[R] Filled contour in a irregular map (shapefile)
Hello All, I want to draw a figure with filled contour in a irregular map. But I found that the contours overlap the boundaries of the map, and also some regions in the map were not filled. I have following data: data1. A shapefile (i.e., a map with boundary, for example, the whole Australia map); data2. A text file with three columns: x, latitude; y,longitude;z,variable (e.g., rainfall); and use following R code: Map-readShapeSpatial(data1) plot(Map) data2.li-interp(data2$x,data2$y,data2$z) filled.contour(data2.li, color=topo.colors, add=TRUE) How can I limits the filled contours just inside the map? Thank very much for that! Zachary [[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] Why don't formulas that work for lm() work for plotmeans?
I know that simple line plots showing a point representing the mean + an error bar are difficult in R, but I am clearly missing something. I simply want to show how a the mean and 95% CI of a chemical concentration (y) vary over space (x) under four temperature regimes (T; a categorical factor). plotmeans, in the gplots library, should allow for such a figure, right? After all, it invokes lm() in the help file for the formula, so any formula that works in lm() (e.g., y~x | T) should work in plotmeans. Obviously this is not so - can anyone suggest an alternative command or help me understand how the syntac differs? Thanks... -- View this message in context: http://www.nabble.com/Why-don%27t-formulas-that-work-for-lm%28%29-work-for-plotmeans--tp25517081p25517081.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] Emacs and ESS help
Any and all help is deeply appreciated. If you do not want to learn all the inns and outs of Emacs, just download the Emacs distribution provided by Vincent Goulet - it has ESS. Uninstall your present Emacs, go to http://vgoulet.act.ulaval.ca/en/ressources/emacs/ download Vincent's distribution, install it, and your are set! Jarek __ 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 avoid copy-paste when copying code from this list?
Hi, How do you people avoid copy-pasting and manual editing of the code posted in this list? I mean that if some one post a solution for an answer like this: a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 I have to copy-paste it to e.g. Tinn-R and remove part of the line to try it in my R. When you keep doing this it gets quite annoying. How do you people avoid this (search and replace, perhaps?). The best way would be to able to send this straight from your e-mail reader into R (e.g. from gmail). -Johannes __ 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 avoid copy-paste when copying code from this list?
At least in windows, if you right click directly in the r console, there's a command for 'Paste commands only' which may be one solution... Not sure about other platforms.. hth c johannes rara wrote: Hi, How do you people avoid copy-pasting and manual editing of the code posted in this list? I mean that if some one post a solution for an answer like this: a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 I have to copy-paste it to e.g. Tinn-R and remove part of the line to try it in my R. When you keep doing this it gets quite annoying. How do you people avoid this (search and replace, perhaps?). The best way would be to able to send this straight from your e-mail reader into R (e.g. from gmail). -Johannes __ 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 avoid copy-paste when copying code from this list
On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote: At least in windows, if you right click directly in the r console, there's a command for 'Paste commands only' which may be one solution... Not sure about other platforms.. hth c It was precisely for this kind of reason that, when including R code in postings to the list, I took to formatting it in the following kind of way: a - 1:10 a # [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] # [1] 1 2 3 4 5 In this way, any R commands copy-pasted into R will work as-is, anything else is a comment and will not interfere. I notice that some other people also post their code in this way. I recommend it to all! If the code has been copy-pasted into the email from an R console, then of course the prompts will be there. But then I just edit these out of the email. A bit more trouble for me, but a lot less trouble for others. For instance, if someone had posted the above as copied from the R console in its original form a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 and I wanted to try it out, then I would either have to re-open the email in edit mode so as to edit the email itself, or else copy-paste the above into a text-edit window[*] and pre-edit it there before copying into R. [*] I would be using 'vim' in a Linux xterm. Removal of the prompts (or + continuation prompts) from a long series of commands is relatively easy: Just higlight a column-block of the first two columns, then press d to delete them. But you would first need to enter # for other stuff by hand. Best wishes to all, Ted. johannes rara wrote: Hi, How do you people avoid copy-pasting and manual editing of the code posted in this list? I mean that if some one post a solution for an answer like this: a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 I have to copy-paste it to e.g. Tinn-R and remove part of the line to try it in my R. When you keep doing this it gets quite annoying. How do you people avoid this (search and replace, perhaps?). The best way would be to able to send this straight from your e-mail reader into R (e.g. from gmail). -Johannes E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 19-Sep-09 Time: 09:33:48 -- XFMail -- __ 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 avoid copy-paste when copying code from this list
The R help mailing list posting guide http://www.r-project.org/posting-guide.html suggests to give an example in this form ...snip... f I have a matrix x as follows: x - matrix(1:8, nrow=4, ncol=2, dimnames=list(c(A,B,C,D), c(x,y)) x x y A 1 5 B 2 6 C 3 7 D 4 8 ...snip... Would it be reasonable to consider changing this guide about this matter? 2009/9/19 Ted Harding ted.hard...@manchester.ac.uk: On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote: At least in windows, if you right click directly in the r console, there's a command for 'Paste commands only' which may be one solution... Not sure about other platforms.. hth c It was precisely for this kind of reason that, when including R code in postings to the list, I took to formatting it in the following kind of way: a - 1:10 a # [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] # [1] 1 2 3 4 5 In this way, any R commands copy-pasted into R will work as-is, anything else is a comment and will not interfere. I notice that some other people also post their code in this way. I recommend it to all! If the code has been copy-pasted into the email from an R console, then of course the prompts will be there. But then I just edit these out of the email. A bit more trouble for me, but a lot less trouble for others. For instance, if someone had posted the above as copied from the R console in its original form a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 and I wanted to try it out, then I would either have to re-open the email in edit mode so as to edit the email itself, or else copy-paste the above into a text-edit window[*] and pre-edit it there before copying into R. [*] I would be using 'vim' in a Linux xterm. Removal of the prompts (or + continuation prompts) from a long series of commands is relatively easy: Just higlight a column-block of the first two columns, then press d to delete them. But you would first need to enter # for other stuff by hand. Best wishes to all, Ted. johannes rara wrote: Hi, How do you people avoid copy-pasting and manual editing of the code posted in this list? I mean that if some one post a solution for an answer like this: a - 1:10 a [1] 1 2 3 4 5 6 7 8 9 10 a[1:5] [1] 1 2 3 4 5 I have to copy-paste it to e.g. Tinn-R and remove part of the line to try it in my R. When you keep doing this it gets quite annoying. How do you people avoid this (search and replace, perhaps?). The best way would be to able to send this straight from your e-mail reader into R (e.g. from gmail). -Johannes E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 19-Sep-09 Time: 09:33:48 -- XFMail -- __ 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] Creating histograms from factors using a for loop
# I have a dataframe with data and factors similar to the following:
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
# I am trying to write a 'for' loop which will produce a jpeg histogram
for each factor. I can individually isolate the data from a factor and
produce a jpeg histogram like so:
fnc - function(x){
x - df[df$f==a, d]
}
y - fnc(df[df$f==a, d])
jpeg(filename=foo.jpeg)
hist(y)
dev.off()
# I'm having trouble creating a loop repeating the process for all the
other factors. The following is the best I could come up with. It
produces a single jpeg histogram of the first factor titled with a list
of all the factors.
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
for (i in levels(df[,f])){
y - df[df$f==i, 2]
jpeg(filename=(levels(df[i,f])))
hist(y, main=levels(df[i,f]))
dev.off()
}
# I'm obviously not understanding how loops work with factors. Can
anybody point me in the right direction?
--
Sam Player, B.Sc.(Hons.) B.A.
Ph.D. Candidate, Faculty of Agriculture, Food Natural Resources, University
of Sydney
Email: spla...@usyd.edu.au
Agroecosystems Research Group
Room 214 J.R.A. McMillan Building A05
University of Sydney NSW 2006, Australia
Angkor Research Program
Room 305 Old Teachers College A22
University of Sydney NSW 2006, Australia
__
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] Counting observations of a combined factor
#I have a dataset with two factor. I want to combine those factors into a single factor and count the number of data values for each new factor. The following gives a comparable dataframe: a - rep(c(a, b), c(6,6)) b - rep(c(c, d), c(6,6)) df - data.frame(f1=a, f2=b, d=rnorm(12)) df # I use the 'interaction' function to combine factors f1 and f2: df2 - data.frame(f3=interaction(df[,f1], df[,f2]), d=df[,d]) df2 # A count of the first data.frame using factor f1 returns the kind of results I am looking for: count - as.data.frame(table(df$f1)) count # Var1 Freq #1a6 #2b6 # As does a count using factor2: count2 - as.data.frame(table(df$f2)) count2 # Var1 Freq #1a6 #2b6 # The same procedure on the second dataframe does not treat the levels of factor f3 discreetly, instead giving all possible combinations of f1 and f2. count3 - as.data.frame(table(df2$f3)) count3 # Var1 Freq #1 a.c6 #2 b.c0 #3 a.d0 #4 b.d6 I need the results to be: # Var1 Freq #1a6 #2b6 # Any suggestions? -- Sam Player, B.Sc.(Hons.) B.A. Ph.D. Candidate, Faculty of Agriculture, Food Natural Resources, University of Sydney Email: spla...@usyd.edu.au Agroecosystems Research Group Room 214 J.R.A. McMillan Building A05 University of Sydney NSW 2006, Australia Angkor Research Program Room 305 Old Teachers College A22 University of Sydney NSW 2006, Australia __ 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 avoid copy-paste when copying code from this list
On 19-Sep-09 08:48:45, johannes rara wrote: The R help mailing list posting guide http://www.r-project.org/posting-guide.html suggests to give an example in this form ...snip... f I have a matrix x as follows: x - matrix(1:8, nrow=4, ncol=2, dimnames=list(c(A,B,C,D), c(x,y)) x x y A 1 5 B 2 6 C 3 7 D 4 8 ...snip... Would it be reasonable to consider changing this guide about this matter? Yes, I think there is a case for a change. I must have read the above myself, once, but ignored it later for the reasons I gave below. In any case, that citation is not in the context of advice about how to format R code when posting (there is no such advice explicitly given in the posting-guide), but in the context that it can be helpful to provide an example: Examples: Sometimes it helps to provide a small example that someone can actually run. For example: (then the example above). Possibly, people may tend to read that example as if it were advice on formatting the code. So maybe the change which could be helpful in the present context would be to follow the above example with a section which advised on how to format the code for examples which someone can actually run (they cannot actually run the code as given in the example). In other words, on the lines of When posting R code for examples, when this is copied from an R console remove any command prompts and continuation prompts + from the code as it appears on the R console, and precede each line of R output, messages, etc., with # (to make it a comment, so that if the code is copy-pasted from R-help into an R console it will work as-is without the need for further editing. Example: [...] What do other people (in particular the maintainers of the posting guide) think? Some might argue that the and + prompts serve to mark the presence of R code and distinguish it from message text. But then the result is something that nobody can actually run. I think, myself, that (especially with indenting of the code by a couple of spaces) the format I describe is clearly enough distinguished. Ted. 2009/9/19 Ted Harding ted.hard...@manchester.ac.uk: On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote: At least in windows, if you right click directly in the r console, there's a command for 'Paste commands only' which may be one solution... Not sure about other platforms.. hth c It was precisely for this kind of reason that, when including R code in postings to the list, I took to formatting it in the following kind of way: _a - 1:10 _a _# [1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10 _a[1:5] _# [1] 1 2 3 4 5 In this way, any R commands copy-pasted into R will work as-is, anything else is a comment and will not interfere. I notice that some other people also post their code in this way. I recommend it to all! If the code has been copy-pasted into the email from an R console, then of course the prompts will be there. But then I just edit these out of the email. A bit more trouble for me, but a lot less trouble for others. For instance, if someone had posted the above as copied from the R console in its original form a - 1:10 a _[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10 a[1:5] [1] 1 2 3 4 5 and I wanted to try it out, then I would either have to re-open the email in edit mode so as to edit the email itself, or else copy-paste the above into a text-edit window[*] and pre-edit it there before copying into R. [*] I would be using 'vim' in a Linux xterm. Removal of the prompts (or + continuation prompts) from a long series of commands is relatively easy: Just higlight a column-block of the first two columns, then press d to delete them. But you would first need to enter _# for other stuff by hand. Best wishes to all, Ted. johannes rara wrote: Hi, How do you people avoid copy-pasting and manual editing of the code posted in this list? I mean that if some one post a solution for an answer like this: a - 1:10 a _[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10 a[1:5] [1] 1 2 3 4 5 I have to copy-paste it to e.g. Tinn-R and remove part of the line to try it in my R. When you keep doing this it gets quite annoying. How do you people avoid this (search and replace, perhaps?). The best way would be to able to send this straight from your e-mail reader into R (e.g. from gmail). -Johannes E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 19-Sep-09 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Time: 09:33:48 -- XFMail -- __ 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 avoid copy-paste when copying code from this list
it might be possible to set up a particular mode before copying the history,
### start example ###
email = function(op){
if(!missing(op)) {
options(op) } else {
op - options()
options(prompt = )
options(continue = )
op
}
}
op = email()
a = 1:10
a
email(op)
a = 1:10
a
### end example ###
I'm not sure how one would add # to the result lines.
