Re: [R] Print plot to pdf, jpg or any other format when using scatter3d error
On 04.01.2011 08:37, David Winsemius wrote:
On Jan 3, 2011, at 8:17 PM, Jurica Seva wrote:
Hi,
I have been trying to output my graphs to a file (jpeg, pdf, ps, it
doesnt matter) but i cant seem to be able to get it to output. I tried
a few things but none of them worked and am lost as what to do now. I
am using the scatter3d function, and it prints out the graphs on tot
he screen without any problems, but when it comes to writing them to a
file i cant make it work. Is there any other way of producing
3dimensional graphs (they dont have to be rotatable/interactive after
the print out)?
The code is fairly simple and is listed down :
#libraries
library(RMySQL)
library(rgl)
library(scatterplot3d)
library(Rcmdr)
##
#database connection
mycon - dbConnect(MySQL(),
user='root',dbname='test',host='localhost',password='')
#distinct sessions
rsSessionsU01 - dbSendQuery(mycon, select distinct sessionID from
actiontimes where userID = 'ID01')
sessionU01 -fetch(rsSessionsU01)
sessionU01[2,]
#user01 data
mycon - dbConnect(MySQL(),
user='root',dbname='test',host='localhost',password='')
rsUser01 - dbSendQuery(mycon, select
a.userID,a.sessionID,a.actionTaken,a.timelineMSEC,a.durationMSEC,b.X,b.Y,b.Rel__dist_,b.Total_dist_
from `actiontimes` as a , `ulogdata` as b where a.originalRECNO =
b.RECNO and a.userID='ID01')
user01 - fetch(rsUser01, n= -1)
user01[1,1]
#plot loop
for (i in 1:10){
userSubset-subset(user01,sessionID ==
sessionU01[i,],select=c(timelineMSEC,X,Y))
userSubset
x-as.numeric(userSubset$X)
y-as.numeric(userSubset$Y)
scatter3d(
#??? I thought the function was scatterplot3d()
scatter3d() is provided by Rcmdr and an interface to the rgl package.
x,y,userSubset$timeline,xlim = c(0,1280), ylim = c(0,1024),
zlim=c(0,180),type=h,main=sessionU01[i,],sub=sessionU01[i,])
tmp6=rep(.ps)
Why name it .ps when you are using pdf.dev()?
Actually he is not using it (at least it is in comments).
tmp7=paste(sessionU01[i,],tmp6,sep=)
tmp7
rgl.postscript(tmp7,ps,drawText=FALSE)
That should be correct code, according to the rgl documentation.
When you want to get output to the file device, you need to surround
the plotting commands. the pdf call goes at the beginning of the loop
and the dev.odd at the end. It seems dangerous to specify the number to
dev.off since there might be no or more than one device already open. If
you just use dev.off() you will close the last device that was opened,'
Using R standard devices will not work for rgl graphics.
Best wishes,
Uwe
#pdf(file=tmp7) # Move before the scatterplot3d call
#dev.print(file=tmp7, device=pdf, width=600)
# you should also make sure you created a valid file string. We cannot
check since you have not offered a reproducible example.
#dev.off(2)
}
David Winsemius, MD
West Hartford, CT
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[R] Odp: how to subset unique factor combinations from a data frame.
Hi r-help-boun...@r-project.org napsal dne 04.01.2011 05:21:25: Hi All I have these questions and request members expert view on this. a) I have a dataframe (df) with five factors (identity variables) and value (measured value). The id variables are Year, Country, Commodity, Attribute, Unit. Value is a value for each combination of this. I would like to get just the unique combination of Commodity, Attribute and Unit. I just need the unique factor combination into a dataframe or a table. I know aggregate and subset but dont how to use them in this context. aggregate(Value, list(Comoditiy, Atribute, Unit), function) b) Is it possible to inclue non- aggregate columns with aggregate function say in the above case aggregate(Value ~ Commodity + Attribute, data = df, FUN = count). The use of count(Value) is just a round about to return the combinations of Commodity Attribute, and I would like to include 'Unit' column in the returned data frame? Hm. Maybe xtabs? But without any example it is only a guess. c) Is it possible to subset based on unique combination, some thing like this. subset(df, unique(Commodity), select = c(Commodity, Attribute, Unit)). I know this is not correct as it returns an error 'subset needs a logical evaluation'. Trying various ways to accomplish the task. Probably sqldf package has tools for doing it but I do not use it so you have to try yourself. df[Comodity==something, c(Commodity, Attribute, Unit)] can be other way. Anyway your explanation is ambiguous. Let say you have three rows with the same Commodity. Which row do you want to select? Regards Petr will be grateful for any ideas and help Regards, SNVK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Please, need help with a plot
On 03.01.2011 14:25, Victor F Seabra wrote:
although the code somehow didn't work on my Vista / R 2.8,
it did work perfectly on a XP machine / R 2.10
An when you update both machines to a recent R-2.12.1 you will find how
much more will work in the end!
Uwe Ligges
I've been trying to fix this for days,
Thank you very much for your help!
__
02/01/2011 19:30, David Winsemius dwinsem...@comcast.net wrote:
On Jan 2, 2011, at 1:15 PM, Ben Bolker wrote:
This is a little bit more 'magic' than I would like, but seems
to work. Perhaps someone else can suggest a cleaner solution.
Here's the best I could come up with but will admit that there were
many failed attempts before success:
expr.vec- as.expression(parse(text=table1$var1))
plot(x=table1$var2 ,y=1:11, xlim=c(0,20), pch=20)
text(x=table1$var2, y=1:11, labels=expr.vec, pos=4)
title(x=15, y=5, expression(Yet another way to process strings with
operators like '=' )
(The title expression works on my machine, but perhaps not on the OP's
machine, given differences in encoding that have so far been exhibited.)
ages- gsub([^0-9]+,,table1$var1)
rel- gsub(age\\s*([=]+)\\s*[0-9]+,\\1,table1$var1,perl=TRUE)
with(table1,plot(var2,1:11,xlim=c(0,20),pch=20))
invisible(with(table1,
mapply(function(x,y,a,r) {
text(x=x,y=y,
switch(r,
`=`=bquote(age= .(a)),
``=bquote(age .(a)),
`=`=bquote(age= .(a))),
pos=4)},
var2,1:11,ages,rel)))
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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and provide commented, minimal, self-contained, reproducible code.
[R] Default Working directory on windows 7?
Hi, Just installed R on a new Windows 7 machine (as admin). I feel quite uncomfortable knowing that the default WD when starting R is: getwd() [1] C:/Windows/system32 I guess I did something wrong when installing R... How to change R's default working directory? regards Eryk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Default Working directory on windows 7?
Change the Start in: property on the shortcut you used to start R with. Right-click on the R icon and click Properties (you may need to right click once, then again if you are using the pinned start menu icon in Windows 7). Then when you start R again with that shortcut it will use the directory you choose. I'm not sure if you can control this during the install, but mine is set to use the Documents folder in my user account. Cheers, Mike. On Tue, Jan 4, 2011 at 8:35 PM, W Eryk Wolski wewol...@gmail.com wrote: Hi, Just installed R on a new Windows 7 machine (as admin). I feel quite uncomfortable knowing that the default WD when starting R is: getwd() [1] C:/Windows/system32 I guess I did something wrong when installing R... How to change R's default working directory? regards Eryk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Sumner Institute for Marine and Antarctic Studies, University of Tasmania Hobart, Australia e-mail: mdsum...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fw: Re: Default Working directory on windows 7?
Suppose your working R directory is C:\My Working Directory I hope now that you have installed the R, you must be having R ICON on your desktop. Right click on this icon, then click on Properties. Once that box is opened, you will find a tab called Start in. There within the type C:\My Working Directory. So it should look like C:\My Working Directory Then click on OK. So whenever you execute R henceforth, this will remain your working directory till the time you change it using above process. I hope I have addressed your query. Of course others may be having different efficient methods to do it. HTH Amy --- On Tue, 1/4/11, W Eryk Wolski wewol...@gmail.com wrote: From: W Eryk Wolski wewol...@gmail.com Subject: [R] Default Working directory on windows 7? To: r-help@r-project.org Date: Tuesday, January 4, 2011, 9:35 AM Hi, Just installed R on a new Windows 7 machine (as admin). I feel quite uncomfortable knowing that the default WD when starting R is: getwd() [1] C:/Windows/system32 I guess I did something wrong when installing R... How to change R's default working directory? regards Eryk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lattice: how to center a title?
Dear expeRts, As you can see from this example... trellis.device(pdf, width = 5, height = 5) print(xyplot(0 ~ 0, main = This title is not 'centered' for the human's eye, scales = list(alternating = c(1,1), tck = c(1,0 dev.off() ... the title does not seem to be centered for the human's eye [although it is centered when the plot (width) is considered with the y-axis label]. I could not easily (via trellis.par.get()) find a way to adjust this. Of course one could include more spaces in the title string, but is there a more elegant way to slightly shift the title to the right? Cheers, Marius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Default Working directory on windows 7?
Hi r-help-boun...@r-project.org napsal dne 04.01.2011 10:35:23: Hi, Just installed R on a new Windows 7 machine (as admin). I feel quite uncomfortable knowing that the default WD when starting R is: getwd() [1] C:/Windows/system32 Something was set incorrectly. I believe that with default setting R shall be somewhere in Program Files directory (but you can install it to any directory without problems). Try to remove it and reinstall if it is in some inconvenient place. There is one file .RData which is used as starting workspace. So make any directory, copy this file to it, start R by double click on it and now the new directory is working directory. Quite useful when working on several projects. Regards Petr I guess I did something wrong when installing R... How to change R's default working directory? regards Eryk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to subset unique factor combinations from a data frame.
Hi, Sorry that my example is not clear. I will give an example of what each variable holds. I hope this clearly explains the case. Names of the dataframe (df) and description Year :- Year is calendar year, from 1980 to 2010 Country :- is the country name, total no. (levels) of countries is ~ 190 Commodity :- Crude oil, Sugar, Rubber, Coffee No. (levels) of commodities is 20 Attribute: - Production, Consumption, Stock, Import, Export... Levels ~ 20 Unit :- this is actually not a factor. It describes the unit of Attribute. Say the unit for Coffee (commodity) - Production (attribute) is 60 kgs. While the unit for Crude oil - Production is 1000 barrels Value :- value tail(df, n = 10) // example data// YearCountry Commodity Attribute Unit Value 1991United Kingdom Wheat, DurumTotal Supply(1000 MT) 70 1991United Kingdom Wheat, DurumTY Exports (1000 MT) 0 1991United Kingdom Wheat, DurumTY Imp. from U (1000 MT) 0 1991United Kingdom Wheat, DurumTY Imports (1000 MT) 60 1991United Kingdom Wheat, DurumYield (MT/HA) 5 Wish this is clear. Any suggestion Regards, SNVK -Original Message- From: Petr PIKAL [mailto:petr.pi...@precheza.cz] Sent: Tuesday, January 04, 2011 4:06 PM To: SNV Krishna Cc: r-help@r-project.org Subject: Odp: [R] how to subset unique factor combinations from a data frame. Hi r-help-boun...@r-project.org napsal dne 04.01.2011 05:21:25: Hi All I have these questions and request members expert view on this. a) I have a dataframe (df) with five factors (identity variables) and value (measured value). The id variables are Year, Country, Commodity, Attribute, Unit. Value is a value for each combination of this. I would like to get just the unique combination of Commodity, Attribute and Unit. I just need the unique factor combination into a dataframe or a table. I know aggregate and subset but dont how to use them in this context. aggregate(Value, list(Comoditiy, Atribute, Unit), function) b) Is it possible to inclue non- aggregate columns with aggregate function say in the above case aggregate(Value ~ Commodity + Attribute, data = df, FUN = count). The use of count(Value) is just a round about to return the combinations of Commodity Attribute, and I would like to include 'Unit' column in the returned data frame? Hm. Maybe xtabs? But without any example it is only a guess. c) Is it possible to subset based on unique combination, some thing like this. subset(df, unique(Commodity), select = c(Commodity, Attribute, Unit)). I know this is not correct as it returns an error 'subset needs a logical evaluation'. Trying various ways to accomplish the task. Probably sqldf package has tools for doing it but I do not use it so you have to try yourself. df[Comodity==something, c(Commodity, Attribute, Unit)] can be other way. Anyway your explanation is ambiguous. Let say you have three rows with the same Commodity. Which row do you want to select? Regards Petr will be grateful for any ideas and help Regards, SNVK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Writing do and resample functions
Hi,
I'm trying to take a function from a workspace download provided in a
stats textbook book, so I have it in my workspace to use all the time.
I opened the workspace and typed the names of the two functions to get
the code that makes them up:
-
resample
function(d, size, replace=TRUE,prob=NULL,within=NULL) {
if (!is.null(within)) return( resample.within(d,
within,replace=replace) )
if (is.null(dim(d))) {
# it's just a vector
if (missing(size)) size=length(d)
return( d[ sample(1:length(d),size, replace=replace, prob=prob)])
}
else {
if (missing(size)) size = dim(d)[1];
inds = sample(1:(dim(d))[1], size, replace=replace, prob=prob)
if (is.data.frame(d) | is.matrix(d)) {
return(d[inds,]);
} else {
return(d[inds]);
}
}
}
-
do
function(n=10){
as.repeater(n)
}
-
as.repeater
function(n=5){
foo = list(n=n)
class(foo) = 'repeater'
return(foo)
}
Then I made the functions in my workspace by choosing the name (same
name), and then = and then copied and pasted the function, beginning
with function( and ending with the final }'s.
But when I try to do the following in my workspace afterwards:
samps = do(500)* coef(lm(MIC.~1+Challenge+Cleaner+Replicate,
data=resample(ecoli)))
sd(samps)
I get an error:
Error in do(500) * coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate, :
non-numeric argument to binary operator.
But in the workspace that comes with that book, I get a decent output:
sd(samps)
(Intercept) Challenge CleanerGarlic ReplicateFirst
ReplicateFourth
3.9455401 0.7178385 1.6830641 5.4564926
5.4320998
ReplicateSecond ReplicateThird
5.3895562 5.5422622
Is there anybody out there who know a lot more about programming
functions in R than I do, that might know why this is giving me the
error? I don't understand why one workspace would accept the model
formula, when the other give me the non-numeric argument to binary
vector, the only vector that's not numerical is Replicate, but I don't
that's what the error is talking about.
Thanks,
Ben Ward.
