages: (that's not how to translate Ich bekomme...) . Something must have gone before this! A linker error perhaps? Entering directory `/root/R-2.5.1/tests' make[2]: Entering directory `/root/R-2.5.1/tests' make[3]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: *** No rule to make target `../../lib/libR.so', needed by `base-Ex.Rout'. Stop. Did you really run make. This looks like make check output. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/root/R-2.5.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/root/R-2.5.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/root/R-2.5.1/tests' make: *** [check] Error 2 Make check all - I become following messages: Entering directory `/root/R-2.5.1/tests' make[2]: Entering directory `/root/R-2.5.1/tests' make[3]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[4]: Entering directory `/root/R-2.5.1/tests/Examples' make[4]: *** No rule to make target `../../lib/libR.so', needed by `base-Ex.Rout'. Stop. make[4]: Leaving directory `/root/R-2.5.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/root/R-2.5.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/root/R-2.5.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/root/R-2.5.1/tests' make: *** [check] Error 2 Can you help me? With best regards Andreas Hey _ Tel:030/2093-1463 Email: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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] [R-pkgs] 'fda' 1.2.2 is now available on CRAN.
The fda package supports Functional Data Analysis and Applied Functional Data Analysis by Bernard Silverman and James Ramsay. Functional data analysis, which lots of us like to call FDA, is about the analysis of information on curves or functions. FDA is a collection statistical techniques for answering questions like, What are the main ways in which the curves vary from one to another? In fact, most of the questions and problems associated with multivariate data (PCA, LDA, clustering, ...) have functional counterparts. More information about FDA can be found at http://www.psych.mcgill.ca/misc/fda/. This version (and the previous 1.2.1) includes bug fixes plus a scripts subdirectory with R code to reproduce some of the analyses in the two functional data analysis books by Ramsay and Silverman and a Continuously Stirred Tank Reactor (CSTR) simulation discussed in a Ramsay, et al., discussion paper to appear soon in the Journal of the Royal Statistical Society-series B. It also includes the draft of a presentation on fda in Matlab R (in PowerPoint and Adobe Acrobat PDF formats) for the UseR! 2007 conference this Friday, Aug. 10, 1:55 - 2:20 PM in Ames, IA. Regards Hadley Wickham James Ramsey Spencer Graves ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R^2 for multilevel models
Hi there, In multiple regression one way to view R^2 is as (the square of) the correlation between original y's and the estimated y's. Suppose you fit a multilevel model with random intercept for each cluster. Would it be valid to compute an R^2 by using fixed effects plus the group intercepts to reduce the residuals? I suspect this has been done and, given its absence from the lmer output, refuted somewhere. A reference would be lovely. Code below. Many thanks, Andy # require(lme4) # First generate some data people = 100 obs = 4 # The random intercepts: sub_noise = data.frame(id = 1:people, rand_int = rnorm(people,0,60)) # Merge everything id = rep(1:people,obs) thedata = data.frame(id) thedata = merge(sub_noise, thedata) thedata$x = rep(1:obs,people) # Setup the relationship between x and y thedata$y = 23*thedata$x + 20 + thedata$rand_int + rnorm(people*obs, 0, 20) # plus residuals # Have a look plot(y~x, data = thedata) # Now fit a standard regression model lm1 = lm(y ~ x, data = thedata) summary(lm1) # Use the model to get the R^2 predicted = coef(lm1)[1] + thedata$x * coef(lm1)[2] plot(thedata$y, predicted) # It's a noisy mess cor(thedata$y, predicted)^2 # Now how about adjusting everyone's intercept towards the group # intercept? lmer1 = lmer(y ~ x + (1|id), data=thedata) summary(lmer1) # Get the random intercepts and stick them in a table ran_effects = data.frame(rownames(ranef(lmer1)$id), ranef(lmer1)$id[1]) names(ran_effects) = c(id, b) ran_effects_data = merge(thedata, ran_effects) # Now compute predicted.ml = fixef(lmer1)[1] + ran_effects_data$x * fixef(lmer1)[2] + ran_effects_data$b plot(thedata$y, predicted.ml) cor(thedata$y, predicted.ml)^2 # Looks much nicer __ R-help@stat.math.ethz.ch 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] R Weka and cobweb
adschai at optonline.net writes: Hi, I never use cobweb before and I'm quite new to this. I have a couple of questions around the cobweb implementation in R Weka. If you could supply answer or insight, I would really appreciate. 1. From Fisher's paper in 1987, it seems that Cobweb only deals with nominal data. In R Weka cobweb, is it allowed to accommodate real/continuous value? 2. My understanding is that Cobweb clusters based on Category Utility function. However, if I would like to specify my own objective function, how can I do so? 3. I have about 130,000 data points (each with about 50 attributes) for training and another same amount for testing. Would this cause any memory or performance problem? Thank you, - adschai RWeka is simply an interface to the WEKA data mining software. Why don't you just put your question to the Weka mailing list at https://list.scms.waikato.ac.nz/mailman/listinfo/wekalist? From my own former experience I would say that Cobweb is never applicable to large data sets (and was not meant for that) and for numerical attributes the results are not very meaningful. Hans Werner Borchers __ R-help@stat.math.ethz.ch 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] R-excel
On Fri, 10 Aug 2007, Peter Wickham wrote: I am running R 2.5.1 using Mac OSX 10.4.10. xlsReadWrite is a Windows binary. Instead, install and load packages: (1) gtools:(2) gdata. These are both Windows and Mac binaries. gdata depends on gtools, so be sure to load gtools first or set the installation depends parameters. Then you The R default *is* to install dependencies in R = 2.5.0. can use read.xls. Thus, in Mac: data-read.xls(/Users/your name/Documents/data.xls,sheet=1). For Windows, substitute the appropriate filepath and file name in the first argument of read.xls: e.g., data-read.xls(A:/filename.xls,sheet-1). Thanks to correspondents for You mean sheet=1 There are other platforms, and the usage of gdata::read.xls is common to all platforms. their advice; but I hope that this may alleviate some of the frustration (referred to in the R Import/Export Manual) associated with dealing with That is described in the 'R Data Import/Export Manual' (sic). It *increases* the frustration of those who WTFM to see it and its contents misdescribed in this way. Further, people who search the list archives are liable to make use of buggy posts like this one, so it seems necessary to put the corrections and frustration on the record. Please just point people to the appropriate manual EXCEL files in R. Erika Frigo wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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__ R-help@stat.math.ethz.ch 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] R Weka and cobweb
Hi, I never use cobweb before and I'm quite new to this. I have a couple of questions around the cobweb implementation in R Weka. If you could supply answer or insight, I would really appreciate. 1. From Fisher's paper in 1987, it seems that Cobweb only deals with nominal data. In R Weka cobweb, is it allowed to accommodate real/continuous value? 2. My understanding is that Cobweb clusters based on Category Utility function. However, if I would like to specify my own objective function, how can I do so? 3. I have about 130,000 data points (each with about 50 attributes) for training and another same amount for testing. Would this cause any memory or performance problem? Thank you, - adschai __ R-help@stat.math.ethz.ch 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] R-excel