Best,
baptiste
2009/9/19 Ted Harding ted.hard...@manchester.ac.uk:
On 19-Sep-09 08:48:45, johannes rara wrote:
The R help mailing list posting guide
http://www.r-project.org/posting-guide.html
suggests to give an example in this form
...snip...
f I have a matrix x as follows:
x - matrix(1:8, nrow=4, ncol=2,
dimnames=list(c(A,B,C,D), c(x,y))
x
x y
A 1 5
B 2 6
C 3 7
D 4 8
...snip...
Would it be reasonable to consider changing this guide about this
matter?
Yes, I think there is a case for a change. I must have read the
above myself, once, but ignored it later for the reasons I gave
below. In any case, that citation is not in the context of advice
about how to format R code when posting (there is no such advice
explicitly given in the posting-guide), but in the context that it
can be helpful to provide an example:
Examples: Sometimes it helps to provide a small example that
someone can actually run. For example:
(then the example above). Possibly, people may tend to read that
example as if it were advice on formatting the code.
So maybe the change which could be helpful in the present context
would be to follow the above example with a section which advised
on how to format the code for examples which someone can actually
run (they cannot actually run the code as given in the example).
In other words, on the lines of
When posting R code for examples, when this is copied from an R
console remove any command prompts and continuation prompts
+ from the code as it appears on the R console, and precede
each line of R output, messages, etc., with # (to make it a
comment, so that if the code is copy-pasted from R-help into an
R console it will work as-is without the need for further editing.
Example:
[...]
What do other people (in particular the maintainers of the posting
guide) think?
Some might argue that the and + prompts serve to mark the
presence of R code and distinguish it from message text. But then
the result is something that nobody can actually run. I think,
myself, that (especially with indenting of the code by a couple
of spaces) the format I describe is clearly enough distinguished.
Ted.
2009/9/19 Ted Harding ted.hard...@manchester.ac.uk:
On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote:
At least in windows, if you right click directly in the r console,
there's a command for 'Paste commands only' which may be one
solution...
Not sure about other platforms..
hth
c
It was precisely for this kind of reason that, when including
R code in postings to the list, I took to formatting it in the
following kind of way:
_a - 1:10
_a
_# [1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
_a[1:5]
_# [1] 1 2 3 4 5
In this way, any R commands copy-pasted into R will work as-is,
anything else is a comment and will not interfere. I notice that
some other people also post their code in this way.
I recommend it to all! If the code has been copy-pasted into the
email from an R console, then of course the prompts will be
there. But then I just edit these out of the email. A bit more
trouble for me, but a lot less trouble for others.
For instance, if someone had posted the above as copied from the
R console in its original form
a - 1:10
a
_[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
a[1:5]
[1] 1 2 3 4 5
and I wanted to try it out, then I would either have to re-open the
email in edit mode so as to edit the email itself, or else
copy-paste
the above into a text-edit window[*] and pre-edit it there before
copying into R.
[*] I would be using 'vim' in a Linux xterm. Removal of the
prompts (or + continuation prompts) from a long series of commands
is relatively easy: Just higlight a column-block of the first two
columns, then press d to delete them. But you would first need to
enter _# for other stuff by hand.
Best wishes to all,
Ted.
johannes rara wrote:
Hi,
How do you people avoid copy-pasting and manual editing of the code
posted in this list? I mean that if some one post a solution for an
answer like this:
a - 1:10
a
_[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
a[1:5]
[1] 1 2 3 4 5
I have to copy-paste it to e.g. Tinn-R and remove part of the
line to try it in my R. When you keep doing this it gets quite
annoying. How do you people avoid this (search and replace,
perhaps?).
The best way would be to able to send this straight from your e-mail
reader into R (e.g. from gmail).
-Johannes
E-Mail: (Ted Harding)
[R] graphing help
Hello: I am very new to R, and I am trying to plot a large data set. I would like to get a line graph. My data looks like this in a csv file (no header): 07/03/23,05:00,23 07/03/23,06:00,32 07/03/23,07:00,33 07/03/23,08:00,25 07/03/23,09:00,26 07/03/23,10:00,21 07/03/23,11:00,23 07/03/23,12:00,24 07/03/23,13:00,25 07/03/23,14:00,29 07/03/23,15:00,23 07/03/23,16:00,23 TIA __ 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] graphing help
stephen sefick wrote: ?read.csv ?paste ?as.Date ?as.dataframe library(ggplot2) ?qplot Also: library(zoo) ?zoo Stefan __ 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] graphing help
Mag Gam wrote: Hello: I am very new to R, and I am trying to plot a large data set. I would like to get a line graph. My data looks like this in a csv file (no header): 07/03/23,05:00,23 07/03/23,06:00,32 07/03/23,07:00,33 07/03/23,08:00,25 07/03/23,09:00,26 07/03/23,10:00,21 07/03/23,11:00,23 07/03/23,12:00,24 07/03/23,13:00,25 07/03/23,14:00,29 07/03/23,15:00,23 07/03/23,16:00,23 TIA __ 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. Let's see... dd - read.csv(clipboard, header=F) dd names(dd)- c(D,TOD,Y) dd$T - as.POSIXct(paste(dd$D, dd$TOD), format=%y/%m/%d %H:%M) plot(Y~T,data=dd, type=b) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] Why don't formulas that work for lm() work for plotmeans?
Did lm(y ~ x | T) work for you? Let's see a reproducible example. Peter jrflanders wrote: I know that simple line plots showing a point representing the mean + an error bar are difficult in R, but I am clearly missing something. I simply want to show how a the mean and 95% CI of a chemical concentration (y) vary over space (x) under four temperature regimes (T; a categorical factor). plotmeans, in the gplots library, should allow for such a figure, right? After all, it invokes lm() in the help file for the formula, so any formula that works in lm() (e.g., y~x | T) should work in plotmeans. Obviously this is not so - can anyone suggest an alternative command or help me understand how the syntac differs? Thanks... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of R in Schools
On Sat, Sep 19, 2009 at 6:28 AM, John Maindonald john.maindon...@anu.edu.au wrote: I am looking for information on experimentation with the use of R in the teaching of statistics and science in schools. Any leads would be very welcome. I am certain that there is such experimentation. I read this paper http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000482 some days ago. It's quite interesting, and it links to some excellent slides that look great as templates for making your own R course. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Replacing values in dataframes
I think this is what you want NAD$Sample.Id - t(Prot.amount[NAD$Sample.Id]) HTH Schalk Heunis On Sat, Sep 19, 2009 at 12:18 PM, Monna Nygård monn...@hotmail.com wrote: Hi, This is a question of a newbie getting into the exciting world of R. I have several dataframes in the same format as NAD: NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 148 10a 0.04836 0.04994 167 11a_1109 0.32245 0.36541 173 11b_1109 0.29293 0.32815 What I want to do is to replace the Sample.Id with a corresponding number.The number i have in another file,called Prot.amount Prot.amount[1:3,1] 10a 11a_1109 11b_1109 15.516 38.248 42.297 row.names(NAD)-(NAD[,1]) NAD$Sample.Id - replace(NAD$Sample.Id, NAD$Sample.Id==10a,Prot.amount[10a,1]) NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 10a 15.516 0.04836 0.04994 11a_1109 11a_1109 0.32245 0.36541 11b_1109 11b_1109 0.29293 0.32815 So what I have tried to do is to write a function that would allow me to replace the values automatically of all dataframes. This I just can't get to work. Thank you so much in advance! _ [[elided Hotmail spam]] [[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] Use of R in Schools
I cannot offer direct experience with schools, but perhaps you are interested in having a look at RExcel (I am the author) which makes R accessible within Excel on Windows. One of the reasons of writing it was to make R more easily accessible for statistics education. rcom.univie.ac.at has more information John Maindonald wrote: I am looking for information on experimentation with the use of R in the teaching of statistics and science in schools. Any leads would be very welcome. I am certain that there is such experimentation. I've made this inquiry on r-sig-teaching, with no response. John. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ 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] Creating histograms from factors using a for loop
Sam,
Your loop produces two jpegs but the second overwrites the first.
What do you expect
levels(df[i,f])
to produce? (Think about it.)
Try
jpeg(filename=paste(i,.jpg,sep=))
and you may want to fix the titles as well.
Peter
Sam Player wrote:
# I have a dataframe with data and factors similar to the following:
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
# I am trying to write a 'for' loop which will produce a jpeg histogram
for each factor. I can individually isolate the data from a factor and
produce a jpeg histogram like so:
fnc - function(x){
x - df[df$f==a, d]
}
y - fnc(df[df$f==a, d])
jpeg(filename=foo.jpeg)
hist(y)
dev.off()
# I'm having trouble creating a loop repeating the process for all the
other factors. The following is the best I could come up with. It
produces a single jpeg histogram of the first factor titled with a list
of all the factors.
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
for (i in levels(df[,f])){
y - df[df$f==i, 2]
jpeg(filename=(levels(df[i,f])))
hist(y, main=levels(df[i,f]))
dev.off()
}
# I'm obviously not understanding how loops work with factors. Can
anybody point me in the right direction?
__
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 avoid copy-paste when copying code from this list
One solution would be to have a portable version of the
Windows
Edit | Paste commands only
functionality that works on all platforms.
For example if a command such as this were available:
source.commands - function(echo = TRUE, ...) {
L - readLines(clipboard)
L - grep(^[+] , L, value = TRUE)
L - gsub(^.., , L)
source(textConnection(L), echo = echo, ...)
}
one could just copy the email snippet and the issue this command in
the R session:
source.commands()
Building this directly into source as an option might be nice.
On Sat, Sep 19, 2009 at 5:46 AM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 19-Sep-09 08:48:45, johannes rara wrote:
The R help mailing list posting guide
http://www.r-project.org/posting-guide.html
suggests to give an example in this form
...snip...
f I have a matrix x as follows:
x - matrix(1:8, nrow=4, ncol=2,
dimnames=list(c(A,B,C,D), c(x,y))
x
x y
A 1 5
B 2 6
C 3 7
D 4 8
...snip...
Would it be reasonable to consider changing this guide about this
matter?
Yes, I think there is a case for a change. I must have read the
above myself, once, but ignored it later for the reasons I gave
below. In any case, that citation is not in the context of advice
about how to format R code when posting (there is no such advice
explicitly given in the posting-guide), but in the context that it
can be helpful to provide an example:
Examples: Sometimes it helps to provide a small example that
someone can actually run. For example:
(then the example above). Possibly, people may tend to read that
example as if it were advice on formatting the code.
So maybe the change which could be helpful in the present context
would be to follow the above example with a section which advised
on how to format the code for examples which someone can actually
run (they cannot actually run the code as given in the example).
In other words, on the lines of
When posting R code for examples, when this is copied from an R
console remove any command prompts and continuation prompts
+ from the code as it appears on the R console, and precede
each line of R output, messages, etc., with # (to make it a
comment, so that if the code is copy-pasted from R-help into an
R console it will work as-is without the need for further editing.
Example:
[...]
What do other people (in particular the maintainers of the posting
guide) think?
Some might argue that the and + prompts serve to mark the
presence of R code and distinguish it from message text. But then
the result is something that nobody can actually run. I think,
myself, that (especially with indenting of the code by a couple
of spaces) the format I describe is clearly enough distinguished.
Ted.
2009/9/19 Ted Harding ted.hard...@manchester.ac.uk:
On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote:
At least in windows, if you right click directly in the r console,
there's a command for 'Paste commands only' which may be one
solution...
