[R] subset and or operator
Hello, I'm trying to subset a dataframe where I have many observation taken in different years. I would like to subset the dataframe (in this example called table) to get a new dataframe containing only the observation of year 1995, 1998 and 2000. I've tried to use subset and the or operator | like this: subset(table, year==1995|1998|2000)--table2 but the dataframe didn't subset and I get an object called table2 that is identical to table. I guess I'm doing something wrong!! Thank in advance for any suggestions! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mean over previous cells
If, suppose, the name of your dataframe is dataframe , you could try
something like:
mean60days-c()
for(i in 1:length(dataframe$SST))
+ {
+ mean60days[[i]]-mean(dataframe$SST[i-10:i])
+ }
I'm not really sure it will work... my skills aren't that great...
Anyway, it worked on a sample I tried it on, but you have to be careful and
discard the first 60 values!!
Hope it works,
ciao
Laura
Dear RUsers,
I guess this is an easy question for someone a little familiar with
programming...(which I am not)...
I've got 2 colummns, one shows just dates(SST_date, Class 'Date' num), the
other one shows the SeaSurfaceTemperature (SST, num) at that certain date.
SST_dateSST
2008-01-01 22.2
2008-01-02 21.8
2008-01-03 22.8
2008-01-04 22.9
2008-01-05 23.1
2008-01-06 23.2
...
...
now, I would like to add a column that shows the mean SST over the last
(e.g.) 60 days (for that specific date).
My biological question is, whether the birthweight of an animal at a
specific birthdate changes due to the SST over the last 60 days before
birth. (SST is an indicator for food abundance - if food is scarce, mothers
can't feed much and hence, pups are born lighter!?)
Up to now, I can only show, whether the SeaSurfaceTemperatures on the
birthdate can have an influence on birthweight, which is not what I want to
do...
Can anybody tell me, how to start, where to look it up or help me even more?
thanks in advance.
Birte
--
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] mean over previous cells
Sorry, I meant:
If, suppose, the name of your dataframe is dataframe , you could try
something like:
mean60days-c()
for(i in 1:length(dataframe$SST))
+ {
+ mean60days[[i]]-mean(dataframe$SST[i-60:i])
+ }
I'm not really sure it will work... my skills aren't that great...
Anyway, it worked on a sample I tried it on, but you have to be careful and
discard the first 60 values!!
Hope it works,
ciao
Laura
Dear RUsers,
I guess this is an easy question for someone a little familiar with
programming...(which I am not)...
I've got 2 colummns, one shows just dates(SST_date, Class 'Date' num), the
other one shows the SeaSurfaceTemperature (SST, num) at that certain date.
SST_dateSST
2008-01-01 22.2
2008-01-02 21.8
2008-01-03 22.8
2008-01-04 22.9
2008-01-05 23.1
2008-01-06 23.2
...
...
now, I would like to add a column that shows the mean SST over the last
(e.g.) 60 days (for that specific date).
My biological question is, whether the birthweight of an animal at a
specific birthdate changes due to the SST over the last 60 days before
birth. (SST is an indicator for food abundance - if food is scarce, mothers
can't feed much and hence, pups are born lighter!?)
Up to now, I can only show, whether the SeaSurfaceTemperatures on the
birthdate can have an influence on birthweight, which is not what I want to
do...
Can anybody tell me, how to start, where to look it up or help me even more?
thanks in advance.
Birte
--
View this message in context:
http://www.nabble.com/mean-over-previous-cells-tp22116807p22116807.html
Sent from the R help mailing list archive at Nabble.com.
__
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] write.table
Sorry, I'm using R 2.8.1 on Microsoft Windows XP professional 2002 Service Pack 2. The error I get is Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' The problem is that I can' t manage to save the dataframe... With other dataframe I usually have no problems!!! Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done: as.vector(c(unique(portate$Anno)))-anno as.vector(loadListPO4)-loadPO4 as.vector(loadListPTG)-loadPTG as.vector(loadListNT)-loadNT as.vector(loadListNH4)-loadNH4 as.vector(loadListNO3)-loadNO3 as.vector(loadListBOD5)-loadBOD5 as.vector(loadListSiO2)-loadSiO2 cbind(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loa dSiO2)-carichi as.data.frame(carichi)-carichi.annui #if I type carichi.annui #I get anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 1 2002 3.399518 1.382235 390.6959 22.07992 256.2244 492.9177 150.6505 2 2003 1.559606 0.6271712 202.9181 6.198592 145.9498 63.07578 68.08632 3 2004 2.363862 0.9493779 292.0841 12.21207 200.2545 141.0533 105.2409 4 2005 1.64 0.6570313 217.2192 6.58045 155.7393 66.44154 73.0394 5 2006 1.827174 0.7290634 235.7914 7.858396 166.8327 79.2474 80.92576 6 2007 1.742629 0.6891045 228.0253 7.130082 162.6692 71.91434 77.22507 7 2008 0.8382246 0.3612176 110.9079 2.024197 86.60459 25.46127 32.9733 #which looks lika a data frame #And if I type is.data.frame(carichi.annui) # I get this: [1] TRUE #but if I try write.table(carichi.annui, carichi.annui.lav) #It doesn't work?!?!?! Does someone have an explanation? Thanks a lot for any help!! Laura Laura, What do you mean by It doesn't work? Do you get error messages? Or, do you just not get what you want? And if so, what is that you want? Dan Daniel Nordlund Bothell, WA USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] write.table
