[R] Partial loop?
My dear R buddies,
I'm writing a loop program like this:
for(i in 1:n){
for(j in 1:i){
...
}
}
I wonder if there is any simple apply()-like function to make the loop
a little bit easier and faster. Thanks a lot.
Best wishes,
--
彭河森 Hesen Peng
http://hesen.peng.googlepages.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.
[R] compressing the plot's white space
I need to fit a graph into a column of a 2-column paper. I found that just specifying width and height parameters (3.2in x 3.5in) to plot doesn't decrease the fonts of the main title, axis titles, and labeling numbers, and tick sizes. So I have to add cex to all labels and titles and manage ticks. However, I can't decrease the space between axis label and numbers on ticks. Is there a way to place those numbers inside the plot, and/or explicitly remove most of the space between the numbers and the axis title? Also, how should I specify the margins to achieve best white space elimination? On Quartz, decreasing margins seem to squeeze the titles properly, on postscript device, the axis titles simply move outside the plot. Cheers, Alexy __ 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] 50993 point distance matrix, too big to as.matrix, looking for another way to calculate point-level summary
Hi, If you are only interested in row means, you can work the distance matrix at the c level. You might like to adapt this post: http://tolstoy.newcastle.edu.au/R/e6/devel/09/04/1378.html Romain On 06/26/2009 09:40 PM, leif olson wrote: Hello, Im working on a 50933 point count bird abundance dataset. I've succeeded in calculating a distance matrix for this entire set, but I don't have sufficient memory to convert this to a matrix, as below... abun.dist- dist(abun.mat[1:50993,1:235) test- rowMeans(as.matrix(abun.dist)) Error in matrix(0, size, size) : too many elements specified ive been able to run a hclust() clustering procedure, due to the fact that hclust() makes a call to fortran code, but id like to be able to generate a calinski index for each of the clusters to assess the validity. Unfortunately, all the validation routines I have found are all native R code, and usually call as.matrix, resulting in the same error i receive above. What I'd like to figure out is how to just go through, one point at a time, and calculate the values i need. But I've been unable to come up with code to call the correct positions in the dist vector, can anyone suggest some code that might do this? Thanks... ...leif -- Romain Francois Independent R Consultant +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.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.
Re: [R] Partial loop?
Finally I ended up doing this:
temp - expand.grid(1:n,1:n)
temp-temp[temp[,1]temp[,2]]
apply(temp,1, ... )
and it seems much faster :)
On Sat, Jun 27, 2009 at 3:26 PM, Patrick Burnspbu...@pburns.seanet.com wrote:
See 'The R Inferno'.
Patrick Burns
patr...@burns-stat.com
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of The R Inferno and A Guide for the Unwilling S User)
Hesen Peng wrote:
My dear R buddies,
I'm writing a loop program like this:
for(i in 1:n){
for(j in 1:i){
...
}
}
I wonder if there is any simple apply()-like function to make the loop
a little bit easier and faster. Thanks a lot.
Best wishes,
--
彭河森 Hesen Peng
http://hesen.peng.googlepages.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] Compute correlation matrix for panel data with specific ordering
Hello All, I have a panel date - here a small-scale example: df - data.frame(cbind(rep(c(AUT,BEL,DEN,GER),4),cbind(rep(c(1999,2000,2001,2002),4)),sample(10,16,replace=T))) names(df) - c(country,year,x) SORT - c(GER,BEL,DEN,AUT) I need to compute the correlation between countries in the variable x in such a way that the rows columns of the resulting correlation matrix are not in an alphabetical order but in the order of a given factor vector - here SORT. How can I do this? Greatly appreciate any help! Serguei Kaniovski __ 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] questions about meta-analysis
Le samedi 27 juin 2009 à 13:02 +0800, sdzhangping a écrit : Dear R users: In the example of meta-analysis (cochrane, package rmeta), I can not found the p-value of Test for overall effect, and some other indices (Z, I, weight and et al). How can I get the these indices listed? library(rmeta) data(cochrane) cochrane name ev.trt n.trt ev.ctrl n.ctrl 1 Auckland 36 532 60538 2Block 169 5 61 3Doran 481 11 63 4Gamsu 14 131 20137 5 Morrison 367 7 59 6 Papageorgiou 171 7 75 7 Tauesch 856 10 71 a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) summary(a) Fixed effects ( Mantel-Haenszel ) meta-analysis Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = ev.ctrl, names = name, data = cochrane) OR (lower 95% upper) Auckland 0.580.38 0.89 Block0.160.02 1.45 Doran0.250.07 0.81 Gamsu0.700.34 1.45 Morrison 0.350.09 1.41 Papageorgiou 0.140.02 1.16 Tauesch 1.020.37 2.77 Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p-value ?) Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) You might easily recompute them : use the confidence interval to guesstimate the standard deviation of OR, its value and the damn Z and p you long for... Remember that it's log(OR) that is (asymptotically) normally distributed. The weights are proportional to inverse of variance and sum to 1. You might peek at the source code for enlightment... Alternatively, you may grow lazy an use the meta package, whose function metabin() will give you all that. The recent metafor package seems also quite interesting. Another (smarter(?)) alternative is to ask yourself *why* you need Z and p. Z is just a computing device allowing you to use a known density. And the real meaning of p and its usefulness has been discussed, disputed and fought over at exceedingly large lengths in the past 80 years. Of course, if you have an instructor to please ... HTH, Emmanuel Charpentier __ 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] Compute correlation matrix for panel data with specific ordering