I am running R 2.5.1 using Mac OSX 10.4.10. xlsReadWrite is a Windows binary. Instead, install and load packages: (1) gtools:(2) gdata. These are both Windows and Mac binaries. gdata depends on gtools, so be sure to load gtools first or set the installation depends parameters. Then you can use read.xls. Thus, in Mac: data-read.xls(/Users/your name/Documents/data.xls,sheet=1). For Windows, substitute the appropriate filepath and file name in the first argument of read.xls: e.g., data-read.xls(A:/filename.xls,sheet-1). Thanks to correspondents for their advice; but I hope that this may alleviate some of the frustration (referred to in the R Import/Export Manual) associated with dealing with EXCEL files in R. Erika Frigo wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- View this message in context: http://www.nabble.com/R-excel-tf3975982.html#a12101349 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] R memory usage
See ?gc ?Memory-limits On Wed, 8 Aug 2007, Jun Ding wrote: Hi All, I have two questions in terms of the memory usage in R (sorry if the questions are naive, I am not familiar with this at all). 1) I am running R in a linux cluster. By reading the R helps, it seems there are no default upper limits for vsize or nsize. Is this right? Is there an upper limit for whole memory usage? How can I know the default in my specific linux environment? And can I increase the default? See ?Memory-limits, but that is principally a Linux question. 2) I use R to read in several big files (~200Mb each), and then I run: gc() I get: used (Mb) gc trigger (Mb) max used Ncells 23083130 616.4 51411332 1372.9 51411332 Vcells 106644603 813.7 240815267 1837.3 227550003 (Mb) 1372.9 1736.1 What do columns of used, gc trigger and max used mean? It seems to me I have used 616Mb of Ncells and 813.7Mb of Vcells. Comparing with the numbers of max used, I still should have enough memory. But when I try object.size(area.results) ## area.results is a big data.frame I get an error message: Error: cannot allocate vector of size 32768 Kb Why is that? Looks like I am running out of memory. Is there a way to solve this problem? Thank you very much! Jun -- 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 __ R-help@stat.math.ethz.ch 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] R memory usage
Hi All, I have two questions in terms of the memory usage in R (sorry if the questions are naive, I am not familiar with this at all). 1) I am running R in a linux cluster. By reading the R helps, it seems there are no default upper limits for vsize or nsize. Is this right? Is there an upper limit for whole memory usage? How can I know the default in my specific linux environment? And can I increase the default? 2) I use R to read in several big files (~200Mb each), and then I run: gc() I get: used (Mb) gc trigger (Mb) max used Ncells 23083130 616.4 51411332 1372.9 51411332 Vcells 106644603 813.7 240815267 1837.3 227550003 (Mb) 1372.9 1736.1 What do columns of used, gc trigger and max used mean? It seems to me I have used 616Mb of Ncells and 813.7Mb of Vcells. Comparing with the numbers of max used, I still should have enough memory. But when I try object.size(area.results) ## area.results is a big data.frame I get an error message: Error: cannot allocate vector of size 32768 Kb Why is that? Looks like I am running out of memory. Is there a way to solve this problem? Thank you very much! Jun __ R-help@stat.math.ethz.ch 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] R and excell differences in calculation F distributionfunction
R-help, I'm trying to work out the density function by doing: df(5.22245, 3, 22) [1] 0.005896862 df(15.20675, 6, 4) [1] 0.001223825 In excell the result is : 0.0071060464 * FDIST(5.22245,3,22) 0.011406 -- FDIST(15.20675,6,4) From my point of view the differences in the second case are substantial. Can anyone give me a hint on this? Thanks in advance Luis Ridao Cruz Faroese Fisheries Laboratory Nóatún 1, P.O. Box 3051 FR-110 Tórshavn Faroe Islands Tel : (+298) 353900, Tel (direct) : (+298) 353912 Mob.:(+298) 580800, Fax: : (+298) 353901 E-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] R and excell differences in calculation F distributionfunction
I think you'll have to compare FDIST to pf() and not df() Best regards Frede Aakmann Tøgersen Scientist UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1878 E-mail: [EMAIL PROTECTED] Web: http://www.agrsci.org This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. -Oprindelig meddelelse- Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne af Luis Ridao Cruz Sendt: 7. august 2007 12:27 Til: r-help@stat.math.ethz.ch Emne: [R] R and excell differences in calculation F distributionfunction R-help, I'm trying to work out the density function by doing: df(5.22245, 3, 22) [1] 0.005896862 df(15.20675, 6, 4) [1] 0.001223825 In excell the result is : 0.0071060464 * FDIST(5.22245,3,22) 0.011406 -- FDIST(15.20675,6,4) From my point of view the differences in the second case are substantial. Can anyone give me a hint on this? Thanks in advance Luis Ridao Cruz Faroese Fisheries Laboratory Nóatún 1, P.O. Box 3051 FR-110 Tórshavn Faroe Islands Tel : (+298) 353900, Tel (direct) : (+298) 353912 Mob.:(+298) 580800, Fax: : (+298) 353901 E-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R and excell differences in calculation F distributionfu
On 07-Aug-07 10:27:06, Luis Ridao Cruz wrote: R-help, I'm trying to work out the density function by doing: df(5.22245, 3, 22) [1] 0.005896862 df(15.20675, 6, 4) [1] 0.001223825 In excell the result is : 0.0071060464 * FDIST(5.22245,3,22) 0.011406 -- FDIST(15.20675,6,4) From my point of view the differences in the second case are substantial. Can anyone give me a hint on this? Thanks in advance It would seem that Excel is giving you the upper tail of the F-distribution (cumulative distribution, not density), i.e. what R would calculate as pf(5.22245,3,22,lower.tail=FALSE) [1] 0.007106046 pf(15.20675,6,4,lower.tail=FALSE) [1] 0.0114 so in effect using pf rather than df. If you want the density function (corresponding to df) from Excel, then that's not something I know how to do (nor want to know ... ). Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 07-Aug-07 Time: 11:47:52 -- XFMail -- __ R-help@stat.math.ethz.ch 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] R script for obtaining standard errors for marginal effects of multinomial logit
Deat R users, Could you please help me with how to get standard errors (or asymptotic variances) of marginal effects of multinomial logit model? So far I do have estimated coeficients of multinomial logit (using multinom function) and covariance matrix of coefficients. I did also manage to obtain probabilities and marginal effects. However, getting standard errors (which in theory has to be done using delta method) seems to be a little bit tricky and complicated to me. Thanks a lot in advance, David -- View this message in context: http://www.nabble.com/R-script-for-obtaining-standard-errors-for-marginal-effects-of-multinomial-logit-tf4217461.html#a11998475 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] [R-pkgs] surveyNG (and survey)
'surveyNG' version 0.3 is on CRAN. This package provides experimental features for survey analysis that may be incorporated in the survey package in the future. Currently there are facilities for analysis of complex surveys using (possibly large) data sets stored in a SQLite database. However, analysis facilities for these SQL-backed survey designs are rather more limited than in the 'survey' package. Version 0.3 adds hexagonal binning plots and kernel smoothing. Also, the 'survey' package hasn't been announced on this list since version 2.9 in 2005 and verison 3.6-11 was recently posted. It provides fairly comprehensive facilities for analysis of complex survey designs. Major additions since 2.9 are calibration estimators (aka GREG or generalized raking), simple two-phase designs, and smoothing. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-SIG-Finance] question on analyzing of correlation structure
I don't understand your question but there is a package called VARs
that may be helpful to you.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of liu lu
Sent: Friday, August 03, 2007 8:39 AM
To: [EMAIL PROTECTED]
Subject: [R-SIG-Finance] question on analyzing of correlation structure
I am currently working on an empirical analysis of the respective A and
B series in the three markets: X, Y, and Z. Suppose the correlation of
the A B series in market X shows a different pattern for the
significant short-run adjustment as the impulse reponse fuctions
indicate (Haan, Wouter J. den. 2000. The comovement between output and
prices. Journal of Monetary Economics 46:3-30.).
