[R] force pdf()
Hi is there a way to generate a pdf, e.g. pdf(test.pdf), even if the file test.pdf is open? (e.g. with acrobat) i.e. I would have to close test.pdf in the viewer without any user interaction, than override the file and maybe open it again. thx Christof __ 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] optimize integer function parameters
Hi I have observations obs - (11455, 11536, 11582, 11825, 11900, ...) and a simulation function f(A,B,C,D,E,F), so sim - f(A,B,C,D,E,F) e.g. sim = c(11464, 11554, 11603, 11831, 11907, ...) now I would like to fit A,B,C,D,E,F such that obs and f(A,B,C,D,E,F) match as well as possible. A,..,F should be integers and have bounds. How would you solve this problem without bruteforce in an acceptable time? thx Christof __ 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] optimize integer function parameters
Hi
the integer values in the vectors sim and obs are dates
when I set sim - f(TS0,TS1,TS2,TB0,TB1,TB2) my A,..,F below
then TS0 and TB0 are depend (and so on)
the main thing in f(...) is something like
for (i in c(1:length(temperature))) {
Temp - temperature[i]
if (DS 0) {
DS - DS + max(Temp-TB0,0) / TS0
} else if (DS 1) {
... date0 - i
DS - DS + max(Temp-TB1,0) / TS1
} else if (DS 2) {
... date1 - i
DS - DS + max(Temp-TB2,0) / TS2
} else {
... date2 - i
break
}
}
this produced a vector sim = c(date0,date1,date2,...)
now I would like to minimize RMSE(sim,obs) or something like that
thx
Christof
for brute force I would do something like
obs - ...
act - 1000
for (TS0 in seq(50,100,10))
for (TS1 in seq(750,850,10))
for (TS2 in seq(400,600,10))
for (TB0 in c(5:7))
for (TB1 in c(5:7))
for (TB2 in c(4:9)) {
sim - foosim(dat,TS0,TS1,TS2,TB0,TB1,TB2)
rmse - sqrt(mean((sim - obs)^2, na.rm = TRUE))
if (rmse act) {
print(paste(rmse,TS0,TS1,TS2,TB0,TB1,TB2))
act - rmse
}
}
Am 23-07-2013 13:20, schrieb Enrico Schumann:
On Tue, 23 Jul 2013, Christof Kluß ckl...@email.uni-kiel.de writes:
I have observations obs - (11455, 11536, 11582, 11825, 11900, ...)
and a simulation function f(A,B,C,D,E,F), so sim - f(A,B,C,D,E,F)
e.g. sim = c(11464, 11554, 11603, 11831, 11907, ...)
now I would like to fit A,B,C,D,E,F such that obs and f(A,B,C,D,E,F)
match as well as possible. A,..,F should be integers and have bounds.
How would you solve this problem without bruteforce in an acceptable time?
That depends on what your simulation function looks like. Could you
post a (small) self-contained example?
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[R] make R program faster
Hi
there are some good tips in The R Inferno
http://www.burns-stat.com/documents/books/the-r-inferno/
or connect C++ to R with Rcpp
http://dirk.eddelbuettel.com/code/rcpp.html
or byte code compiler (library(compiler))
or library(data.table)
but do you have an idea to fasten standard R source code, with the
following Rprof output
self.time self.pct total.time total.pct
[-.data.frame 1.3429.13 1.78 38.70
[.data.frame 0.26 5.65 1.02 22.17
[[ 0.12 2.61 0.44 9.57
NextMethod 0.12 2.61 0.12 2.61
match0.10 2.17 0.16 3.48
Anonymous 0.10 2.17 0.10 2.17
c0.10 2.17 0.10 2.17
[[.data.frame0.08 1.74 0.32 6.96
[.Date 0.06 1.30 0.10 2.17
FUN 0.06 1.30 0.10 2.17
[- 0.04 0.87 1.82 39.57
[0.04 0.87 1.04 22.61
[-.Date 0.04 0.87 0.18 3.91
vapply 0.04 0.87 0.14 3.04
%in% 0.02 0.43 0.18 3.91
+0.02 0.43 0.10 2.17
It comes from a simulation algorithmus that calculates day wise values
(values are depenend from the output of the day before). First I create
a data.frame with NAs. Finally each row contains the daily values.
output - as.data.frame(matrix(nrow = 365, ncol = 50))
for (day in (1:365)) {
...
r - list(Date=d,daylength=daylength,TempSum=tempsum, ...)
output[day,] - r
}
Is there an better (faster) way to do such things in R?