Not sure about other platforms..
hth
c
It was precisely for this kind of reason that, when including
R code in postings to the list, I took to formatting it in the
following kind of way:
_a - 1:10
_a
_# [1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
_a[1:5]
_# [1] 1 2 3 4 5
In this way, any R commands copy-pasted into R will work as-is,
anything else is a comment and will not interfere. I notice that
some other people also post their code in this way.
I recommend it to all! If the code has been copy-pasted into the
email from an R console, then of course the prompts will be
there. But then I just edit these out of the email. A bit more
trouble for me, but a lot less trouble for others.
For instance, if someone had posted the above as copied from the
R console in its original form
a - 1:10
a
_[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
a[1:5]
[1] 1 2 3 4 5
and I wanted to try it out, then I would either have to re-open the
email in edit mode so as to edit the email itself, or else
copy-paste
the above into a text-edit window[*] and pre-edit it there before
copying into R.
[*] I would be using 'vim' in a Linux xterm. Removal of the
prompts (or + continuation prompts) from a long series of commands
is relatively easy: Just higlight a column-block of the first two
columns, then press d to delete them. But you would first need to
enter _# for other stuff by hand.
Best wishes to all,
Ted.
johannes rara wrote:
Hi,
How do you people avoid copy-pasting and manual editing of the code
posted in this list? I mean that if some one post a solution for an
answer like this:
a - 1:10
a
_[1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
a[1:5]
[1] 1 2 3 4 5
I have to copy-paste it to e.g. Tinn-R and remove part of the
line to try it in my R. When you keep doing this it gets quite
annoying. How do you people avoid this (search and replace,
perhaps?).
The best way would be to able to send
Re: [R] Creating histograms from factors using a for loop
On Sep 19, 2009, at 5:37 AM, Sam Player wrote:
# I have a dataframe with data and factors similar to the following:
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
# I am trying to write a 'for' loop which will produce a jpeg
histogram for each factor. I can individually isolate the data from
a factor and produce a jpeg histogram like so:
fnc - function(x){
x - df[df$f==a, d]
}
y - fnc(df[df$f==a, d])
jpeg(filename=foo.jpeg)
hist(y)
dev.off()
# I'm having trouble creating a loop repeating the process for all
the other factors. The following is the best I could come up with.
It produces a single jpeg histogram of the first factor titled with
a list of all the factors.
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
for (i in levels(df[,f])){
y - df[df$f==i, 2]
jpeg(filename=(levels(df[i,f])))
hist(y, main=levels(df[i,f]))
dev.off()
}
You are a bit unclear about what you are seeking but if you want
separate file names and titles that are factor-specifich, then why not
use i inside the loop as itself?
for (i in levels(df[,f])){
y - df[df$f==i, 2]
jpeg(filename=paste(file_,i,sep=))
hist(y, main=paste(Factor =,i,sep=))
dev.off()
}
# I'm obviously not understanding how loops work with factors.
It seems that you are unclear about loop indices. You are not really
passing factors anyway, but rather elements of a character vector,
levels(df[,f]).
Can anybody point me in the right direction?
--
Sam Player, B.Sc.(Hons.) B.A.
Ph.D. Candidate, Faculty of Agriculture, Food Natural Resources,
University of Sydney
Email: spla...@usyd.edu.au
Agroecosystems Research Group
Room 214 J.R.A. McMillan Building A05
University of Sydney NSW 2006, Australia
Angkor Research Program
Room 305 Old Teachers College A22
University of Sydney NSW 2006, Australia
__
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] Counting observations of a combined factor
Sam, Depending on what your ultimate aim is, perhaps you just want to add the 'drop=TRUE' argument to your interaction call. Peter Sam Player wrote: #I have a dataset with two factor. I want to combine those factors into a single factor and count the number of data values for each new factor. The following gives a comparable dataframe: a - rep(c(a, b), c(6,6)) b - rep(c(c, d), c(6,6)) df - data.frame(f1=a, f2=b, d=rnorm(12)) df # I use the 'interaction' function to combine factors f1 and f2: df2 - data.frame(f3=interaction(df[,f1], df[,f2]), d=df[,d]) df2 # A count of the first data.frame using factor f1 returns the kind of results I am looking for: count - as.data.frame(table(df$f1)) count # Var1 Freq #1a6 #2b6 # As does a count using factor2: count2 - as.data.frame(table(df$f2)) count2 # Var1 Freq #1a6 #2b6 # The same procedure on the second dataframe does not treat the levels of factor f3 discreetly, instead giving all possible combinations of f1 and f2. count3 - as.data.frame(table(df2$f3)) count3 # Var1 Freq #1 a.c6 #2 b.c0 #3 a.d0 #4 b.d6 I need the results to be: # Var1 Freq #1a6 #2b6 # Any suggestions? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating histograms from factors using a for loop
You could plot both histograms into the same file using this:
library(lattice)
jpeg(filename=combined.jpeg)
histogram(~d|f, data = df)
dev.off()
Schalk Heunis
On Sat, Sep 19, 2009 at 11:37 AM, Sam Player samtpla...@gmail.com wrote:
# I have a dataframe with data and factors similar to the following:
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
# I am trying to write a 'for' loop which will produce a jpeg histogram for
each factor. I can individually isolate the data from a factor and produce a
jpeg histogram like so:
fnc - function(x){
x - df[df$f==a, d]
}
y - fnc(df[df$f==a, d])
jpeg(filename=foo.jpeg)
hist(y)
dev.off()
# I'm having trouble creating a loop repeating the process for all the
other factors. The following is the best I could come up with. It produces a
single jpeg histogram of the first factor titled with a list of all the
factors.
a - rep(c(a, b), c(6,6))
df - data.frame(f=a, d=rnorm(12))
df
for (i in levels(df[,f])){
y - df[df$f==i, 2]
jpeg(filename=(levels(df[i,f])))
hist(y, main=levels(df[i,f]))
dev.off()
}
# I'm obviously not understanding how loops work with factors. Can anybody
point me in the right direction?
--
Sam Player, B.Sc.(Hons.) B.A.
Ph.D. Candidate, Faculty of Agriculture, Food Natural Resources,
University of Sydney
Email: spla...@usyd.edu.au
Agroecosystems Research Group
Room 214 J.R.A. McMillan Building A05
University of Sydney NSW 2006, Australia
Angkor Research Program
Room 305 Old Teachers College A22
University of Sydney NSW 2006, Australia
__
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] Counting observations of a combined factor
On Sep 19, 2009, at 5:39 AM, Sam Player wrote: #I have a dataset with two factor. I want to combine those factors into a single factor and count the number of data values for each new factor. The following gives a comparable dataframe: a - rep(c(a, b), c(6,6)) b - rep(c(c, d), c(6,6)) df - data.frame(f1=a, f2=b, d=rnorm(12)) df # I use the 'interaction' function to combine factors f1 and f2: df2 - data.frame(f3=interaction(df[,f1], df[,f2]), d=df[,d]) df2 # A count of the first data.frame using factor f1 returns the kind of results I am looking for: count - as.data.frame(table(df$f1)) count # Var1 Freq #1a6 #2b6 # As does a count using factor2: count2 - as.data.frame(table(df$f2)) count2 # Var1 Freq #1a6 #2b6 # The same procedure on the second dataframe does not treat the levels of factor f3 discreetly, instead giving all possible combinations of f1 and f2. We appear to have a different understanding of the term discrete. The interaction function produces all possible combinations of factors and then table() counts the occurrences of such. count3 - as.data.frame(table(df2$f3)) count3 # Var1 Freq #1 a.c6 #2 b.c0 #3 a.d0 #4 b.d6 I need the results to be: # Var1 Freq #1a6 #2b6 Puzzled. You already have such. Why would you want the interaction function to behave differently? Did you just want to create a label from f1 and f2? That can be achieved: df2 - df df2$f12 - with( df2, paste(f1,f2,sep=.) ) df2 f1 f2 d f12 1 a c -0.52902802 a.c 2 a c -1.07351118 a.c 3 a c 0.63463011 a.c 4 a c 0.26857599 a.c 5 a c 1.57677999 a.c 6 a c 1.08645153 a.c 7 b d -0.60400852 b.d 8 b d -0.06611533 b.d 9 b d 1.00787048 b.d 10 b d 1.48289305 b.d 11 b d 0.5465 b.d 12 b d -0.67630052 b.d count3 - as.data.frame(table(df2$f12)) count3 Var1 Freq 1 a.c6 2 b.d6 # Any suggestions? -- Sam Player, B.Sc.(Hons.) B.A. Ph.D. Candidate, Faculty of Agriculture, Food Natural Resources, University of Sydney Email: spla...@usyd.edu.au Agroecosystems Research Group Room 214 J.R.A. McMillan Building A05 University of Sydney NSW 2006, Australia Angkor Research Program Room 305 Old Teachers College A22 University of Sydney NSW 2006, Australia __ 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] How to avoid copy-paste when copying code from this list
On 19-Sep-09 14:12:08, Gabor Grothendieck wrote:
One solution would be to have a portable version of the
Windows
Edit | Paste commands only
functionality that works on all platforms.
For example if a command such as this were available:
source.commands - function(echo = TRUE, ...) {
L - readLines(clipboard)
L - grep(^[+] , L, value = TRUE)
L - gsub(^.., , L)
source(textConnection(L), echo = echo, ...)
}
one could just copy the email snippet and the issue this command in
the R session:
source.commands()
Building this directly into source as an option might be nice.
Neat, Gabor! I just tried it out on the following:
TP - function(x){
+ L - length(x)
+ which( ((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L]))
+ |((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L])) ) + 1
+ }
y-c(93,93,93,93,93,93,93,93,93,93,93,
+ 93,93,93,93,93,93,93,93,93,93,93)
m-c(02,02,02,02,02,02,02,02,02,02,02,
+ 02,02,02,02,02,02,02,02,02,02,02)
d-c(07,08,09,10,11,12,13,14,15,16,17,
+ 18,19,20,21,22,23,24,25,26,27,28)
ix - TP(count)
rbind(d[ix],count[ix])
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,]8.0 10 12.0 13 15 17.0 20.0 23.0 27.0
[2,] 3976.7 3955 3972.8 3961 4008 3981.2 4029.5 3848.3 3936.7
(which was the basis of my response on 17 Sept 2009 to Ogbos Okike's
query about turning-points, though then I edited out the prompts, etc.).
After entering the definition of your function source.commands(),
with the above already executed in an R session running in a Linux
xterm, I highlighted all the above with the mouse (which puts it in
the clipboard) and then, leaving it highlighted, entered the
command souce.commands().
This was the result (as it appeared on-screen):
source.commands()
TP - function(x){
+ L - length(x)
+ which( ((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L]))
+ |((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L [TRUNCATED]
y - c(93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93,
+ 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93)
m - c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+ 2, 2, 2, 2, 2, 2, 2)
d - c(7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
+ 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
ix - TP(count)
rbind(d[ix], count[ix])
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,]8.0 10 12.0 13 15 17.0 20.0 23.0 27.0
[2,] 3976.7 3955 3972.8 3961 4008 3981.2 4029.5 3848.3 3936.7
To check again, I opened Jens Oehlschlägel'e query on 18 Sept.
about basename, which contains the lines:
dirname(./.)
[1] .
basename(./.)
[1] .
dirname(./)
[1] .
basename(./)
[1] .
I highlighted these, went back to the R window, and again issued
your command. Result:
source.commands()
dirname(./.)
[1] .
basename(./.)
[1] .
dirname(./)
[1] .
basename(./)
[1] .
So it seems to work fine!
At any rate for basic use. I think it could have problems in some
cases, such as if the user had executed
cat( rbind(d[ix], count[ix]))
8 3976.7 10 3955 12 3972.8 13 3961 15 4008 17 3981.2 20 4029.5 23 3848.3
27 3936.7
But, most of the time, it should just work.
Thanks for the tip. One for my .Rprofile, I think!
Ted.
On Sat, Sep 19, 2009 at 5:46 AM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 19-Sep-09 08:48:45, johannes rara wrote:
The R help mailing list posting guide
http://www.r-project.org/posting-guide.html
suggests to give an example in this form
...snip...
f I have a matrix x as follows:
_ x - matrix(1:8, nrow=4, ncol=2,
_ _ _ _ _ _ _ _ dimnames=list(c(A,B,C,D), c(x,y))
_ x
_ _ x y
_ A 1 5
_ B 2 6
_ C 3 7
_ D 4 8
_
...snip...
Would it be reasonable to consider changing this guide about this
matter?