Could somebody share some ideas about any package can do the following:
(1) to work out the factors contributing the disparity; (2) to contrast
and highlight the difference.
Many thanks to your kind attention.
Wei-han Liu
[[alternative HTML version deleted]]
___
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-finance
-- Subscriber-posting only.
-- If you want to post, subscribe first.
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
__
R-help@stat.math.ethz.ch 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] [R-pkgs] new package plotAndPlayGTK
Package plotAndPlayGTK provides a graphical user interface for R
plots. Wrap it around your plot commands, like playwith(plot(mydata)).
A window pops up with a Cairo plot device and a toolbar with buttons
to interact with the plot. The default buttons allow you to add
persistent labels to data points, zoom in and out and around, save the
plot to a file, and so on. Furthermore, you can edit the plot call on
the fly. There are buttons to work with multiple panels and pages of a
Lattice plot. For multi-variate scatterplots ('splom' only) there is a
brush function, and for 3D plots ('wireframe' / 'cloud' only) there
is a simple zoom and rotate.
New buttons can also be defined; actually any GTK+ widget can be added
to the toolbar. An example is given of a numeric input widget to
choose a number of clusters to show.
Note: code to generate the plot will need to be wrapped up into a
single call with some standard arguments, and the interaction features
do not work well with multiple-plot layouts in traditional graphics.
As yet it does not work with grid-based plots other than Lattice (such
as ggplot2), but button handlers could be written. This package is
based on RGtk2, and so requires the GTK+ libraries.
v0.8.42 is on CRAN.
http://code.google.com/p/plotandplay-gtk/
--
Felix Andrews / 安福立
PhD candidate
Integrated Catchment Assessment and Management Centre
The Fenner School of Environment and Society
The Australian National University (Building 48A), ACT 0200
Beijing Bag, Locked Bag 40, Kingston ACT 2604
http://www.neurofractal.org/felix/
xmpp:[EMAIL PROTECTED]
3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8
___
R-packages mailing list
[EMAIL PROTECTED]
https://stat.ethz.ch/mailman/listinfo/r-packages
__
R-help@stat.math.ethz.ch 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] [R-pkgs] new package plotAndPlayGTK
Felix Andrews felix at nfrac.org writes: Package plotAndPlayGTK provides a graphical user interface for R . This package is based on RGtk2, and so requires the GTK+ libraries. Warning for Windows users: When I installed GTK+ from http://gladewin32.sourceforge.net/modules/wfdownloads/visit.php?lid=111 (Win2K) the installation erased all my paths settings, leaving only the the GTK path. I had to restore it via registry manipulation from the old control set. The plotAndPlayGTK worked after the recovery. Dieter __ R-help@stat.math.ethz.ch 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] [R-pkgs] new package plotAndPlayGTK
It did not do that for me. Maybe its specific to Win 2K? I am using XP. On 8/2/07, Dieter Menne [EMAIL PROTECTED] wrote: Felix Andrews felix at nfrac.org writes: Package plotAndPlayGTK provides a graphical user interface for R . This package is based on RGtk2, and so requires the GTK+ libraries. Warning for Windows users: When I installed GTK+ from http://gladewin32.sourceforge.net/modules/wfdownloads/visit.php?lid=111 (Win2K) the installation erased all my paths settings, leaving only the the GTK path. I had to restore it via registry manipulation from the old control set. The plotAndPlayGTK worked after the recovery. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] [R-pkgs] New R package sqldf
On 8/1/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Extremely cool and useful I immediately saw uses for it in some of the work I do. So went to look at it. I especially liked the examples with joins! I observed a few small bugs in the documentation: - The help references The sqldf home page URL: http://code.google.com/p/batchfiles/ but it should be of course .../p/sqldf Thanks. Its fixed in the svn repository now. Will be part of next release. - Example 5 there didn't work for me. Maybe I don't have something loaded? minSL - 7 limit - 3 fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Error: attempt to apply non-function Works for me. What versions are you using? library(sqldf) minSL - 7 limit - 3 fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Sepal_Length Sepal_Width Petal_Length Petal_Width Species 1 7.1 3.0 5.9 2.1 virginica 2 7.6 3.0 6.6 2.1 virginica 3 7.3 2.9 6.3 1.8 virginica packageDescription(gsubfn)$Version [1] 0.3-3 packageDescription(sqldf)$Version [1] 0-1.1 packageDescription(DBI)$Version [1] 0.2-3 packageDescription(RSQLite)$Version [1] 0.5-5 R.version.string # Windows XP [1] R version 2.5.1 (2007-06-27) Also, not shown, but example(fn) works for me. Other things to try are try it on a new R session and if that still does not work try sourcing it from the repository first: library(gsubfn) source(http://gsubfn.googlecode.com/svn/trunk/R/fn.R;) fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Let me know if any of these things work or not. None of the examples in ?fn work for me either, giving the same error message. The examples in gsubfn work as do the rest of the sqldf examples. As mentioned, they all work for me. Let me know what the result is of trying the previous suggestions. I am on Windows XP with R version 2.5.1 version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.1 year 2007 month 06 day27 svn rev42083 language R version.string R version 2.5.1 (2007-06-27) David L. Reiner Rho Trading Securities, LLC -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Grothendieck Sent: Tuesday, July 31, 2007 7:43 PM To: [EMAIL PROTECTED] Subject: [R] [R-pkgs] New R package sqldf sqldf is an R package for running SQL select statements on one or more R data frames. It is optimized for convenience making it useful for ad hoc queries against R data frames. Given an SQL select statement whose tables are the names of R data frames it: - sets up the database (by default it transparently sets up an in memory SQLite database using RSQLite; however, MySQL via RMySQL, can be specified as an alternative. MySQL has not been tested.) - imports the data frames found in SQL select statement into the database - runs the SQL select statement - outputs the result back to a data frame - uses a heuristic to assign the appropriate column classes to the result - removes the database so that all the user has to do is issue a one line function call with one argument, the select statement. Here is an example which processes an SQL select statement whose functionality is similar to the R aggregate function. Note that although the iris dataset (which is built into R) uses the name Sepal.Length the R database interface, DBI, converts that to Sepal_Length. Just install the sqldf package from CRAN and type these two lines into R without the prompts: library(sqldf) sqldf(select Species, avg(Sepal_Length) from iris group by Species) Species avg(Sepal_Length) 1 setosa 5.006 2 versicolor 5.936 3 virginica 6.588 As can be seen from the example, there is: - no database setup - no importing and exporting into the database - no coercing of the returned columns to the appropriate class (in most cases) It can be used: - as an alternate syntax for data frame manipulation - learning SQL if you know R - learning R if you know SQL The sqldf package has a single function, sqldf. More information is available by issuing the command ?sqldf from within R. More examples and useful links are available at the sqldf home page: http://code.google.com/p/sqldf/ ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-pkgs] New R package sqldf