Greetings
Christof
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Re: [R] read tab delimited file from a certain line
Hi Henrik, that's perfect, thanks! Greetings Christof Am 18-01-2013 19:26, schrieb Henrik Bengtsson: Christof, I've added support for this to the R.filesets package. In your case, then all you need to do is: library(R.filesets) dlf - readDataFrame(filename, skip=^year) No need to specify any other arguments - they're all automagically inferred - and the default is stringsAsFactors=FALSE. This is in R.filesets v2.0.0 which I still haven't published on CRAN. In the meanwhile, you can install it via: source(http://aroma-project.org/hbLite.R;) hbLite(R.filesets) /Henrik On Thu, Jan 17, 2013 at 1:34 AM, Christof Kluß ckl...@email.uni-kiel.de wrote: Hello thank you for the fast and helpful answer! Now the following works fine for me x - readLines(filename) i - grep(^year, x) dlf - read.table(textConnection(x[i:length(x)]), header = T, stringsAsFactors=F,sep=\t) Greetings Christof Am 16-01-2013 16:55, schrieb Rui Barradas: Hello, Read the file using readLines, then grep ^year. You can then use a textConnection to read.table: x - readLines(con = textConnection( informations (unknown count of lines) ... and at some point the table -- year month mday value 2013 1 16 0 )) # This is it i - grep(^year, x) read.table(textConnection(x[i:length(x)]), header = TRUE) Hope this helps, Rui Barradas Em 16-01-2013 14:17, Christof Kluß escreveu: Hi I would like to read table data from a text-files with extra informations in the header (of unknown line count). Example: informations (unknown count of lines) ... and at some point the table -- year month mday value 2013 1 16 0 ... If it was an excel file I could use something like read.xls(..., pattern=year) But it is a simple tab seperated text-file. Is there an easy way to read only the table? (Without dirty things ;)) Thx Christof __ 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] read tab delimited file from a certain line
Hello thank you for the fast and helpful answer! Now the following works fine for me x - readLines(filename) i - grep(^year, x) dlf - read.table(textConnection(x[i:length(x)]), header = T, stringsAsFactors=F,sep=\t) Greetings Christof Am 16-01-2013 16:55, schrieb Rui Barradas: Hello, Read the file using readLines, then grep ^year. You can then use a textConnection to read.table: x - readLines(con = textConnection( informations (unknown count of lines) ... and at some point the table -- year month mday value 2013 1 16 0 )) # This is it i - grep(^year, x) read.table(textConnection(x[i:length(x)]), header = TRUE) Hope this helps, Rui Barradas Em 16-01-2013 14:17, Christof Kluß escreveu: Hi I would like to read table data from a text-files with extra informations in the header (of unknown line count). Example: informations (unknown count of lines) ... and at some point the table -- year month mday value 2013 1 16 0 ... If it was an excel file I could use something like read.xls(..., pattern=year) But it is a simple tab seperated text-file. Is there an easy way to read only the table? (Without dirty things ;)) Thx Christof __ 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] read tab delimited file from a certain line
Hi I would like to read table data from a text-files with extra informations in the header (of unknown line count). Example: informations (unknown count of lines) ... and at some point the table -- year month mday value 2013 1 16 0 ... If it was an excel file I could use something like read.xls(..., pattern=year) But it is a simple tab seperated text-file. Is there an easy way to read only the table? (Without dirty things ;)) Thx Christof __ 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] connect points in charts
Hi is there a automatic way that long distances between points are not connected. I have something like plot(x,y,type=o,...) atx - seq(as.Date(2009-04-01),as.Date(2011-04-01),month) axis.Date(1, at=atx,labels=format(atx, %b\n%Y), padj=0.5 ) but I do not want lines between points whose distance is greater than two weeks. thx Christof __ 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] mark sections on a time chart
Hi is there a comfortable way to mark periods on time chart (axis.Date)? To do it with arrows(...), seems to be irritating. I want to have something like ---winterspringsummer-- thx Christof __ 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] mark sections on a time chart
Hello Rui Barradas
thank you very much. That is exactly what I was looking for.