Yes, I think there is a case for a change. I must have read the
above myself, once, but ignored it later for the reasons I gave
below. In any case, that citation is not in the context of advice
about how to format R code when posting (there is no such advice
explicitly given in the posting-guide), but in the context that it
can be helpful to provide an example:
_Examples: Sometimes it helps to provide a small example that
_ someone can actually run. For example:
(then the example above). Possibly, people may tend to read that
example as if it were advice on formatting the code.
So maybe the change which could be helpful in the present context
would be to follow the above example with a section which advised
on how to format the code for examples which someone can actually
run (they cannot actually run the code as given in the example).
In other words, on the lines of
_When posting R code for examples, when this is copied from an R
_console remove any command prompts and continuation prompts
_+ from the code as it appears on the R console, and precede
_each line of R output, messages, etc., with # (to make it a
_comment, so that if the code is copy-pasted from R-help into an
_R console it will work as-is without
Re: [R] How to avoid copy-paste when copying code from this list
On 19/09/2009 10:12 AM, Gabor Grothendieck wrote:
One solution would be to have a portable version of the
Windows
Edit | Paste commands only
functionality that works on all platforms.
For example if a command such as this were available:
source.commands - function(echo = TRUE, ...) {
L - readLines(clipboard)
L - grep(^[+] , L, value = TRUE)
L - gsub(^.., , L)
source(textConnection(L), echo = echo, ...)
}
one could just copy the email snippet and the issue this command in
the R session:
source.commands()
Building this directly into source as an option might be nice.
The Windows Rgui is uses slightly more general patterns than those so it
can take output from running examples, e.g.
example(mean)
mean x - c(0:10, 50)
mean xm - mean(x)
m
[1] 8.75 5.50
mean mean(USArrests, trim = 0.2)
Murder Assault UrbanPop Rape
7.42 167.6066.2020.16
(and does it in C code, not using grep/gsub; see CleanTranscript in
https://svn.r-project.org/R/trunk/src/gnuwin32/console.c), but that's
basically what it does.
However, it's hard to do this in a portable way, because not all systems
support clipboard as the name of the clipboard for cut and paste. I
think Unix/Linux systems need to be running X11, and OSX systems don't
normally support it in the GUI. So it might makes sense to have a
portable version of the CleanTranscript function available, but it's
really up to each different system to connect it up to cut and paste.
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems.
And even this will sometimes mess up, e.g. it will sometimes
misinterpret output that contains or + as input.
Duncan Murdoch
On Sat, Sep 19, 2009 at 5:46 AM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 19-Sep-09 08:48:45, johannes rara wrote:
The R help mailing list posting guide
http://www.r-project.org/posting-guide.html
suggests to give an example in this form
...snip...
f I have a matrix x as follows:
x - matrix(1:8, nrow=4, ncol=2,
dimnames=list(c(A,B,C,D), c(x,y))
x
x y
A 1 5
B 2 6
C 3 7
D 4 8
...snip...
Would it be reasonable to consider changing this guide about this
matter?
Yes, I think there is a case for a change. I must have read the
above myself, once, but ignored it later for the reasons I gave
below. In any case, that citation is not in the context of advice
about how to format R code when posting (there is no such advice
explicitly given in the posting-guide), but in the context that it
can be helpful to provide an example:
Examples: Sometimes it helps to provide a small example that
someone can actually run. For example:
(then the example above). Possibly, people may tend to read that
example as if it were advice on formatting the code.
So maybe the change which could be helpful in the present context
would be to follow the above example with a section which advised
on how to format the code for examples which someone can actually
run (they cannot actually run the code as given in the example).
In other words, on the lines of
When posting R code for examples, when this is copied from an R
console remove any command prompts and continuation prompts
+ from the code as it appears on the R console, and precede
each line of R output, messages, etc., with # (to make it a
comment, so that if the code is copy-pasted from R-help into an
R console it will work as-is without the need for further editing.
Example:
[...]
What do other people (in particular the maintainers of the posting
guide) think?
Some might argue that the and + prompts serve to mark the
presence of R code and distinguish it from message text. But then
the result is something that nobody can actually run. I think,
myself, that (especially with indenting of the code by a couple
of spaces) the format I describe is clearly enough distinguished.
Ted.
2009/9/19 Ted Harding ted.hard...@manchester.ac.uk:
On 19-Sep-09 08:00:18, Cedrick W. Johnson wrote:
At least in windows, if you right click directly in the r console,
there's a command for 'Paste commands only' which may be one
solution...
Not sure about other platforms..
hth
c
It was precisely for this kind of reason that, when including
R code in postings to the list, I took to formatting it in the
following kind of way:
_a - 1:10
_a
_# [1] _1 _2 _3 _4 _5 _6 _7 _8 _9 10
_a[1:5]
_# [1] 1 2 3 4 5
In this way, any R commands copy-pasted into R will work as-is,
anything else is a comment and will not interfere. I
Re: [R] How to avoid copy-paste when copying code from this list
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
On 19/09/2009 10:12 AM, Gabor Grothendieck wrote:
One solution would be to have a portable version of the
Windows
Edit | Paste commands only
functionality that works on all platforms.
For example if a command such as this were available:
source.commands - function(echo = TRUE, ...) {
L - readLines(clipboard)
L - grep(^[+] , L, value = TRUE)
L - gsub(^.., , L)
source(textConnection(L), echo = echo, ...)
}
one could just copy the email snippet and the issue this command in
the R session:
source.commands()
Building this directly into source as an option might be nice.
The Windows Rgui is uses slightly more general patterns than those
so it can take output from running examples, e.g.
example(mean)
mean x - c(0:10, 50)
mean xm - mean(x)
m
[1] 8.75 5.50
mean mean(USArrests, trim = 0.2)
Murder Assault UrbanPop Rape
7.42 167.6066.2020.16
(and does it in C code, not using grep/gsub; see CleanTranscript in https://svn.r-project.org/R/trunk/src/gnuwin32/console.c)
, but that's basically what it does.
However, it's hard to do this in a portable way, because not all
systems support clipboard as the name of the clipboard for cut and
paste. I think Unix/Linux systems need to be running X11, and OSX
systems don't normally support it in the GUI. So it might makes
sense to have a portable version of the CleanTranscript function
available, but it's really up to each different system to connect it
up to cut and paste.
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value =
TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only
menu option does, but you'd need a different incantation on other
systems. And even this will sometimes mess up, e.g. it will
sometimes misinterpret output that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining
CleanTranscript produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+echo = TRUE, max.deparse.length=Inf)
example(mean)
mean x - c(0:10, 50)
mean xm - mean(x)
mean c(xm, mean(x, trim = 0.10))
[1] 8.75 5.50
mean mean(USArrests, trim = 0.2)
Murder Assault UrbanPop Rape
7.42 167.6066.2020.16
x - c(0:10, 50)
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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https://stat.ethz.ch/mailman/listinfo/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] matrix operations on grobs and grid units
Dear list,
As a minimal test of a more complex grid layout, I'm trying to find a
clean and efficient way to arrange text grobs in a rectangular layout.
The labels may be expressions, or text with a fontsize different of
the default, which means that the cell sizes should probably be
calculated using grobWidth() and grobHeight() as opposed to simpler
stringWidth() and stringHeight(). (Correct?).
The input of this function is a vector of labels, which are arranged
into a matrix layout. Below is my current version, followed by a few
questions.
e = expression(alpha,testing very large width, hat(beta),
integral(f(x)*dx, a, b))
rowMax.units - function(u, nrow){ # rowMax with a fake matrix of units
matrix.indices - matrix(seq_along(u), nrow=nrow)
do.call(unit.c, lapply(seq(1, nrow), function(ii) {
max(u[matrix.indices[ii, ]])
}))
}
colMax.units - function(u, ncol){ # colMax with a fake matrix of units
matrix.indices - matrix(seq_along(u), ncol=ncol)
do.call(unit.c, lapply(seq(1, ncol), function(ii) {
max(u[matrix.indices[, ii]])
}))
}
makeTableGrobs - function(e, ncol, nrow,
just = c(center, center),
gpar.text = gpar(col=black, cex=1),
gpar.fill = gpar(fill = grey95, col=white, lwd=1.5)) {
n - length(e) # number of labels
stopifnot(!n%%2) # only rectangular layouts
if(missing(ncol) missing(nrow)){
nm - n2mfrow(n) # pretty default layout
ncol = nm[1]
nrow = nm[2]
}
makeOneLabel - function(label.ind){
textGrob(label=e[label.ind], gp=gpar.text,
name=paste(cells-label-,label.ind, sep=))
}
lg - lapply(seq_along(e), makeOneLabel) # list of grobs
wg - lapply(lg, grobWidth) # list of grob widths
hg - lapply(lg, grobHeight) # list of grob heights
widths.all - do.call(unit.c, wg)
heights.all - do.call(unit.c, hg)
widths - colMax.units(widths.all, ncol)
heights - rowMax.units(heights.all, nrow)
gcells = frameGrob(name=table.cells, vp = cells,
layout = grid.layout(nrow, ncol, just=just,
widths = widths,
heights = heights) )
label.ind - 1 # index running for the vector of labels
for (ii in seq(1, ncol, 1)) {
for (jj in seq(1, nrow, 1)) {
gcells = placeGrob(gcells, rectGrob(gp=gpar.fill,
name=paste(cells-fill-r,ii, -c,jj,sep=)),
row=jj, col=ii)
text.grob.ij = textGrob(label=e[label.ind],
gp=gpar.text, name=paste(cells-label-r,ii,
-c,jj,sep=))
gcells = placeGrob(gcells, text.grob.ij, row=jj, col=ii)
label.ind - label.ind + 1
}
}
gList( gcells)
}
# tests
vp = viewport(name=cells)
grid.draw(gTree(children=makeTableGrobs(e), childrenvp=vp))
grid.newpage()
grid.draw(gTree(children=makeTableGrobs(e, 1, 4), childrenvp=vp))
grid.newpage()
grid.draw(gTree(children=makeTableGrobs(e, 4, 1), childrenvp=vp))
This works as expected, however I would like some advice before going
any further,
- because this layout seems quite common, would it make sense to
provide methods for the following objects? (i) a matrix of grobs; (ii)
a matrix of units; (iii) cbind, rbind, rowMax, colMax methods for a
matrix of units.
- is there a better, recommended way to achieve the same thing?
(examples would be great)
Any other comments are very welcome.
Best regards,
baptiste
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Re-order columns
Dear R'sians,
Would really appreciate if you could suggest a more efficient way to order
the columns of a dataset. The column names of the dataset contain indices
separated by a period. Following are examples of my code and the dataset.
oC - function(tg=x2) {
lth- length(grep(T,names(tg)))
thix - match(paste(T,seq(lth),sep=),names(tg))
soi- c(grep(O,names(tg),fixed=T),grep(S,names(tg),fixed=T))
oi -
data.frame(t(data.frame(strsplit(names(tg)[soi],\\.),stringsAsFactors=F)),stringsAsFactors=F)
names(oi) - c(par,ix1,ix2);row.names(oi) - NULL
oi$cnm - sub(^\\s+((.*\\S)\\s+)?$, \\2, paste(
,paste(oi$par,oi$ix1,oi$ix2, ,sep=.),sep=))
oi1- oi[order(oi$par,as.integer(oi$ix1),as.integer(oi$ix2)),]
return(list(oi1=oi1,thix=thix))
}
x1 - c(TABLE NO. 1: Gold ,
RT2 T1 O.4.1. O.3.1.
S.1.1. ,
0 3.68000E+01 1.41000E+03 4.94000E+03 2.33000E+01
4.9E+01,
43 3.77870E+01 2.46260E+03 4.44227E+03 2.31390E+01
4.84272E+01,
-1 3.67870E+01 1.46260E+03 4.44227E+03 2.31390E+01
4.84271E+01)
x2 - read.table(textConnection(x1),as.is=T,head=T,skip=1)
x3 - oC(x2)
pcols - c(names(x2)[x3$thix],x3$oi1$cnm)
x4 - x2[,match(c(setdiff(names(x2),pcols),pcols),names(x2))]
Thanks a TON
Santosh
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-order columns
I'm not sure I understand what you are doing below but to rearrange columns of
a data.frame you can just rearrange the indices. Is this what you mean?