It works after rm(list=ls()) I had a function called 'fn'; if I had paid close attention when I loaded gsubfn, I would have seen the warning. My fault. Thanks again for a most useful package! David L. Reiner Rho Trading Securities, LLC -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Wednesday, August 01, 2007 10:27 AM To: David Reiner [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] [R-pkgs] New R package sqldf On 8/1/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Extremely cool and useful I immediately saw uses for it in some of the work I do. So went to look at it. I especially liked the examples with joins! I observed a few small bugs in the documentation: - The help references The sqldf home page URL: http://code.google.com/p/batchfiles/ but it should be of course .../p/sqldf Thanks. Its fixed in the svn repository now. Will be part of next release. - Example 5 there didn't work for me. Maybe I don't have something loaded? minSL - 7 limit - 3 fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Error: attempt to apply non-function Works for me. What versions are you using? library(sqldf) minSL - 7 limit - 3 fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Sepal_Length Sepal_Width Petal_Length Petal_Width Species 1 7.1 3.0 5.9 2.1 virginica 2 7.6 3.0 6.6 2.1 virginica 3 7.3 2.9 6.3 1.8 virginica packageDescription(gsubfn)$Version [1] 0.3-3 packageDescription(sqldf)$Version [1] 0-1.1 packageDescription(DBI)$Version [1] 0.2-3 packageDescription(RSQLite)$Version [1] 0.5-5 R.version.string # Windows XP [1] R version 2.5.1 (2007-06-27) Also, not shown, but example(fn) works for me. Other things to try are try it on a new R session and if that still does not work try sourcing it from the repository first: library(gsubfn) source(http://gsubfn.googlecode.com/svn/trunk/R/fn.R;) fn$sqldf(select * from iris where Sepal_Length $minSL limit $limit) Let me know if any of these things work or not. None of the examples in ?fn work for me either, giving the same error message. The examples in gsubfn work as do the rest of the sqldf examples. As mentioned, they all work for me. Let me know what the result is of trying the previous suggestions. I am on Windows XP with R version 2.5.1 version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.1 year 2007 month 06 day27 svn rev42083 language R version.string R version 2.5.1 (2007-06-27) David L. Reiner Rho Trading Securities, LLC -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Grothendieck Sent: Tuesday, July 31, 2007 7:43 PM To: [EMAIL PROTECTED] Subject: [R] [R-pkgs] New R package sqldf sqldf is an R package for running SQL select statements on one or more R data frames. It is optimized for convenience making it useful for ad hoc queries against R data frames. Given an SQL select statement whose tables are the names of R data frames it: - sets up the database (by default it transparently sets up an in memory SQLite database using RSQLite; however, MySQL via RMySQL, can be specified as an alternative. MySQL has not been tested.) - imports the data frames found in SQL select statement into the database - runs the SQL select statement - outputs the result back to a data frame - uses a heuristic to assign the appropriate column classes to the result - removes the database so that all the user has to do is issue a one line function call with one argument, the select statement. Here is an example which processes an SQL select statement whose functionality is similar to the R aggregate function. Note that although the iris dataset (which is built into R) uses the name Sepal.Length the R database interface, DBI, converts that to Sepal_Length. Just install the sqldf package from CRAN and type these two lines into R without the prompts: library(sqldf) sqldf(select Species, avg(Sepal_Length) from iris group by Species) Species avg(Sepal_Length) 1 setosa 5.006 2 versicolor 5.936 3 virginica 6.588 As can be seen from the example, there is: - no database setup - no importing and exporting into the database - no coercing of the returned columns to the appropriate class (in most cases) It can be used: - as an alternate syntax for data frame manipulation - learning SQL if you know R - learning R if you know SQL The sqldf package has a single function, sqldf. More information is available by issuing the command ?sqldf from within R. More examples and useful links are available at the sqldf home
[R] [R-pkgs] randomSurvivalForest 3.0.0 now available
Dear useRs: Release 3.0.0 of the randomSurvivalForest, an ensemble tree method for the analysis of right censored survival data, package is now available. - CHANGES TO RELEASE 3.0.0 Release 3.0.0 represents a major upgrade in the functionality of the 2.x releases. Key changes are as follows: o Missing data can be imputed in both grow and predict mode. This applies to variables as well as time and censoring outcome values. Values are imputed dynamically as the tree is grown using a new tree imputation methodology. This produces an imputed forest which can be used for prediction purposes on test data sets with missing data. o Importance values for variables are returned in predict mode when test data contains outcomes as well as variables. o Fixed some bugs in plot.variable(). Thanks to Andy J. Minn for pointing this out. o Minor modification of PMML representation of RSF forest output to accomodate imputation. The method of random seed chain recovery has been altered. Note that forests produced with prior releases will have to be regenerated using this release. We apologize for the inconvenience. - Thanks. ubk [EMAIL PROTECTED] Udaya B. Kogalur, Ph.D. Kogalur Shear Corporation 5425 Nestleway Drive, Suite L1 Clemmons, NC 27012 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R on QNX
Hi, Has anyone attempted to compile R on QNX 4.x or 6.x ? It would be particularly cool if there is a precompiled version somewhere on the QNX software archives. Thank you very much !! Suresh ps. Please cc replies to my address if possible... __ R-help@stat.math.ethz.ch 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] [R-pkgs] New R package sqldf