Serguei Kaniovski Serguei.Kaniovski at wifo.ac.at writes: df - data.frame(cbind(rep(c(AUT,BEL,DEN,GER),4), cbind(rep(c(1999,2000,2001,2002),4)),sample(10,16,replace=T))) names(df) - c(country,year,x) SORT - c(GER,BEL,DEN,AUT) I need to compute the correlation between countries in the variable x in such a way that the rows columns of the resulting correlation matrix are not in an alphabetical order but in the order of a given factor vector - here SORT. This boils down to : how do I reorder a factor not to use alphabetical order? There are several reorders around, and you could do it with base function in R, but I find the following solution using package gdata the most readable: library(gdata) df - data.frame(country = sample(c(AUT,BEL,DEN,GER),10,TRUE)) str(df) SORT - c(GER,BEL,DEN,AUT) df$countryS = reorder(df$country, new.order=SORT) Dieter __ 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 automatically placing a legend in empty space
Jason Rupert jasonkrupert at yahoo.com writes: At one point I believe I heard of an R package that would automatically find the most empty space in a plot, and then that answer could then be used to intelligently place a legend. Have a look a some of the plotting function in package Hmisc. Dieter __ 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] Creating Excel-Charts via RDCOMClient
Hi R-users! I'm trying to create an easy Excel chart using the package RDCOMClient. The following example is working fine: #--- library(RDCOMClient) xlLocationAsObject -2 xlXYScatterSmoothNoMarkers - 73 ex - COMCreate(Excel.Application) wb - ex[[Workbooks]]$Add() sh - ex$ActiveSheet() ex[[Visible]] - TRUE r - sh$Range(A1:D1) r[[Value]] - c(1:4) ch - ex$Charts() ch$Add() ac - ex$ActiveChart() ac[[ChartType]] - xlXYScatterSmoothNoMarkers ac$Location(Where=xlLocationAsObject, Name=Tabelle1) ac$SeriesCollection()$NewSeries() ac$SeriesCollection(1)[[XValues]] - r ac$SeriesCollection(1)[[Values]] - r #--- But I don't perfer this way writing calculated values like c(1:4) to the Excel Sheet and calling them via SeriesCollection. I'm looking for direct adressing to SeriesCollection. But codes like ac$SeriesCollection(1)[[XValues]] - asCOMArray(c(1:4)) ac$SeriesCollection(1)[[Values]] - asCOMArray(c(1:4)) were not successfull. E.g. the code above produces the error message OLE error 0x800a01a8. Ok, I know that there are better ways to solve my problem by using the RExcel/statconn tools. Unfortunately the conditions under which I work (partly using other computers by adressing R on my working computer) permit the use of these tools. As I see, my best chance is a solution with RDCOMClient. (A clipboard solution which I developed some month ago are very slow when using large data matrices.) So, could anyone help me solving the problem? Thanks, Michael Wolf Von-Schonebeck-Ring 18 D-48161 Muenster __ 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] questions about meta-analysis
The object a has log.estimates and selog.estimates: str(a) List of 10 $ logOR : num [1:7] -0.548 -1.804 -1.404 -0.357 -1.055 ... $ selogOR : num [1:7] 0.22 1.11 0.611 0.372 0.715 ... $ logMH : num -0.632 $ selogMH : num 0.16 snipped remainder of output. You can also look at the the code of meta.MH: meta.MH On Jun 27, 2009, at 1:02 AM, sdzhangping wrote: Dear R users: In the example of meta-analysis (cochrane, package rmeta), I can not found the p-value of Test for overall effect, and some other indices (Z, I, weight and et al). How can I get the these indices listed? library(rmeta) data(cochrane) cochrane name ev.trt n.trt ev.ctrl n.ctrl 1 Auckland 36 532 60538 2Block 169 5 61 3Doran 481 11 63 4Gamsu 14 131 20137 5 Morrison 367 7 59 6 Papageorgiou 171 7 75 7 Tauesch 856 10 71 a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) summary(a) Fixed effects ( Mantel-Haenszel ) meta-analysis Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = ev.ctrl, names = name, data = cochrane) OR (lower 95% upper) Auckland 0.580.38 0.89 Block0.160.02 1.45 Doran0.250.07 0.81 Gamsu0.700.34 1.45 Morrison 0.350.09 1.41 Papageorgiou 0.140.02 1.16 Tauesch 1.020.37 2.77 Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p- value ?) Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) David Winsemius, MD Heritage Laboratories 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] Regression; how to get t-values for all parameters estimates
Dear all, Even after a couple of hours looking at old messages I still haven't found a solution for my problem. I'm trying to fit an additive linear regression model with 2 effects, both fixed, to some dataset. The function contrasts(effectA) - contr.sum can gaurantee that the coefficients per parameter sum to one, and the function dummy.coef provices the estimates of all coefficientss. But I would also like to be able to obtain the corresponding t-values for ALL parameters (not just the number of effects minus 1, provided by summary()). Does anyone know how to get (all of) them? Here comes what I've already tried: ## Try data: Data - rbinom(1000,50,.9); Dates - Sys.Date()-(1000:1) facweek - factor(weekdays(Dates,abbreviate=TRUE)) facmonth - factor(months(Dates,abbreviate=TRUE)) contrasts(facweek) - contr.sum ; contrasts(facmonth) - contr.sum ; fit - lm(formula = Data ~ facweek + facmonth) summary(fit) Call: lm(formula = Data ~ facweek + facmonth) Residuals: Min 1Q Median 3Q Max -8.7498 -1.3774 0.1778 1.5108 5.1643 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 45.014520.06976 645.252 2e-16 *** facweek1-0.371140.16836 -2.204 0.0277 * facweek2 0.403600.16836 2.397 0.0167 * facweek3-0.199180.16885 -1.180 0.2384 facweek4-0.136890.16834 -0.813 0.4163 facweek5-0.070490.16835 -0.419 0.6755 facweek6 0.409740.16836 2.434 0.0151 * facmonth1 -0.120460.22053 -0.546 0.5850 facmonth2 -0.108320.26155 -0.414 0.6789 facmonth30.252810.21731 1.163 0.2450 facmonth40.401610.22627 1.775 0.0762 . facmonth5 -0.374090.21731 -1.721 0.0855 . facmonth60.066450.26155 0.254 0.7995 facmonth70.136270.22509 0.605 0.5451 facmonth8 -0.047890.21731 -0.220 0.8256 facmonth9 -0.229100.21731 -1.054 0.2920 facmonth10 0.117520.22053 0.533 0.5942 facmonth11 -0.272330.21731 -1.253 0.2104 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 2.174 on 982 degrees of freedom Multiple R-squared: 0.02673,Adjusted R-squared: 0.009879 F-statistic: 1.586 on 17 and 982 DF, p-value: 0.06097 print(dummy.coef(fit),digits=3) Full coefficients are (Intercept): 45 facweek:Fri Mon Sat Sun Thu Tue -0.3711 0.4036 -0.1992 -0.1369 -0.0705 0.4097 facmonth: Apr Aug Dec Feb Jan Jul -0.1205 -0.1083 0.2528 0.4016 -0.3741 0.0664 (Intercept): facweek:Wed -0.0357 facmonth: Jun Mar May Nov Oct Sep 0.1363 -0.0479 -0.2291 0.1175 -0.2723 0.1775 __ 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 do I define the method for gcheckboxgroup in gWidgets?