Christof
Am 20-10-2012 14:19, schrieb Rui Barradas:
library(zoo)
arrowsRange - function(from, to, at = 1, labels = NULL,
length = 1/8, horizontal = TRUE, border = FALSE, ...){
require(plotrix)
f1 - function(){
if(horizontal)
arrows(from, at, to, at, length = length, code = 3, ...)
else
arrows(at, from, at, to, length = length, code = 3, ...)
}
f2 - function(){
f1()
if(horizontal){
x - rowMeans(cbind(from, to))
y - at
}else{
x - at
y - rowMeans(cbind(from, to))
}
boxed.labels(x, y, labels = labels, border = border)
}
if(is.null(text)) f1() else f2()
}
# Make up some test data
set.seed(9365)
z - zoo(cumsum(rnorm(365)))
index(z) - Sys.Date() + 1:365
start - as.Date(c(2012-12-21, 2013-03-21, 2013-06-22))
end - as.Date(c(2013-03-20, 2013-06-21, 2013-09-21))
seasons - c(Winter, Spring, Summer)
plot(z)
abline(v = c(start[1], end))
arrowsRange(start, end, at = 0, labels = seasons)
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[R] lattice xyplot, get current level
Hi
xyplot(y ~ x | subject) plots a separate graph of y against x for each
level of subject. But I would like to have an own function for each
level. Something like
xyplot(y ~ x | subject,
panel = function(x,y) {
panel.xyplot(x,y)
panel.curve(x,y) {
# something that dependents on the current subject
...
}
})
How I get the current subject? (The current subject is the title of the
graph, too)
thx
Christof
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Re: [R] lattice xyplot, get current level
subj - levels(subject)
subj[panel.number()]
seems to be a good solution
is there something like panel.legend (instead of panel.text)?
Am 02-10-2012 12:59, schrieb Christof Kluß:
Hi
xyplot(y ~ x | subject) plots a separate graph of y against x for each
level of subject. But I would like to have an own function for each
level. Something like
xyplot(y ~ x | subject,
panel = function(x,y) {
panel.xyplot(x,y)
panel.curve(x,y) {
# something that dependents on the current subject
...
}
})
How I get the current subject? (The current subject is the title of the
graph, too)
thx
Christof
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[R] nlme function examples for dose-respone
Hi, I want to fit nonlinear dose-response curves, as fun(X,a,b,c), for each of our 5 trail locations. Our data basis is something like location plot year dose response For each location there are 4 plots as repetitions (over 3 years). So the interactions location*year and location*plot should be random effects. There are some examples in Mixed-Effects Models in S and S-PLUS (Pinheiro and Bates), but I do not see how they can help me for my model. Of course I can start with something like mod - nlme(response ~ fun(dose,a,b,c) , fixed = list(a ~ 1, b ~ 1, c ~ 1) , random = list(a ~ 1, b ~ 1, c ~ 1) , groups = ~location , data=dat , start= ... ) But that is not what I want. How do you describe that you want one fit for each of the five locations and that location*year and location*plot or something similar are random effects? Do you have some other examples that fit better to this problem setting? I welcome any tips. thx Christof __ 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] nlme function examples for dose-respone
Hi, thx Bert, I forward the question. I forgot a detail. For each (location, plot, year) combination there are 6 (dose, response) pairs. $ plot: Factor w/ 4 levels 1,2,3,4: $ location : Factor w/ 5 levels loc1,loc2,..: $ year: Factor w/ 3 levels 2009,2010,..: $ dose: num 27.3 32.7 57.2 33 183.1 ... $ response: num 54.2 64.9 74.3 62 92.2 ... So I can fit each (location, plot, year) with 6 points and make a bottom up approach. But I would be glad to have one overall model, like mod - nlme(response ~ fun(dose,a,b,c) , fixed = list(a ~ 1, b ~ 1, c ~ 1) , random = list(a ~ 1, b ~ 1, c ~ 1) , groups = ~location , data=dat , start= ... ) and location*plot and location*year as random and for each location one best fitted curve. But unfortunately I did not know how to formulate this in nlme. Christof Am 25-09-2012 18:13, schrieb Bert Gunter: 1. Post on R-sig-mixed-models instead. Much more expertise and relevance there. 2. I would forget about mixed effects and treat the locations as fixed. With only 5, you don't have enough information to estimate the variance component with any precision anyway. 3. Feel free to ignore (2) and defer to the experts at (1). Cheers, Bert On Tue, Sep 25, 2012 at 8:52 AM, Christof Kluß ckl...