A couple of examples:
(mydata - data.frame(aa=as.character(c(a, b, c, d, e)), bb = 1:5))
(mydata - mydata[,2:1])
df1 - structure(list(site = c(1, 1, 4, 4, 1, 4), id = structure(c(1L,
2L, 2L, 3L, 1L, 2L), .Label = c(a, b, c), class = factor),
cata = c(1, 1, 6, 1, 1, NA), catb = c(1, 2, 3, 4, 5, 6),
doga = c(3, 5, 3, 6, 4, 0), dogb = c(2, 4, 6, 8, 10, 12),
rata = c(NA, 9, 9, 8, 9, 8), ratb = c(1, 2, 3, 4, 5, 6),
bata = c(12, 42, NA, 45, 32, 54), batb = c(13, 15, 17, 19,
21, 23)), .Names = c(site, id, cata, catb, doga,
dogb, rata, ratb, bata, batb), row.names = c(aa,
bb, cc, dd, ee, ff), class = data.frame)
df1
(df1 - df1[,rev(1:10)])
--- On Sat, 9/19/09, Santosh santosh2...@gmail.com wrote:
From: Santosh santosh2...@gmail.com
Subject: [R] Re-order columns
To: r-help@r-project.org
Received: Saturday, September 19, 2009, 11:25 AM
Dear R'sians,
Would really appreciate if you could suggest a more
efficient way to order
the columns of a dataset. The column names of the dataset
contain indices
separated by a period. Following are examples of my code
and the dataset.
oC - function(tg=x2) {
lth -
length(grep(T,names(tg)))
thix -
match(paste(T,seq(lth),sep=),names(tg))
soi -
c(grep(O,names(tg),fixed=T),grep(S,names(tg),fixed=T))
oi -
data.frame(t(data.frame(strsplit(names(tg)[soi],\\.),stringsAsFactors=F)),stringsAsFactors=F)
names(oi) -
c(par,ix1,ix2);row.names(oi) - NULL
oi$cnm - sub(^\\s+((.*\\S)\\s+)?$,
\\2, paste(
,paste(oi$par,oi$ix1,oi$ix2, ,sep=.),sep=))
oi1 -
oi[order(oi$par,as.integer(oi$ix1),as.integer(oi$ix2)),]
return(list(oi1=oi1,thix=thix))
}
x1 - c(TABLE NO. 1: Gold ,
R T2
T1
O.4.1.
O.3.1.
S.1.1. ,
0
3.68000E+01 1.41000E+03 4.94000E+03
2.33000E+01
4.9E+01,
43
3.77870E+01 2.46260E+03 4.44227E+03
2.31390E+01
4.84272E+01,
-1
3.67870E+01 1.46260E+03 4.44227E+03
2.31390E+01
4.84271E+01)
x2 -
read.table(textConnection(x1),as.is=T,head=T,skip=1)
x3 - oC(x2)
pcols - c(names(x2)[x3$thix],x3$oi1$cnm)
x4 -
x2[,match(c(setdiff(names(x2),pcols),pcols),names(x2))]
Thanks a TON
Santosh
[[alternative HTML version deleted]]
__
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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.
__
Get a
__
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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] How to avoid copy-paste when copying code from this list
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
On 19/09/2009 10:12 AM, Gabor Grothendieck wrote:
One solution would be to have a portable version of the
Windows
Edit | Paste commands only
functionality that works on all platforms.
For example if a command such as this were available:
source.commands - function(echo = TRUE, ...) {
L - readLines(clipboard)
L - grep(^[+] , L, value = TRUE)
L - gsub(^.., , L)
source(textConnection(L), echo = echo, ...)
}
one could just copy the email snippet and the issue this command in
the R session:
source.commands()
Building this directly into source as an option might be nice.
The Windows Rgui is uses slightly more general patterns than those so it
can take output from running examples, e.g.
example(mean)
mean x - c(0:10, 50)
mean xm - mean(x)
m
[1] 8.75 5.50
mean mean(USArrests, trim = 0.2)
Murder Assault UrbanPop Rape
7.42 167.60 66.20 20.16
(and does it in C code, not using grep/gsub; see CleanTranscript in
https://svn.r-project.org/R/trunk/src/gnuwin32/console.c), but that's
basically what it does.
However, it's hard to do this in a portable way, because not all systems
support clipboard as the name of the clipboard for cut and paste. I think
Unix/Linux systems need to be running X11, and OSX systems don't normally
support it in the GUI. So it might makes sense to have a portable version
of the CleanTranscript function available, but it's really up to each
different system to connect it up to cut and paste.
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems. And
even this will sometimes mess up, e.g. it will sometimes misinterpret output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+ echo = TRUE, max.deparse.length=Inf)
example(mean)
mean x - c(0:10, 50)
mean xm - mean(x)
mean c(xm, mean(x, trim = 0.10))
[1] 8.75 5.50
mean mean(USArrests, trim = 0.2)
Murder Assault UrbanPop Rape
7.42 167.60 66.20 20.16
x - c(0:10, 50)
--
David Winsemius, MD
Heritage Laboratories
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.
__
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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] How to avoid copy-paste when copying code from this list
On Sep 19, 2009, at 11:58 AM, johannes rara wrote:
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
I agree entirely but trying to change posting behavior appears to be a
difficult exercise. It would also be much preferred if people would
learn to post the output of dput on an object, rather than what is
displayed on the console when the object is print()ed.
--
David.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
snip
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value =
TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands
only menu
option does, but you'd need a different incantation on other
systems. And
even this will sometimes mess up, e.g. it will sometimes
misinterpret output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from
the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining
CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+echo = TRUE, max.deparse.length=Inf)
example(mean)
snip
David Winsemius, MD
Heritage Laboratories
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] How to avoid copy-paste when copying code from this list
Combining the code posted by myself, Duncan and David we have:
# Usage: copy code from r-help to clipboard, then in R enter this:
# source.commands()
#
source.commands - function(echo = TRUE, max.deparse.length = Inf, ...) {
# L - readLines(pipe(pbpaste)) # use this instead for Mac
L - readLines(clipboard)
L - grep(^[[:blank:]]*[^+[:blank:]]*[+], L, value = TRUE)
L - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , L)
source(textConnection(L), echo = echo,
max.deparse.length = max.deparse.length, ...)
}
It might be possible to automate the check for Mac using .Platform$GUI
On Sat, Sep 19, 2009 at 12:08 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Sep 19, 2009, at 11:58 AM, johannes rara wrote:
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
I agree entirely but trying to change posting behavior appears to be a
difficult exercise. It would also be much preferred if people would learn to
post the output of dput on an object, rather than what is displayed on the
console when the object is print()ed.
--
David.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
snip
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems.
And
even this will sometimes mess up, e.g. it will sometimes misinterpret
output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+ echo = TRUE, max.deparse.length=Inf)
example(mean)
snip
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-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] reducing space between charts in lattice graphics
Hi, I'm trying to create a lattice plot with three xyplots in one vertical column. I would like to reduce the vertical space between the charts. My code is below. There seems to be a between parameter for lattice.options, but I can't find any examples. Aside from the data setup, the code is below. Can anyone provide an example showing how to reduce the white space between the charts? Thanks. total_chart - xyplot(total ~ date, xlab=list(label=), ylab=list(label=Total Work) ) balance_chart - xyplot(bal ~ date, xlab=list(label=), ylab=list(label=Remaining Work) ) index_chart - xyplot(index ~ date, col=red, type=b, pch=15) print(total_chart, split=c(1,1,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(balance_chart, split=c(1,2,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(index_chart, split=c(1,3,1,3), position=c(0, 0, 1, 1), newpage=TRUE, more=FALSE) [[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 avoid copy-paste when copying code from this list
Neat!
What if, instead, one wanted to format his/her code in the console
before sending it by email? Any tips for that?
(I proposed something like options(prompt= ) above, but got stuck
with adding a comment # to printed results)
Thanks,
baptiste
2009/9/19 Gabor Grothendieck ggrothendi...@gmail.com:
Combining the code posted by myself, Duncan and David we have:
# Usage: copy code from r-help to clipboard, then in R enter this:
# source.commands()
#
source.commands - function(echo = TRUE, max.deparse.length = Inf, ...) {
# L - readLines(pipe(pbpaste)) # use this instead for Mac
L - readLines(clipboard)
L - grep(^[[:blank:]]*[^+[:blank:]]*[+], L, value = TRUE)
L - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , L)
source(textConnection(L), echo = echo,
max.deparse.length = max.deparse.length, ...)
}
It might be possible to automate the check for Mac using .Platform$GUI
On Sat, Sep 19, 2009 at 12:08 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Sep 19, 2009, at 11:58 AM, johannes rara wrote:
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
I agree entirely but trying to change posting behavior appears to be a
difficult exercise. It would also be much preferred if people would learn to
post the output of dput on an object, rather than what is displayed on the
console when the object is print()ed.
--
David.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
snip
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems.
And
even this will sometimes mess up, e.g. it will sometimes misinterpret
output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+ echo = TRUE, max.deparse.length=Inf)
example(mean)
snip
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-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] reducing space between charts in lattice graphics
The Lattice book shows different uses of the layout and between parameters in the early examples in chapter 2. Why not go to the book's website and take a look? -- David. On Sep 19, 2009, at 12:42 PM, Larry White wrote: Hi, I'm trying to create a lattice plot with three xyplots in one vertical column. I would like to reduce the vertical space between the charts. My code is below. There seems to be a between parameter for lattice.options, but I can't find any examples. Aside from the data setup, the code is below. Can anyone provide an example showing how to reduce the white space between the charts? Thanks. total_chart - xyplot(total ~ date, xlab=list(label=), ylab=list(label=Total Work) ) balance_chart - xyplot(bal ~ date, xlab=list(label=), ylab=list(label=Remaining Work) ) index_chart - xyplot(index ~ date, col=red, type=b, pch=15) print(total_chart, split=c(1,1,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(balance_chart, split=c(1,2,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(index_chart, split=c(1,3,1,3), position=c(0, 0, 1, 1), newpage=TRUE, more=FALSE) [[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 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] Amazon SimpleDB and R
As far as I know there isn't anything available for this, but I thought I'd check before working up something of my own. Is there a way to query Amazon SimpleDB and import the data results directly into R? Cheers, Tim. __ 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] reducing space between charts in lattice graphics
xyplot.zoo does that by default. library(lattice) library(zoo) z - zoo(cbind(1:4, 2:5, 3:6)) xyplot(z, type = l) On Sat, Sep 19, 2009 at 12:42 PM, Larry White ljw1...@gmail.com wrote: Hi, I'm trying to create a lattice plot with three xyplots in one vertical column. I would like to reduce the vertical space between the charts. My code is below. There seems to be a between parameter for lattice.options, but I can't find any examples. Aside from the data setup, the code is below. Can anyone provide an example showing how to reduce the white space between the charts? Thanks. total_chart - xyplot(total ~ date, xlab=list(label=), ylab=list(label=Total Work) ) balance_chart - xyplot(bal ~ date, xlab=list(label=), ylab=list(label=Remaining Work) ) index_chart - xyplot(index ~ date, col=red, type=b, pch=15) print(total_chart, split=c(1,1,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(balance_chart, split=c(1,2,1,3), position=c(0, 0, 1, 1), newpage=FALSE, more=TRUE) print(index_chart, split=c(1,3,1,3), position=c(0, 0, 1, 1), newpage=TRUE, more=FALSE) [[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] Converting matrices into row vectors and saving as ASCII text
Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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] Rcmdr
Is there a UseR! manual in the works for the outstanding Rcmdr? -- Oscar Oscar A. Linares, MD Translational Medicine Unit Bolles Harbor Monroe, Michigan [[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] Rcmdr
Dear Oscar, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of oscar linares Sent: September-19-09 1:14 PM To: r-h...@stat.math.ethz.ch Subject: [R] Rcmdr Is there a UseR! manual in the works for the outstanding Rcmdr? First, thanks for the kind phrasing of your question. I'm not aware of a book specifically on the Rcmdr, nor do I plan to write one. It's my intention that the Rcmdr be largely self-explanatory, and I hope that it doesn't require a book for people to use it. That said, Heiberger and Neuwirth's recently published book, R Through Excel, in the Springer Use R! series, makes use of the Rcmdr menus and describes them. Regards, John -- Oscar Oscar A. Linares, MD Translational Medicine Unit Bolles Harbor Monroe, Michigan [[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] How to avoid copy-paste when copying code from this list
I made a python script to parse and + marks, if someone is interested:
#- start --
#!/Python26/
# -*- coding: utf-8 -*-
import sys
def main(argv):
if len(argv) 2:
sys.stderr.write(Usage: %s file.txt % (argv[0],))
return 1
f = open(sys.argv[1])
lines = f.readlines()
f.close()
for line in lines:
line = line.strip()
if not (line[:1] == or line[:1] == +):
continue
print line[2:]
if __name__ == __main__:
sys.exit(main(sys.argv))
#- end --
And to use it:
~ python strip_r-help.py code_from_r-help.txt
TP - function(x){
L - length(x)
which( ((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L]))
|((x[1:(L-2)]x[2:(N-1)])(x[2:(L-1)]x[3:L])) ) + 1
}
y-c(93,93,93,93,93,93,93,93,93,93,93,
93,93,93,93,93,93,93,93,93,93,93)
m-c(02,02,02,02,02,02,02,02,02,02,02,
02,02,02,02,02,02,02,02,02,02,02)
d-c(07,08,09,10,11,12,13,14,15,16,17,
18,19,20,21,22,23,24,25,26,27,28)
ix - TP(count)
rbind(d[ix],count[ix])
~
This is not a good solutions, but works especially when there is lots
of code to parse.