On Thu, Jun 25, 2009 at 8:29 AM, Bryan Hanson han...@depauw.edu wrote:
Hi All...
I¹m trying to build a small demo using gWidgets which permits interactive
scaling and selection among different things to plot. I can get the
widgets
for scaling to work just fine. I am using gcheckboxgroup to make the
(possibly multiple) selections. However, I can¹t seem to figure out how to
properly define the gcheckboxgroup; I can draw the widget properly, I think
my handler would use the svalue right if it actually received it. Part of
the problem is using the index of the possible values rather than the
values
themselves, but I'm pretty sure this is not all of the problem. I've been
unable to find an example like this in any of the various resources I've
come across.
BTW, report.which is really only there for troubleshooting. It works to
return the values, I can't get it to return the indices, which are probably
what I need in this case.
A demo script is at the bottom and the error is just below.
tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
+ checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel)
The above code should define the gcheckboxgroup.
add(tmp, value = 1, expand = TRUE)
I'm not sure what you are trying to add here.
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function .add, for signature
gCheckboxgroupRGtk, guiWidgetsToolkitRGtk2, numeric
This error suggests that I don't have a method - I agree, but I don't know
what goes into the method for gcheckboxgroup.
For the sliders, it's clear to me how the actions and drawing of the
widgets
differ, but not so for gcheckboxgroup.
A big TIA, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
DePauw University, Greencastle IN USA
Full Script:
x - 1:10
y1 - x
y2 - x^2
y3 - x^0.5
y4 - y^3
df - as.data.frame(cbind(x, y1, y2, y3, y4))
stuff - c(y = x, y = x^2, y = x^0.5, y = x^3)
which.y - 2 # inital value, to be changed later by the widget
# Define a function for the widget handlers
update.Plot - function(h,...) {
plot(df[,1], df[,svalue(which.y)], type = l,
ylim = c(0, svalue(yrange)), main = Interactive Selection Scaling,
xlab = x values, ylab = y values)
}
report.which - function(h, ...) { print(svalue(h$obj), index = TRUE) }
In the above handler, do you mean to pass the 'index' parameter to the
svalue() function?
# Define the actions type of widget, along with returned values.
# Must be done before packing widgets.
yrange - gslider(from = 0, to = max(y), by = 1.0,
value = max(y), handler = update.Plot)
which.y - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
checked = c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Assemble the graphics window groups of containers
mainWin - gwindow(Interactive Plotting)
bigGroup - ggroup(cont = mainWin)
leftPanel - ggroup(horizontal = FALSE, container = bigGroup)
# Format and pack the widgets, link to their actions/type
tmp - gframe(y range, container = leftPanel)
add(tmp, yrange, expand = TRUE)
tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel)
add(tmp, value = 1, expand = TRUE)
# Put it all together
add(mainWin, ggraphics()) # puts the active graphic window w/i mainWin
__
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.
[[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] parallel R?
For cross-validation, the caret package was designed to easily go between sequential and parallel processing (using nws, mpi or anything else). See the last examples in ?train. Max On Jun 26, 2009, at 11:28 AM, Michael comtech@gmail.com wrote: I guess when we move to Amazon AWS, we have to rewrite the whole R programs? On Fri, Jun 26, 2009 at 8:05 AM, Dirk Eddelbuettele...@debian.org wrote: On 26 June 2009 at 07:40, Michael wrote: | Hi all, | | Lots of big IT companies are renting out their computing facilities. | Amazon has one such service. In my understanding, this will | dramatically improve the speed of my R program -- currently the cross | validation and model selection part is the bottle neck. It take a few | days to just finish optimal parameter tuning via CV. | | Could anybody shed some lights on this? Is it completely transparent | to move my R program to a rented parallel computing facility? | | Moreover, at my PC level, I have a 4-core PC, is there anything we | could do in R to speed up my CV programs? Try this link: http://lmgtfy.com/?q=parallel+computing+with+R A survey paper on parallel computing with R by Schmidberger et al will be fortcoming shortly in Journal of Statistical Software -- that is at http://jstatsoft.org and a Google query will lead to preprints. Also note that R has a support site network called 'CRAN' which contains so called 'Task Views'. Amnong these you may find this one of interest: http://cran.r-project.org/web/views/HighPerformanceComputing.html As to your initial question: yes, people do use R on the Amazon service. Dirk -- Three out of two people have difficulties with fractions. __ 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 do I define the method for gcheckboxgroup in gWidgets?
Thanks Michael...
I was working by analogy to the gbuttons, so I was trying to ³add² the
gcheckboxgroup, which is apparently not necessary (due to, I guess, the
intrinsic differences between the widgets). The index thing I was just
screwed up on! I have it working now.
Nice package. Bryan
On 6/27/09 8:25 AM, Michael Lawrence mflaw...@fhcrc.org wrote:
On Thu, Jun 25, 2009 at 8:29 AM, Bryan Hanson han...@depauw.edu wrote:
Hi All...
I¹m trying to build a small demo using gWidgets which permits interactive
scaling and selection among different things to plot. I can get the widgets
for scaling to work just fine. I am using gcheckboxgroup to make the
(possibly multiple) selections. However, I can¹t seem to figure out how to
properly define the gcheckboxgroup; I can draw the widget properly, I think
my handler would use the svalue right if it actually received it. Part of
the problem is using the index of the possible values rather than the values
themselves, but I'm pretty sure this is not all of the problem. I've been
unable to find an example like this in any of the various resources I've
come across.