@email.uni-kiel.de wrote: Hi, I want to fit nonlinear dose-response curves, as fun(X,a,b,c), for each of our 5 trail locations. Our data basis is something like location plot year dose response For each location there are 4 plots as repetitions (over 3 years). So the interactions location*year and location*plot should be random effects. There are some examples in Mixed-Effects Models in S and S-PLUS (Pinheiro and Bates), but I do not see how they can help me for my model. Of course I can start with something like mod - nlme(response ~ fun(dose,a,b,c) , fixed = list(a ~ 1, b ~ 1, c ~ 1) , random = list(a ~ 1, b ~ 1, c ~ 1) , groups = ~location , data=dat , start= ... ) But that is not what I want. How do you describe that you want one fit for each of the five locations and that location*year and location*plot or something similar are random effects? Do you have some other examples that fit better to this problem setting? I welcome any tips. thx Christof __ 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] eval(parse(...)) only once in a function
Hi Thomas thx, already the e - parse(text=df$str==12)[[1]] is nice. So I have not to call parse in my function! (The function is called very often, so it makes the program much faster.) And eval(bquote(function(df) b-.(e))) is great! That's exactly what I was looking for. Christof Am 17-09-2012 22:52, schrieb Thomas Lumley: On Mon, Sep 17, 2012 at 6:27 PM, Christof Kluß ckl...@email.uni-kiel.de wrote: but for performance eval(parse(a)) should not be evaluated at each function call, but should work as You can do it with bquote() e-parse(text=df$str==12)[[1]] e df$str == 12 bquote(function(df) b-.(e)) function(df) b - df$str == 12 eval(bquote(function(df) b-.(e))) function (df) b - df$str == 12 This saves more time than I expected, about 100ms per evaluation on my computer. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] eval(parse(...)) only once in a function
Hi
I would like to have something like
str - df$JT == 12
fun - function(df) {
b - eval(parse(str))
return(b)
}
but for performance eval(parse(a)) should not be evaluated at each
function call, but should work as
fun - function(df) {
b - df$JT == 12
return(b)
}
Do you have an idea how I can implement this?
Thx
Christof
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[R] self-starter functions for y = a + b * c^x
Hi there are some predefined self-start functions, like SSmicmen, SSbiexp, SSasymp, SSasympOff, SSasympOrig, SSgompertz, SSflp, SSlogis, SSweibull, Quadratic, Qubic, SSexp (nlrwr) Btw, do you know graphic examples for this functions? The SSexpDecay (exponential decay) for y = (y0 - plateau)*exp(-k*x) + plateau from http://stats.stackexchange.com/questions/17126/how-can-i-make-my-r-nls-model-more-stable works fine, too. But now I search a self-starter for y = a + b * c^x Do you know a package that implement such self-starter or is there a easy way to do it myself? thx Christof __ 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] self-starter functions for y = a + b * c^x
Hi Ken Am 14-08-2012 11:50, schrieb ken knoblauch: Christof Kluß ckluss at email.uni-kiel.de writes: But now I search a self-starter for y = a + b * c^x You might be able to adapt the SS.calib function from the psyphy package for this. It was designed to fit gamma functions to the luminance vs frame buffer values measured on CRT screens. But the functional form is similar. thank you for the hint. I will test that function too. But it seems to be something like y = a + b * x^c and not y = a + b * c^x Greetings Christof __ 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] self-starter functions for y = a + b * c^x
Am 14-08-2012 19:40, schrieb Peter Ehlers: On 2012-08-14 00:09, Christof Kluß wrote: But now I search a self-starter for y = a + b * c^x Can't you just reparameterize with c^x = exp(x * log(c)) ? oh, I've missed this... thank you very much! Greetings Christof __ 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] alternative to rbind for data.table
Hi
I want to add a row to a data.table in each round of a for loop.
rbind seems to be a inefficient way to implement this.
How would you do this? The slow solution:
library(data.table)
Rprof(test.out)
dt - data.table()
for (i in (1:1)) {
# algorithm that generates a list with different values,
# but same key-names, each round, for example
l - list(A=1,B=2,C=3,E=4,F=5)
dt - rbind(dt,l) # very slow :(
}
Rprof(NULL)
summaryRprof(test.out)
thx
Christof
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Re: [R] save conditions in a list
Hi Rui Barradas
thank you very much, that's what I searched for
result - lapply(conds, fun, DF) works, if
day - DF$day
val - DF$val
Thanks
Christof
Am 02-07-2012 20:44, schrieb Rui Barradas:
Hello,
I'm not sure if this is what you want.