sqldf is an R package for running SQL select statements on one or more R data frames. It is optimized for convenience making it useful for ad hoc queries against R data frames. Given an SQL select statement whose tables are the names of R data frames it: - sets up the database (by default it transparently sets up an in memory SQLite database using RSQLite; however, MySQL via RMySQL, can be specified as an alternative. MySQL has not been tested.) - imports the data frames found in SQL select statement into the database - runs the SQL select statement - outputs the result back to a data frame - uses a heuristic to assign the appropriate column classes to the result - removes the database so that all the user has to do is issue a one line function call with one argument, the select statement. Here is an example which processes an SQL select statement whose functionality is similar to the R aggregate function. Note that although the iris dataset (which is built into R) uses the name Sepal.Length the R database interface, DBI, converts that to Sepal_Length. Just install the sqldf package from CRAN and type these two lines into R without the prompts: library(sqldf) sqldf(select Species, avg(Sepal_Length) from iris group by Species) Species avg(Sepal_Length) 1 setosa 5.006 2 versicolor 5.936 3 virginica 6.588 As can be seen from the example, there is: - no database setup - no importing and exporting into the database - no coercing of the returned columns to the appropriate class (in most cases) It can be used: - as an alternate syntax for data frame manipulation - learning SQL if you know R - learning R if you know SQL The sqldf package has a single function, sqldf. More information is available by issuing the command ?sqldf from within R. More examples and useful links are available at the sqldf home page: http://code.google.com/p/sqldf/ ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] [R-pkgs] New versions for the distr-family of packages and of package startupmsg
We would like to announce the availability on CRAN (with possibly a minor delay until on every mirror) of new versions of our packages in the distrXXX-family (version 1.9), i.e.; distr, distrEx, distrSim, distrTEst, and distrDoc as well as of package for managing startup messages, startupmsg (0.5). [all of them require R = 2.2.0] - * Changes *** of distr (1.9), distrEx (1.9), distrSim (1.9), distrTEst (1.9), distrDoc (1.9) * - There are major changes in distr and distrEx from this release on; the more important ones can be inspected at http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR and the pages linked to on this page. Special thanks go to Spencer Graves for spotting some errors in 1.8 (which should be fixed by now) and to G.Jay Kerns for detecting some further bugs and providing code for exact kurtosis and skewness functionals. After package installation you may also have a look at NEWS(pkg-name) for each of the packages mentioned in this mail. - * Changes *** of startupmsg (0.5) * - This may be interesting to those annoyed by our chatty startup messages ;-) - From this version on, you may use suppressPackageStartupMessages() to suppress the startup-messages issued by our packages--- compare http://tolstoy.newcastle.edu.au/R/e2/devel/07/04/3039.html - Short Descriptions - distr: distr is to provide a conceptual treatment of random variables (r.v.'s) by means of S4--classes. A virtual mother class Distribution is introduced. All distributions of the stats package are implemented as subclasses of either AbscontDistribution or DiscreteDistribution. Using these classes, we also provide (default) methods to automatically generate the image distributions under unary mathematical operations as well as a general convolution algorithm. - distrSim: Classes and methods are provided for a standardized treatment of simulations (also under contaminations) . - distrTEst: Classes and methods are provided for a standardized treatment of the evaluation of statistical procedures (up to now only estimators) at data/simulations - distrEx: This package provides some extensions to package distr like: * extreme value distribution classes, * expectations +in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median, kurtosis, skewness * truncated moments * distances between distributions (Hellinger, Kolmogorov, total variation, convex contamination) * conditional distributions in factorized form * conditional expectations in factorized form - distrDoc: distrDoc provides a common vignette to the distrXXX family - startupmsg: provides utilities for start-up messages for packages - We look forward to receiving questions, comments and suggestions Peter Ruckdeschel Matthias Kohl Thomas Stabla Florian Camphausen ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R codes for g-and-h distribution
filame uyaco filams0704 at yahoo.com writes:
hi!
I would like to ask help how to generate numbers from g-and-h distribution.
This distribution is like
normal distribution but span more of the kurtosis and skewness plane. Has R
any package on how to generate
them?
Someone else asked for this in 2005, but I didn't see any
answers. If the wiki weren't down I would put this up there ...
## http://www.itl.nist.gov/div898/software/dataplot/refman2/auxillar/ghpdf.htm
## G(p,g,h) = exp((g*Zp)-1)*exp((h*Zp^2)/2)/g
[n.b. formatting on this page is very confusing, I inserted
parentheses]
## with Zp denoting the normal percent point function of p. When g = 0
## and h = 0, the g-and-h distribution reduces to a standard normal
## distribution.
## The g-and-h probability density function is computed by taking the
## numerical derivative of the cumulative distribution function (which is
## turn computed by numerically inverting the percent point function
## using a bisection method).
## [from
## http://www.itl.nist.gov/div898/handbook/eda/section3/eda362.htm:
## The percent point function (ppf) is the inverse of the cumulative
## distribution function. For this reason, the percent point function
## is also commonly referred to as the inverse distribution function.
## thus R's q functions are percent point functions
qgh - function(q,g,h) {
Zp - qnorm(q)
## not vectorized!
if (g==0) Zp else (exp(g*Zp)-1)*exp((h*Zp^2/2))/g
}
## since the quantile function is defined, it makes generating
## random values easy!
rgh - function(n,g,h) {
qgh(runif(n),g,h)
}
## eps sets distance from 1 for searching
## strategy could probably be improved (first approx. based on
## qnorm??)
pgh - function(p,g,h,eps=1e-7) {
uniroot(function(z) { qgh(z,g,h) - p}, interval=c(eps,1-eps))$root
}
dgh - function(x,g,h,log=FALSE,ndep=1e-3,...) {
## crude vectorization in x (not g or h)
if (length(x)1) return(sapply(x,dgh,g=g,h=h,log=log,ndep=ndep,...))