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[R] RSQLite to input dataframe
Dear r helpers, At first, I apologize for raising a query which seems to be a stupid interpretation on my part. I am trying to learn SQLite. Following is an example given in the RSQLite.zip file (Page # 4) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(USArrests) dbWriteTable(con, arrests, USArrests) On the similar line I am trying to read my data. Suppose I have a dataframe as given below. DF = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(DF) dbWriteTable(con, ..., ...) # Didn't know what to write here. I understand I have raised a query in a stupid manner. I need to understand is there any way I can use SQLite to read dataframe or for that matter any csv file say e.g. 'DF.csv'. Please enlighten me. Amy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to invert the axes in the wireframe() plot
thank you very much, I am now closer to the result I would like to achieve. Still, I have to figure out how to invert the n axes, see figure: http://www.digitaldust.it/materiali/mine2.pdf is panel.3dwire the function I have to study for this last step? thanks, simone Il giorno 04/gen/2011, alle ore 01.26, David Winsemius ha scritto: On Jan 3, 2011, at 7:07 PM, Simone Gabbriellini wrote: I am trying to reproduce this graph: http://www.digitaldust.it/materiali/their.png the default axes orientation of wireframe gives me this: http://www.digitaldust.it/materiali/mine.pdf I am trying to understand if I can reproduce the axes orientation of the first figure. Well, there is more to reproducing that figure than just rotating around the z axis by 180, which is what I now take your question to be: ?panel.3dwire Run the 2nd example in ?wireframe and then compare to this minor modification of the screen arguments: wireframe(z ~ x * y, data = g, groups = gr, scales = list(arrows = FALSE), drape = TRUE, colorkey = TRUE, screen = list(z = 30+180, x = -60), ) (Rotated 180 around the z-axis.) -- Best; David. many thanks, simone Il giorno 03/gen/2011, alle ore 23.45, David Winsemius ha scritto: On Jan 3, 2011, at 5:06 PM, Simone Gabbriellini wrote: Dear List, I am using the wireframe function in the lattice package, and I am wondering if it is possible to invert the default axes orientation for x and y axes... what parameter should I look for? Perhaps you should define invert. -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lattice: par.settings with standard.theme() + additional arguments?
Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Cheers, Marius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to subset unique factor combinations from a data frame.
Hi r-help-boun...@r-project.org napsal dne 04.01.2011 11:19:02: Hi, Sorry that my example is not clear. I will give an example of what each variable holds. I hope this clearly explains the case. Names of the dataframe (df) and description Year :- Year is calendar year, from 1980 to 2010 Country :- is the country name, total no. (levels) of countries is ~ 190 Commodity :- Crude oil, Sugar, Rubber, Coffee No. (levels) of commodities is 20 Attribute: - Production, Consumption, Stock, Import, Export... Levels ~ 20 Unit :- this is actually not a factor. It describes the unit of Attribute. Say the unit for Coffee (commodity) - Production (attribute) is 60 kgs. While the unit for Crude oil - Production is 1000 barrels Value :- value tail(df, n = 10) // example data// Year Country Commodity Attribute Unit Value 1991 United Kingdom Wheat, Durum Total Supply (1000 MT) 70 1991 United Kingdom Wheat, Durum TY Exports (1000 MT) 0 1991 United Kingdom Wheat, Durum TY Imp. from U (1000 MT) 0 1991 United Kingdom Wheat, Durum TY Imports (1000 MT) 60 1991 United Kingdom Wheat, Durum Yield (MT/HA) 5 Wish this is clear. Any suggestion suggestion is still the same, use aggregate on any other similar function maybe from plyr package. No matter how exactly you will describe your data if you fail to show any code you used and how this code failed in delivering desired result you will get only vague responses. Regards Petr Regards, SNVK -Original Message- From: Petr PIKAL [mailto:petr.pi...@precheza.cz] Sent: Tuesday, January 04, 2011 4:06 PM To: SNV Krishna Cc: r-help@r-project.org Subject: Odp: [R] how to subset unique factor combinations from a data frame. Hi r-help-boun...@r-project.org napsal dne 04.01.2011 05:21:25: Hi All I have these questions and request members expert view on this. a) I have a dataframe (df) with five factors (identity variables) and value (measured value). The id variables are Year, Country, Commodity, Attribute, Unit. Value is a value for each combination of this. I would like to get just the unique combination of Commodity, Attribute and Unit. I just need the unique factor combination into a dataframe or a table. I know aggregate and subset but dont how to use them in this context. aggregate(Value, list(Comoditiy, Atribute, Unit), function) b) Is it possible to inclue non- aggregate columns with aggregate function say in the above case aggregate(Value ~ Commodity + Attribute, data = df, FUN = count). The use of count(Value) is just a round about to return the combinations of Commodity Attribute, and I would like to include 'Unit' column in the returned data frame? Hm. Maybe xtabs? But without any example it is only a guess. c) Is it possible to subset based on unique combination, some thing like this. subset(df, unique(Commodity), select = c(Commodity, Attribute, Unit)). I know this is not correct as it returns an error 'subset needs a logical evaluation'. Trying various ways to accomplish the task. Probably sqldf package has tools for doing it but I do not use it so you have to try yourself. df[Comodity==something, c(Commodity, Attribute, Unit)] can be other way. Anyway your explanation is ambiguous. Let say you have three rows with the same Commodity. Which row do you want to select? Regards Petr will be grateful for any ideas and help Regards, SNVK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 95% CI of the Predicted values from the GLS Model
Dear all, I have just constructed the GLS model in R . How do I print the 95% confidence intervals for the vector of predicted values R code/s for GLS CI? See the model below: Please advice Regards Peter South Africa +2712 422 7357 +2782 456 4669 Generalized least squares fit by maximum likelihood Model: log(y) ~ log(x) + d1 + d3 Data: NULL AIC BIC logLik -166.2344 -147.8469 92.1172 Correlation Structure: ARMA(2,2) Formula: ~1 Parameter estimate(s): Phi1Phi2 Theta1 Theta2 0.65960193 0.26221313 -0.02561896 -0.37995110 Coefficients: Value Std.Errort-valuep-value (Intercept) -2.4304969 0.8078837 -3.0084740.004 log(x)1.0558775 0.068438915.428027 0.000 d10.2105713 0.011025019.099466 0.000 d30.1012744 0.01095029.2485960.000 Correlation: (Intr) lg(cm) d1 log(x) -0.999 d1 -0.208 0.204 d3 -0.094 0.093 -0.323 Standardized residuals: Min Q1Med Q3Max -1.6668631 -0.9549670 -0.1153022 0.7962635 2.0764581 Residual standard error: 0.07542025 Degrees of freedom: 57 total; 53 residual Please Note: This email and its contents are subject to our email legal notice which can be viewed at http://www.sars.gov.za/Email_Disclaimer.pdf [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RSQLite to input dataframe
Hi Amy, I'm not sure if I understand your question correctly so let me know if the following is off track. Starting with your example, here is how to create a data.frame and write it to a new table in a new database file... my.data = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) con - dbConnect(drv, myfilename.db) dbWriteTable(con, sometablename, my.data) To verify that the table is now in the file... dbListTables(con) To check the fields in the table (should match the colnames in your data.frame)... dbListFields(con, sometablename) To read the whole table into the workspace as a new data.frame my.data.copy - dbReadTable(con, sometablename) If you have data in a CSV file, and the contents are small enough to read in one go, you would use the read.csv function to read the contents of the file into a data.frame and then use dbWriteTable to transfer this to your database. Hope this helps, Michael On 4 January 2011 21:43, Amy Milano milano_...@yahoo.com wrote: Dear r helpers, At first, I apologize for raising a query which seems to be a stupid interpretation on my part. I am trying to learn SQLite. Following is an example given in the RSQLite.zip file (Page # 4) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(USArrests) dbWriteTable(con, arrests, USArrests) On the similar line I am trying to read my data. Suppose I have a dataframe as given below. DF = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(DF) dbWriteTable(con, ..., ...) # Didn't know what to write here. I understand I have raised a query in a stupid manner. I need to understand is there any way I can use SQLite to read dataframe or for that matter any csv file say e.g. 'DF.csv'. Please enlighten me. Amy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving objects inside a list
Message: 42 Date: Mon, 3 Jan 2011 18:58:04 -0200 From: Eduardo de Oliveira Hortaeduardo.oliveiraho...@gmail.com To: r-helpr-help@r-project.org Subject: Re: [R] Saving objects inside a list Message-ID: aanlktimbxmr0rusiws1grorhjh=wstofzqdoc-90z...@mail.gmail.com Content-Type: text/plain sapply(ls(),get) works fine. Thanks. ps: the as.list and the eapply suggestions didn't work. Hi Eduardo (and all the best for this new year), are you sure the as.list and eapply solutions didn't work ? On my machine they produce a list but in reverse order compared to the result of ls(),...maybe it's the same with you : names(as.list(.GlobalEnv))[6] is the name of the 6th variable FROM THE END of ls(). Regards. Olivier -- Olivier ETERRADOSSI Maître-Assistant animateur du groupe Sensomines (Institut Carnot M.I.N.E.S) - CMGD Pôle Matériaux Polymères Avancés axe Propriétés Psycho-Sensorielles des Matériaux - Ecole des Mines d'Alès Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9 tel std: +33 (0)5.59.30.54.25 tel direct: +33 (0)5.59.30.90.35 fax: +33 (0)5.59.30.63.68 http://www.mines-ales.fr e-mail : olivier.eterrado...@mines-ales.fr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Listing of available functions
Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Writing do and resample functions
It seems that the textbook workspace you are using as a method
definition for * for class repeater. Load the workspace and try
methods(`*`)
If you get something like '*.repeater' this suspicion is confirmed
On 1/4/2011 11:36 AM, Ben Ward wrote:
Hi,
I'm trying to take a function from a workspace download provided in a
stats textbook book, so I have it in my workspace to use all the time.
I opened the workspace and typed the names of the two functions to get
the code that makes them up:
-
resample
function(d, size, replace=TRUE,prob=NULL,within=NULL) {
if (!is.null(within)) return( resample.within(d,
within,replace=replace) )
if (is.null(dim(d))) {
# it's just a vector
if (missing(size)) size=length(d)
return( d[ sample(1:length(d),size, replace=replace, prob=prob)])
}
else {
if (missing(size)) size = dim(d)[1];
inds = sample(1:(dim(d))[1], size, replace=replace, prob=prob)
if (is.data.frame(d) | is.matrix(d)) {
return(d[inds,]);
} else {
return(d[inds]);
}
}
}
-
do
function(n=10){
as.repeater(n)
}
-
as.repeater
function(n=5){
foo = list(n=n)
class(foo) = 'repeater'
return(foo)
}
Then I made the functions in my workspace by choosing the name (same
name), and then = and then copied and pasted the function, beginning
with function( and ending with the final }'s.
But when I try to do the following in my workspace afterwards:
samps = do(500)* coef(lm(MIC.~1+Challenge+Cleaner+Replicate,
data=resample(ecoli)))
sd(samps)
I get an error:
Error in do(500) * coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate, :
non-numeric argument to binary operator.
But in the workspace that comes with that book, I get a decent output:
sd(samps)
(Intercept) Challenge CleanerGarlic ReplicateFirst
ReplicateFourth
3.9455401 0.7178385 1.6830641 5.4564926
5.4320998
ReplicateSecond ReplicateThird
5.3895562 5.5422622
Is there anybody out there who know a lot more about programming
functions in R than I do, that might know why this is giving me the
error? I don't understand why one workspace would accept the model
formula, when the other give me the non-numeric argument to binary
vector, the only vector that's not numerical is Replicate, but I don't
that's what the error is talking about.
Thanks,
Ben Ward.
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Re: [R] RSQLite to input dataframe
Hi Amy, Suppose I have a dataframe as given below. DF = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(DF) dbWriteTable(con, ..., ...) # Didn't know what to write here. data() loads data sets which ship with R or an extension package. Your data frame DF is already in the working environment, hence it is neither possible nor necessary to load it, the expression data(DF) is an error. The command to write DF to a database would be something like dbWriteTable(con, DF, DF) where the second argument is the name of the database table to write to, the third argument the data frame you want to write (please have a look at the documentation). I understand I have raised a query in a stupid manner. I need to understand is there any way I can use SQLite to read dataframe or for that matter any csv file say e.g. 'DF.csv'. To copy a CSV file to SQLite, read it via read.table() or read.csv() first, then copy the result with dbWriteTable. There might be a way to read files directly from SQLite, but I don't know about that. Best regards, Andreas -- Andreas Borg Medizinische Informatik UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Medizinische Biometrie, Epidemiologie und Informatik Obere Zahlbacher Straße 69, 55131 Mainz www.imbei.uni-mainz.de Telefon +49 (0) 6131 175062 E-Mail: b...@imbei.uni-mainz.de Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Listing of available functions
Try : objects(package:base) Also, as it happens, a new package called unknownR is in development on R-Forge. It's description says : Do you know how many functions there are in base R? How many of them do you know you don't know? Run unk() to discover your unknown unknowns. It's fast and it's fun ! It's not ready to try yet (and may not live up to it's promises) but hopefully should be ready soon. Matthew Sébastien Bihorel pomc...@free.fr wrote in message news:aanlktinfpmthb2osgjckeo3jwsqhw+-zdyd0xtdmk...@mail.gmail.com... Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Listing of available functions
Try this: sapply(search(), ls, all.names = TRUE) This show all the functions in the search() path On Tue, Jan 4, 2011 at 10:13 AM, Sébastien Bihorel pomc...@free.fr wrote: Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Writing do and resample functions
I've just loaded the workspace and done
methods('*')
And got the ouptut
[1] *.difftime *.repeater
I'm not entirely sure on what this repeater and as.repeater is. From my
reading when one want to repeat stuff for say bootstrapping, you have to
use repeat as part of a function and put in some sort of qualification
that end the repetitions. Coding functions is a bit beyond what is
taught on my BSc Biology course. However, I do know that if I do the
same in a new R session:
methods('*')
[1] *.difftime
*.repeater is missing. So to clarify my understanding, the * is the
problem because it hasn't got this .repeater value attributed to it?
Thanks,
Ben Ward.
On 04/01/2011 12:30, Erich Neuwirth wrote:
It seems that the textbook workspace you are using as a method
definition for * for class repeater. Load the workspace and try
methods(`*`)
If you get something like '*.repeater' this suspicion is confirmed
On 1/4/2011 11:36 AM, Ben Ward wrote:
Hi,
I'm trying to take a function from a workspace download provided in a
stats textbook book, so I have it in my workspace to use all the time.
I opened the workspace and typed the names of the two functions to get
the code that makes them up:
-
resample
function(d, size, replace=TRUE,prob=NULL,within=NULL) {
if (!is.null(within)) return( resample.within(d,
within,replace=replace) )
if (is.null(dim(d))) {
# it's just a vector
if (missing(size)) size=length(d)
return( d[ sample(1:length(d),size, replace=replace, prob=prob)])
}
else {
if (missing(size)) size = dim(d)[1];
inds = sample(1:(dim(d))[1], size, replace=replace, prob=prob)
if (is.data.frame(d) | is.matrix(d)) {
return(d[inds,]);
} else {
return(d[inds]);
}
}
}
-
do
function(n=10){
as.repeater(n)
}
-
as.repeater
function(n=5){
foo = list(n=n)
class(foo) = 'repeater'
return(foo)
}
Then I made the functions in my workspace by choosing the name (same
name), and then = and then copied and pasted the function, beginning
with function( and ending with the final }'s.