BTW, report.which is really only there for troubleshooting. It works to
return the values, I can't get it to return the indices, which are probably
what I need in this case.
A demo script is at the bottom and the error is just below.
tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
+ checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel)
The above code should define the gcheckboxgroup.
add(tmp, value = 1, expand = TRUE)
I'm not sure what you are trying to add here.
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function .add, for signature
gCheckboxgroupRGtk, guiWidgetsToolkitRGtk2, numeric
This error suggests that I don't have a method - I agree, but I don't know
what goes into the method for gcheckboxgroup.
For the sliders, it's clear to me how the actions and drawing of the widgets
differ, but not so for gcheckboxgroup.
A big TIA, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
DePauw University, Greencastle IN USA
Full Script:
x - 1:10
y1 - x
y2 - x^2
y3 - x^0.5
y4 - y^3
df - as.data.frame(cbind(x, y1, y2, y3, y4))
stuff - c(y = x, y = x^2, y = x^0.5, y = x^3)
which.y - 2 # inital value, to be changed later by the widget
# Define a function for the widget handlers
update.Plot - function(h,...) {
plot(df[,1], df[,svalue(which.y)], type = l,
ylim = c(0, svalue(yrange)), main = Interactive Selection Scaling,
xlab = x values, ylab = y values)
}
report.which - function(h, ...) { print(svalue(h$obj), index = TRUE) }
In the above handler, do you mean to pass the 'index' parameter to the
svalue() function?
# Define the actions type of widget, along with returned values.
# Must be done before packing widgets.
yrange - gslider(from = 0, to = max(y), by = 1.0,
value = max(y), handler = update.Plot)
which.y - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
checked = c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Assemble the graphics window groups of containers
mainWin - gwindow(Interactive Plotting)
bigGroup - ggroup(cont = mainWin)
leftPanel - ggroup(horizontal = FALSE, container = bigGroup)
# Format and pack the widgets, link to their actions/type
tmp - gframe(y range, container = leftPanel)
add(tmp, yrange, expand = TRUE)
tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE,
checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel)
add(tmp, value = 1, expand = TRUE)
# Put it all together
add(mainWin, ggraphics()) # puts the active graphic window w/i mainWin
__
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] compressing the plot's white space
On 27/06/2009 3:06 AM, Alexy Khrabrov wrote: I need to fit a graph into a column of a 2-column paper. I found that just specifying width and height parameters (3.2in x 3.5in) to plot doesn't decrease the fonts of the main title, axis titles, and labeling numbers, and tick sizes. I normally plot somewhat larger than I'd like the plot displayed, and shrink it to fit. This reduces everything proportionally. So I have to add cex to all labels and titles and manage ticks. However, I can't decrease the space between axis label and numbers on ticks. That is controlled by par(mgp). Duncan Murdoch Is there a way to place those numbers inside the plot, and/or explicitly remove most of the space between the numbers and the axis title? Also, how should I specify the margins to achieve best white space elimination? On Quartz, decreasing margins seem to squeeze the titles properly, on postscript device, the axis titles simply move outside the plot. Cheers, Alexy __ 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] Creating Excel-Charts via RDCOMClient
The statconn tools allow you configure your application with the Excel client on one machine and the R server on another machine. In (D)COM, the D stands for distributed COM. Dr. Michael Wolf wrote: Hi R-users! I'm trying to create an easy Excel chart using the package RDCOMClient. The following example is working fine: #--- library(RDCOMClient) xlLocationAsObject -2 xlXYScatterSmoothNoMarkers - 73 ex - COMCreate(Excel.Application) wb - ex[[Workbooks]]$Add() sh - ex$ActiveSheet() ex[[Visible]] - TRUE r - sh$Range(A1:D1) r[[Value]] - c(1:4) ch - ex$Charts() ch$Add() ac - ex$ActiveChart() ac[[ChartType]] - xlXYScatterSmoothNoMarkers ac$Location(Where=xlLocationAsObject, Name=Tabelle1) ac$SeriesCollection()$NewSeries() ac$SeriesCollection(1)[[XValues]] - r ac$SeriesCollection(1)[[Values]] - r #--- But I don't perfer this way writing calculated values like c(1:4) to the Excel Sheet and calling them via SeriesCollection. I'm looking for direct adressing to SeriesCollection. But codes like ac$SeriesCollection(1)[[XValues]] - asCOMArray(c(1:4)) ac$SeriesCollection(1)[[Values]] - asCOMArray(c(1:4)) were not successfull. E.g. the code above produces the error message OLE error 0x800a01a8. Ok, I know that there are better ways to solve my problem by using the RExcel/statconn tools. Unfortunately the conditions under which I work (partly using other computers by adressing R on my working computer) permit the use of these tools. As I see, my best chance is a solution with RDCOMClient. (A clipboard solution which I developed some month ago are very slow when using large data matrices.) So, could anyone help me solving the problem? Thanks, Michael Wolf Von-Schonebeck-Ring 18 D-48161 Muenster __ 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. -- Erich Neuwirth, University of Vienna Faculty of Computer Science Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-39459 __ 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] questions about meta-analysis
At 06:02 27/06/2009, sdzhangping wrote: Dear R users: In the example of meta-analysis (cochrane, package rmeta), I can not found the p-value of Test for overall effect, and some other indices (Z, I, weight and et al). How can I get the these indices listed? library(rmeta) data(cochrane) cochrane name ev.trt n.trt ev.ctrl n.ctrl 1 Auckland 36 532 60538 2Block 169 5 61 3Doran 481 11 63 4Gamsu 14 131 20137 5 Morrison 367 7 59 6 Papageorgiou 171 7 75 7 Tauesch 856 10 71 a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) If at this point you do str(a) you will find what a contains which may or may not help you answer your question. Similarly str(summary(a)) may also be revealing. Of course R lets you do anything you want but if the author did not print out a test and a p-value you might like to ask yourself whether that suggests anything (as someone has already pointed out in another reply). summary(a) Fixed effects ( Mantel-Haenszel ) meta-analysis Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = ev.ctrl, names = name, data = cochrane) OR (lower 95% upper) Auckland 0.580.38 0.89 Block0.160.02 1.45 Doran0.250.07 0.81 Gamsu0.700.34 1.45 Morrison 0.350.09 1.41 Papageorgiou 0.140.02 1.16 Tauesch 1.020.37 2.77 Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p-value ?) Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) Thanks Yours Ping Zhang [[alternative HTML version deleted]] Michael Dewey http://www.aghmed.fsnet.co.uk __ 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] changing default arguments of a function and return the modified function as a result
see also `%but%.character` in the operators package. rnorm %but% list( mean = 3 ) function (n, mean = 3, sd = 1) .Internal(rnorm(n, mean, sd)) environment: namespace:stats baptiste [[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 read a specific dataset, not the entire data, from HDF5?