#-- Make up a dataset
set.seed(1)
n - 1e2
DF - data.frame(year=2010 + sample(3, n, TRUE),
day=sample(365, n, TRUE),
val=sample(100, n, TRUE))
a = day 100; b = val 50; c = year == 2012
conds - list(a=a, b=b, c=c)
#-- This does it
fun - function(condition, x){
f - function(){}
if(class(x) == matrix) x - data.frame(x)
if(class(x) == data.frame)
body(f) - with(x, parse(text=condition))
else
body(f) - parse(text=condition)
f()
}
#-- Test the function
year - DF$year # See if it works with vectors
fun(b, year)# Must throw error
fun(c, year)# Should work
# And now with data.frames
result - lapply(conds, fun, DF)
Reduce(``, result) # combine the results
Reduce(`|`, result) #
Hope this helps,
Rui Barradas
Em 02-07-2012 18:04, Christof Kluß escreveu:
Hi
how would you save conditions like
a = day 100; b = val 50; c = year == 2012
in a list? I like to have variables like day, val, year and a list
of conditions list(a,b,c). Then I want to check if a b c is true or
if a | b | c is true or similar things.
Greetings
Christof
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[R] save conditions in a list
Hi how would you save conditions like a = day 100; b = val 50; c = year == 2012 in a list? I like to have variables like day, val, year and a list of conditions list(a,b,c). Then I want to check if a b c is true or if a | b | c is true or similar things. Greetings Christof __ 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] lm without intercept, false R-squared
Hi is there a command that calculates the correct adjusted R-squared, when I work without intercept? (The R-squared from lm without intercept is false.) Greetings Chrsitof __ 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] lm without intercept, false R-squared
for example the same model with intercept R² = 0.6, without intercept R² = 0.9 and higher. In my definition of R², R² has to be equal or less without intercept I do not know what R shows, but in the summary of the model without intercept it does not show the R² of the regression line. When I run a regression I like to have the R² of the regression line and not something else. ;) Am 27-06-2012 10:25, schrieb Uwe Ligges: On 27.06.2012 09:33, Christof Kluß wrote: Hi is there a command that calculates the correct adjusted R-squared, when I work without intercept? (The R-squared from lm without intercept is false.) Then we need your definition of your version of correct - we know the definition of your version of false. Best, Uwe Ligges Greetings Chrsitof __ 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. -- Dipl.-Inf. Christof Kluß (Raum 223) | Universität Kiel Inst. für Pflanzenbau und -züchtung | www.gfo.uni-kiel.de Grünland u. Futterbau/Ökol. Landbau | ckl...@gfo.uni-kiel.de Hermann-Rodewald Str. 9, 24118 Kiel | Tel. 0431 880-2197 __ 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] lm without intercept, false R-squared
for example the same model with intercept R² = 0.6, without intercept R² = 0.9 and higher. In my definition of R², R² has to be equal or less without intercept I do not know what R shows, but in the summary of the model without intercept it does not show the R² of the regression line. When I run a regression I like to have the R² of the regression line and not something else. ;) Am 27-06-2012 10:25, schrieb Uwe Ligges: On 27.06.2012 09:33, Christof Kluß wrote: Hi is there a command that calculates the correct adjusted R-squared, when I work without intercept? (The R-squared from lm without intercept is false.) Then we need your definition of your version of correct - we know the definition of your version of false. Best, Uwe Ligges Greetings Chrsitof __ 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. -- Dipl.-Inf. Christof Kluß (Raum 223) | Universität Kiel Inst. für Pflanzenbau und -züchtung | www.gfo.uni-kiel.de Grünland u. Futterbau/Ökol. Landbau | ckl...@gfo.uni-kiel.de Hermann-Rodewald Str. 9, 24118 Kiel | Tel. 0431 880-2197 __ 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] visualize correlation matrix
Hi is there a easy way to get something like http://addictedtor.free.fr/graphiques/graphcode.php?graph=137 pairs(USJudgeRatings[,c(2:3,6,1,7)], lower.panel=panel.smooth, upper.panel=panel.cor) but without the lower.panel (and without numbers and ticks at the border.) thx Christof __ 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] lme: extract result-function
Hi,
mod - lme(A ~ -1 + B+C+D+E+F+G, random = ~1 | ...)
results in summary(mod)$coeff
B C D E F G (Intercept)
b c d e f g i
Now I'm interested in the function
f - function(B,C,D,E,F,G) - {
return(i + b*B + c*C + d*D + e*E + f*F + g*G)
}
Is there a easier way to create such function with flexible number of
coefficient, than do it by hand?
thx
Christof
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[R] plotting dates, incorrectly scaled x-axis?