But when I try to do the following in my workspace afterwards:
samps = do(500)* coef(lm(MIC.~1+Challenge+Cleaner+Replicate,
data=resample(ecoli)))
sd(samps)
I get an error:
Error in do(500) * coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate, :
non-numeric argument to binary operator.
But in the workspace that comes with that book, I get a decent output:
sd(samps)
(Intercept) Challenge CleanerGarlic ReplicateFirst
ReplicateFourth
3.9455401 0.7178385 1.6830641 5.4564926
5.4320998
ReplicateSecond ReplicateThird
5.3895562 5.5422622
Is there anybody out there who know a lot more about programming
functions in R than I do, that might know why this is giving me the
error? I don't understand why one workspace would accept the model
formula, when the other give me the non-numeric argument to binary
vector, the only vector that's not numerical is Replicate, but I don't
that's what the error is talking about.
Thanks,
Ben Ward.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
Hi thank you all. I think I have what I need to solve my problem. Regards, A.Dias -- View this message in context: http://r.789695.n4.nabble.com/Help-with-For-instruction-tp3173074p3173386.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inverse Gaussian Distribution
Thank you! But i'm wondering: if you run area - factor(area, levels=c(C, A,B,D,E,F) ) then you are transforming only 'area', aren't you? isn't it possible to transform the whole data like i did for agecat but now for area and area C as baseline, or are you doing so when you run area - factor(area, levels=c(C, A,B,D,E,F) ) attach(data) and then run the model with area as predictorvariable: model - glm(Y~ agecat+gender+area,...) My question is if i can run it as follows and still have a right solution : data -transform(data, area=(factor(area, levels=c(C, A,B,D,E,F) ) ) I'll be very grateful for any help you can provide! Kind regards, Louisa -- View this message in context: http://r.789695.n4.nabble.com/Inverse-Gaussian-Distribution-tp3172533p3173468.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] S4 plot function (Package)...
Hello,
I have a problem programming 2 plot methods for 2 classes.
1. I have 2 classes. Each class has its own plot method. !!! How the
plot,xxx-method.R -files have to look like,
so that the plot method for class 1 und plot methods for class 2 can act
for each belonging class. Prob
My example for plot_class1.R for class labeled class1 (class2
equivalent):
if (!isGeneric(plot)) {
setGeneric(plot, function(x=class1, y=ANY, ...)
standardGeneric(plot), package=the_package_name);
}
setMethod(plot, signature(x=class1, y=ANY),
function(x, y, type=xy, method = names(x...@misclass), anno=symbol,
...)
{
... #code
}
}
#DOCS
\name{plot,class1-method}
\docType{methods}
\alias{plot}
\alias{plot,class1-method}
...
Looks it correct?
thx so far.
Dan
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Re: [R] RSQLite to input dataframe
Dear sir, When I was going through RSQLite.pdf file, I was just wondering if at all I will understand this. But you have explained it in such a simple and lucid manner, that although I am yet to go thoroughly through the mail, I am filled with confidence that yes now i can do it and I am going to circulate your mail through my office so that all will be benefited. Thanks a lot sir once again. Must say that was The Guidnace. Regards Amy --- On Tue, 1/4/11, Michael Bedward michael.bedw...@gmail.com wrote: From: Michael Bedward michael.bedw...@gmail.com Subject: Re: [R] RSQLite to input dataframe To: Amy Milano milano_...@yahoo.com, Rhelp r-help@r-project.org Date: Tuesday, January 4, 2011, 11:32 AM Hi Amy, I'm not sure if I understand your question correctly so let me know if the following is off track. Starting with your example, here is how to create a data.frame and write it to a new table in a new database file... my.data = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) con - dbConnect(drv, myfilename.db) dbWriteTable(con, sometablename, my.data) To verify that the table is now in the file... dbListTables(con) To check the fields in the table (should match the colnames in your data.frame)... dbListFields(con, sometablename) To read the whole table into the workspace as a new data.frame my.data.copy - dbReadTable(con, sometablename) If you have data in a CSV file, and the contents are small enough to read in one go, you would use the read.csv function to read the contents of the file into a data.frame and then use dbWriteTable to transfer this to your database. Hope this helps, Michael On 4 January 2011 21:43, Amy Milano milano_...@yahoo.com wrote: Dear r helpers, At first, I apologize for raising a query which seems to be a stupid interpretation on my part. I am trying to learn SQLite. Following is an example given in the RSQLite.zip file (Page # 4) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(USArrests) dbWriteTable(con, arrests, USArrests) On the similar line I am trying to read my data. Suppose I have a dataframe as given below. DF = data.frame(X = c(US, UK, Canada, Australia, Newzealand), Y = c(52, 36, 74, 10, 98)) drv - dbDriver(SQLite) tfile - tempfile() con - dbConnect(drv, dbname = tfile) data(DF) dbWriteTable(con, ..., ...) # Didn't know what to write here. I understand I have raised a query in a stupid manner. I need to understand is there any way I can use SQLite to read dataframe or for that matter any csv file say e.g. 'DF.csv'. Please enlighten me. Amy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ARIMA simulation including a constant
That output is not from arima(), which is the function paired with arima.sim(). Nor is it from arima0(), so I don't believe it is 'ouptut from R' (perhaps from a contributed package you have not mentioned?). With arima(), the intercept is 'm' in the notation on the help page and not 'a' in your personal re-definition. You can easily go from one to the other by some trivial algebra ( a = m*(1-sum(ar)) ), but you do need to be sure what the unstated function you use is using. On Mon, 3 Jan 2011, Paolo Rossi wrote: Sorry I am not really sure I have been taht clear. I meant ARMA which is not bound to have zero mean. More precisely, suppose I estimate y(t) = a + by(t-1) + e(t) + ce(t-1) , i.e. and ARMA(1,1). My question is how do I simulate values for yt given the values for a, b and c? My problem with arima.sim is that I cannot find a way to pass the value for the constant a. Output from R is: Coefficient(s): Estimate Std. Error t value Pr(|t|) ar1 0.82978 0.01033 80.297 2e-16 *** ma1 0.46347 0.01548 29.942 2e-16 *** intercept -0.02666 0.01012 -2.635 0.00841 ** --- Intercept is significant and I suppose it should be used if I want simulate values from this ARMA(1,1) Thanks and Apologies for not being clear Paolo On 3 January 2011 16:46, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Mon, 3 Jan 2011, Paolo Rossi wrote: Hi, I have been looking at arima.sim to simulate the output from an ARMA model fed with a normal and uncorrelated input series but I cannot find a way to pass an intercept / constant into the model. In other words, the model input in the function allows only for the AR and MA components but I need to pass a constant. Can anyone help? Well, an ARIMA model by definition has zero mean (as the link on the help page for arima.sim to the exact definition tells you). Perhaps you mean that (X-m) = Z follows an ARIMA model, in which case simulate Z and add m. For a differenced ARIMA model it is not clear if you meant that you wanted an intercept for the original or differenced series: for the latter simply simulate the differenced series, add the intercept and use diffinv(). Thanks Paolo [[alternative HTML version deleted]] Please do as we asked in the posting guide and not send HTML. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to subset unique factor combinations from a data frame.
Hi: Did you try something like summdf - as.data.frame(with(df, table(Commodity, Attribute, Unit))) ? The rows of the table should represent the unique combinations of the three variables Here's a simple toy example to illustrate: x - sample(LETTERS[1:6], 1000, replace = TRUE) xx - sample(letters[1:6], 1000, replace = TRUE) u - as.data.frame(table(x, xx)) dim(u) [1] 36 3 head(u) x xx Freq 1 A a 26 2 B a 29 3 C a 25 4 D a 25 5 E a 27 6 F a 29 HTH, Dennis On Tue, Jan 4, 2011 at 2:19 AM, SNV Krishna kris...@primps.com.sg wrote: Hi, Sorry that my example is not clear. I will give an example of what each variable holds. I hope this clearly explains the case. Names of the dataframe (df) and description Year :- Year is calendar year, from 1980 to 2010 Country :- is the country name, total no. (levels) of countries is ~ 190 Commodity :- Crude oil, Sugar, Rubber, Coffee No. (levels) of commodities is 20 Attribute: - Production, Consumption, Stock, Import, Export... Levels ~ 20 Unit :- this is actually not a factor. It describes the unit of Attribute. Say the unit for Coffee (commodity) - Production (attribute) is 60 kgs. While the unit for Crude oil - Production is 1000 barrels Value :- value tail(df, n = 10) // example data// YearCountry Commodity Attribute Unit Value 1991United Kingdom Wheat, DurumTotal Supply(1000 MT) 70 1991United Kingdom Wheat, DurumTY Exports (1000 MT) 0 1991United Kingdom Wheat, DurumTY Imp. from U (1000 MT) 0 1991United Kingdom Wheat, DurumTY Imports (1000 MT) 60 1991United Kingdom Wheat, DurumYield (MT/HA) 5 Wish this is clear. Any suggestion Regards, SNVK -Original Message- From: Petr PIKAL [mailto:petr.pi...@precheza.cz] Sent: Tuesday, January 04, 2011 4:06 PM To: SNV Krishna Cc: r-help@r-project.org Subject: Odp: [R] how to subset unique factor combinations from a data frame. Hi r-help-boun...@r-project.org napsal dne 04.01.2011 05:21:25: Hi All I have these questions and request members expert view on this. a) I have a dataframe (df) with five factors (identity variables) and value (measured value). The id variables are Year, Country, Commodity, Attribute, Unit. Value is a value for each combination of this. I would like to get just the unique combination of Commodity, Attribute and Unit. I just need the unique factor combination into a dataframe or a table. I know aggregate and subset but dont how to use them in this context. aggregate(Value, list(Comoditiy, Atribute, Unit), function) b) Is it possible to inclue non- aggregate columns with aggregate function say in the above case aggregate(Value ~ Commodity + Attribute, data = df, FUN = count). The use of count(Value) is just a round about to return the combinations of Commodity Attribute, and I would like to include 'Unit' column in the returned data frame? Hm. Maybe xtabs? But without any example it is only a guess. c) Is it possible to subset based on unique combination, some thing like this. subset(df, unique(Commodity), select = c(Commodity, Attribute, Unit)). I know this is not correct as it returns an error 'subset needs a logical evaluation'. Trying various ways to accomplish the task. Probably sqldf package has tools for doing it but I do not use it so you have to try yourself. df[Comodity==something, c(Commodity, Attribute, Unit)] can be other way. Anyway your explanation is ambiguous. Let say you have three rows with the same Commodity. Which row do you want to select? Regards Petr will be grateful for any ideas and help Regards, SNVK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to keep keep matching column in output of merge
How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. thanks Nevil Amos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Print plot to pdf, jpg or any other format when using scatter3d error
On 03/01/2011 8:17 PM, Jurica Seva wrote:
Hi,
I have been trying to output my graphs to a file (jpeg, pdf, ps, it
doesnt matter) but i cant seem to be able to get it to output.
As Uwe said, you are using rgl graphics, not base graphics. So none of
the standard devices work, you need to use the tools built into rgl.
Attach that package, and then read ?rgl.postscript (for graphics in
various vector formats, not just Postscript) and ?rgl.snapshot (for
bitmapped graphics).
Some notes:
- For a while rgl.snapshot wasn't working in the Windows builds with R
2.12.1; that is now fixed, so you should update rgl before getting
frustrated.
- rgl.snapshot just takes a copy of the graphics buffer that is
showing on screen, so it is limited to the size you can display
- rgl.postscript does a better job for the parts of an image that it
can handle, but it is not a perfect OpenGL emulator, so it doesn't
always include all components of a graph properly.
Duncan Murdoch
I tried a
few things but none of them worked and am lost as what to do now. I am
using the scatter3d function, and it prints out the graphs on tot he
screen without any problems, but when it comes to writing them to a file
i cant make it work. Is there any other way of producing 3dimensional
graphs (they dont have to be rotatable/interactive after the print out)?
The code is fairly simple and is listed down :
#libraries
library(RMySQL)
library(rgl)
library(scatterplot3d)
library(Rcmdr)
##
#database connection
mycon- dbConnect(MySQL(),
user='root',dbname='test',host='localhost',password='')
#distinct sessions
rsSessionsU01- dbSendQuery(mycon, select distinct sessionID from
actiontimes where userID = 'ID01')
sessionU01-fetch(rsSessionsU01)
sessionU01[2,]
#user01 data
mycon- dbConnect(MySQL(),
user='root',dbname='test',host='localhost',password='')
rsUser01- dbSendQuery(mycon, select
a.userID,a.sessionID,a.actionTaken,a.timelineMSEC,a.durationMSEC,b.X,b.Y,b.Rel__dist_,b.Total_dist_
from `actiontimes` as a , `ulogdata` as b where a.originalRECNO =
b.RECNO and a.userID='ID01')
user01- fetch(rsUser01, n= -1)
user01[1,1]
#plot loop
for (i in 1:10){
userSubset-subset(user01,sessionID ==
sessionU01[i,],select=c(timelineMSEC,X,Y))
userSubset
x-as.numeric(userSubset$X)
y-as.numeric(userSubset$Y)
scatter3d(x,y,userSubset$timeline,xlim = c(0,1280), ylim =
c(0,1024),
zlim=c(0,180),type=h,main=sessionU01[i,],sub=sessionU01[i,])
tmp6=rep(.ps)
tmp7=paste(sessionU01[i,],tmp6,sep=)
tmp7
rgl.postscript(tmp7,ps,drawText=FALSE)
#pdf(file=tmp7)
#dev.print(file=tmp7, device=pdf, width=600)
#dev.off(2)
}
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Re: [R] lattice: par.settings with standard.theme() + additional arguments?
On Jan 4, 2011, at 5:57 AM, Marius Hofert wrote: Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Add it as a list element: xyplot(x ~ 1:10, type = l, par.settings = list(standard.theme(color = FALSE), par.xlab.text = list(cex = 5, col = blue))) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Listing of available functions
On 04/01/2011 7:13 AM, Sébastien Bihorel wrote: Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. This requires a two level search, but is probably more useful than just a list of function names: Run help.start() to get into the main help page. Click on Packages. Now you'll see a list of all installed packages and their titles. Choose an interesting package, and click on its name. Now you'll see a list of most help aliases (generally all functions, plus some other things) and the title of the associated help page. You don't see all help aliases: S4 method documentation tends to have a lot of aliases, and some of those are suppressed. But you should see all help pages at least once. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Listing of available functions
You can also search for a cheatsheet. There are several out there searching on cheatsheet r This one at Oregon State is presented as a web page http://www.science.oregonstate.edu/~shenr/Rhelp/00cheat.htm Others are available as pdf's. On Jan 4, 2011, at 7:13 AM, Sébastien Bihorel wrote: Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: par.settings with standard.theme() + additional arguments?