Thanks, Felix. You are watching new questions here. I will give a try to rgdal and let you know the result. BTW, it is surprising to me that there seems no R package handling HDF5 like PyTables does for Python community, considering HDF5 is as popular as NetCDF as a file format for scientific data. I hope the gap will be filled in near future. Regards, DH 2009/6/27 Felix Andrews fe...@nfrac.org: Hi DH I recommend the rgdal package, which provides R bindings for the Geospatial Data Abstraction Library (GDAL). This does handle HDF5, according to the list at http://www.gdal.org/formats_list.html I have not ever used HDF5 myself, but that it what I would try. -Felix 2009/6/27 Daehyok Shin sdh...@gmail.com: Hi. Recently I am working for a project to generate massive numeric data. After storing them in HDF5 using PyTables, we are trying to use R for data analysis and visualisation. Surprising to me, however, I could not find a R package to allow the reading of a specific dataset (or its slide) in a HDF5 file. I found I can read and write only the entire data using hdf5 package and I could not locate rhdf5 in bioconductor. Each dataset is huge, so selecting a specific dataset is a mandatory function for my project. Could you give me a hint for the solution? Thanks. -- DH __ 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. -- Felix Andrews / 安福立 Post-Doctoral Fellow Integrated Catchment Assessment and Management (iCAM) Centre Fenner School of Environment and Society [Bldg 48a] The Australian National University Canberra ACT 0200 Australia M: +61 410 400 963 T: + 61 2 6125 1670 E: felix.andr...@anu.edu.au CRICOS Provider No. 00120C -- http://www.neurofractal.org/felix/ -- Daehyok Shin, PhD Geography Department University of North Carolina-Chapel Hill USA __ 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] panel.text and saving to pdf
If it is not the device then it's probably just the usage of an unexpected unit somewhere - as reported in another reply by another helper to your original question on R-help. Best, Uwe Ligges willem vervoort wrote: Hi Uwe, I should send these messages from my member e-mail number Thanks for that. As you can see from the last bit of my code, I tried that, but it gave the same results. I had a look at pdf.options() but didn't see anything there either to make the text stay on the same spot. It seems to also happen if you use png(). Willem From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Fri 6/26/2009 6:47 PM To: Willem Vervoort Cc: r-help@r-project.org Subject: Re: [R] panel.text and saving to pdf To get reproducible results, I highly recommend to print the lattice graphics directly into the desired device, i.e. start the pdf (or jpeg or whatever) device before printing. Best, Uwe Ligges Willem Vervoort wrote: Dear all, I am not sure what I am doing wrong, but I have some unexplained behaviour when saving a lattice graph including text to a pdf file. The text seems to move around. It must have something to do with the way coordinates are set in devices other than jpg. Any suggestions would be helpful Willem Here is some example code setwd(c:/willem/research/misc) today - format(Sys.Date(),%Y%m%d) x - runif(500) y - rnorm(500) foo - data.frame(x = x, y = y, z = rep(c(a,b),250)) require(lattice) xyplot(x~y|z,data=foo) panel.text(370,470,silly graph,cex=1.2,font=2) savePlot(paste(today, jpgplot,sep=_),type=jpg) # this plots fine and text is as on the screen savePlot(paste(today, pdfplot,sep=_),type=pdf) # text has moved pdf(paste(today,pdfplot2.pdf,sep=_)) # no difference using pdf xyplot(x~y|z,data=foo) panel.text(370,470,silly graph,cex=1.2,font=2) dev.off() # There is also no difference _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 9.0 year 2009 month 04 day17 svn rev48333 language R version.string R version 2.9.0 (2009-04-17) - Dr. R.W. Vervoort McCaughey Senior Lecturer Hydrology and Catchment Management Faculty of Agriculture, Food and Natural Resources, Bldg A04, The University of Sydney, NSW 2006 http://tinyurl.com/mccaughey http://blogs.usyd.edu.au/waterhydrosu ph: +61 2 9351 8744 fax: +61 2 9351 4953 __ 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] Re gression; how to get t-values for all parameters estimates
gzf200 wrote: Even after a couple of hours looking at old messages I still haven't found a solution for my problem. I'm trying to fit an additive linear regression model with 2 effects, both fixed, to some dataset. The function contrasts(effectA) - contr.sum can gaurantee that the coefficients per parameter sum to one, and the function dummy.coef provices the estimates of all coefficientss. But I would also like to be able to obtain the corresponding t-values for ALL parameters (not just the number of effects minus 1, provided by summary()). Does anyone know how to get (all of) them? Trying to fit months and weeks as a series of categorical variables and picking the asterisks is a path to disaster and hopefully not used to model the future economic of our economy. If you must, you can check function estimable in package gmodels, package multcomp, package contrast, and several functions in Hmisc. Dieter -- View this message in context: http://www.nabble.com/Regression--how-to-get-t-values-for-all-parameters-estimates-tp24232820p24234659.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] Looking for Rdonlp2
Dear All, I tried to download the package Rdonlp2 from the address given at CRAN Task View: Optimization and Mathematical Programming: http://arumat.net/Rdonlp2/ However, this link seems to be dead. Any ideas? Thanks in advance, Paul __ 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] a plot of stacked boxes
check out 'map.market' in the 'portfolio' package. On Fri, Jun 26, 2009 at 11:27 PM, Osman Al-Radi osman.al.r...@gmail.comwrote: Dear Richard and David, Thanks for this reference. I looked into vcd and mosaic plot, it is a nice plot for investigating associations between two or more variables. However, I just need to plot the frequency of a single variable as the area of the box. boxes are stacked to fill a larger box that represents the entire population. The axes are non-informative. I am trying to recreate the plot in the following website, used to represent the market capital of public companies. I would like to use a similar plot for a totally different application. The website: http://finviz.com/map.ashx The color code in the above link represents daily change in the stocks, in my intended plot I would like the color shade to represent the outcome (probability of an event in a predefined time usually 1 year). I am again grateful for your assistance. Osman Osman O. Al-Radi, MD, MSc, FRCSC Staff Cardiovascular Surgeon Co-medical director, Tissue Bank The Hospital for Sick Children University of Toronto, Canada On Fri, Jun 19, 2009 at 6:55 PM, Richard M. Heiberger r...@temple.edu wrote: I think you are looking for mosaic() table(df) library(vcd) mosaic(outcome ~ group, data=df) Rich [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] gradient fill of a grid.polygon
Following up on my previous post.