Hi, I want to plot with axis.Date(), but something is scaled incorrectly. The red vertical line in is put on a totally wrong position. (sample below) Do you have an idea what I'm doing wrong? Thx Christof x11(width=30, height=20) x-seq(as.Date(2010-02-27), as.Date(2011-03-28),month) y - seq(0,100,length=length(x)) plot(y ~ x, type=o, tck=1, xaxt=n) axis.Date(1, at=x, labels=format(x,%b\n%Y), padj=0.5) abline(v=as.Date(2011-01-01), col=red, lty=dashed) __ 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 dates, incorrectly scaled x-axis?
Hi, I want to plot with axis.Date(), but something is scaled incorrectly. The red vertical line in is put on a totally wrong position. (sample below) Do you have an idea what I'm doing wrong? Thx Christof x11(width=30, height=20) x-seq(as.Date(2010-02-27), as.Date(2011-03-28),month) y - seq(0,100,length=length(x)) plot(y ~ x, type=o, tck=1, xaxt=n) axis.Date(1, at=x, labels=format(x,%b\n%Y), padj=0.5) abline(v=as.Date(2011-01-01), col=red, lty=dashed) attachment: plot.png__ 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] visualize lme results
Hi for each measurement day we use lme for our four repetitions. Now it would be great if we can represent the error too. The following seems to be good. Unfortunately, there is not the full example source code. Maybe someone has done it before. (from http://anthony.darrouzet-nardi.net/scienceblog/?p=406 ) Finally, here's a graph of the results for the ammonium data, showing the mean differences±95%CI between each of our three treatments and the control http://anthony.darrouzet-nardi.net/scienceblog/wp-content/uploads/2011/08/rm_analysis_demo.png thx Christof __ 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] break an axis.POSIXct
Hi I like to use axis.POSIXct to plot days from 2006 till 2008. But I only have datas for the summer months. Is it possible to get two axis breaks, to have not so long distances without points? thx Christof __ 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] selection part of subset
Hi
thank you very much for your useful answers! In this case I solved it
with Sarah's suggestion
tab[tab[[name]] == v,]
that works fine
Greetings
Christof
Am 05-01-2012 16:51, schrieb Christof Kluß:
Hi
I want to do something like
a - c(10,20,15,43,76,41,25,46)
tab - data.frame(a)
name - a
for (v in unique(tab[[name]])) {
r - subset(tab, name==v) # this does not work
...
}
i.e. a string on the left side of the select expression (subset). How
could I solve this?
thx
Christof
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[R] RODBC vs gdata
Hi one col in my Excel file contains many numbers. But on line 3000 and some other lines are strings like FG 1. RODBS seems to omit this lines. gdata works, but is much slower. Is this a bug of RODBC or do I apply it wrong? Example with the same file.xlsx library(RODBC); excel - odbcConnectExcel2007(file.xlsx) tab - sqlQuery(excel, 'select * from Table 1$'); str(tab) col1: num 1 2 3 4 5 6 7 8 9 10 ... library(gdata); tab - read.xls(file.xlsx, sheet=1); str(tab) col1: Factor w/ 51 levels 1,10,11,..: 1 12 23 34 41 42 43... greeting Christof __ 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] RODBC vs gdata
Hi Enrico, thank you very much, so it is a known problem with the Microsoft Excel ODBC drivers :( 7 Excel Drivers ... There are at least two known problems with reading columns that do not have a format set before data entry, and so start with format `General'. First, the driver uses the fi rst few rows to determined the column type, and is over-fond of declaring `Numeric' even when there are non-numeric entries. ... Second, if a column is declared as `Text', numeric entries will be read as SQL nulls and hence R NAs. Unfortunately, in neither case does reformatting the column help. So I think I have to use gdata to be sure to read all datas. regards Christof Am 09-01-2012 19:29, schrieb Enrico Schumann: Hi Christof, have a look at the manual of RODBC, and in particular the section on Excel drivers. RShowDoc(RODBC, package=RODBC) Regards, Enrico Am 09.01.2012 19:02, schrieb Christof Kluß: Hi one col in my Excel file contains many numbers. But on line 3000 and some other lines are strings like FG 1. RODBS seems to omit this lines. gdata works, but is much slower. Is this a bug of RODBC or do I apply it wrong? Example with the same file.xlsx library(RODBC); excel- odbcConnectExcel2007(file.xlsx) tab- sqlQuery(excel, 'select * from Table 1$'); str(tab) col1: num 1 2 3 4 5 6 7 8 9 10 ... library(gdata); tab- read.xls(file.xlsx, sheet=1); str(tab) col1: Factor w/ 51 levels 1,10,11,..: 1 12 23 34 41 42 43... greeting Christof __ 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] selection part of subset
Hi
I want to do something like
a - c(10,20,15,43,76,41,25,46)
tab - data.frame(a)
name - a
for (v in unique(tab[[name]])) {
r - subset(tab, name==v) # this does not work
...