Dear David, this I already tried. But as you can see, the plot itself *is* colored. However, I want to have color = FALSE, so, unfortunately, this approach does not work... Cheers, Marius On 2011-01-04, at 14:32 , David Winsemius wrote: On Jan 4, 2011, at 5:57 AM, Marius Hofert wrote: Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Add it as a list element: xyplot(x ~ 1:10, type = l, par.settings = list(standard.theme(color = FALSE), par.xlab.text = list(cex = 5, col = blue))) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inverse Gaussian Distribution
On Jan 4, 2011, at 7:50 AM, Louisa wrote: Thank you! But i'm wondering: if you run area - factor(area, levels=c(C, A,B,D,E,F) ) then you are transforming only 'area', aren't you? isn't it possible to transform the whole data like i did for agecat but now for area and area C as baseline, Of course, but may I point out that you did no earlier say that you may have attached a dataframe containing area. There are many confusing situations that arise when using attached dataframes and this may be one of them. Many experienced R users avoid attaching data objects like the plague. or are you doing so when you run area - factor(area, levels=c(C, A,B,D,E,F) ) attach(data) and then run the model with area as predictorvariable: model - glm(Y~ agecat+gender+area,...) My question is if i can run it as follows and still have a right solution : data -transform(data, area=(factor(area, levels=c(C, A,B,D,E,F) ) ) Is there any reason that you suspect this will not work? Why not try it ... now assumimg that you failed to tell us that area was a column in a dataframe that is. (One set of parentheses appear extraneous.) data -transform(data, area = factor(area, levels=c(C, A,B,D,E,F) ) (Untested in the absence of reproducible example ,,, but it looks as though it might work.) I'll be very grateful for any help you can provide! Kind regards, Louisa -- View this message in context: http://r.789695.n4.nabble.com/Inverse-Gaussian-Distribution-tp3172533p3173468.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lasso/lars error
I'm having the same error too, but it's very rare though... (especially when using datasets with many variables, say 25). A somewhat odd, but seemingly effective, way to solve this, is by writing try(lars(x,y),silent = T). The try-command in this shape will not generate an error on the console and therefore, any running programs are not aborted. When there is no error, you simply get the LARS object. When there is an error, you get a character string (can be checked by 'is.character()'). I suggest to perturb the data a little to get it to work... Best Regards, Timmie Smet B.A.P. Operations Research and Business Statistics University of Leuven, Belgium -- View this message in context: http://r.789695.n4.nabble.com/lasso-lars-error-tp831400p3173480.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to keep keep matching column in output of merge
Nevil Amos nevil.amos at gmail.com writes: How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. simple reproducible example please? (e.g. make up a couple of 4-row datasets that show what you want, what you are trying, and what you are getting instead). __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to keep keep matching column in output of merge
Hi Nevil, We really need an example here of what you're doing, since merge() does keep the id column by default. x - data.frame(id = c(a, b, c, d), x=c(1,2,3,4)) y - data.frame(id = c(b, a, d, c), y=c(101, 102, 103, 104)) merge(x, y) id x y 1 a 1 102 2 b 2 101 3 c 3 104 4 d 4 103 Sarah On Tue, Jan 4, 2011 at 8:31 AM, Nevil Amos nevil.a...@gmail.com wrote: How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. thanks Nevil Amos -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving objects inside a list
Hello, (and a happy new year for you too!)
Apparently the problem is happening only within my RKWard sessions:
B = 1000
oblist = as.list(.GlobalEnv)
str(oblist)
List of 1
$ B:function (value)
oblist$B
function (value)
{
if (!missing(value)) {
assign(k, value, envir = .rk.watched.symbols)
.rk.do.call(ws, k)
invisible(value)
}
else {
get(k, envir = .rk.watched.symbols)
}
}
environment: 0x08cc9eec
Now the same code in a regular Rgui session:
B = 1000
oblist = as.list(.GlobalEnv)
str(oblist)
List of 1
$ B: num 1000
oblist$B
[1] 1000
Problem solved?
Best regards,
Eduardo Horta
On Tue, Jan 4, 2011 at 9:41 AM, Olivier ETERRADOSSI
olivier.eterrado...@mines-ales.fr wrote:
Message: 42
Date: Mon, 3 Jan 2011 18:58:04 -0200
From: Eduardo de Oliveira Hortaeduardo.oliveiraho...@gmail.com
To: r-helpr-help@r-project.org
Subject: Re: [R] Saving objects inside a list
Message-ID:
aanlktimbxmr0rusiws1grorhjh=wstofzqdoc-90z...@mail.gmail.com
Content-Type: text/plain
sapply(ls(),get) works fine. Thanks.
ps: the as.list and the eapply suggestions didn't work.
Hi Eduardo (and all the best for this new year),
are you sure the as.list and eapply solutions didn't work ? On my machine
they produce a list but in reverse order compared to the result of
ls(),...maybe it's the same with you :
names(as.list(.GlobalEnv))[6] is the name of the 6th variable FROM THE END
of ls().
Regards. Olivier
--
Olivier ETERRADOSSI
Maître-Assistant
animateur du groupe Sensomines (Institut Carnot M.I.N.E.S)
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CMGD
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axe Propriétés Psycho-Sensorielles des Matériaux
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Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9
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[R] How to make a Cluster of Clusters
Dear R-help, In my Master thesis I measured 10 variables from 18 lakes. These measurements were taken 4 times a year in 3 depths, so I have 12 samples from each lake. I know that 12 samples can not be treated as replications, since they don't correspond to the same environmental characteristics and are not statistically independent, but I want to use these 12 samples as an estimate of an annual range the 18 lakes have of the 10 variables. I want to make a cluster analysis of the 18 lakes and my known possibilities were: 1- Make an average of the 12 samples from each lake and make the cluster (Using ward's method); 2- Use all 216 samples (18*12) to make the cluster (Which yields a mess). But I thought I could begin the cluster algorithm already with 18 clusters (Lakes) each with 12 individuals (samples) and normally proceed with the calculations (using ward's method). So I will obtain a cluster of the 18 lakes, but using the 12 samples. I got the cluster Fortran algorithm and I'm trying to translate it to the R language to see how it works and maybe implement this kind of cluster of cluster analysis. Does anyone knows if there is an algorithm that does this? Actually I did it by hand and got very good and meaningful results, but I want to implement it to try another merging criterias. Thanks Diego Pujoni Zooplankton Ecology Laboratory Biological Sciences Institute Federal University of Minas Gerais Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calendar in R-program
Hey. I have to do calendar in program R. I was looking for examples on this forum but havent found it. Can someone help me in this thing ? I would be really appreciate for that. Calendar should be the same as we have in Windows but I really dont know how to begin it. Hope u can show me the best way to do it. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Calendar-in-R-program-tp3173566p3173566.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] plyr 1.4
# plyr plyr is a set of tools for a common set of problems: you need to __split__ up a big data structure into homogeneous pieces, __apply__ a function to each piece and then __combine__ all the results back together. For example, you might want to: * fit the same model each patient subsets of a data frame * quickly calculate summary statistics for each group * perform group-wise transformations like scaling or standardising It's already possible to do this with base R functions (like split and the apply family of functions), but plyr makes it all a bit easier with: * totally consistent names, arguments and outputs * convenient parallelisation through the foreach package * input from and output to data.frames, matrices and lists * progress bars to keep track of long running operations * built-in error recovery, and informative error messages * labels that are maintained across all transformations Considerable effort has been put into making plyr fast and memory efficient, and in many cases plyr is as fast as, or faster than, the built-in functions. You can find out more at http://had.co.nz/plyr/, including a 20 page introductory guide, http://had.co.nz/plyr/plyr-intro.pdf. You can ask questions about plyr (and data-manipulation in general) on the plyr mailing list. Sign up at http://groups.google.com/group/manipulatr Version 1.4 (2011-01-03) -- * `count` now takes an additional parameter `wt_var` which allows you to compute weighted sums. This is as fast, or faster than, `tapply` or `xtabs`. * Really fix bug in `names.quoted` * `.` now captures the environment in which it was evaluated. This should fix an esoteric class of bugs which no-one probably ever encountered, but will form the basis for an improved version of `ggplot2::aes`. Version 1.3.1 (2010-12-30) -- * Fix bug in `names.quoted` that interfered with ggplot2 Version 1.3 (2010-12-28) -- NEW FEATURES * new function `mutate` that works like transform to add new columns or overwrite existing columns, but computes new columns iteratively so later transformations can use columns created by earlier transformations. (It's also about 10x faster) (Fixes #21) BUG FIXES * split column names are no longer coerced to valid R names. * `quickdf` now adds names if missing * `summarise` preserves variable names if explicit names not provided (Fixes #17) * `arrays` with names should be sorted correctly once again (also fixed a bug in the test case that prevented me from catching this automatically) * `m_ply` no longer possesses .parallel argument (mistakenly added) * `ldply` (and hence `adply` and `ddply`) now correctly passes on .parallel argument (Fixes #16) * `id` uses a better strategy for converting to integers, making it possible to use for cases with larger potential numbers of combinations -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] reshape2 1.1
Reshape2 is a reboot of the reshape package. It's been over five years since the first release of the package, and in that time I've learned a tremendous amount about R programming, and how to work with data in R. Reshape2 uses that knowledge to make a new package for reshaping data that is much more focussed and much much faster. This version improves speed at the cost of functionality, so I have renamed it to `reshape2` to avoid causing problems for existing users. Based on user feedback I may reintroduce some of these features. What's new in `reshape2`: * considerably faster and more memory efficient thanks to a much better underlying algorithm that uses the power and speed of subsetting to the fullest extent, in most cases only making a single copy of the data. * cast is replaced by two functions depending on the output type: `dcast` produces data frames, and `acast` produces matrices/arrays. * multidimensional margins are now possible: `grand_row` and `grand_col` have been dropped: now the name of the margin refers to the variable that has its value set to (all). * some features have been removed such as the `|` cast operator, and the ability to return multiple values from an aggregation function. I'm reasonably sure both these operations are better performed by plyr. * a new cast syntax which allows you to reshape based on functions of variables (based on the same underlying syntax as plyr): * better development practices like namespaces and tests. Initial benchmarking has shown `melt` to be up to 10x faster, pure reshaping `cast` up to 100x faster, and aggregating `cast()` up to 10x faster. This work has been generously supported by BD (Becton Dickinson). Version 1.1 --- * `melt.data.frame` no longer turns characters into factors * All melt methods gain a `na.rm` and `value.name` arguments - these previously were only possessed by `melt.data.frame` (Fixes #5) -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Page eject and clearing the console
(1) I know that \n when used in cat, e.g. cat(\n) produces a line feed (i.e.
skips to the next line). Is there any escape sequence that will go to the top
of the next page?
(2) I know that control L will clear the console. Is there an equivalent
function or other means that can be used in R code to clear the console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
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Re: [R] Inverse Gaussian Distribution
Thank you again David! I did not try it yet, cause neither the dataset nor R is on this computer. I'll try it in a few hours, as soon as possible, when I'm on my personal computer. I'll let you know if it works. I'm really curious! Thank you for your time! Best Wishes, Louisa -- View this message in context: http://r.789695.n4.nabble.com/Inverse-Gaussian-Distribution-tp3172533p3173579.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] uroot Package and R 2.12.1
Hello friends. I'm wondering what happened to package uroot. I worked quite well with older versions of R, however with 2.12.1 version it simply doesn't work. The worst thing is that I look for it in the contributed packages and it simply doesn't appear. I want to develop ADF test with seasonal (centered) dummies, is there any other possible package that contains this test? Thanks a lot. Regards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] uroot Package and R 2.12.1
On 04.01.2011 16:15, CALEF ALEJANDRO RODRIGUEZ CUEVAS wrote: Hello friends. I'm wondering what happened to package uroot. I worked quite well with older versions of R, however with 2.12.1 version it simply doesn't work. The worst thing is that I look for it in the contributed packages and it simply doesn't appear. It was removed from the main repository since it did not work and was not fixed by its maintainer. Given the compatible license: Feel free to get it from the archives, fix it, and re-upload a new version to CRAN. Best, Uwe Ligges I want to develop ADF test with seasonal (centered) dummies, is there any other possible package that contains this test? Thanks a lot. Regards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] an error about JRI
Hi everyone, I try to run my R script in Java, thus I installed JRI. and run
the example, I am using Eclipse on 64 bits windows 7. part of the example
code is as follows:
public static void main(String[] args) {
System.out.println(Creating Rengine (with arguments));
Rengine re=new Rengine(args, false, null);
System.out.println(Rengine created, waiting for R);
if (!re.waitForR()) {
System.out.println(Cannot load R);
return;
}
However, everytime I run it. it teminated after print out Creating Rengine
(with arguments) never successfully print out Rengine created, waiting for
R
I do not know what is right argument to input, I have tried to add
--no-save under the Program arguments of eclipse run configuration, but
still does not help.
any suggestions? Many thanks
Ying
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: how to center a title?
mhofert wrote: trellis.device(pdf, width = 5, height = 5) print(xyplot(0 ~ 0, main = This title is not 'centered' for the human's eye, scales = list(alternating = c(1,1), tck = c(1,0 dev.off() ... the title does not seem to be centered for the human's eye [although it is centered when the plot (width) is considered with the y-axis label]. This is because there is a y label, and centering is on the page (as you noted). One way around this would be to add a similar padding at the right side. See the example below, where I have exaggerated the effect. Try a padding of 5 instead. Dieter library(lattice) trellis.device(pdf, width = 5, height = 5) trellis.par.set(layout.widths = list(right.padding = 10)) print(xyplot(0 ~ 0, main = This title is not 'centered' for the human's eye, scales = list(alternating = c(1,1), tck = c(1,0 dev.off() -- View this message in context: http://r.789695.n4.nabble.com/lattice-how-to-center-a-title-tp3173271p3173800.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: par.settings with standard.theme() + additional arguments?
On Jan 4, 2011, at 8:39 AM, Marius Hofert wrote: Dear David, this I already tried. But as you can see, the plot itself *is* colored. However, I want to have color = FALSE, so, unfortunately, this approach does not work... Quite right. I didn't see that until you pointed it out. I had many failed attempts at a solution and then searched for prior positngs using par.settings and standard.theme and found one by Ehlers earlier this year that seems to work when modified to your ends: xyplot(x ~ 1:10, type = l, par.settings = modifyList(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5) ))) I had tried various constructions that I thought would be equivalent, but I think I was getting the levels of the list structure wrong. This also works: xyplot(x ~ 1:10, type = l, par.setting=c(list(par.xlab.text = list(cex = 5), standard.theme(color = FALSE)) ) Notice the use of c() rather than list() to bind them together. When I looked at the output of standard.theme(color=FALSE), there was no par.xlab.text element so it seemed as though there should be no conflict and in fact there wasn't (except for the asynchrony between my brain and the R interpreter.) best; David. Cheers, Marius On 2011-01-04, at 14:32 , David Winsemius wrote: On Jan 4, 2011, at 5:57 AM, Marius Hofert wrote: Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Add it as a list element: xyplot(x ~ 1:10, type = l, par.settings = list(standard.theme(color = FALSE), par.xlab.text = list(cex = 5, col = blue))) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Resampling to find Confidence intervals
Axolotl9250 wrote:
...
resampled_ecoli = sample(ecoli, 500, replace=T)
coefs = (coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate,
data=resampled_ecoli)))
sd(coefs)
...