I've managed to have the function return a gList rather than plot everything
directly, but I get a rather obscure error message when I try to wrap the
grobs in a gTree with a rotated viewport,
Error in x$children[[i]] : attempt to select less than one element
however the same syntax works for simpler gTree such as,
g -
polygonGrob(x=c(0, 0.5, 1), y=c(0.5, 1, 0.5), gp=gpar(fill=NA,
col=grey90))
gg - gTree(children=gList(gList(clipGrob(), g)))
grid.draw(gg)
Any idea?
Below is the new code,
library(grid)
rotate.polygon - function(g, angle=0){
matR - matrix(c(cos(angle), -sin(angle), sin(angle), cos(angle)),
nrow = 2)
gravity.x = unit(mean(g$x),npc)
gravity.y = unit(mean(g$y),npc)
x.center = convertX(g$x - gravity.x ,npc,TRUE)
y.center = convertY(g$y - gravity.y ,npc,TRUE)
new.xy - matrix(c(x.center, y.center),
ncol=2) %*% matR
editGrob(g, x=unit(new.xy[,1],npc) + gravity.x,
y=unit(new.xy[,2],npc) + gravity.y)
}
gradient.polygon - function(g, n=10,
cols=colorRampPalette(c(#E41A1C, #377EB8, #4DAF4A, #984EA3))(n),
alpha=0.5,
stripe=FALSE, angle=pi/3){
gx - grobWidth(g)
gy - grobHeight(g)
dx - unit(convertX(gx, npc, valueOnly = TRUE)/(n-1), npc)
startx - min(g$x)
starty - min(g$y)
vp = viewport(angle = angle)
g = rotate.polygon(g, - angle)
g.all - gList()
for(ii in seq(1, n)){
clip.tmp - clipGrob(x= startx + (ii-1) * dx , y=starty,
width= 1.0*dx, # fudge factor to overlap well
height=gy,
just=bottom)
if(stripe){
if(ii%%2)# testing with every other masked
g.tmp - editGrob(g, gp=gpar(fill=cols[ii], col=cols[ii], alpha=alpha))
}else{
g.tmp - editGrob(g, gp=gpar(fill=cols[ii], col=NA,lwd=0, alpha=alpha))
}
g.all[[ii]] - gList(clip.tmp, g.tmp)
}
## return(gTree(children=g.all, vp=vp)) # this fails
g.all # simply return the gList for now
}
g -
polygonGrob(x=c(0, 0.5, 1), y=c(0.5, 1, 0.5), gp=gpar(fill=NA,
col=grey90))
g4 - gradient.polygon(g)
grid.draw(g4) # fine but not in the correct orientation
g6 - gTree(children=g4, vp=viewport(angle=30))
grid.draw(g6)
# Error in x$children[[i]] : attempt to select less than one element
grid.ls(g6) # looks similar to the minimal example of above
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[R] Bayesian Model Averaging
Two questions pertaining to the iBMA.glm procedure: 1) Does prior.param=1 force variables into the model as it does in S-Plus? If not, how can I force the first p variables into every model? 2) Is there some way in which to suppress the intercept as in the case of origin models? [[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] data formatting
All, I have three columns of data: id, date, hab. I am trying to set up a matrix that has the id as the rows, date as columns, and the hab value as the data values. Each id/date combination can only have one hab value. I would like for it to look something like this date 1, date 2, date 3. id 0001 21 2 0002 3 56 I don't know how to set this up properly. I am pretty sure dates cannot be used in a matrix, but I can easily convert this to an integer. I am mainly unsure of the functions to use to do this operation. Thank you [[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] Looking for Rdonlp2
Not sure what word in my prior message triggered the list-filter but this is what I got after a bit of cutting and pasting on the link offered: This directory does not contain anymore the source of DONLP2. The code is available for some users from its author, Peter Spellucci, spellu...@mathematik.tu-darmstadt.de -- DW On Jun 27, 2009, at 2:06 PM, Paul Smith wrote: Dear All, I tried to download the package Rdonlp2 from the address given at CRAN Task View: Optimization and Mathematical Programming: http://arumat.net/Rdonlp2/ However, this link seems to be dead. Any ideas? Thanks in advance, Paul __ 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 Heritage Laboratories 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] data formatting
Is this what you are after (uses the reshape package)
# test data
x - expand.grid(id=1:5, date=seq(as.Date('2009-01-01'), by='1 day',
length=5))
x$hab - seq(nrow(x)) # add hab
head(x)
id date hab
1 1 2009-01-01 1
2 2 2009-01-01 2
3 3 2009-01-01 3
4 4 2009-01-01 4
5 5 2009-01-01 5
6 1 2009-01-02 6
require(reshape)
x.melt - melt(x, measure='hab')
cast(x.melt, id ~ date)
id 2009-01-01 2009-01-02 2009-01-03 2009-01-04 2009-01-05
1 1 1 6 11 16 21
2 2 2 7 12 17 22
3 3 3 8 13 18 23
4 4 4 9 14 19 24
5 5 5 10 15 20 25
On Sat, Jun 27, 2009 at 7:40 PM, James Martin just.strut...@gmail.comwrote:
All,
I have three columns of data: id, date, hab. I am trying to set up a matrix
that has the id as the rows, date as columns, and the hab value as the data
values. Each id/date combination can only have one hab value. I would
like
for it to look something like this
date 1, date 2, date 3.
id
0001 21 2
0002 3 56
I don't know how to set this up properly. I am pretty sure dates cannot be
used in a matrix, but I can easily convert this to an integer. I am mainly
unsure of the functions to use to do this operation.