-Johannes
2009/9/19 baptiste auguie baptiste.aug...@googlemail.com:
Neat!
What if, instead, one wanted to format his/her code in the console
before sending it by email? Any tips for that?
(I proposed something like options(prompt= ) above, but got stuck
with adding a comment # to printed results)
Thanks,
baptiste
2009/9/19 Gabor Grothendieck ggrothendi...@gmail.com:
Combining the code posted by myself, Duncan and David we have:
# Usage: copy code from r-help to clipboard, then in R enter this:
# source.commands()
#
source.commands - function(echo = TRUE, max.deparse.length = Inf, ...) {
# L - readLines(pipe(pbpaste)) # use this instead for Mac
L - readLines(clipboard)
L - grep(^[[:blank:]]*[^+[:blank:]]*[+], L, value = TRUE)
L - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , L)
source(textConnection(L), echo = echo,
max.deparse.length = max.deparse.length, ...)
}
It might be possible to automate the check for Mac using .Platform$GUI
On Sat, Sep 19, 2009 at 12:08 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Sep 19, 2009, at 11:58 AM, johannes rara wrote:
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
I agree entirely but trying to change posting behavior appears to be a
difficult exercise. It would also be much preferred if people would learn to
post the output of dput on an object, rather than what is displayed on the
console when the object is print()ed.
--
David.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
snip
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems.
And
even this will sometimes mess up, e.g. it will sometimes misinterpret
output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+ echo = TRUE, max.deparse.length=Inf)
example(mean)
snip
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-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] Converting matrices into row vectors and saving as ASCII text
XYT - array(1:150, dim=c(3,5,10)) XYbyT= matrix(apply(XYT, 3, I), ncol=10) ...or even... XYbyT= matrix(XYT, ncol=10) -- David. On Sep 19, 2009, at 1:11 PM, Xi Ang wrote: Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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 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] generic methods - in particular the summary function
Hi all, I'm currently working on the fitdistrplus package (that basically fit distributions). There is something I do not understand about the generic function summary. In the current version on CRAN, there is no NAMESPACE saying S3method(summary, fitdist) . However if we use summary on an object send by fitdist function it works fine... According to R-lang, we have The most common use of generic functions is to provide print and summary methods for statistical ob jects, generally the output of some model fitting process. To do this, each model attaches a class attribute to its output and then provides a special method that takes that output and provides a nice readable version of it. The user then needs only remember that print or summary will provide nice output for the results of any analysis. I would like to be sure, that if the summary.fitdist is not exported in the NAMESPACE, then we must use declare it with S3method. Thanks in advance Christophe -- Christophe Dutang Ph.D. student at ISFA, Lyon, France website: http://dutangc.free.fr [[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] Windows RGui line editing
I've been using RGui and Tinn-R on Windows for a while now, but it continues to be a hassle that RGui supports only very rudimentary line editing. I can't even use Shift+arrows to select text, let alone use things like Ctrl+arrows to jump left or right a word at a time. I searched in the list archives and found what seem to be a few earlier references to this problem, but I couldn't find a clear answer on why it is or whether there's some workaround. I saw something in the docs about it being due to a lack of readline support on Windows, but it's hard for me to understand how this can be a deal-breaker, given that there are tons of programs that run on Windows with full line editing (e.g., cmd.exe, text editors, Python's IDLE). So, my question is, is there a way to use R in Windows with full line editing capabilities, or does every single person who uses R on Windows just suffer with this limitation? (The main reason I'm asking is that it seems hard for me to believe the latter is true, so I feel like I must be missing something.) Thanks, -- --OKB (not okblacke) Brendan Barnwell Do not follow where the path may lead. Go, instead, where there is no path, and leave a trail. --author unknown __ 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] matrix operations on grobs and grid units
A few amendments might make this improved code more readable,
e = expression(alpha,testing very large width, hat(beta),
integral(f(x)*dx, a, b))
library(grid)
rowMax.units - function(u, nrow){ # rowMax with a fake matrix of units
matrix.indices - matrix(seq_along(u), nrow=nrow)
do.call(unit.c, lapply(seq(1, nrow), function(ii) {
max(u[matrix.indices[ii, ]])
}))
}
colMax.units - function(u, ncol){ # colMax with a fake matrix of units
matrix.indices - matrix(seq_along(u), ncol=ncol)
do.call(unit.c, lapply(seq(1, ncol), function(ii) {
max(u[matrix.indices[, ii]])
}))
}
makeTableGrobs - function(e, ncol, nrow, equal.width = F, equal.height=F,
just = c(center, center),
gpar.text = gpar(col=black, cex=1),
gpar.fill = gpar(fill = grey95, col=white, lwd=1.5)) {
n - length(e) # number of labels
stopifnot(!n%%2) # only rectangular layouts
if(missing(ncol) missing(nrow)){
nm - n2mfrow(n) # pretty default layout
ncol = nm[1]
nrow = nm[2]
}
makeOneLabel - function(label.ind){
textGrob(label=e[label.ind], gp=gpar.text,
name=paste(cells-label-,label.ind, sep=))
}
makeOneCell - function(label.ind){
rectGrob(gp=gpar.fill, name=paste(cells-fill-,label.ind, sep=))
}
lg - lapply(seq_along(e), makeOneLabel) # list of text grobs
lf - lapply(seq_along(e), makeOneCell) # list of rect grobs
wg - lapply(lg, grobWidth) # list of grob widths
hg - lapply(lg, grobHeight) # list of grob heights
widths.all - do.call(unit.c, wg) # all grob widths
heights.all - do.call(unit.c, hg) #all grob heights
widths - colMax.units(widths.all, ncol) # all column widths
heights - rowMax.units(heights.all, nrow) # all row heights
if(equal.width)
widths - rep(max(widths), length(widths))
if(equal.height)
heights - rep(max(heights), length(heights))
gcells = frameGrob(name=table.cells, vp = cells,
layout = grid.layout(nrow, ncol, just=just,
widths = widths, heights = heights) )
label.ind - 1 # index running accross labels
for (ii in seq(1, ncol, 1)) {
for (jj in seq(1, nrow, 1)) {
gcells = placeGrob(gcells, lf[[label.ind]], row=jj, col=ii)
gcells = placeGrob(gcells, lg[[label.ind]], row=jj, col=ii)
label.ind - label.ind + 1
}
}
gl = gList( gcells)
gl
}
# tests
vp = viewport(name=cells)
g1 - gTree(children=makeTableGrobs(e), childrenvp=vp)
g2 - gTree(children=makeTableGrobs(e, 4, 1), childrenvp=vp)
g3 - gTree(children=makeTableGrobs(e, 1, 4), childrenvp=vp)
g4 - gTree(children=makeTableGrobs(e, equal.w=T), childrenvp=vp)
g5 - gTree(children=makeTableGrobs(e, equal.h=T), childrenvp=vp)
g6 - gTree(children=makeTableGrobs(e, equal.h=T, equal.w=T), childrenvp=vp)
source(http://gridextra.googlecode.com/svn-history/r21/trunk/R/arrange2.r;)
# wrapper around grid.layout and grid.draw
arrange2(g1, g2, g3, g4, g5, g6, main=Testing different fitting arrangements)
This works as expected, however I would like some advice before going
any further,
- because this layout seems quite common, would it make sense to
provide methods for the following objects? (i) a matrix of grobs; (ii)
a matrix of units; (iii) cbind, rbind, rowMax, colMax methods for a
matrix of units.
- is there a better, recommended way to achieve the same thing?
(examples would be great)
Any comments and suggestions are very welcome.
Best regards,
baptiste
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[R] [R-pkgs] homals package and core loop
The homals package http://www.jstatsoft.org/v31/i04 will get a major programming overhaul. This will take some time, but what's a few years on a 40-year project. Suggestions from the audience are welcome. homals() has a core loop over the m variables in which 1. tapply is used to compute category quantification (centroids) 2. category quantifications are then adjusted to satisfy the rank and level constraints The idea is to replace 1 by least squares fitting of a B-spline and to adjust 2 accordingly. The core will be re-programmed in C and/or FORTRAN (sometimes using existing routines), and the loop over variables will be parallelized using OpenMP or Grand Central Dispatch. For ordinal variables this requires some alternative quadratic programming routines to be linked in (which could then also become part of the isotone package). In addition the basic homals code will have object (individual) weights (minor addition) and the prehom routines (from the jacobi package) will be added. Because of the use of B splines the variables in homals will no longer be all factors, some can now be numerical (continuous). Otherwise the package will keep its many analysis options (multi-set non-metric canonical analysis, non-metric discriminant analysis, non-metric regression, multiple correspondence analysis, non-metric principal components analysis, non-metric additive conjoint analysis) and its many plot options. Jan de Leeuw, 11667 Steinhoff Rd, Frazier Park, CA 93225 home 661-245-1725 mobile 661-231-5416 work 310-825-9550 .mac: jdeleeuw +++ aim: deleeuwjan +++ skype: j_deleeuw If I wanted you to understand it, I would have explained it better. -- Johan Cruijff ___ 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] Poisson Regression - Query
Hi All, My dependent variable is a ratio that takes a value of 0 (zero) for 95% of the observations and positive non-integer values for the other 5%. What model would be appropriate? I'm thinking of fitting a GLM with a Poisson ~. Now, becuase it takes non-integer values, using the glm function with Poisson family issues warning messages. Warning messages: 1: In dpois(y, mu, log = TRUE) : non-integer x = 0.430783 2: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 3: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 4: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 5: In dpois(y, mu, log = TRUE) : non-integer x = 0.371564 I'll appreciate your thoughts. Thanks! Axel. [[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] Poisson Regression - Query
On Sat, 19 Sep 2009, Axel Urbiz wrote: Hi All, My dependent variable is a ratio that takes a value of 0 (zero) for 95% of the observations and positive non-integer values for the other 5%. What model would be appropriate? I'm thinking of fitting a GLM with a Poisson ~. Now, becuase it takes non-integer values, using the glm function with Poisson family issues warning messages. If it is a ratio of (integer-valued) counts in the numerator and some known denominator, say ratio = count/denom then one standard approach would be to fit glm(count ~ ..., offset = log(denom), data = ..., family = poisson) because this corresponds to log(count) = x'beta + log(denom) = log(count/denom) = x'beta To address the excess zeros, you could use a hurdle model or a zero-inflated model. See http://www.jstatsoft.org/v27/i08/ Best, Z Warning messages: 1: In dpois(y, mu, log = TRUE) : non-integer x = 0.430783 2: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 3: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 4: In dpois(y, mu, log = TRUE) : non-integer x = 0.162519 5: In dpois(y, mu, log = TRUE) : non-integer x = 0.371564 I'll appreciate your thoughts. Thanks! Axel. [[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] eval(expr) without printing to screen?
Hi,
I have a script which I source, which evaluates a changing expression
call hundreds of times. It works, but it prints to screen each time,
which is annoying. There must be simple way to suppress this, or to use
a slightly different set of commands, which will be obvious to those
wiser than I...
Here is a simpler mockup which shows the issue:
x = data.frame(rbind(c(1,2,3),c(1,2,3)))
xnames = c(a, b, c)
names(x) = xnames
for(i in 1:length(x))
{
# Create a varying string expression
expr = paste(y = x$, xnames[i], [1], sep=)
# evaluate expression
eval(parse(text=print(expr)))
# This command prints the expression to screen even when embedded in a
function in a sourced script. I would prefer it didn't!