Below a simplified and self-consistent version of your code, and some
changes
Dieter
# resample
d = data.frame(x=rnorm(10))
d$y = d$x*3+rnorm(10,0.01)
# if you do this, you only get ONE bootstrap sample
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
d1.coef
# No error below, because you compute the sd of (Intercept) and slope
# but result is wrong!
sd(d1.coef)
# We have to do this over and over
# Check ?replicate for a more R-ish approach
nsamples = 1000
allboot = NULL
for (i in 1:1000) {
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
allboot = rbind(allboot,d1.coef) # Not very efficient, preallocate!
}
head(allboot) # display first of nsamples lines
apply(allboot,2,mean) # Compute mean
apply(allboot,2,sd) # compute sd
# After you are sure you understood the above, you might try package boot.
--
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Re: [R] randomForest speed improvements
If you have multiple cores, one poor man's solution is to run separate
forests in different R sessions, save the RF objects, load them into the
same session and combine() them. You can do this less clumsily if you
use things like Rmpi or other distributed computing packages.
Another consideration is to increase nodesize (which reduces the sizes
of trees). The problem with numeric predictors for tree-based
algorithms is that the number of computations to find the best splitting
point increases by that much _at each node_. Some algorithms try to
save on this by using only certain quantiles. The current RF code
doesn't do this.
Andy
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of apresley
Sent: Monday, January 03, 2011 6:28 PM
To: r-help@r-project.org
Subject: Re: [R] randomForest speed improvements
I haven't tried changing the mtry or ntree at all ... though
I suppose with
only 6 variables, and tens-of-thousands of rows, we can
probably do less
than 500 tree's (the default?).
Although tossing the forest does speed things up a bit, seems
to be about 15
- 20% faster in some cases, I need to keep the forest to do
the prediction,
otherwise, it complains that there is no forest component in
the object.
--
Anthony
--
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tp3172523p3172834.html
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[R] Cost-benefit/value for money analysis
I assume this has a proper name, but I don't know what it is and wondered if anyone knew of a package that might do the following, or something similar. As an example, assume I have borrowed and read 10 books on R , and I have subjectively given each of them a value score in terms of how useful I think they are. I also know how much each costs in terms of money. What I would like to do is to calculate the costs of every possible combination of the 10 books, and plot the total monetary value for each of these possible combination with their associated subjective value totals, to help decide which combination of books represents the best value for money. I know that some specialist decision analysis software does this sort of thing, but was hoping R might have an appropriate package. Many thanks, Graham [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] an error about JRI
AFAIK JRI is part of rJava (and you installed rJava), which has its
own mailing list: plasea use it. (http://rosuda.org/lists.shtml, I
believe).
There are tricky things with JRI on multi-architecture platforms, so
you do need to be sure you are using the right versions (and rJava
0.8-8 is needed for 64-bit Windows R, for example).
On Tue, 4 Jan 2011, ying zhang wrote:
Hi everyone, I try to run my R script in Java, thus I installed JRI. and run
the example, I am using Eclipse on 64 bits windows 7. part of the example
code is as follows:
public static void main(String[] args) {
System.out.println(Creating Rengine (with arguments));
Rengine re=new Rengine(args, false, null);
System.out.println(Rengine created, waiting for R);
if (!re.waitForR()) {
System.out.println(Cannot load R);
return;
}
However, everytime I run it. it teminated after print out Creating Rengine
(with arguments) never successfully print out Rengine created, waiting for
R
I do not know what is right argument to input, I have tried to add
--no-save under the Program arguments of eclipse run configuration, but
still does not help.
any suggestions? Many thanks
Ying
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] lattice: par.settings with standard.theme() + additional arguments?
On Jan 4, 2011, at 11:08 AM, David Winsemius wrote: On Jan 4, 2011, at 8:39 AM, Marius Hofert wrote: Dear David, this I already tried. But as you can see, the plot itself *is* colored. However, I want to have color = FALSE, so, unfortunately, this approach does not work... Quite right. I didn't see that until you pointed it out. I had many failed attempts at a solution and then searched for prior positngs using par.settings and standard.theme and found one by Ehlers earlier this year that seems to work when modified to your ends: xyplot(x ~ 1:10, type = l, par.settings = modifyList(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5) ))) I had tried various constructions that I thought would be equivalent, but I think I was getting the levels of the list structure wrong. This also works: ### NO, it doesn't. I failed to notice that the command was incomplete so was looking at my prior plot. xyplot(x ~ 1:10, type = l, par.setting=c(list(par.xlab.text = list(cex = 5), standard.theme(color = FALSE)) ) Proving that I still do not really understand why the modifyList approach works and what seemed to be equivalents do not. (Next paragraph is wrong.) Notice the use of c() rather than list() to bind them together. When I looked at the output of standard.theme(color=FALSE), there was no par.xlab.text element so it seemed as though there should be no conflict and in fact there wasn't (except for the asynchrony between my brain and the R interpreter.) best; David. Cheers, Marius On 2011-01-04, at 14:32 , David Winsemius wrote: On Jan 4, 2011, at 5:57 AM, Marius Hofert wrote: Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Add it as a list element: xyplot(x ~ 1:10, type = l, par.settings = list(standard.theme(color = FALSE), par.xlab.text = list(cex = 5, col = blue))) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot without points overlap
Hi, I'm trying to plot a grid of points of different dimensions using the simple plot() function. I want to plot the points such that they DO NOT overlap, I guess there should be a way to set a maximum distance between the points, but I cannot find it. Can you help? Thanks a lot! g PS: Is it possible to produce device regions of different dimensions? (i.e. a rectangular one with height width) -- View this message in context: http://r.789695.n4.nabble.com/plot-without-points-overlap-tp3173894p3173894.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: par.settings with standard.theme() + additional arguments?
Dear David, that's funny to read. I guess we did pretty much the same. I also thought I got the list structure wrong and I also tried c()... (since I recently learned from Gabor that a list is only a vector of mode list) and I also searched for posts with exactly the same words [but wasn't as successful as you :-)]. Thanks for the modifyList()-trick! Cheers, Marius On 2011-01-04, at 17:37 , David Winsemius wrote: On Jan 4, 2011, at 11:08 AM, David Winsemius wrote: On Jan 4, 2011, at 8:39 AM, Marius Hofert wrote: Dear David, this I already tried. But as you can see, the plot itself *is* colored. However, I want to have color = FALSE, so, unfortunately, this approach does not work... Quite right. I didn't see that until you pointed it out. I had many failed attempts at a solution and then searched for prior positngs using par.settings and standard.theme and found one by Ehlers earlier this year that seems to work when modified to your ends: xyplot(x ~ 1:10, type = l, par.settings = modifyList(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5) ))) I had tried various constructions that I thought would be equivalent, but I think I was getting the levels of the list structure wrong. This also works: ### NO, it doesn't. I failed to notice that the command was incomplete so was looking at my prior plot. xyplot(x ~ 1:10, type = l, par.setting=c(list(par.xlab.text = list(cex = 5), standard.theme(color = FALSE)) ) Proving that I still do not really understand why the modifyList approach works and what seemed to be equivalents do not. (Next paragraph is wrong.) Notice the use of c() rather than list() to bind them together. When I looked at the output of standard.theme(color=FALSE), there was no par.xlab.text element so it seemed as though there should be no conflict and in fact there wasn't (except for the asynchrony between my brain and the R interpreter.) best; David. Cheers, Marius On 2011-01-04, at 14:32 , David Winsemius wrote: On Jan 4, 2011, at 5:57 AM, Marius Hofert wrote: Dear expeRts, I usually use par.settings = standard.theme(color = FALSE) to create lattice graphics without colors, so something like library(lattice) x - runif(10) xyplot(x ~ 1:10, type = l, par.settings = standard.theme(color = FALSE)) Now I would like to use an additional component in par.settings. I tried several things like xyplot(x ~ 1:10, type = l, par.settings = c(standard.theme(color = FALSE), list(par.xlab.text = list(cex = 5, col = blue but it doesn't work. I know I could use lattice.options() but is there a way to get it right (locally) with par.settings? Add it as a list element: xyplot(x ~ 1:10, type = l, par.settings = list(standard.theme(color = FALSE), par.xlab.text = list(cex = 5, col = blue))) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Page eject and clearing the console
(1) I know that \n when used in cat, e.g. cat(\n) produces a line feed (i.e.
skips to the next line). Is there any escape sequence that will go to the top
of the next page?
(2) I know that control L will clear the console. Is there an equivalent
function or other means that can be used in R code to clear the console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Page eject and clearing the console
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line feed
(i.e. skips to the next line). Is there any escape sequence that will go to
the top of the next page?
(2) I know that control L will clear the console. Is there an equivalent
function or other means that can be used in R code to clear the console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:20}}
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
Hi John, I don't understand what you mean by top of the next page, or rather, how that differs from clearing the screen. And for the latter, that is dependent on OS, and on GUI/console usage, and has been discussed several times on the list. The easiest solution is to invoke the system command if running in a console. For linux, that would be: system(clear) A Google search using the exact words from your question found several more options, including a discussion of doing this in Windows. http://www.google.com/search?q=R+code+to+clear+the+console I can't test them for you, but since I don't know if you're using Windows or not it may not matter. Sarah On Tue, Jan 4, 2011 at 11:54 AM, John Sorkin jsor...@grecc.umaryland.edu wrote: (1) I know that \n when used in cat, e.g. cat(\n) produces a line feed (i.e. skips to the next line). Is there any escape sequence that will go to the top of the next page? (2) I know that control L will clear the console. Is there an equivalent function or other means that can be used in R code to clear the console? Thanks, John -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
Hi, Still with the above problem: But for instance, i have a data base with 30 variables and I created an object each with one varibale missing: DataBase - has 30 variables DataBase1 has 29 variables with the 1st variable gone DataBase2 has 29 variables with the 2nd variable gone for(i in 1:length(database)) assign(paste(database,i,sep=),database[-i]) Now, I wish to create the 30 distance matrix: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(database[i])) But doing like this - database[i] - I am just refering to the 1st value on the object database and not to the entire database i. How do I do this? thanks Regards, A.Dias -- View this message in context: http://r.789695.n4.nabble.com/Help-with-For-instruction-tp3173074p3173914.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving objects inside a list
Hello,
I've contacted the guys from RKWard. Below I paste the answer Thomas
Friedrichsmeier gave me.
---
Hi,
the problem appears to be our use of active bindings (see
?makeActiveBinding). Internally, RKWard replaces all objects inside
.GlobalEnv
by active bindings. This allows us to find out, when the objects get
modified.
For almost all purposes, these active bindings behave just like the regular
object, but apparently, as.list() copies the accessor functions, instead. I
do
wonder whether that is the expected behavior of as.list()...
Either way, RKWard will probably switch to a different strategy for
detecting
when objects get modified, in the not-too-distant future. The problem should
go
away, then. Meanwhile, perhaps you can work around the problem using code
like
this:
oblist - sapply (ls (all.names=TRUE), function (x) get (x), simplify=FALSE)
Regards
Thomas
On Tue, Jan 4, 2011 at 2:54 PM, William Dunlap wdun...@tibco.com wrote:
Under RKWard, do you get (at the command line)
environment()
environment: R_GlobalEnv
If environment() doesn't evaluate to .GlobalEnv's
value then
as.list(environment())
may show the B=1000. It may be that RKWard doesn't
use .GlobalEnv in the usual way.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Eduardo de
Oliveira Horta
Sent: Tuesday, January 04, 2011 6:25 AM
To: r-help@r-project.org
Subject: Re: [R] Saving objects inside a list
Hello, (and a happy new year for you too!)
Apparently the problem is happening only within my RKWard sessions:
B = 1000
oblist = as.list(.GlobalEnv)
str(oblist)
List of 1
$ B:function (value)
oblist$B
function (value)
{
if (!missing(value)) {
assign(k, value, envir = .rk.watched.symbols)
.rk.do.call(ws, k)
invisible(value)
}
else {
get(k, envir = .rk.watched.symbols)
}
}
environment: 0x08cc9eec
Now the same code in a regular Rgui session:
B = 1000
oblist = as.list(.GlobalEnv)
str(oblist)
List of 1
$ B: num 1000
oblist$B
[1] 1000
Problem solved?
Best regards,
Eduardo Horta
On Tue, Jan 4, 2011 at 9:41 AM, Olivier ETERRADOSSI
olivier.eterrado...@mines-ales.fr wrote:
Message: 42
Date: Mon, 3 Jan 2011 18:58:04 -0200
From: Eduardo de Oliveira Hortaeduardo.oliveiraho...@gmail.com
To: r-helpr-help@r-project.org
Subject: Re: [R] Saving objects inside a list
Message-ID:
aanlktimbxmr0rusiws1grorhjh=wstofzqdoc-90z...@mail.gmail.com
Content-Type: text/plain
sapply(ls(),get) works fine. Thanks.
ps: the as.list and the eapply suggestions didn't work.
Hi Eduardo (and all the best for this new year),
are you sure the as.list and eapply solutions didn't work ?
On my machine
they produce a list but in reverse order compared to the result of
ls(),...maybe it's the same with you :
names(as.list(.GlobalEnv))[6] is the name of the 6th
variable FROM THE END
of ls().