r - (pgh(x+ndep,g,h)-pgh(x,g,h))/ndep
if (log) log(r) else r
}
## examples ...
set.seed(1001)
## should be approx. normal
r1 = rgh(1,1e-5,0)
r2 = rgh(1,1e-5,0)
r3 = rgh(1,1e-5,0)
## plot 3 different samples
plot(density(r1))
lines(density(r2))
lines(density(r3))
curve(dnorm(x),col=2,add=TRUE)
curve(dgh(x,1e-5,0),col=4,add=TRUE)
## some slight numerical glitches -- e.g. around
## x=-2.6
r4 = rgh(5,0.4,0.4)
plot(density(r4,n=1024),xlim=c(-10,10))
curve(dnorm(x),add=TRUE,col=2)
curve(dgh(x,0.4,0.4),add=TRUE,col=4)
legend(topleft,c(density,g-h,normal),
lty=rep(1,3),col=c(1,4,2))
## note glitch again, this time around
## y=-3.89
__
R-help@stat.math.ethz.ch 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] R CMD check sh: line 1: make: command not found
On Thu, 26 Jul 2007, David Peltier wrote: hello, I am using R 2.5.0 under OS X. I am having sh: line 1: make: command not found error message when I run R CMD check : Any help would be appreciated. Well, that is easy: 'make' is missing. It should be there in the OS, so you need to talk to your OS support for help in finding/installing it. BTW, the list for MacOS-specific questions if r-sig-mac. R CMD check backtest * checking for working latex ... OK * using log directory '/backtest/trunk/backtest.Rcheck' * using R version 2.5.0 (2007-04-23) * checking for file 'backtest/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'backtest' version '0.2-0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'backtest' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * creating backtest-Ex.R ... OK * checking examples ... OK * checking tests ... sh: line 1: make: command not found ERROR [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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 __ R-help@stat.math.ethz.ch 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] R CMD check sh: line 1: make: command not found
hello, I am using R 2.5.0 under OS X. I am having sh: line 1: make: command not found error message when I run R CMD check : Any help would be appreciated. R CMD check backtest * checking for working latex ... OK * using log directory '/backtest/trunk/backtest.Rcheck' * using R version 2.5.0 (2007-04-23) * checking for file 'backtest/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'backtest' version '0.2-0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'backtest' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * creating backtest-Ex.R ... OK * checking examples ... OK * checking tests ... sh: line 1: make: command not found ERROR [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R codes for g-and-h distribution
hi! I would like to ask help how to generate numbers from g-and-h distribution. This distribution is like normal distribution but span more of the kurtosis and skewness plane. Has R any package on how to generate them? Any help will be greatly appreciated. Thank you so much! Form, Filame Uyaco - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] [R-pkgs] New package: pomp, inference for partially-observed Markov processes
To: [EMAIL PROTECTED] Subject: New package: pomp, inference for partially-observed Markov processes The new package 'pomp' is built around a very general realization of nonlinear partially-observed Markov processes (AKA state-space models, nonlinear stochastic dynamical systems). The user provides functions specifying the model's process and measurement components. The package's algorithms are built on top of these functions. At the moment, algorithms are provided for particle filtering (AKA sequential importance sampling or sequential Monte Carlo) and the likelihood maximization by iterated filtering (MIF) method of Ionides, Breto, and King (PNAS, 103:18438-18443, 2006). Future support for a variety of other algorithms is envisioned. A working group of the National Center for Ecological Analysis and Synthesis (NCEAS), Inference for Mechanistic Models, is currently implementing additional methods for this package. Simple worked examples are provided in the form of a vignette, random_walk_example. The package is provided under the GPL. Contributions are welcome, as are comments, suggestions, examples, and bug reports. The development of this package has been aided by support from the U.S. N.S.F (Grants #EF-0545276, #EF-0430120) and by the Inference for Mechanistic Models Working Group supported by the National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California. -- Aaron A. King, Ph.D. Ecology Evolutionary Biology University of Michigan http://www.umich.edu/~kingaa GPG Public Key: 0x2B00840F ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] R and mysql
Gabor Grothendieck wrote: To run with R 2.5.1 you need the Windows binary of RMySQL 0.6-0 but I don't think that that is available on either CRAN or BioConductor currently. But on the CRAN extras repository which is provided by Brian Ripley. You can even select it from the menu (and it should be the default). Hence install.packages(RMySQL) shoudl work. Uwe Ligges however, one does exist and I suggest you contact the maintainer, David James or the r-sig-db list. If those don't get it for you send me an email off list and I will send you mine. I have only used the Windows version on XP so I can't say whether there would be any problems on W2k. On 7/22/07, along zeng [EMAIL PROTECTED] wrote: Hi all, I want to visit MySQL in R use RMySQL package on Windows 2k.I got RMySQL and DBI packages from a cran,but only the package RMySQL is built on MasOS.I extracted both and put them under the folder of library,started R and typed string as , require(RMySQL); R told me DBI was loaded,but RMySQL was't loaded because R not found it. Thank very much! along __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R and Excel
Dear all, Someone knows what's the command in R corresponding to the vlookup in Excel? Thank you in advance. Claudia [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R and Excel
Dear all, Someone knows what's the command in R corresponding to the vlookup in Excel? Thank you in advance. Claudia __ R-help@stat.math.ethz.ch 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. As far as I discovered from a quick google query the Excel command you cite selects some values from a table according to some conditions. So if you have a data frame called example you could do something like example[example$var15,] Perhaps you need something like example[example$var15,2:5] or example[example$var15,]$var2. Anyway you should follow the advice you'll find at the end of the message: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ... or at least a good example of what you would like to obtain! You'll find a lot of informations on the manipulation of data frames in the manuals. go to http://www.r-project.org/, select manuals, go to the Contributed Documentation. You'll find various manuals, also ones in italian. Ciao Sandro __ R-help@stat.math.ethz.ch 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] R and Excel
On 23/07/07, D ANIELLO CLAUDIA (MPS - 05966) claudia.d'[EMAIL PROTECTED] wrote: Dear all, Someone knows what's the command in R corresponding to the vlookup in Excel? Thank you in advance. Claudia Dear Claudia, Depending on the dataset, it is possible to achieve the same results by using merge(). It is a different way of thinking, but can effectively lookup corresponding values in one data frame into another. If you give a sample of data then I could be a bit more specific! Best wishes, Mark -- Dr. Mark Wardle Clinical research fellow and specialist registrar, Neurology Cardiff, UK __ R-help@stat.math.ethz.ch 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] R and Copula
:
###PART B###
par(op)
for (i in seq(1:360)){
persp(x, dmvdc, xlim = c(-4, 4), ylim=c(0, 1),theta=i)
}
Regards,
Gaurav Yadav
+++
Assistant Manager, CCIL, Mumbai (India)
Mob: +919821286118 Email: [EMAIL PROTECTED]
Bhagavad Gita: Man is made by his Belief, as He believes, so He is
copula [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
07/17/2007 12:53 PM
To
r-help@stat.math.ethz.ch
cc
Subject
Re: [R] R and Copula
it would be great when somebody will help me
thanks
copula wrote:
hi,
first I want to say that I'm new here, and new with copula and R.
That is the reason why I'm writing, if somebody can help me.
I have to make an example of Copula.
On internet I've found this forum and that copula can calculate with
R.
Can somebody help me with the thing how can I start and where can
read
about these stuffs.
Thank to all who can help!
--
View this message in context:
http://www.nabble.com/R-and-Copula-tf4085867.html#a11644534
Sent from the R help mailing list archive at Nabble.com.
__
R-help@stat.math.ethz.ch 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.
DISCLAIMER AND CONFIDENTIALITY CAUTION:\ \ This message and
...{{dropped}}
__
R-help@stat.math.ethz.ch 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.
Quoted from:
http://www.nabble.com/R-and-Copula-tf4085867.html#a11645614
DISCLAIMER AND CONFIDENTIALITY CAUTION:\ \ This message and
...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch 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.
--
View this message in context:
http://www.nabble.com/R-and-Copula-tf4085867.html#a11741607
Sent from the R help mailing list archive at Nabble.com.