}
PS: I have to go through this rigamarole:
expr = y1 = x$c[1]
eval(parse(text=print(expr)))
Because the following doesn't work, even though it seems like it should:
expr = y = x$c[2]
eval(expr)
--
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
-
[W]hen people thought the earth was flat, they were wrong. When people
thought the earth was spherical, they were wrong. But if you think that
thinking the earth is spherical is just as wrong as thinking the earth
is flat, then your view is wronger than both of them put together.
Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer,
14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] eval(expr) without printing to screen?
Hi,
What about this,
eval(parse(text=expr))
(no print)
HTH,
baptiste
2009/9/19 Nick Matzke mat...@berkeley.edu:
Hi,
I have a script which I source, which evaluates a changing expression call
hundreds of times. It works, but it prints to screen each time, which is
annoying. There must be simple way to suppress this, or to use a slightly
different set of commands, which will be obvious to those wiser than I...
Here is a simpler mockup which shows the issue:
x = data.frame(rbind(c(1,2,3),c(1,2,3)))
xnames = c(a, b, c)
names(x) = xnames
for(i in 1:length(x))
{
# Create a varying string expression
expr = paste(y = x$, xnames[i], [1], sep=)
# evaluate expression
eval(parse(text=print(expr)))
# This command prints the expression to screen even when embedded in a
function in a sourced script. I would prefer it didn't!
}
PS: I have to go through this rigamarole:
expr = y1 = x$c[1]
eval(parse(text=print(expr)))
Because the following doesn't work, even though it seems like it should:
expr = y = x$c[2]
eval(expr)
--
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
-
[W]hen people thought the earth was flat, they were wrong. When people
thought the earth was spherical, they were wrong. But if you think that
thinking the earth is spherical is just as wrong as thinking the earth is
flat, then your view is wronger than both of them put together.
Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer,
14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
__
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] eval(expr) without printing to screen?
On Sep 19, 2009, at 4:48 PM, Nick Matzke wrote:
Hi,
I have a script which I source, which evaluates a changing
expression call hundreds of times. It works, but it prints to
screen each time, which is annoying. There must be simple way to
suppress this, or to use a slightly different set of commands, which
will be obvious to those wiser than I...
Here is a simpler mockup which shows the issue:
x = data.frame(rbind(c(1,2,3),c(1,2,3)))
xnames = c(a, b, c)
names(x) = xnames
for(i in 1:length(x))
{
# Create a varying string expression
expr = paste(y = x$, xnames[i], [1], sep=)
# evaluate expression
eval(parse(text=print(expr)))
Why are you printing expr? Seems that you are making it difficult to
achieve your goal of quiet execution if you print the expressions
inside the parse function.
# This command prints the expression to screen even when embedded in
a function in a sourced script. I would prefer it didn't!
}
PS: I have to go through this rigamarole:
expr = y1 = x$c[1]
eval(parse(text=print(expr)))
Because the following doesn't work, even though it seems like it
should:
expr = y = x$c[2]
eval(expr)
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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Re: [R] eval(expr) without printing to screen?
David,
You can used the sink function to direct the output to a file. When you do
this, nothing is printed on the screen.
e.g.
sink(c:\\RResu.txt) #Defines location to which output is to be written
#R code goes here
sink() #Turns off redirection, any code after this
will print to the screen
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
David Winsemius dwinsem...@comcast.net 9/19/2009 5:01 PM
On Sep 19, 2009, at 4:48 PM, Nick Matzke wrote:
Hi,
I have a script which I source, which evaluates a changing
expression call hundreds of times. It works, but it prints to
screen each time, which is annoying. There must be simple way to
suppress this, or to use a slightly different set of commands, which
will be obvious to those wiser than I...
Here is a simpler mockup which shows the issue:
x = data.frame(rbind(c(1,2,3),c(1,2,3)))
xnames = c(a, b, c)
names(x) = xnames
for(i in 1:length(x))
{
# Create a varying string expression
expr = paste(y = x$, xnames[i], [1], sep=)
# evaluate expression
eval(parse(text=print(expr)))
Why are you printing expr? Seems that you are making it difficult to
achieve your goal of quiet execution if you print the expressions
inside the parse function.
# This command prints the expression to screen even when embedded in
a function in a sourced script. I would prefer it didn't!
}
PS: I have to go through this rigamarole:
expr = y1 = x$c[1]
eval(parse(text=print(expr)))
Because the following doesn't work, even though it seems like it
should:
expr = y = x$c[2]
eval(expr)
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
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[R] Lattice: combine the same strip?
Hello R helpers, I am producing a figure with dual strips, i.e., x~y | S1 + S2, where S1 and S2 are two strips. For example, in figure 2.1 at http://lmdvr.r-forge.r-project.org/figures/figures.html. In this case, I would like to combine the the top strip, since all three pictures in the same row have the same level based on the first strip. In other words, instead of | -- S11 -- | -- S11 -- | -- S11 -- | | -- S21 -- | -- S22 -- | -- S23 -- | I would like my graph to look like | - S11 | | -- S21 -- | -- S22 -- | -- S23 -- | In there a way I can do it? Thanks! JD [[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] Processing strings
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Processing strings
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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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.
Re: [R] Processing strings
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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https://stat.ethz.ch/mailman/listinfo/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] Processing strings
On 19/09/2009 6:51 PM, tzygmund mcfarlane wrote:
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
You must not have entered them correctly. His answer is fine.
Duncan Murdoch
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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https://stat.ethz.ch/mailman/listinfo/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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https://stat.ethz.ch/mailman/listinfo/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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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Processing strings
Ah, apologies. In the backing and forthing, I assigned the names to
the matrices. All sorted. Thanks!
On Sat, Sep 19, 2009 at 11:55 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 19/09/2009 6:51 PM, tzygmund mcfarlane wrote:
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
You must not have entered them correctly. His answer is fine.
Duncan Murdoch
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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.
__
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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] Processing strings
Try this:
sapply(ls(pattern = 'Table[0-9]'), get)
On Sat, Sep 19, 2009 at 7:51 PM, tzygmund mcfarlane
tzygm...@googlemail.com wrote:
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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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https://stat.ethz.ch/mailman/listinfo/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
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Re: [R] Processing strings
Hi tzygmund,
You can avoid the print() part and the result would be pretty much the same:
# Data
x1 - x2- x3 - matrix( rnorm(20), ncol = 5)
# Names to print
Names - paste('x', 1:3, sep=)
# New suggestion
sapply( Names, function( y ) list( get( y ) ) )
Best,
Jorge
On Sat, Sep 19, 2009 at 6:51 PM, tzygmund mcfarlane wrote:
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
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Re: [R] Processing strings
Thanks again!
On Sun, Sep 20, 2009 at 12:04 AM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Hi tzygmund,
You can avoid the print() part and the result would be pretty much the same:
# Data
x1 - x2- x3 - matrix( rnorm(20), ncol = 5)
# Names to print
Names - paste('x', 1:3, sep=)
# New suggestion
sapply( Names, function( y ) list( get( y ) ) )
Best,
Jorge
On Sat, Sep 19, 2009 at 6:51 PM, tzygmund mcfarlane wrote:
Jorge,
Your suggestions produce the names of the matrices and not the
contents. Sorry if this was not clear in the question.
On Sat, Sep 19, 2009 at 11:46 PM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Dear tzygmund,
Here are two suggestions:
# Suggestion 1
for (i in 1:10){
disp-paste(Table, i, sep=)
print(get(disp))
}
# Suggestion 2
disp - paste(Table, 1:10, sep=)
sapply(disp, function(x) print( get(x) ) )
See ?print and ?get for more information.
HTH,
Jorge
On Sat, Sep 19, 2009 at 6:40 PM, tzygmund mcfarlane wrote:
Hi,
I am unable to do something fairly simple. I have matrices called
Table1,..., Table10. I want to be able to print them using a loop. So
I wrote:
##
for (i in 1:10){
disp-paste(Table, i, sep=)
eval(parse(text=disp))
}
##
but this produces no output. Any ideas?
__
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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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Re: [R] Converting matrices into row vectors and saving as ASCII text
Thanks for your reply. Is there a way I can save the data to an ascii file without losing the row/column structure? I have tried save(...) and write.table(...) but the output file seems to jumble up the order of the matrix. Thanks Xi David Winsemius wrote: XYT - array(1:150, dim=c(3,5,10)) XYbyT= matrix(apply(XYT, 3, I), ncol=10) ...or even... XYbyT= matrix(XYT, ncol=10) -- David. On Sep 19, 2009, at 1:11 PM, Xi Ang wrote: Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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 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. -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25526729.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] plotting least-squares regression against x-axis
Hi, I want to plot the residuals of a least-squares regression. plot(lm(y~x), which=1) does this, but it plots the y-axis of my data on the x-axis of the residuals plot. That is, it plots the residual for each y-value in the data. Can I instead use the x-axis of my data as the x-axis of the residuals plot, showing the residual for a given x? Thanks! Jason Priem University of North Carolina at Chapel Hill School of Information and Library Science __ 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] plotting least-squares regression against x-axis
x - seq(50) y - 10 + x * 2 + rnorm(50,0,10) plot(y~x) mylm = lm(y~x) # Use str(mylm) to see how to get the residuals plot(x,mylm$residuals) On Sat, Sep 19, 2009 at 8:35 PM, Jason Priem pr...@email.unc.edu wrote: Hi, I want to plot the residuals of a least-squares regression. plot(lm(y~x), which=1) does this, but it plots the y-axis of my data on the x-axis of the residuals plot. That is, it plots the residual for each y-value in the data. Can I instead use the x-axis of my data as the x-axis of the residuals plot, showing the residual for a given x? Thanks! Jason Priem University of North Carolina at Chapel Hill School of Information and Library Science __ 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] Converting matrices into row vectors and saving as ASCII text
?cat ?apply ?t You could follow each row of the transposed matrix with a newline: apply(t(XYbyT), 1, function(x) cat(x, \n, file=output.txt, append=TRUE) ) On Sep 19, 2009, at 8:11 PM, Xi Ang wrote: Thanks for your reply. Is there a way I can save the data to an ascii file without losing the row/column structure? I have tried save(...) and write.table(...) but the output file seems to jumble up the order of the matrix. Thanks Xi David Winsemius wrote: XYT - array(1:150, dim=c(3,5,10)) XYbyT= matrix(apply(XYT, 3, I), ncol=10) ...or even... XYbyT= matrix(XYT, ncol=10) -- David. On Sep 19, 2009, at 1:11 PM, Xi Ang wrote: Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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 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. -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25526729.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 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] Converting matrices into row vectors and saving as ASCII text
Another possiblity: write.table( t(XYbyT), file=outcsv.csv, sep=\t) On Sep 19, 2009, at 9:16 PM, David Winsemius wrote: ?cat ?apply ?t You could follow each row of the transposed matrix with a newline: apply(t(XYbyT), 1, function(x) cat(x, \n, file=output.txt, append=TRUE) ) On Sep 19, 2009, at 8:11 PM, Xi Ang wrote: Thanks for your reply. Is there a way I can save the data to an ascii file without losing the row/column structure? I have tried save(...) and write.table(...) but the output file seems to jumble up the order of the matrix. Thanks Xi David Winsemius wrote: XYT - array(1:150, dim=c(3,5,10)) XYbyT= matrix(apply(XYT, 3, I), ncol=10) ...or even... XYbyT= matrix(XYT, ncol=10) -- David. On Sep 19, 2009, at 1:11 PM, Xi Ang wrote: Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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 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. -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25526729.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 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. 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] Converting matrices into row vectors and saving as ASCII text
If the only reason you want to save it is to later read it back into R later then see ?dump or even ?save On Sat, Sep 19, 2009 at 8:11 PM, Xi Ang slideprojec...@gmail.com wrote: Thanks for your reply. Is there a way I can save the data to an ascii file without losing the row/column structure? I have tried save(...) and write.table(...) but the output file seems to jumble up the order of the matrix. Thanks Xi David Winsemius wrote: XYT - array(1:150, dim=c(3,5,10)) XYbyT= matrix(apply(XYT, 3, I), ncol=10) ...or even... XYbyT= matrix(XYT, ncol=10) -- David. On Sep 19, 2009, at 1:11 PM, Xi Ang wrote: Hi I have some data with these dimensions: 5 3 100 which correspond to the x, y, and time dimensions, for a variable, p. I need the data in this format: 100 rows (1 row per time unit), and 15 values in each row. I have attempted to reshape my data dim(data) 5 3 100 attr(data,'dim')-c(dim(data)[3],dim(data)[1]*dimdata[2]) So I get data with 100 rows, 15 columns. I need to use this data outside of R, and so have to save it as an ASCII file that retains the row-column structure of the data, but I do not know how to. It would be ideal if I could end up with a text file that also has an additional column that labels which time unit (1-100) the row belongs to, i.e. 1 a1,1 a1,2 ... a1,15 2 a2,1 a2,2 ... a2,15 3 a3,1 a3,2 ... a3,15 4 a4,1 a4,2 ... a4,15 . . . 99 100 Any suggestions would be appreciated. Thanks Xi -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25523562.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 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. -- View this message in context: http://www.nabble.com/Converting-matrices-into-row-vectors-and-saving-as-ASCII-text-tp25523562p25526729.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.