Thank you
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] how to interpret coefficients for a natural spline smooth function in a GLM
I have not seen a reply to this question, so I will offer a comment; someone who knows more than I may correct or add to my comments. There are many different kinds of splines. Perhaps the most common are B-splines, which sum to 1 inside their range of definition and are 0 outside. Natural splines are similar, but support extrapolation outside the (finite) range of definition. A natural cubic spline extrapolates as straight lines (http://en.wikipedia.org/wiki/Spline_interpolation). The coefficients are weights for a B-spline basis for the natural spline, defined in terms of the knots. The fda package includes a TaylorSpline function to translate spline coefficients into the coefficients of Taylor expansions about the midpoints of the intervals between knots. However, I do not know if it will work with a natural spline. This is far from a complete answer to your question, but I hope it helps. Spencer Graves ltracy wrote: Hello- I am trying to model infections counts over 120 months using a GLM in R. The model is simple really including a factor variable for year (10 yrs in total) and another variable consisting of a natural spline function for time in months. My code for the GLM is as follows: model1-glm(ALL_COUNT~factor(FY)+ns(1:120, 10), offset=log(TOTAL_PTS), family=poisson, data=TS1) The summary output pertaining to the smooth function consists of 10 coefficients for each df in the model. Here are the coefficients: ns(1:120, 10)1 -0.724380.32773 -2.210 0.027084 * ns(1:120, 10)2 -1.190970.37492 -3.177 0.001490 ** ns(1:120, 10)3 -1.402500.42366 -3.310 0.000931 *** ns(1:120, 10)4 -0.827220.47459 -1.743 0.081334 . ns(1:120, 10)5 -0.461390.49657 -0.929 0.352812 ns(1:120, 10)6 -0.448920.51909 -0.865 0.387137 ns(1:120, 10)7 -0.530600.54783 -0.969 0.332778 ns(1:120, 10)8 -0.256990.55582 -0.462 0.643814 ns(1:120, 10)9 -0.740910.63899 -1.160 0.246249 ns(1:120, 10)10 0.411420.56317 0.731 0.465054 What is still unclear to me is what these 10 coefficients from the natural spline represent. Thanks in advace- __ 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] Defining class as a member of another class
Hi, When I define a new class (through setClass), members defined in representation argument doesn't seem to like a class. For example, if I do the following: setClass(NotWork,representation=(x=zoo)) It seems to me that representation members will take in only primitive type to R. Is there any way to stuff a class as a member in another class? Thank you. - adschai __ 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] Defining class as a member of another class
Try this: setClass(zoo) [1] zoo setClass(Work,representation=(x=zoo)) [1] Work On Sat, Jun 27, 2009 at 10:01 PM, R_help Helprhelp...@gmail.com wrote: Hi, When I define a new class (through setClass), members defined in representation argument doesn't seem to like a class. For example, if I do the following: setClass(NotWork,representation=(x=zoo)) It seems to me that representation members will take in only primitive type to R. Is there any way to stuff a class as a member in another class? Thank you. - adschai __ 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] Defining class as a member of another class
Thank you Gabor. It works. I read a bit more and understood what you're doing. One more question, I want to know more about .Data property of a class. I know that it defines type of the class when asking typeof. But I don't know much how to use them. Would you mind pointing me to some reference and example? Thank you again! ads On Sat, Jun 27, 2009 at 10:29 PM, Gabor Grothendieckggrothendi...@gmail.com wrote: Try this: setClass(zoo) [1] zoo setClass(Work,representation=(x=zoo)) [1] Work On Sat, Jun 27, 2009 at 10:01 PM, R_help Helprhelp...@gmail.com wrote: Hi, When I define a new class (through setClass), members defined in representation argument doesn't seem to like a class. For example, if I do the following: setClass(NotWork,representation=(x=zoo)) It seems to me that representation members will take in only primitive type to R. Is there any way to stuff a class as a member in another class? Thank you. - adschai __ 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 automatically placing a legend in empty space
I really apprecaite the suggestion. I just downloaded the Hmisc.pdf document and looked through it. Do you have any further thoughts about a specific function within the Hmisc package? I looked at largest.empty, but not sure how that is applicable to my data points. x = seq(0, 1000, by = 1) y1_vals-rnorm(1000, mean = 0, sd = 50) y2_vals-rnorm(1000, mean = 25, sd = 40) y3_vals-rnorm(1000, mean = 115, sd = 40) plot(x_vals, y1_vals, pch=22, col=dark red, bg = dark red, cex =0.3) points(x_vals, y2_vals, pch=22, col=dark blue, bg = dark blue, cex =0.3) points(x_vals, y3_vals, pch=22, col=dark green, bg = dark green, cex =0.3) abline(h=0, col=dark red, lwd=1.5, lty=6) abline(h=25, col=dark blue, lwd=1.5, lty=6) abline(h=115, col=dark green, lwd=1.5, lty=6) legend(topright, c(Best Guess 1 , Best Guess 2, Best Guess 3), bg=white, lwd = 2, title = Randomness:) Is there any chance you can provide a suggestion? Thanks again. --- On Sat, 6/27/09, Dieter Menne dieter.me...@menne-biomed.de wrote: From: Dieter Menne dieter.me...@menne-biomed.de Subject: Re: [R] How to automatically placing a legend in empty space To: r-h...@stat.math.ethz.ch Date: Saturday, June 27, 2009, 5:37 AM Jason Rupert jasonkrupert at yahoo.com writes: At one point I believe I heard of an R package that would automatically find the most empty space in a plot, and then that answer could then be used to intelligently place a legend. Have a look a some of the plotting function in package Hmisc. Dieter __ 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] applying a function to a pair of components for each row of a list