__
R-help@stat.math.ethz.ch 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] ?R: Removing white space betwen multiple plots, traditional graphics
You could try par(mar=c(0,5,0,2), mfrow = c(6,1), oma=c(5,0,2,0)) ##...then, your plots...## --- Mr Natural [EMAIL PROTECTED] wrote: I would appreciate suggestions for removing the white spaces the graphs in a stack: par(mar=c(2,2,1,1), mfrow = c(6,1)) mydates-dates(1:20,origin=c(month = 1, day = 1, year = 1986)) plot(rnorm(20,0.1,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.2,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.3,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.5,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.7,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.8,0.1)~mydates, type=b,xlab=,ylim=c(0,1) ) Thanx, Don -- View this message in context: http://www.nabble.com/-R%3A--Removing-white-space-betwen-multiple-plots%2C-traditional-graphics-tf4119626.html#a11716176 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] ?R: Removing white space betwen multiple plots, traditional graphics
Dear List: Thank you for the several helpful comments on my original post of this title. Most to the point, 1. that from z, who is a coauthor of zoo was very kind. I have spent a morning learning zoo and find it a very cool package. With zoo, one can make very neat time series graphs with a minimum of code. I had great fun downloading and plotting financial data from the web. I still have two problems with zoo for my particular application as per the original post of this title. First, my dates are slightly different for each series. Neither of the two suggestions for dealing different-dates-for-different-series that I have found are appropriate (na.approx(m), na.locf.(m)). Is there a way that the NAs can be skipped by each plot, with lines plotted between the dates that exist, as in my original code below? Second, I have complex standard errors for each point, which are either read in as a distinct column for each y value or calculated in R and plotted with code such as (for the first two series): plot(MP~dmp, type=b,xlab=,ylim=c(0,1),xaxt = n) arrows(dmp,MP+semp,dmp,MP-semp,length=.02,angle=90,code=3) plot(C~dc, type=b,xlab=,ylim=c(0,1),xaxt = n) arrows(dc,C+sec,dc,C-sec,length=.02,angle=90,code=3) I cannot get zoo to do this. 2. The second helpful comment is from Steven Tucker, and this solves my problem completely and elegantly. He suggests changing my parameter statements to: par(mar=c(0,5,0,2), mfrow = c(6,1), oma=c(5,0,2,0)) Thank you Steven! Warm regards, Don ps. This forum is very valuable to the growth of R usage among those of us who are not programmers. Mr Natural wrote: I would appreciate suggestions for removing the white spaces the graphs in a stack: par(mar=c(2,2,1,1), mfrow = c(6,1)) mydates-dates(1:20,origin=c(month = 1, day = 1, year = 1986)) plot(rnorm(20,0.1,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.2,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.3,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.5,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.7,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.8,0.1)~mydates, type=b,xlab=,ylim=c(0,1) ) Thanx, Don -- View this message in context: http://www.nabble.com/-R%3A--Removing-white-space-betwen-multiple-plots%2C-traditional-graphics-tf4119626.html#a11732080 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] ?R: Removing white space betwen multiple plots, traditional graphics
On 7/22/07, Mr Natural [EMAIL PROTECTED] wrote: I still have two problems with zoo for my particular application as per the original post of this title. First, my dates are slightly different for each series. Neither of the two suggestions for dealing different-dates-for-different-series that I have found are appropriate (na.approx(m), na.locf.(m)). Is there a way that the NAs can be skipped by each plot, with lines plotted between the dates that exist, as in my original code below? But that is precisely what na.approx does. Here is an example: library(zoo) z - as.zoo(ldeaths) z[c(4, 8, 17)] - NA zz - cbind(z, lag(z, -5)) plot(na.approx(zz), col = 1:2) # classic library(lattice) xyplot(na.approx(zz), col = 1:2) # lattice Second, I have complex standard errors for each point, which are either read in as a distinct column for each y value or calculated in R and plotted with code such as (for the first two series): plot(MP~dmp, type=b,xlab=,ylim=c(0,1),xaxt = n) arrows(dmp,MP+semp,dmp,MP-semp,length=.02,angle=90,code=3) plot(C~dc, type=b,xlab=,ylim=c(0,1),xaxt = n) arrows(dc,C+sec,dc,C-sec,length=.02,angle=90,code=3) I cannot get zoo to do this. Please provide the data. __ R-help@stat.math.ethz.ch 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] R and mysql
Hi all, I want to visit MySQL in R use RMySQL package on Windows 2k.I got RMySQL and DBI packages from a cran,but only the package RMySQL is built on MasOS.I extracted both and put them under the folder of library,started R and typed string as , require(RMySQL); R told me DBI was loaded,but RMySQL was't loaded because R not found it. Thank very much! along __ R-help@stat.math.ethz.ch 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] R and mysql
To run with R 2.5.1 you need the Windows binary of RMySQL 0.6-0 but I don't think that that is available on either CRAN or BioConductor currently. however, one does exist and I suggest you contact the maintainer, David James or the r-sig-db list. If those don't get it for you send me an email off list and I will send you mine. I have only used the Windows version on XP so I can't say whether there would be any problems on W2k. On 7/22/07, along zeng [EMAIL PROTECTED] wrote: Hi all, I want to visit MySQL in R use RMySQL package on Windows 2k.I got RMySQL and DBI packages from a cran,but only the package RMySQL is built on MasOS.I extracted both and put them under the folder of library,started R and typed string as , require(RMySQL); R told me DBI was loaded,but RMySQL was't loaded because R not found it. Thank very much! along __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] (R) Using arguments for the empirical cumulative distribution function
Is there no one who can help me? :,( -- View this message in context: http://www.nabble.com/%28R%29-Using-arguments-for-the-empirical-cumulative-distribution-function-tf4111355.html#a11705448 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] (R) Using arguments for the empirical cumulative distribution function
?plot.ecdf() On 20-Jul-07, at 6:57 AM, squall44 wrote: Is there no one who can help me? :,( -- View this message in context: http://www.nabble.com/%28R%29-Using- arguments-for-the-empirical-cumulative-distribution-function- tf4111355.html#a11705448 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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. -- Mike Lawrence Graduate Student, Department of Psychology, Dalhousie University Website: http://memetic.ca Public calendar: http://icalx.com/public/informavore/Public The road to wisdom? Well, it's plain and simple to express: Err and err and err again, but less and less and less. - Piet Hein __ R-help@stat.math.ethz.ch 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] (R) Using arguments for the empirical cumulative distribution function
Hi Tobias, Maybe I do not understand the issue here but the following line adds main and xlab plot(F10,verticals = TRUE, do.p = TRUE, lwd = 3, main = myTitle, xlab = myXlab) You could find all this in the introduction manual. see r-project.org in the documentation section. Good luck AA. - Original Message - From: squall44 [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Thursday, July 19, 2007 10:13 AM Subject: [R] (R) Using arguments for the empirical cumulative distribution function Hi, I have just started using R. Now I have the following problem: I want to create an Empirical Cumulative Distribution Function and I only came so far: F10 - ecdf(x) plot(F10, verticals= TRUE, do.p = TRUE, lwd=3) x=c(1.6,1.8,2.4,2.7,2.9,3.3,3.4,3.4,4,5.2) Now I'd like to use arguments such as xlabs and main but I don't know how to integrate them. I hope someone can help me, I am really stuck! -- View this message in context: http://www.nabble.com/%28R%29-Using-arguments-for-the-empirical-cumulative-distribution-function-tf4111355.html#a11690150 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R CMD SHLIB problem [make: *** No rule to make target ]
Hy all,
I apologize for my ingenuity in regard to interfaces in R, but I do need it for
my work. In that respect I took a simple and small example from the net (the
hello world, one) to interface R with C.
I have a Windows XP OS using R.2.5.0 and in that regard I have installed the
Perl and RTools files to my PC. I also wrote a proper path file, as suggested.
The C program is:
#include C:/Archivos de programa/R-2.5.0/include/R.h
void hello(int *n){
int i;
for(i=0;i*n;i++){
Rprintf(Hello, world!\n);
}
}
However when trying to compile the a C file in the command window:
R CMD SHLIB holla.c
I get the following message:
make: *** No rule to make target `holla.d', needed by `makeMakedeps'. Stop.