Regards. Olivier
--
Olivier ETERRADOSSI
Maître-Assistant
animateur du groupe Sensomines (Institut Carnot M.I.N.E.S)
-
CMGD
Pôle Matériaux Polymères Avancés
axe Propriétés Psycho-Sensorielles des Matériaux
-
Ecole des Mines d'Alès
Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9
tel std: +33 (0)5.59.30.54.25
tel direct: +33 (0)5.59.30.90.35
fax: +33 (0)5.59.30.63.68
http://www.mines-ales.fr
e-mail : olivier.eterrado...@mines-ales.fr
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Re: [R] Page eject and clearing the console
On Tue, Jan 4, 2011 at 9:48 AM, John Sorkin jsor...@grecc.umaryland.edu wrote: (1) I know that \n when used in cat, e.g. cat(\n) produces a line feed (i.e. skips to the next line). Is there any escape sequence that will go to the top of the next page? (2) I know that control L will clear the console. Is there an equivalent function or other means that can be used in R code to clear the console? Its always a good idea to look through the archives before posting. I had posted this 5 years ago. It uses RDCOMClient: http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg57802.html and also posted a second version using rcom in the same thread. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot without points overlap
Hi, You can set the device region in inches using the pin argument (see ?par maybe halfway down or so). You can also set the aspect ratio in plot(), but I am not sure that is really what you want (see ?plot.window for that). Two Examples ### par(pin = c(2, 4)) plot(1:10) dev.off() plot(1:10, asp = 2) ### Hope that helps, Josh On Tue, Jan 4, 2011 at 8:46 AM, joonR joon...@gmail.com wrote: Hi, I'm trying to plot a grid of points of different dimensions using the simple plot() function. I want to plot the points such that they DO NOT overlap, I guess there should be a way to set a maximum distance between the points, but I cannot find it. Can you help? Thanks a lot! g PS: Is it possible to produce device regions of different dimensions? (i.e. a rectangular one with height width) -- View this message in context: http://r.789695.n4.nabble.com/plot-without-points-overlap-tp3173894p3173894.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: how to center a title?
Dear Dieter, many thanks, exactly what I was looking for. Cheers, Marius -- View this message in context: http://r.789695.n4.nabble.com/lattice-how-to-center-a-title-tp3173271p3173931.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calendar in R-program
Look at the lubridate package from Hadley Wickham for great basic routines for handling date objects. Mark R. Mark Sharp, Ph.D. msh...@sfbr.orgmailto:msh...@sfbr.org On Jan 4, 2011, at 8:02 AM, LOON88 wrote: Hey. I have to do calendar in program R. I was looking for examples on this forum but havent found it. Can someone help me in this thing ? I would be really appreciate for that. Calendar should be the same as we have in Windows but I really dont know how to begin it. Hope u can show me the best way to do it. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Calendar-in-R-program-tp3173566p3173566.html Sent from the R help mailing list archive at Nabble.comhttp://Nabble.com. __ R-help@r-project.orgmailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] packagename:::functionname vs. importFrom
Thanks Luke. By the namespace from which you import is loaded when your package is I take it that you are saying that all such referenced packages are loaded up front, which is not what I hoped. And it's too bad you can't import unexported objects, as that rather defeats the purpose of importFrom. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/packagename-functionname-vs-importFrom-tp3172684p3174003.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] packagename:::functionname vs. importFrom
Thanks Hadley, Luke, Martin, and Bill. Bill captured the essence of my reasons for needing an unexported function. Other reasons include occasional overrides of dispatching rules, and providing parallel versions of some functions that exist in other packages to make them easier to use in some sense. I could ask the package creator to export those functions but it would not make sense to him to do so. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/packagename-functionname-vs-importFrom-tp3172684p3174011.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
hi how do I exactly use the get(). I am reading the help for get() but the way I am using it causes an error/ thanks ADias 2011/1/4 Sarah Goslee sarah.gos...@gmail.com With get(). On Tue, Jan 4, 2011 at 11:58 AM, ADias diasan...@gmail.com wrote: Hi, Still with the above problem: But for instance, i have a data base with 30 variables and I created an object each with one varibale missing: DataBase - has 30 variables DataBase1 has 29 variables with the 1st variable gone DataBase2 has 29 variables with the 2nd variable gone for(i in 1:length(database)) assign(paste(database,i,sep=),database[-i]) Now, I wish to create the 30 distance matrix: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(database[i])) But doing like this - database[i] - I am just refering to the 1st value on the object database and not to the entire database i. How do I do this? thanks Regards, A.Dias -- -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Resampling to find Confidence intervals
Ok I'll check I understand:
So it's using sample, to resample d once, 10 values, because the rnorm
has 10 values, with replacement (I assume thats the TRUE part).
Then a for loop has this to resample the data - in the loop's case its
1000 times. Then it does a lm to get the coefficients and add them to
d1.coef. I'm guessing that the allboot bit with rbind, which is null at
the start of the loop, is the collection of d1.coef values, as I think
that without it, every cycle of the loop the d1.coef from the previous
cycle round the loop would be gone?
On 04/01/2011 16:24, Dieter Menne wrote:
Axolotl9250 wrote:
...
resampled_ecoli = sample(ecoli, 500, replace=T)
coefs = (coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate,
data=resampled_ecoli)))
sd(coefs)
...
Below a simplified and self-consistent version of your code, and some
changes
Dieter
# resample
d = data.frame(x=rnorm(10))
d$y = d$x*3+rnorm(10,0.01)
# if you do this, you only get ONE bootstrap sample
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
d1.coef
# No error below, because you compute the sd of (Intercept) and slope
# but result is wrong!
sd(d1.coef)
# We have to do this over and over
# Check ?replicate for a more R-ish approach
nsamples = 1000
allboot = NULL
for (i in 1:1000) {
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
allboot = rbind(allboot,d1.coef) # Not very efficient, preallocate!
}
head(allboot) # display first of nsamples lines
apply(allboot,2,mean) # Compute mean
apply(allboot,2,sd) # compute sd
# After you are sure you understood the above, you might try package boot.
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Re: [R] Help with For instruction
2011/1/4 André Dias diasan...@gmail.com: hi how do I exactly use the get(). I am reading the help for get() but the way I am using it causes an error/ So how are you using it? It's so much easier to explain what you're doing wrong if I know what you're doing. Without a reproducible example I can't show you exactly, but something like: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(get(paste(database, i, sep= get() is the counterpart of assign(), though there are better (more R-ish) ways of doing what you want. Sarah thanks ADias 2011/1/4 Sarah Goslee sarah.gos...@gmail.com With get(). On Tue, Jan 4, 2011 at 11:58 AM, ADias diasan...@gmail.com wrote: Hi, Still with the above problem: But for instance, i have a data base with 30 variables and I created an object each with one varibale missing: DataBase - has 30 variables DataBase1 has 29 variables with the 1st variable gone DataBase2 has 29 variables with the 2nd variable gone for(i in 1:length(database)) assign(paste(database,i,sep=),database[-i]) Now, I wish to create the 30 distance matrix: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(database[i])) But doing like this - database[i] - I am just refering to the 1st value on the object database and not to the entire database i. How do I do this? thanks Regards, A.Dias -- -- -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inverse Gaussian Distribution
Dear David, It works! Thank you so much for your help! Louisa -- View this message in context: http://r.789695.n4.nabble.com/Inverse-Gaussian-Distribution-tp3172533p3174015.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
If you had followed David's advice and put everything into a list or other structure instead of using the assign function (see fortune(236)) then you could just access the list element instead of needing get. In the long run (or even medium and short run) life will be much easier for you if you learn to use proper data structures and not programmatically create global variables. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of André Dias Sent: Tuesday, January 04, 2011 10:55 AM To: Sarah Goslee Cc: r-help@r-project.org Subject: Re: [R] Help with For instruction hi how do I exactly use the get(). I am reading the help for get() but the way I am using it causes an error/ thanks ADias 2011/1/4 Sarah Goslee sarah.gos...@gmail.com With get(). On Tue, Jan 4, 2011 at 11:58 AM, ADias diasan...@gmail.com wrote: Hi, Still with the above problem: But for instance, i have a data base with 30 variables and I created an object each with one varibale missing: DataBase - has 30 variables DataBase1 has 29 variables with the 1st variable gone DataBase2 has 29 variables with the 2nd variable gone for(i in 1:length(database)) assign(paste(database,i,sep=),database[-i]) Now, I wish to create the 30 distance matrix: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(database[i])) But doing like this - database[i] - I am just refering to the 1st value on the object database and not to the entire database i. How do I do this? thanks Regards, A.Dias -- -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
Hi I was doing for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(paste(get(database, i, sep=) but i really did not know what I was doing. I will try your way. But I still don't understnad how the get function works. What woud be more r-ish then get() ? thanks ADias No dia 4 de Janeiro de 2011 17:58, Sarah Goslee sarah.gos...@gmail.comescreveu: 2011/1/4 André Dias diasan...@gmail.com: hi how do I exactly use the get(). I am reading the help for get() but the way I am using it causes an error/ So how are you using it? It's so much easier to explain what you're doing wrong if I know what you're doing. Without a reproducible example I can't show you exactly, but something like: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(get(paste(database, i, sep= get() is the counterpart of assign(), though there are better (more R-ish) ways of doing what you want. Sarah thanks ADias 2011/1/4 Sarah Goslee sarah.gos...@gmail.com With get(). On Tue, Jan 4, 2011 at 11:58 AM, ADias diasan...@gmail.com wrote: Hi, Still with the above problem: But for instance, i have a data base with 30 variables and I created an object each with one varibale missing: DataBase - has 30 variables DataBase1 has 29 variables with the 1st variable gone DataBase2 has 29 variables with the 2nd variable gone for(i in 1:length(database)) assign(paste(database,i,sep=),database[-i]) Now, I wish to create the 30 distance matrix: for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(database[i])) But doing like this - database[i] - I am just refering to the 1st value on the object database and not to the entire database i. How do I do this? thanks Regards, A.Dias -- -- -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with For instruction
You need to swap the get and paste commands - paste() creates the string filename that get() acts on. As already explained, using a list is much nicer. Sarah 2011/1/4 André Dias diasan...@gmail.com: Hi I was doing for (i in 1:length(database)) assign(paste(distancematrix,i,sep=), dist(paste(get(database, i, sep=) but i really did not know what I was doing. I will try your way. But I still don't understnad how the get function works. What woud be more r-ish then get() ? thanks ADias -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calendar in R-program
If all you want is a calendar Date, the simplest may be the
Date class in the base package. Try help('as.Date').
Dates and times can be extremely difficult to use for many
reasons. For example, some months have 30 days, others have 31, and
February usually has 28 days, but every 4th year, it has 29, except if
the year is a century year, except ... . Times involve arithmetic to
multiple bases. In addition, there are occasional leap seconds
introduced by irregularities in the rotation of the earth. Then don't
forget timezones and holidays, which vary between countries and
sometimes between regions within a country. Holidays further depend on
the occupation. Financial markets have their own rules.
This complexity is met by a wide range of alternative systems in
R for coding dates and times. A great overview of the options appeared
in R News a few years ago. To find it,
go to r-project.org - The R Journal - Archive - Table of
Contents (all issues) - Search for date. The second match should be
Gabor Grothendieck and Thomas Petzoldt. R Help Desk: Date and time
classes in R. R News, 4(1):29-32, June 2004.
There have been many additions since 2004. Probably the quickest
way to find other options is to use the sos package.
library(sos)
(cndr - ???calendar)
#found 238 matches; retrieving 12 pages
# This will open a table in a web browser showing the 238 matches
# sorted by package.
# A function from the lubridate package is match # 229 on this list.
The sos package also has a vignette, which provides examples of
how to combine searches, write results to an Excel file with the first
sheet being a summary by package, etc.
Hope this helps.
Spencer
On 1/4/2011 9:32 AM, Mark Sharp wrote:
Look at the lubridate package from Hadley Wickham for great basic routines for
handling date objects.
Mark
R. Mark Sharp, Ph.D.
msh...@sfbr.orgmailto:msh...@sfbr.org
On Jan 4, 2011, at 8:02 AM, LOON88 wrote:
Hey.
I have to do calendar in program R. I was looking for examples on this forum
but havent found it. Can someone help me in this thing ? I would be really
appreciate for that. Calendar should be the same as we have in Windows but I
really dont know how to begin it. Hope u can show me the best way to do it.
Cheers
--
View this message in context:
http://r.789695.n4.nabble.com/Calendar-in-R-program-tp3173566p3173566.html
Sent from the R help mailing list archive at Nabble.comhttp://Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
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Re: [R] Page eject and clearing the console
I have received help on one of my questions (thank you Henrique Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the next
page, i.e. cat(\n) skips to the next line, is there an equivalent way
to skip to the top of the next page?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line
feed
(i.e. skips to the next line). Is there any escape sequence that will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for\...{{dropped:25}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
On Jan 4, 2011, at 1:19 PM, John Sorkin wrote:
I have received help on one of my questions (thank you Henrique Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the next
page, i.e. cat(\n) skips to the next line, is there an equivalent
way
to skip to the top of the next page?
\n does NOT skip to the next line. It is a character and it is
interpreted by some sort of program, say a a plotting program or a
word-processor as a line feed. You need to specify what sort of
program you intend to do this skipping-to-next-page action and also
provide the character sequence that that program uses to signal that
action. (There are not any pages in R except perhaps multi-page plots
but you seem to be in character mode at the moment.)
--
David.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line
feed
(i.e. skips to the next line). Is there any escape sequence that will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for\...{{dropped:
25}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
On Jan 4, 2011, at 1:27 PM, David Winsemius wrote:
On Jan 4, 2011, at 1:19 PM, John Sorkin wrote:
I have received help on one of my questions (thank you Henrique Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the next
page, i.e. cat(\n) skips to the next line, is there an equivalent
way
to skip to the top of the next page?
\n does NOT skip to the next line. It is a character and it is
interpreted by some sort of program, say a a plotting program or a
word-processor as a line feed. You need to specify what sort of
program you intend to do this skipping-to-next-page action and
also provide the character sequence that that program uses to signal
that action. (There are not any pages in R except perhaps multi-page
plots but you seem to be in character mode at the moment.)
It has occurred to me that you may be asking for something that will
give the illusion of clearing the screen but will in fact be just
printing a page of blank space on a console display, scrolling would
ahve been the name I would have given it. In which case:
scroll - function(lines=40) cat(rep(\n, lines))
scroll()
--
David.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to
faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line
feed
(i.e. skips to the next line). Is there any escape sequence that
will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for\...{{dropped:
25}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
Perhaps merely rephrasing David's comments,
page is not a meaningful physical entity -- it depends on font size,
line spacing, etc. and the physical size of the output surface,
which has no meaning for an infinitely (or at least up to tyhe
screen buffer's limit) scrollable screen viewing area.
But maybe David's scroll function is what you had in mind.
-- Bert
On Tue, Jan 4, 2011 at 10:55 AM, David Winsemius dwinsem...@comcast.net wrote:
On Jan 4, 2011, at 1:27 PM, David Winsemius wrote:
On Jan 4, 2011, at 1:19 PM, John Sorkin wrote:
I have received help on one of my questions (thank you Henrique Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the next
page, i.e. cat(\n) skips to the next line, is there an equivalent way
to skip to the top of the next page?
\n does NOT skip to the next line. It is a character and it is
interpreted by some sort of program, say a a plotting program or a
word-processor as a line feed. You need to specify what sort of program you
intend to do this skipping-to-next-page action and also provide the
character sequence that that program uses to signal that action. (There are
not any pages in R except perhaps multi-page plots but you seem to be in
character mode at the moment.)