Hi, I have a set of (x,y) coordinate pairs that are stored as a list my_list $x [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 $y [1] -8.0866819 -7.3876052 -6.6849311 -5.9837693 -5.2967432 -4.6525466 [7] -4.0999453 -3.6556190 -3.3076102 -3.0360780 -2.8220465 -2.6532085 [13] -2.5192816 -2.4086241 -2.3072977 -2.1969611 -2.0574250 -1.8737694 [19] -1.6357864 -1.3478118 -1.0228402 -0.6708884 -0.2973863 0.0922034 [25] 0.4935457 I would like to plot each of these points onto an existing plot. ie., For each (x,y) pair, I would like to do: points(x,y) How can I do this in a vectorized manner? Thanks! Kavitha [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] applying a function to a pair of components for each row of a list
Hi Kavitha, I must confess you that I not understood well what you are looking for. But.. mylist-list(x=1:25, y=runif(n=25)) plot(mylist, type=n) points(mylist, type=p, col=mylist$x) Hth, miltinho On Sun, Jun 28, 2009 at 1:03 AM, Kavitha Venkatesan kavitha.venkate...@gmail.com wrote: Hi, I have a set of (x,y) coordinate pairs that are stored as a list my_list $x [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 $y [1] -8.0866819 -7.3876052 -6.6849311 -5.9837693 -5.2967432 -4.6525466 [7] -4.0999453 -3.6556190 -3.3076102 -3.0360780 -2.8220465 -2.6532085 [13] -2.5192816 -2.4086241 -2.3072977 -2.1969611 -2.0574250 -1.8737694 [19] -1.6357864 -1.3478118 -1.0228402 -0.6708884 -0.2973863 0.0922034 [25] 0.4935457 I would like to plot each of these points onto an existing plot. ie., For each (x,y) pair, I would like to do: points(x,y) How can I do this in a vectorized manner? Thanks! Kavitha [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] applying a function to a pair of components for each row of a list
Milton, Thanks, the answer was in fact as simple as you pointed out. I was thinking more complicated than needed! Kavitha On Sun, Jun 28, 2009 at 1:11 AM, milton ruser milton.ru...@gmail.comwrote: Hi Kavitha, I must confess you that I not understood well what you are looking for. But.. mylist-list(x=1:25, y=runif(n=25)) plot(mylist, type=n) points(mylist, type=p, col=mylist$x) Hth, miltinho On Sun, Jun 28, 2009 at 1:03 AM, Kavitha Venkatesan kavitha.venkate...@gmail.com wrote: Hi, I have a set of (x,y) coordinate pairs that are stored as a list my_list $x [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 $y [1] -8.0866819 -7.3876052 -6.6849311 -5.9837693 -5.2967432 -4.6525466 [7] -4.0999453 -3.6556190 -3.3076102 -3.0360780 -2.8220465 -2.6532085 [13] -2.5192816 -2.4086241 -2.3072977 -2.1969611 -2.0574250 -1.8737694 [19] -1.6357864 -1.3478118 -1.0228402 -0.6708884 -0.2973863 0.0922034 [25] 0.4935457 I would like to plot each of these points onto an existing plot. ie., For each (x,y) pair, I would like to do: points(x,y) How can I do this in a vectorized manner? Thanks! Kavitha [[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.htmlhttp://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] multiple regression w/ no intercept; strange results
I am writing some software to do multiple regression and am using r to benchmark the results. The results are squaring up nicely for the with-intercept case but not for the no-intercept case. I am not sure what R is doing to get the statistics for the 0 intercept case. For example, I would expect the Multiple R-squared to equal the square of the correlation between the actual values y and the fitted values yprime. For the with-intercept case, they do, but not for the no-intercept case. My sample file and R session output are below dataset = read.table(/Users/jdhunter/tmp/sample1.csv, header=TRUE, sep=,) The with-intercept fit: the Multiple R-Squared is equal to the cor(yprime, y)**2: fit - lm( y~x1+x2, data=dataset) summary(fit) Call: lm(formula = y ~ x1 + x2, data = dataset) Residuals: Min 1Q Median 3Q Max -1.8026 -0.4651 0.1778 0.5241 1.0222 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -4.103581.26103 -3.254 0.00467 ** x1 0.086410.03144 2.748 0.01372 * x2 0.087600.04548 1.926 0.07100 . --- Residual standard error: 0.7589 on 17 degrees of freedom Multiple R-squared: 0.6709, Adjusted R-squared: 0.6322 F-statistic: 17.33 on 2 and 17 DF, p-value: 7.888e-05 yp = fitted.values(fit) cor(yp, dataset$y)**2 [1] 0.6709279 The no-intercept fit: the Multiple R-Squared is not equal to the cor(yprime, y)**2: fitno - lm( y~0+x1+x2, data=dataset) summary(fitno) Call: lm(formula = y ~ 0 + x1 + x2, data = dataset) Residuals: Min 1Q Median 3Q Max -1.69640 -0.58134 0.03650 0.53673 1.33358 Coefficients: Estimate Std. Error t value Pr(|t|) x1 0.036550.03399 1.0750.296 x2 0.043580.05376 0.8110.428 Residual standard error: 0.9395 on 18 degrees of freedom Multiple R-squared: 0.9341, Adjusted R-squared: 0.9267 F-statistic: 127.5 on 2 and 18 DF, p-value: 2.352e-11 ypno = fitted.values(fitno) cor(ypno, dataset$y) [1] 0.6701336 If anyone has some suggestions about how R is computing these summary stats for the no-intercept case, or references to literature or docs, tha would be helpful. It seems odd to me that dropping the intercept would cause the R^2 and F stats to rise so dramatically, and the p value to consequently drop so much. In my implementation, I get the same beta1 and beta2, and the R2 I compute using the variance_regression / variance_total agrees with cor(ypno, dataset$y) but not with the value R reports in the summary, and my F and p values are similarly off for the no-intercept case. Thanks, JDH R version 2.9.1 (2009-06-26) home:~/tmp uname -a Darwin Macintosh-7.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 __ 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.