Can somebody give me a hand on this,
Thanks in advance
Diogo André Alagador
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] R CMD SHLIB problem [make: *** No rule to make target ]
Hy all,
I apologize for my ingenuity in regard to interfaces in R, but I do need it for
my work. In that respect I took a simple and small example from the net (the
hello world, one) to interface R with C.
I have a Windows XP OS using R.2.5.0 and in that regard I have installed the
Perl and RTools files to my PC. I also wrote a proper path file, as suggested.
The C program is:
#include C:/Archivos de programa/R-2.5.0/include/R.h
void hello(int *n){
int i;
for(i=0;i*n;i++){
Rprintf(Hello, world!\n);
}
}
However when trying to compile the a C file in the command window:
R CMD SHLIB holla.c
I get the following message:
make: *** No rule to make target `holla.d', needed by `makeMakedeps'. Stop.
Can somebody give me a hand on this,
Thanks in advance
Diogo André Alagador
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] R CMD SHLIB problem [make: *** No rule to make target ]
Please do *not* use paths in your C code, especially those with spaces in.
(The rw-FAQ did advise you not to install into a path with spaces in if
you wanted to do development work.) The path is not needed for system
include files (you used ) and is likely the problem.
And please do not post multiple times.
On Fri, 20 Jul 2007, Diogo Alagador wrote:
Hy all,
I apologize for my ingenuity in regard to interfaces in R, but I do need it for my work.
In that respect I took a simple and small example from the net (the hello
world, one) to interface R with C.
I have a Windows XP OS using R.2.5.0 and in that regard I have installed the
Perl and RTools files to my PC. I also wrote a proper path file, as suggested.
The C program is:
#include C:/Archivos de programa/R-2.5.0/include/R.h
void hello(int *n){
int i;
for(i=0;i*n;i++){
Rprintf(Hello, world!\n);
}
}
You don't need R.h, but you do need to declare Rprintf, which is in
R_ext/Print.h. So a more legible version of a correct program would be
% cat holla.c
#include R_ext/Print.h
void hello(int *n)
{
int i;
for(i = 0; i *n; i++)
Rprintf(Hello, world!\n);
}
which you could call by
dyn.load(holla.dll)
.C(hello, 10L)
(note the L).
However when trying to compile the a C file in the command window:
R CMD SHLIB holla.c
I get the following message:
make: *** No rule to make target `holla.d', needed by `makeMakedeps'. Stop.
Can somebody give me a hand on this,
Thanks in advance
Diogo André Alagador
[[alternative HTML version deleted]]
--
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__
R-help@stat.math.ethz.ch 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] R CMD SHLIB problem [make: *** No rule to make target ]
Prof. Ripley,
I will follow your suggestion about file spaces. However, as you said the path
declared in the #include row is redundant, so I think the problem did not come
through that.
Meanwhile, after some tries I could compile the file. I just got more attention
to case sensitiveness.
Sorry for the mess.
Cheers,
Diogo Andre' Alagador
Please do *not* use paths in your C code, especially those with spaces in.
(The rw-FAQ did advise you not to install into a path with spaces in if
you wanted to do development work.) The path is not needed for system
include files (you used ) and is likely the problem.
And please do not post multiple times.
On Fri, 20 Jul 2007, Diogo Alagador wrote:
Hy all,
I apologize for my ingenuity in regard to interfaces in R, but I do
need it for my work. In that respect I took a simple and small example
from the net (the hello world, one) to interface R with C. I have a
Windows XP OS using R.2.5.0 and in that regard I have installed the
Perl and RTools files to my PC. I also wrote a proper path file, as
suggested.
The C program is:
#include C:/Archivos de programa/R-2.5.0/include/R.h
void hello(int *n){
int i;
for(i=0;i*n;i++){
Rprintf(Hello, world!\n);
}
}
You don't need R.h, but you do need to declare Rprintf, which is in
R_ext/Print.h. So a more legible version of a correct program would be
% cat holla.c
#include R_ext/Print.h
void hello(int *n)
{
int i;
for(i = 0; i *n; i++)
Rprintf(Hello, world!\n);
}
which you could call by
dyn.load(holla.dll)
.C(hello, 10L)
(note the L).
However when trying to compile the a C file in the command window:
R CMD SHLIB holla.c
I get the following message:
make: *** No rule to make target `holla.d', needed by `makeMakedeps'.
Stop.
Can somebody give me a hand on this,
Thanks in advance
Diogo André Alagador
[[alternative HTML version deleted]]
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] ?R: Removing white space betwen multiple plots, traditional graphics
I would appreciate suggestions for removing the white spaces the graphs in a stack: par(mar=c(2,2,1,1), mfrow = c(6,1)) mydates-dates(1:20,origin=c(month = 1, day = 1, year = 1986)) plot(rnorm(20,0.1,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.2,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.3,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.5,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.7,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.8,0.1)~mydates, type=b,xlab=,ylim=c(0,1) ) Thanx, Don -- View this message in context: http://www.nabble.com/-R%3A--Removing-white-space-betwen-multiple-plots%2C-traditional-graphics-tf4119626.html#a11716176 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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] ?R: Removing white space betwen multiple plots, traditional graphics
On Fri, 20 Jul 2007, Mr Natural wrote: I would appreciate suggestions for removing the white spaces the graphs in a stack: par(mar=c(2,2,1,1), mfrow = c(6,1)) mydates-dates(1:20,origin=c(month = 1, day = 1, year = 1986)) plot(rnorm(20,0.1,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.2,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.3,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.5,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.7,0.1)~mydates, type=b,xlab=,ylim=c(0,1),xaxt = n) plot(rnorm(20,0.8,0.1)~mydates, type=b,xlab=,ylim=c(0,1) ) Really, there is no need to do this all by hand. Please have a look at the zoo package (as recommended earlier this week). Then you can do x - cbind(rnorm(20,0.1,0.1), rnorm(20,0.2,0.1), rnorm(20,0.3,0.1), rnorm(20,0.5,0.1), rnorm(20,0.7,0.1), rnorm(20,0.8,0.1)) z - zoo(x, mydates) plot(z) plot(z, nc = 1, type = b) and much more. Please consult vignette(zoo-quickref, package = zoo) vignette(zoo, package = zoo) as well as the Date and Time Classes article by Gabor Grothendieck and Thomas Petzoldt in R News 4(1), 29-32. (available from your favourite CRAN mirror). Z Thanx, Don -- View this message in context: http://www.nabble.com/-R%3A--Removing-white-space-betwen-multiple-plots%2C-traditional-graphics-tf4119626.html#a11716176 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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] R
Hello! I am using for logistic regression in survey data the svyglm procedure. I wondered how does the strata effect estimates SE (in addition to the weights given proportional to population size). I know that for simple regression measurements of each strata is assumed to have different variance. But in a logistic model this is not the case. Can anyone help me here? Thank you Ron [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