It has occurred to me that you may be asking for something that will give
the illusion of clearing the screen but will in fact be just printing a
page of blank space on a console display, scrolling would ahve been the name
I would have given it. In which case:
scroll - function(lines=40) cat(rep(\n, lines))
scroll()
--
David.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line
feed
(i.e. skips to the next line). Is there any escape sequence that will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for\...{{dropped:25}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] XTS : merge.xts seems to have problem with character vectors
Hi, Please can you tell me what I am doing wrong. When trying to merge two xts objects, one of which has multiple character vectors for columns...I am just getting NAs. str(t) POSIXct[1:1], format: 2011-01-04 11:45:37 y2 = xts(matrix(c(letters[1:10]),5), order.by=as.POSIXct(c(t + 1:5))) names(y2) = c(1,2) y2 1 2 2011-01-04 11:45:38 a f 2011-01-04 11:45:39 b g 2011-01-04 11:45:40 c h 2011-01-04 11:45:41 d i 2011-01-04 11:45:42 e j y1 = xts(c(1:5), order.by=as.POSIXct(c(t + 1:5))) y1 [,1] 2011-01-04 11:45:381 2011-01-04 11:45:392 2011-01-04 11:45:403 2011-01-04 11:45:414 2011-01-04 11:45:425 merge(y1, y2) y1 X1 X2 2011-01-04 11:45:38 1 NA NA 2011-01-04 11:45:39 2 NA NA 2011-01-04 11:45:40 3 NA NA 2011-01-04 11:45:41 4 NA NA 2011-01-04 11:45:42 5 NA NA Warning message: In merge.xts(y1, y2) : NAs introduced by coercion Why do I lose the character columns ? Cheers, Chris -- View this message in context: http://r.789695.n4.nabble.com/XTS-merge-xts-seems-to-have-problem-with-character-vectors-tp3174125p3174125.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Navigating web pages using R
R-Help, I'm trying to obtain some data from a webpage which masks the URL from the user, so an explicit URL will not work. For example, when one navigates to the web page the URL looks something like: http://137.113.141.205/rpt34s.php?flags=1 (changed for privacy, but i'm not sure you could access it anyways since it's internal to the agency I work for). The site has three drop-down menus for Site, Month, and Year. When a combination is selected of these, the resulting URL is always http://137.113.141.205/rpt34s (nothing changes, except flags=1 is dropped, so what I need to be able to do is write something that will navigate to the original URL, then select some combination of Site, Month, and Year, and then submit the query to the site to navigate to the page with the data. Is this a capability that R has as a language? Unfortunately, I'm unfamiliar with html or php programming, so if this question belongs in a forum on that I apologize. I'm trying to centralize all of my code for my analysis in R! Thank you, -Erik Gregory Student Assistant, California EPA CSU Sacramento, Mathematics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] XTS : merge.xts seems to have problem with character vectors
On Tue, Jan 4, 2011 at 12:42 PM, rivercode aqua...@gmail.com wrote: Hi, Please can you tell me what I am doing wrong. When trying to merge two xts objects, one of which has multiple character vectors for columns...I am just getting NAs. str(t) POSIXct[1:1], format: 2011-01-04 11:45:37 y2 = xts(matrix(c(letters[1:10]),5), order.by=as.POSIXct(c(t + 1:5))) names(y2) = c(1,2) y2 1 2 2011-01-04 11:45:38 a f 2011-01-04 11:45:39 b g 2011-01-04 11:45:40 c h 2011-01-04 11:45:41 d i 2011-01-04 11:45:42 e j y1 = xts(c(1:5), order.by=as.POSIXct(c(t + 1:5))) y1 [,1] 2011-01-04 11:45:38 1 2011-01-04 11:45:39 2 2011-01-04 11:45:40 3 2011-01-04 11:45:41 4 2011-01-04 11:45:42 5 merge(y1, y2) y1 X1 X2 2011-01-04 11:45:38 1 NA NA 2011-01-04 11:45:39 2 NA NA 2011-01-04 11:45:40 3 NA NA 2011-01-04 11:45:41 4 NA NA 2011-01-04 11:45:42 5 NA NA Warning message: In merge.xts(y1, y2) : NAs introduced by coercion Why do I lose the character columns ? Because zoo / xts objects are matrices with an ordered index (a time index in the case of xts). You can't mix types in a matrix. -- Joshua Ulrich | FOSS Trading: www.fosstrading.com Cheers, Chris -- View this message in context: http://r.789695.n4.nabble.com/XTS-merge-xts-seems-to-have-problem-with-character-vectors-tp3174125p3174125.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
I am looking for something which will emulate the following:
Back in the old days, when printing to a line printer, the first two characters
in a line controlled printing. For example, a line starting with
1h1 starts printing at the top of the next page.
1h+ indicates overprinting
1h0 results in double
In R \n skips to the next line. Is there some escape sequence that will start
printing at the top of the next page?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) Bert
Gunter gunter.ber...@gene.com 1/4/2011 2:05 PM
Perhaps merely rephrasing David's comments,
page is not a meaningful physical entity -- it depends on font size,
line spacing, etc. and the physical size of the output surface,
which has no meaning for an infinitely (or at least up to tyhe
screen buffer's limit) scrollable screen viewing area.
But maybe David's scroll function is what you had in mind.
-- Bert
On Tue, Jan 4, 2011 at 10:55 AM, David Winsemius dwinsem...@comcast.net wrote:
On Jan 4, 2011, at 1:27 PM, David Winsemius wrote:
On Jan 4, 2011, at 1:19 PM, John Sorkin wrote:
I have received help on one of my questions (thank you Henrique Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the next
page, i.e. cat(\n) skips to the next line, is there an equivalent way
to skip to the top of the next page?
\n does NOT skip to the next line. It is a character and it is
interpreted by some sort of program, say a a plotting program or a
word-processor as a line feed. You need to specify what sort of program you
intend to do this skipping-to-next-page action and also provide the
character sequence that that program uses to signal that action. (There are
not any pages in R except perhaps multi-page plots but you seem to be in
character mode at the moment.)
It has occurred to me that you may be asking for something that will give
the illusion of clearing the screen but will in fact be just printing a
page of blank space on a console display, scrolling would ahve been the name
I would have given it. In which case:
scroll - function(lines=40) cat(rep(\n, lines))
scroll()
--
David.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a line
feed
(i.e. skips to the next line). Is there any escape sequence that will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for\...{{dropped:25}}
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Bert Gunter
Genentech Nonclinical Biostatistics
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and
[R] R implementation of S-distribution
I'm working with data that can exhibit either strong right- or left-skew. I understand the S-distribution is useful in such cases (e.g., Voit and Schwacke, 2000. Random Number Generation from Right-Skewed, Symmetric, and Left-Skewed Distributions. Risk Analysis 20 (1): 59-71). Does anyone know of any R implementation of this distribution? Dr. Seth W. Bigelow Biologist, USDA-FS Pacific Southwest Research Station 1731 Research Park Drive, Davis California sbige...@fs.fed.us / ph. 530 759 1718 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-uniformly distributed plot
Hi Dennise, David and Jorge,
I hope you all had a great holiday season. Thank you so much for the good
comments. I think all your suggestions are sufficient for my current needs. I
guess it is safe to say that there is no easy way to plot the data according to
the x-axis range. By the way, spotfire can achieve this beautifully.
Eric
From: Dennis Murphy [mailto:djmu...@gmail.com]
Sent: Friday, December 24, 2010 12:43 PM
To: Eric Hu
Cc: r-help@r-project.org
Subject: Re: [R] Non-uniformly distributed plot
Hi:
One way to combine Jorge's and David's solutions is to visualize the data in
ggplot2 and/or lattice:
library(ggplot2)
x - c(0.349763, 3.39489, 1.52249, 0.269066, 0.107872, 0.0451689,
0.590268, 0.275755, 0.751845, 1.00599, 0.652409, 2.80664, 0.0269933,
0.137307, 0.282939, 1.23008, 0.436429, 0.0555626, 1.10624, 53,
1.30411, 1.29749, 53, 3.2552, 1.189, 2.23616, 1.13259, 0.505039,
1.05812, 1.18238, 0.500926, 1.0314, 0.733468, 3.13292, 1.26685,
3.10882, 1.01719, 0.13096, 0.0529692, 0.418408, 0.213299, 0.536631,
1.82336, 1.15287, 0.192519, 0.961295, 51, 0.470511, 4.05688,
1.78098, 0.364686, 1.24533)
y - c(0.423279, 0.473681, 0.629478, 1.09712, 0.396239, 0.273577,
0.303214, 0.628386, 0.465841, 0.687251, 0.544569, 0.635805, 0.358983,
0.16519, 0.366217, 1.08421, 0.668939, 0.181861, 0.782656, 13.3816,
1.15256, 0.965943, 20, 2.86051, 0.304939, 1.94654, 0.967576,
0.647599, 0.520811, 1.27434, 0.363666, 0.93621, 0.544573, 0.696733,
1.0031, 3.78895, 0.694053, 0.289111, 0.178439, 0.746576, 0.391725,
0.363901, 1.20297, 0.461934, 0.364011, 0.691368, 20, 0.81947,
1.69594, 1.56381, 0.900398, 0.960948)
d - data.frame(x, y)
g - ggplot(d, aes(log(x), log(y))
g + geom_point() + geom_smooth(colour = 'red', size = 1) +
geom_smooth(method = 'lm', colour = 'blue', size = 1)
The default smooth is a loess curve, which shows the curvature present in the
residual vs. fitted plot from Jorge's solution. The predicted values from the
linear model in the log-log scale lie along the blue line. (To get rid of the
confidence curves, add se = FALSE to both geom_smooth() calls above.) If you
were to fit a model to these data in the log-log scale, the plot indicates that
a quadratic polynomial would be a reasonable next step.
This is pretty easy to do in lattice as well (sans the confidence curves):
library(lattice)
xyplot(log(y) ~ log(x), data = d, type = c('p', 'r', 'smooth'),
pch = 16, col = 'black',
panel = function(x, y, ...) {
panel.xyplot(x, y, ..., col.line = 'blue')
panel.loess(x, y, col.line = 'red')
}
)
I needed to write a small panel function to get separate colors for the least
squares line and loess curves, but maybe there's an easier way (col.line =
c('blue', 'red') by itself doesn't work - I tried that - and it makes sense to
me why it doesn't).
Dennis
On Thu, Dec 23, 2010 at 3:50 PM, David Winsemius
dwinsem...@comcast.netmailto:dwinsem...@comcast.net wrote:
On Dec 23, 2010, at 6:41 PM, David Winsemius wrote:
On Dec 23, 2010, at 5:55 PM, Eric Hu wrote:
Thanks David. I am reposting the data here.
Jorge has already responded masterfully. He's apparently less lazy that I and
did all the editing. A log transformation as he illustrated can be very useful
with bivariate skewed distributions. The only variation I would have suggested
would be to record the default par settings and restore them at the end.
You could also repeat the plot an use abline to look at the predicted values
plot(x,y, log=xy)
lines( log(x), fit$predicted)
It's complementary to the residual plot and the QQ plot in the plot.lm display
for consideration of the possibility that this may not be a truly
log-log-linear relationship.
--
David
Eric
Hi,
I would like to plot a linear relationship between variable x and y.
Can anyone help me with scaled plotting and axes so that all data
points can be visualized somehow evenly? Plaint plot(x,y) will
generate condensed points near (0,0) due to several large data
points. Thank you.
Eric
dput(x)
c(0.349763, 3.39489, 1.52249, 0.269066, 0.107872, 0.0451689,
0.590268, 0.275755, 0.751845, 1.00599, 0.652409, 2.80664, 0.0269933,
0.137307, 0.282939, 1.23008, 0.436429, 0.0555626, 1.10624, 53,
1.30411, 1.29749, 53, 3.2552, 1.189, 2.23616, 1.13259, 0.505039,
1.05812, 1.18238, 0.500926, 1.0314, 0.733468, 3.13292, 1.26685,
3.10882, 1.01719, 0.13096, 0.0529692, 0.418408, 0.213299, 0.536631,
1.82336, 1.15287, 0.192519, 0.961295, 51, 0.470511, 4.05688,
1.78098, 0.364686, 1.24533)
dput(y)
c(0.423279, 0.473681, 0.629478, 1.09712, 0.396239, 0.273577,
0.303214, 0.628386, 0.465841, 0.687251, 0.544569, 0.635805, 0.358983,
0.16519, 0.366217, 1.08421, 0.668939, 0.181861, 0.782656, 13.3816,
1.15256, 0.965943, 20, 2.86051, 0.304939, 1.94654, 0.967576,
0.647599, 0.520811, 1.27434, 0.363666, 0.93621, 0.544573, 0.696733,
1.0031, 3.78895, 0.694053, 0.289111, 0.178439, 0.746576, 0.391725,
0.363901,
[R] R command execution from shell
Dear R-users, Is there a way I can ask R to execute the write(hello world,file=hello.txt) command directly from the UNIX shell, instead of having to save this command to a .R file and execute this file with R CMD BATCH? Thank you Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Listing of available functions
Thank you David, Duncan, and Henrique. This is going to be useful. Sebastien On Tue, Jan 4, 2011 at 8:38 AM, David Winsemius dwinsem...@comcast.netwrote: You can also search for a cheatsheet. There are several out there searching on cheatsheet r This one at Oregon State is presented as a web page http://www.science.oregonstate.edu/~shenr/Rhelp/00cheat.htmhttp://www.science.oregonstate.edu/%7Eshenr/Rhelp/00cheat.htm Others are available as pdf's. On Jan 4, 2011, at 7:13 AM, Sébastien Bihorel wrote: Dear R-users, Is there a easy way to access to a complete listing of available functions from a R session? The help.start() and ? functions are great, but I feel like they require the user to know the answer in advance (especially with respect to function names)... I could not find a easy way to simply browse through a list of functions and randomly pick one function to see what is does. Is there such a possibility in R? Thanks PS: I apologize if this question appears trivial. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Page eject and clearing the console
Well the things most like cat('\n') for starting a new page would be
cat('\013') or cat('\014') (vertical tab and form feed), however on all the
terminals I tried they don't do anything since page is not a concept on a
terminal. However if you outputted one of those into a file and interpreted
the file in a context with pages, then they may do what you want.
The next closest idea to what you are saying that I can find is the wdPageBreak
function in the R2wd package. This will insert a page break into a word
document that is being created from R, there pages make sense and this will
start the next part on a new page.
To be any more help we need to know what context you are using this in and what
you mean by page. Are you preparing stuff to be printed on paper (or at
least to a pdf doc where pages make sense?) or is there some behavior in the
terminal that you want to see? For the last we need to know OS and possibly
how you are running R within that OS (gui vs. terminal, etc.).
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of John Sorkin
Sent: Tuesday, January 04, 2011 12:52 PM
To: David Winsemius; Bert Gunter
Cc: r-help@r-project.org
Subject: Re: [R] Page eject and clearing the console
I am looking for something which will emulate the following:
Back in the old days, when printing to a line printer, the first two
characters in a line controlled printing. For example, a line starting
with
1h1 starts printing at the top of the next page.