}
i.e. a string on the left side of the select expression (subset). How
could I solve this?
thx
Christof
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Re: [R] selection part of subset
Hi
the output should look like r - subset(tab, a==v)
but now I have something like r - subset(tab, a==v)
and r - subset(tab, [[a]]==v)
does not work :(
greetings
Christof
Am 05-01-2012 16:51, schrieb Christof Kluß:
Hi
I want to do something like
a - c(10,20,15,43,76,41,25,46)
tab - data.frame(a)
name - a
for (v in unique(tab[[name]])) {
r - subset(tab, name==v) # this does not work
...
}
i.e. a string on the left side of the select expression (subset). How
could I solve this?
thx
Christof
__
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[R] clear plot linear mixed model
Hi, first a happy new year ;) I would like to plot the regression lines of a model like lme - lme(conc ~ name/time - 1, random=conc~time|nr,method=ML,data=measurements) Ideally a seperate plot for each regression line (respectively name) and seperate colors for the measurements (nr). How would you do that? thx Christof __ 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] clear plot linear mixed model
Am 02-01-2012 10:54, schrieb ken knoblauch: Christof Klußcklussat email.uni-kiel.de writes: lme- lme(conc ~ name/time - 1, random=conc~time|nr,method=ML,data=measurements) see plot.augPred in the nlme package thx, but how to set primary? I always get the error plot(augPred(lme)) augPred.lme without primary can only be used with fits of groupedData objects greetings Christof __ 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] apply on function with vector as result
Hi,
a have some code like
myfunc - function(x) { ...; return c(a,b) }
ys - sapply(0:100,myfunc)
so I get something like c(c(a1,b1),c(a2,b2),...)
But now I need the as and bs in one vector
as - apply(ys, function(c(a,b)) a)
bs - apply(ys, function(c(a,b)) b)
Can you help me with the correct syntax, instead of my pseudo code?
thx
Christof
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Re: [R] apply on function with vector as result
Am 09-12-2011 12:54, schrieb Sarah Goslee:
myfunc- function(x) {a=x; b=x-1; c(a, b) }
ys- sapply(1:5, myfunc)
ys
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]01234
And from there, it's not at all clear what you mean by one vector -
in what order? All of the a then all of the b values? abab?
as.vector(ys) and as.vector(t(ys)) will accomplish those.
Or do you mean simply
as- ys[1,]
bs- ys[2,]
Thank you very much! That is what I was looking for. Sorry that I have
expressed myself so unclear.
Greetings
Christof
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Re: [R] simplify source code
Hi
now I'd like to do
for (colname in c('ColName1','ColName2','ColName3')) {
dat - measurements$colname
But that does not work, though I can write
measurements$C1 (same as measurements$C1)
(but different to measurements[C1]!)
Can you give me a hint?
greetings
Christof
Am 26-11-2011 23:30, schrieb Christof Kluß:
Hi
I would like to shorten
mod1 - nls(ColName2 ~ ColName1, data = table, ...)
mod2 - nls(ColName3 ~ ColName1, data = table, ...)
mod3 - nls(ColName4 ~ ColName1, data = table, ...)
...
is there something like
cols = c(ColName2,ColName3,ColName4,...)
for i in ...
mod[i-1] - nls(ColName[i] ~ ColName1, data = table, ...)
I am looking forward to help
Christof
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Re: [R] simplify source code
Hi Dennis,
thank you very much. That works fine.