[R] Regarding KS Test for Goodness-of-Fit
I have fitted Hyperexponential distribution (HED) and Hypoexponential distribution (HoED) to two different data sets (of size 1000 numeric values each) using a software package called EMpht. I want to use R to perform goodness-of-fit test for the fitted distribution with respect to the empirical CDFs of the data sets using KS test (Kolmogorov-Smirnov test). ks.test() function in R takes the first argument as the data set, and the second argument as the name of the distribution, followed by the distribution parameter values. In case of the CDFs that are already supported by R, this is simple (for example: ks.test(data_set, pnorm, mean, sd)). 1. Can somebody please suggest whether R has in-built support for Hyperexponential and Hypoexponential CDFs (they do not appear in the list of distribution given in An Introduction to R))? 2. If I write an R function to compute HED (or HoED) CDF value, can I use that function name as second argument in ks.test()? For example, if I implement an R function named HED_CDF with parameters parameters..., will it be correct to use ks.test() as follows: ks.test(data_set, HED_CDF, parameters...) Will it give correct result? - Manuj Sharma From cricket scores to your friends. Try the Yahoo! India Homepage! http://in.yahoo.com/trynew [[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] Barplot error with space=0, log=x
Hello, I would like to do a barplot that has a log-scaled x axis, but no space between the bars. I have attempted the following, but it produces an error that seems to indicate that the log scaling is dependent on the space being 0: x-c(1:100) barplot(x,log=x,space=0) Error message: In plot.window(xlim, ylim, log = log, ...) : nonfinite axis limits [GScale(-inf,2,1, .); log=1] Trying something like this does make a plot with effectively no space between bars, but the first bar becomes unacceptably wide: barplot(x,log=x,space=0.001) I get equivalent results with barplot and barplot2. Does anyone know a work-around for this issue? Thank you, Shawn Polson Delaware Biotechnology Institute University of Delaware -- View this message in context: http://www.nabble.com/Barplot-error-with-space%3D0%2C-log%3D%22x%22-tp25527514p25527514.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] Computing the sum of cross products of rows of a matrix
Hi everyone,
I would like to compute the sum of cross products of rows of a
matrix. Does anyone know how to do this without an explicit loop for
computational efficiency? Below is a code example.
Thanks!
Stephan
# I.e., if I have a matrix like this
x - matrix(rep(c(1,2,3),3),ncol=3)
## x
## [,1] [,2] [,3]
## [1,]111
## [2,]222
## [3,]333
## and a storage matrix like this
cross - matrix(rep(0,9),ncol=3)
## then use a loop to sum up the cross products of the rows
for (i in 1:nrow(x)){ cross - cross+tcrossprod(x[i,]) }
## The result
##
## cross
## [,1] [,2] [,3]
## [1,] 14 14 14
## [2,] 14 14 14
## [3,] 14 14 14
--
---
Stephan Lindner
University of Michigan
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Re: [R] Computing the sum of cross products of rows of a matrix
Dear Stephan,
Try
crossprod(x)
HTH,
Jorge
On Sat, Sep 19, 2009 at 11:42 PM, Stephan Lindner wrote:
Hi everyone,
I would like to compute the sum of cross products of rows of a
matrix. Does anyone know how to do this without an explicit loop for
computational efficiency? Below is a code example.
Thanks!
Stephan
# I.e., if I have a matrix like this
x - matrix(rep(c(1,2,3),3),ncol=3)
## x
## [,1] [,2] [,3]
## [1,]111
## [2,]222
## [3,]333
## and a storage matrix like this
cross - matrix(rep(0,9),ncol=3)
## then use a loop to sum up the cross products of the rows
for (i in 1:nrow(x)){ cross - cross+tcrossprod(x[i,]) }
## The result
##
## cross
## [,1] [,2] [,3]
## [1,] 14 14 14
## [2,] 14 14 14
## [3,] 14 14 14
--
---
Stephan Lindner
University of Michigan
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Re: [R] How to avoid copy-paste when copying code from this list
OK. I've combined both approaches into a single process.source()
function. Just place the mixed R code and output in the clipboard
and run:
source.commands()
it will 1. first display clipboard in a suitable manner for pasting into
an r-help post and then 2. execute it.
Thus you can either copy the code from an r-help post into the
clipboard and run the command or you can copy it from earlier
in your session and run the same command. Just ignore whichever
of the two outputs you don't need (or use the action= argument
to select the appropriate one).
# If clipboard contains R source statements prefaced by
# or + (or similar prefaces used in example()) together
# with unprefixed output then:
#source.commands()
# will perform these actions in sequence:
# 1. display the source removing the prefixes and commenting
#out the output and
# 2. run the source
# Alternately the first argument, action, can select only one of these.
# In all cases it invisibly returns the source that would have been
# displayed under #1.
#
process.source - function(action = c(both, run, show), echo = TRUE,
max.deparse.length = Inf, ...) {
# L - readLines(pipe(pbpaste)) # use this instead for Mac
L - readLines(clipboard)
rx - ^[[:blank:]]*[^+[:blank:]]*[+]
is.cmd - grepl(rx, L)
L[is.cmd] - gsub(paste(rx, ?), , L[is.cmd])
L[!is.cmd] - paste(#, L[!is.cmd])
action - match.arg(action)
if (action != run) for(el in L) cat(el, \n)
if (action == both) cat(##\n)
if (action != show) source(textConnection(L), echo = echo,
max.deparse.length = max.deparse.length, ...)
invisible(L)
}
On Sat, Sep 19, 2009 at 12:46 PM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
Neat!
What if, instead, one wanted to format his/her code in the console
before sending it by email? Any tips for that?
(I proposed something like options(prompt= ) above, but got stuck
with adding a comment # to printed results)
Thanks,
baptiste
2009/9/19 Gabor Grothendieck ggrothendi...@gmail.com:
Combining the code posted by myself, Duncan and David we have:
# Usage: copy code from r-help to clipboard, then in R enter this:
# source.commands()
#
source.commands - function(echo = TRUE, max.deparse.length = Inf, ...) {
# L - readLines(pipe(pbpaste)) # use this instead for Mac
L - readLines(clipboard)
L - grep(^[[:blank:]]*[^+[:blank:]]*[+], L, value = TRUE)
L - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , L)
source(textConnection(L), echo = echo,
max.deparse.length = max.deparse.length, ...)
}
It might be possible to automate the check for Mac using .Platform$GUI
On Sat, Sep 19, 2009 at 12:08 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Sep 19, 2009, at 11:58 AM, johannes rara wrote:
Thanks for the responses.
I think that the best way to avoid lots of hassle is that people
copy-paste their solutions from their code editor, NOT from R console.
For example, I usually save those solutions for my code archive, and
if I want to run these later on (using Tinn-R), I have to parse
and + marks anyway.
I agree entirely but trying to change posting behavior appears to be a
difficult exercise. It would also be much preferred if people would learn to
post the output of dput on an object, rather than what is displayed on the
console when the object is print()ed.
--
David.
-Johannes
2009/9/19 David Winsemius dwinsem...@comcast.net:
On Sep 19, 2009, at 10:58 AM, Duncan Murdoch wrote:
snip
Here's a quick version of CleanTranscript, translated to R:
CleanTranscript - function(lines) {
lines - grep(^[[:blank:]]*[^+[:blank:]]*[+], lines, value = TRUE)
lines - sub(^[[:blank:]]*[^+[:blank:]]*[+] ?, , lines)
}
So on systems where clipboard is supported, executing
source(textConnection(CleanTranscript(readLines(clipboard))),
echo = TRUE, max.deparse.length=Inf)
will do something similar to what the Windows Paste commands only menu
option does, but you'd need a different incantation on other systems.
And
even this will sometimes mess up, e.g. it will sometimes misinterpret
output
that contains or + as input.
Duncan Murdoch
On Macs (and possibly other *NIXen) the equivalent to reading from the
clipboard is: pipe(pbpaste)
Testing shows that a simple modification after defining CleanTranscript
produces no error on the example above:
source(textConnection(CleanTranscript(readLines(pipe(pbpaste,
+ echo = TRUE, max.deparse.length=Inf)
example(mean)
snip
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] axis: forcing last label to print
Hello, I often use the axis command to add labels to axes with large numbers of consecutively numbered names: y- barplot (x, log=x) axis(1, at = y, labels = c(1:12345)) Since there are more labels than will fit in the space, the command only prints selected labels. This is what I want, except that it never actually prints a label for the final item. Thus I end up with labels something like this: 1 16 123 1432 2134 3235 6578 11385 when I really want the last label displayed to be the final category number (12345): 1 16 123 1432 2134 3235 6578 12345 Short of manually choosing the labels, does anyone know a way to force the last category to be among those printed when axis selects labels? Thanks, Shawn Polson Delaware Biotechnology Institute University of Delaware -- View this message in context: http://www.nabble.com/axis%3A-forcing-last-label-to-print-tp25527633p25527633.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] plotting least-squares regression against x-axis
By the way, how about: plot(y,mylm$residuals) So you can have an idea of your error distribution across your response variable domain. :-) milton toronto=brazil On Sat, Sep 19, 2009 at 9:02 PM, Sunil Suchindran sunilsuchind...@gmail.com wrote: x - seq(50) y - 10 + x * 2 + rnorm(50,0,10) plot(y~x) mylm = lm(y~x) # Use str(mylm) to see how to get the residuals plot(x,mylm$residuals) On Sat, Sep 19, 2009 at 8:35 PM, Jason Priem pr...@email.unc.edu wrote: Hi, I want to plot the residuals of a least-squares regression. plot(lm(y~x), which=1) does this, but it plots the y-axis of my data on the x-axis of the residuals plot. That is, it plots the residual for each y-value in the data. Can I instead use the x-axis of my data as the x-axis of the residuals plot, showing the residual for a given x? Thanks! Jason Priem University of North Carolina at Chapel Hill School of Information and Library Science __ 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 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.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] Replacing values in dataframes
What I would probably do is along these lines: iddf - data.frame(Sample.id=names(Prot.amount), new.id=Prot.amount[1,]) newNAD - merge( NAD, iddf) This is not tested, but it looks right to me, assuming I understand the structure of what you're trying to do. I'm also assuming that NAD has more than three rows, and that Prot.amount has as many columns as NAD has rows. And that you just showed us the first three rows of NAD and first three columns of Prot.amount in order to keep the email simple. One final note ... if Prot.amount is an object within R, it is *not* a file. You may have read it in from a file, of course, but it isn't a file inside R. I'm assuming it's a dataframe. -Don At 1:18 PM +0300 9/19/09, Monna Nygård wrote: Hi, This is a question of a newbie getting into the exciting world of R. I have several dataframes in the same format as NAD: NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 148 10a 0.04836 0.04994 167 11a_1109 0.32245 0.36541 173 11b_1109 0.29293 0.32815 What I want to do is to replace the Sample.Id with a corresponding number.The number i have in another file,called Prot.amount Prot.amount[1:3,1] 10a 11a_1109 11b_1109 15.516 38.248 42.297 row.names(NAD)-(NAD[,1]) NAD$Sample.Id - replace(NAD$Sample.Id, NAD$Sample.Id==10a,Prot.amount[10a,1]) NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 10a 15.516 0.04836 0.04994 11a_1109 11a_1109 0.32245 0.36541 11b_1109 11b_1109 0.29293 0.32815 So what I have tried to do is to write a function that would allow me to replace the values automatically of all dataframes. This I just can't get to work. Thank you so much in advance! _ [[elided Hotmail spam]] [[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. -- - Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 m...@llnl.gov __ 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.