1h+ indicates overprinting
1h0 results in double
In R \n skips to the next line. Is there some escape sequence that
will start printing at the top of the next page?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Bert Gunter gunter.ber...@gene.com 1/4/2011 2:05 PM
Perhaps merely rephrasing David's comments,
page is not a meaningful physical entity -- it depends on font size,
line spacing, etc. and the physical size of the output surface,
which has no meaning for an infinitely (or at least up to tyhe
screen buffer's limit) scrollable screen viewing area.
But maybe David's scroll function is what you had in mind.
-- Bert
On Tue, Jan 4, 2011 at 10:55 AM, David Winsemius
dwinsem...@comcast.net wrote:
On Jan 4, 2011, at 1:27 PM, David Winsemius wrote:
On Jan 4, 2011, at 1:19 PM, John Sorkin wrote:
I have received help on one of my questions (thank you Henrique
Jorge
and ), viz. how I can clear the console from an R program.
I have not yet received help on how I can skip to the top of the
next
page, i.e. cat(\n) skips to the next line, is there an equivalent
way
to skip to the top of the next page?
\n does NOT skip to the next line. It is a character and it is
interpreted by some sort of program, say a a plotting program or a
word-processor as a line feed. You need to specify what sort of
program you
intend to do this skipping-to-next-page action and also provide
the
character sequence that that program uses to signal that action.
(There are
not any pages in R except perhaps multi-page plots but you seem to
be in
character mode at the moment.)
It has occurred to me that you may be asking for something that will
give
the illusion of clearing the screen but will in fact be just
printing a
page of blank space on a console display, scrolling would ahve been
the name
I would have given it. In which case:
scroll - function(lines=40) cat(rep(\n, lines))
scroll()
--
David.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to
faxing)
Henrique Dallazuanna www...@gmail.com 1/4/2011 11:58 AM
Take a look on:
http://tolstoy.newcastle.edu.au/R/e11/help/10/09/8463.html
On Tue, Jan 4, 2011 at 2:54 PM, John Sorkin
jsor...@grecc.umaryland.eduwrote:
(1) I know that \n when used in cat, e.g. cat(\n) produces a
line
feed
(i.e. skips to the next line). Is there any escape sequence that
will
go to
the top of the next page?
(2) I know that control L will clear the console. Is there an
equivalent
function or other means that can be used in R code to clear the
console?
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Re: [R] R command execution from shell
On 04/01/2011 3:21 PM, Sebastien Bihorel wrote: Dear R-users, Is there a way I can ask R to execute the write(hello world,file=hello.txt) command directly from the UNIX shell, instead of having to save this command to a .R file and execute this file with R CMD BATCH? Yes. Some versions of R support the -e option on the command line to execute a particular command. It's not always easy to work out the escapes so your shell passes all the quotes through... An alternative is to echo the command into the shell, e.g. echo 'cat(hello)' | R --slave (where the outer ' ' are just for bash). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Resampling to find Confidence intervals
You mentioned the boot package, I've just stumbled across a package
called simpleboot, with a function lm.boot. Would this be suitable - it
says I can sample cases from the origional dataset, as well as from the
residuals of a model. Not all the options I understand but I assume the
defaults might be suitable for what I'm doing?
On 04/01/2011 17:56, Ben Ward wrote:
Ok I'll check I understand:
So it's using sample, to resample d once, 10 values, because the rnorm
has 10 values, with replacement (I assume thats the TRUE part).
Then a for loop has this to resample the data - in the loop's case its
1000 times. Then it does a lm to get the coefficients and add them to
d1.coef. I'm guessing that the allboot bit with rbind, which is null
at the start of the loop, is the collection of d1.coef values, as I
think that without it, every cycle of the loop the d1.coef from the
previous cycle round the loop would be gone?
On 04/01/2011 16:24, Dieter Menne wrote:
Axolotl9250 wrote:
...
resampled_ecoli = sample(ecoli, 500, replace=T)
coefs = (coef(lm(MIC. ~ 1 + Challenge + Cleaner + Replicate,
data=resampled_ecoli)))
sd(coefs)
...
Below a simplified and self-consistent version of your code, and some
changes
Dieter
# resample
d = data.frame(x=rnorm(10))
d$y = d$x*3+rnorm(10,0.01)
# if you do this, you only get ONE bootstrap sample
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
d1.coef
# No error below, because you compute the sd of (Intercept) and slope
# but result is wrong!
sd(d1.coef)
# We have to do this over and over
# Check ?replicate for a more R-ish approach
nsamples = 1000
allboot = NULL
for (i in 1:1000) {
d1 = d[sample(1:nrow(d),10,TRUE),]
d1.coef = coef(lm(y~x,data=d1))
allboot = rbind(allboot,d1.coef) # Not very efficient, preallocate!
}
head(allboot) # display first of nsamples lines
apply(allboot,2,mean) # Compute mean
apply(allboot,2,sd) # compute sd
# After you are sure you understood the above, you might try package
boot.
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] error in calling source(): invalid multibyte character in parser
It works fine, thanks.
I was just wondering is there is anyway to include automatically the command
you suggest as a default when I open R.
Thanks,
Luca
Il giorno 03/gen/2011, alle ore 08.36, Phil Spector ha scritto:
Luca -
What happens why you type
Sys.setlocale('LC_ALL','C')
before issuing the source command?
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Mon, 3 Jan 2011, Luca Meyer wrote:
Being italians when writing comments/instructions we use accented letters -
like à, ò, è, etc when running R scripts using such characters I get and
error saying:
invalid multibyte character in parser
I have been looking at the help and searched the r-help archives but I
haven't find anything that I could intelligibly apply to my case.
Can anyone suggest a fix for this error?
Thanks,
Luca
Mr. Luca Meyer
www.lucameyer.com
IBM SPSS Statistics release 19.0.0
R version 2.12.1 (2010-12-16)
Mac OS X 10.6.5 (10H574) - kernel Darwin 10.5.0
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R command execution from shell
Thank you That is exactly what I was looking for. Sebastien Duncan Murdoch wrote: On 04/01/2011 3:21 PM, Sebastien Bihorel wrote: Dear R-users, Is there a way I can ask R to execute the write(hello world,file=hello.txt) command directly from the UNIX shell, instead of having to save this command to a .R file and execute this file with R CMD BATCH? Yes. Some versions of R support the -e option on the command line to execute a particular command. It's not always easy to work out the escapes so your shell passes all the quotes through... An alternative is to echo the command into the shell, e.g. echo 'cat(hello)' | R --slave (where the outer ' ' are just for bash). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] error in calling source(): invalid multibyte character in parser
On Tue, 4 Jan 2011, Luca Meyer wrote: How would I go by doing that? I have tried with: source(file.R, encoding=it_IT.UTF-8) But I get Error in file(file, r, encoding = encoding) : unsupported conversion from 'it_IT.UTF-8' to '' Well, that is not the value I suggested -- so what not simply follow what you were asked to try? Thanks, Luca PS: it_IT.UTF-8 is what I get under locale when I run sessionInfo() Il giorno 03/gen/2011, alle ore 09.48, Prof Brian Ripley ha scritto: On Mon, 3 Jan 2011, peter dalgaard wrote: On Jan 3, 2011, at 08:32 , Luca Meyer wrote: Being italians when writing comments/instructions we use accented letters - like à, ò, è, etc when running R scripts using such characters I get and error saying: invalid multibyte character in parser I have been looking at the help and searched the r-help archives but I haven't find anything that I could intelligibly apply to my case. Can anyone suggest a fix for this error? The most likely cause is that your scripts are written in an 8 bit ASCII encoding (Latin-1 or -9, most likely), while R is running in a UTF8 locale. If that is the cause, the fix is to standardize things to use the same locale. You can convert the encoding of your source file using the iconv utility (in a Terminal window). Or use the 'encoding' argument of source() to tell R what the encoding is, e.g. encoding=latin1 or latin-9 (the inconsistency being in the iconv used on Macs, not in R). -pd Thanks, Luca Mr. Luca Meyer www.lucameyer.com IBM SPSS Statistics release 19.0.0 R version 2.12.1 (2010-12-16) Mac OS X 10.6.5 (10H574) - kernel Darwin 10.5.0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R command execution from shell
On Tue, 4 Jan 2011, Duncan Murdoch wrote:
On 04/01/2011 3:21 PM, Sebastien Bihorel wrote:
Dear R-users,
Is there a way I can ask R to execute the write(hello
world,file=hello.txt) command directly from the UNIX shell, instead
of having to save this command to a .R file and execute this file with R
CMD BATCH?
Yes. Some versions of R support the -e option on the command line to execute
a particular command. It's not always easy to work out the escapes so your
shell passes all the quotes through... An alternative is to echo the command
into the shell, e.g.
echo 'cat(hello)' | R --slave
(where the outer ' ' are just for bash).
It is marginally preferable to use Rscript in place of 'R --slave'.
I think in all known shells
Rscript -e write('hello world', file = 'hello.txt')
will work. (If not, shQuote() will not work for that shell, but this
does work in sh+clones, csh+clones, zsh and Windows' cmd.exe.)
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] ENmisc_1.0
ENmisc contains two utility function mtapply is a hybrid of mapply and tapply. It evaluates summary function for each cell of data defined by a fixed set of factor values. The reason I wrote it was to be able to compute weighted means (using wtd.mean from Hmisc) to groups of data defined by factors, but it accepts any multivariate function as the function argument wtd.boxplot does what the name makes you expect, it computes and draws boxplots for weighted data. It behaves like boxplot, but accepts an additional argument, weights. ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Package animation update (v2.0-0)
Hi,
The animation package 2.0-0 is on CRAN now. This version is a
milestone of the animation package. It includes a new function
saveHTML() which uses a much more elegant interface and is consistent
in syntax with other save*() functions such as saveMovie(), saveSWF()
and saveLatex(). Lots of demos have been added to demonstrate the
flexibility of this package, e.g. now we can get the snapshots of rgl
3D plots and insert them into LaTeX with a single call to saveLatex(),
or even into Sweave documents.
There are some funny demos in this version too, e.g. demo('fireworks')
to set fireworks, or demo('CLEvsLAL') which is a replay of an NBA
game between Cavaliers and Lakers on 2009.
Have fun!
CHANGES IN animation VERSION 2.0-0
NEW FEATURES
o a new demo 'Xmas2': Merry Christmas with snowflakes (see
demo('Xmas2', 'animation'); thanks, Jing Jiao)
o a new function saveHTML() to insert animations into HTML pages
(this was designed to replace the old ani.start() and ani.stop();
the output is much more appealing; the JavaScript is based on the
SciAnimator library and jQuery)
o ani.options() gained a new option 'autoplay' to indicate whether
to autoplay the animation in the HTML page created by saveHTML()
o in fact ani.options() was rewritten, but this should not have
any influence on users; the usage is the same
o ani.options() gained a new option 'use.dev' to decide whether to
use the graphics device provided in ani.options('ani.dev') when
calling saveHTML(), saveLatex(), saveMovie() and saveSWF()
o ani.options() has a couple of hidden options ('convert',
'swftools', 'img.fmt') which can be useful too; see ?ani.options for
details
o a new function ani.pause(): it is a wrapper to
Sys.sleep(interval) but it will not pause when called in a
non-interactive graphics device (usually the off-screen devices);
this is the recommended way to specify the pause in the animation
now -- all the functions in this package have been adjusted to use
ani.pause()
o a new demo('pollen') to show the hidden 'structure' in a large
data (requires the rgl package)
o a new demo('CLEvsLAL') to `replay' the NBA game between CLE and
LAL on 2009 Christmas (with a new dataset 'CLELAL09')
o a new demo('fireworks') to set fireworks using R (thanks,
Weicheng Zhu)
o saveLatex() can work with the rgl package to produce 3D animations
in a PDF document now; see demo('rgl_animation')
o a new demo('rgl_animation') to demonstrate how to insert rgl 3D
animations into a LaTeX document and compile to PDF
o a new demo('use_Cairo') to show how to use the Cairo device in
this package to obtain high-quality output
o a new demo('Sweave_animation') to show how to insert animations
into Sweave documents
o a new demo('game_of_life') to demonstrate the (amusing) Game of
Life (thanks, Linlin Yan)
SIGNIFICANT CHANGES
o the documentation of this package has been tremendously revised;
hopefully it is more clear to read now
o several arguments in saveMovie(), im.convert(), saveSWF() and
saveLatex() were removed, because they can be specified by
ani.options(); this can simplify the usage of these functions
MINOR CHANGES
o the argument 'para' in saveMovie() was removed; the argument
'ani.first' was also removed from all the save*() functions, because
this can be written in 'expr' and there is no need to provide an
additional argument
o the path of the output in im.convert() and gm.convert() will be
quoted, because sometimes users might supply a path containing
spaces (thanks, Phalkun Chheng)
o the option 'filename' in ani.options() was renamed to 'htmlfile'
so that the meaning of this option is more clear; 'footer' was
renamed to 'verbose' too
o ani.options() can accept any arguments now
o im.convert() and gm.convert() will no longer stop() when the
convert utility cannot be found; instead, they only issue warnings;
a hidden option ani.options('convert') can be used to specify the
location of convert.exe in ImageMagick
o saveMovie(), saveHTML(), saveSWF() and saveLatex() will try to
open the output if ani.options('autobrowse') is TRUE; and they will
keep the current working directory untouched when evaluating 'expr'
(i.e. 'expr' will be evaluated under getwd())
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
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Re: [R] randomForest speed improvements
Andy, Thanks for the reply. I had no idea I could combine them back ... that actually will work pretty well. We can have several worker threads load up the RF's on different machines and/or cores, and then re-assemble them. RMPI might be an option down the road, but would be a bit of overhead for us now. Using the method of combine() ... I was able to drastically reduce the amount of time to build randomForest objects. IE, using about 25,000 rows (6 columns), it takes maybe 5 minutes on my laptop. Using 5 randomForest objects (each with 5k rows), and then combining them, takes 1 minute. -- Anthony -- View this message in context: http://r.789695.n4.nabble.com/randomForest-speed-improvements-tp3172523p3174621.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to keep keep matching column in output of merge
Apologies, it is there! On 5/01/2011 1:26 AM, Sarah Goslee wrote: Hi Nevil, We really need an example here of what you're doing, since merge() does keep the id column by default. x- data.frame(id = c(a, b, c, NA), x=c(1,2,3,4)) y- data.frame(id1 = c(NA, a, d, c), y=c(101, 102, 103, 104)) merge(x, y) id x y 1 a 1 102 2 b 2 101 3 c 3 104 4 d 4 103 Sarah On Tue, Jan 4, 2011 at 8:31 AM, Nevil Amosnevil.a...@gmail.com wrote: How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. thanks Nevil Amos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