Is there a possibility that R continue even if one of the models is not
solvable? R currently terminates with an error message.
greetings
Christof
Am 27-11-2011 01:34, schrieb Dennis Murphy:
vars- c('y1', 'y2', 'y3')
# Function to create the model formula by plugging in the
# response y and run the model
mfun- function(y) {
form- as.formula(paste(y, 'cbind(1, exp(x/th))', sep = ' ~ '))
nls(form, data = dg, start = list(th = 0.3), algorithm = 'plinear')
}
# Generate a list of model objects:
mlist- lapply(vars, mfun)
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Re: [R] append to PDF file
Hi Jim, Hi Ken
Am 27-11-2011 00:00, schrieb jim holtman:
There is the 'pdftk' (PDF tool kit) that you will find on the web that
will do the job. I have used it to both combine and split out the
pages in the PDF file.
yes, thx. GUI tools like www.pdfsam.org do the job too. But is there a
possibility to append files directly in R. That is to invoke pdftk
inside R with a shellandwait?
perhaps something like
for (i in ...) {
...
savePlot(filename=temp.pdf, type=pdf)
exec pdftk temp.pdf final.pdf cat output final.pdf
}
greetings
Christof
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[R] simplify source code
Hi I would like to shorten mod1 - nls(ColName2 ~ ColName1, data = table, ...) mod2 - nls(ColName3 ~ ColName1, data = table, ...) mod3 - nls(ColName4 ~ ColName1, data = table, ...) ... is there something like cols = c(ColName2,ColName3,ColName4,...) for i in ... mod[i-1] - nls(ColName[i] ~ ColName1, data = table, ...) I am looking forward to help Christof __ 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] append to PDF file
Hi is there a way to append a plot as PDF to an existing PDF file? savePlot seems not to have this possibility. Christof __ 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] Fwd: linear regression with replication
Probably the question fits better in the lme4 mailing list, so I forwarded it. Original-Nachricht Betreff: linear regression with replication Datum: Mon, 23 May 2011 16:31:54 +0200 Von: Christof Kluß ckl...@email.uni-kiel.de An: r-h...@stat.math.ethz.ch Newsgruppen: gmane.comp.lang.r.general Hi, we want to calculate a linear regression that results from three test series. (The Average linear regression over 3 replication.) Each test serie consists of the values for 3 times (0min, 25min, 50min) and is repeated three times. We need such a regression for each combination of subject and day for a file like this: subject time date replication value 1A0 2011-01-01 1 0.2 2A 25 2011-01-01 1 0.3 3A 50 2011-01-01 1 0.4 4A0 2011-01-01 2 0.2 5A 25 2011-01-01 2 0.2 6A 50 2011-01-01 2 0.3 7A0 2011-01-01 3 0.3 8A 25 2011-01-01 3 0.4 9A 50 2011-01-01 3 0.5 ... 2011-01-02 ... ... 2011-01-02 ... 2011-01-02 [...] B Can you give us a hint how the R-file could look for this example? We think that we should choose the library nlme and the command lme. We are interested in the slope and intercept for each combination of subject and date. Greetings Christof __ 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] linear regression with replication
Hi, we want to calculate a linear regression that results from three test series. (The Average linear regression over 3 replication.) Each test serie consists of the values for 3 times (0min, 25min, 50min) and is repeated three times. We need such a regression for each combination of subject and day for a file like this: subject time date replication value 1A0 2011-01-01 1 0.2 2A 25 2011-01-01 1 0.3 3A 50 2011-01-01 1 0.4 4A0 2011-01-01 2 0.2 5A 25 2011-01-01 2 0.2 6A 50 2011-01-01 2 0.3 7A0 2011-01-01 3 0.3 8A 25 2011-01-01 3 0.4 9A 50 2011-01-01 3 0.5 ... 2011-01-02 ... ... 2011-01-02 ... 2011-01-02 [...] B Can you give us a hint how the R-file could look for this example? We think that we should choose the library nlme and the command lme. We are interested in the slope and intercept for each combination of subject and date. Greetings Christof __ 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] nonlinear regression with an iterativ function
Hi,
we have a function that calculates a value for each day of the year.
For example an iterative function like
actvalue_0 := 0
actvalue_ {t+1} := actvalue_t + f(param_1,param_2,actvalue_t)
and for some days we have measurements. Now we want to choose param_1
and param_2 so that the function values are close to our measured values.
Does anyone know how to solve this problem?
Thanks,
Christof
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