Thank you for your advice, but I didn't manage to make it work... I tried carichi.annui - data.frame(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2) And I got this error message: Error in data.frame(anno, loadPTG, loadPO4, loadNT, loadNH4, loadNO3, : the arguments have a different numer of rows: 4, 1 If I do sapply(carichi.annui, class) I get: anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 list list list list list list list list I thought that the function as.vector() could turn a list of numbers into a vector... was I wrong? Messaggio originale Da: rip...@stats.ox.ac.uk Data: 20.02.2009 12.40 A: lauramorg...@bluewin.chlauramorg...@bluewin.ch Copia: r-help@r-project.org Oggetto: Re: [R] write.table On Fri, 20 Feb 2009, lauramorg...@bluewin.ch wrote: Sorry, I'm using R 2.8.1 on Microsoft Windows XP professional 2002 Service Pack 2. The error I get is Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' The problem is that I can' t manage to save the dataframe... With other dataframe I usually have no problems!!! What does sapply(carichi.annui, class) tell you? It would be better to use carichi.annui - data.frame(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2) as you don't need an intermediate matrix. Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done: as.vector(c(unique(portate$Anno)))-anno as.vector(loadListPO4)-loadPO4 as.vector(loadListPTG)-loadPTG as.vector(loadListNT)-loadNT as.vector(loadListNH4)-loadNH4 as.vector(loadListNO3)-loadNO3 as.vector(loadListBOD5)-loadBOD5 as.vector(loadListSiO2)-loadSiO2 cbind(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loa dSiO2)-carichi as.data.frame(carichi)-carichi.annui #if I type carichi.annui #I get anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 1 2002 3.399518 1.382235 390.6959 22.07992 256.2244 492.9177 150.6505 2 2003 1.559606 0.6271712 202.9181 6.198592 145.9498 63.07578 68.08632 3 2004 2.363862 0.9493779 292.0841 12.21207 200.2545 141.0533 105.2409 4 2005 1.64 0.6570313 217.2192 6.58045 155.7393 66.44154 73.0394 5 2006 1.827174 0.7290634 235.7914 7.858396 166.8327 79.2474 80.92576 6 2007 1.742629 0.6891045 228.0253 7.130082 162.6692 71.91434 77.22507 7 2008 0.8382246 0.3612176 110.9079 2.024197 86.60459 25.46127 32.9733 #which looks lika a data frame #And if I type is.data.frame(carichi.annui) # I get this: [1] TRUE #but if I try write.table(carichi.annui, carichi.annui.lav) #It doesn't work?!?!?! Does someone have an explanation? Thanks a lot for any help!! Laura Laura, What do you mean by It doesn't work? Do you get error messages? Or, do you just not get what you want? And if so, what is that you want? Dan Daniel Nordlund Bothell, WA USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] write.table
Thank you!!! unlist() worked perfectly!!! Have a nice weekend Laura Messaggio originale Da: petr.pi...@precheza.cz Data: 20.02.2009 14.58 A: lauramorg...@bluewin.ch Copia: r-help@r-project.org Oggetto: Re: [R] write.table Hi r-help-boun...@r-project.org napsal dne 20.02.2009 12:54:41: Thank you for your advice, but I didn't manage to make it work... I tried carichi.annui - data.frame (anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2) And I got this error message: Error in data.frame(anno, loadPTG, loadPO4, loadNT, loadNH4, loadNO3, : the arguments have a different numer of rows: 4, 1 If I do sapply(carichi.annui, class) I get: anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 list list list list list list list list Well, here is finally something. You can transfer lists to data frames. lll-list(x=rnorm(5), y=rnorm(5)) do.call(data.frame,lll) or if you have vector list like that x-list(rnorm(5)) x [[1]] [1] -0.7349324 -0.4697276 -1.2026201 -1.4366955 -1.4713526 use unlist unlist(x) [1] -0.7349324 -0.4697276 -1.2026201 -1.4366955 -1.4713526 Regards Petr I thought that the function as.vector() could turn a list of numbers into a vector... was I wrong? Messaggio originale Da: rip...@stats.ox.ac.uk Data: 20.02.2009 12.40 A: lauramorg...@bluewin.chlauramorg...@bluewin.ch Copia: r-help@r-project.org Oggetto: Re: [R] write.table On Fri, 20 Feb 2009, lauramorg...@bluewin.ch wrote: Sorry, I'm using R 2.8.1 on Microsoft Windows XP professional 2002 Service Pack 2. The error I get is Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' The problem is that I can' t manage to save the dataframe... With other dataframe I usually have no problems!!! What does sapply(carichi.annui, class) tell you? It would be better to use carichi.annui - data.frame(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2) as you don't need an intermediate matrix. Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done: as.vector(c(unique(portate$Anno)))-anno as.vector(loadListPO4)-loadPO4 as.vector(loadListPTG)-loadPTG as.vector(loadListNT)-loadNT as.vector(loadListNH4)-loadNH4 as.vector(loadListNO3)-loadNO3 as.vector(loadListBOD5)-loadBOD5 as.vector(loadListSiO2)-loadSiO2 cbind(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loa dSiO2)-carichi as.data.frame(carichi)-carichi.annui #if I type carichi.annui #I get anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 1 2002 3.399518 1.382235 390.6959 22.07992 256.2244 492.9177 150.6505 2 2003 1.559606 0.6271712 202.9181 6.198592 145.9498 63.07578 68.08632 3 2004 2.363862 0.9493779 292.0841 12.21207 200.2545 141.0533 105.2409 4 2005 1.64 0.6570313 217.2192 6.58045 155.7393 66.44154 73.0394 5 2006 1.827174 0.7290634 235.7914 7.858396 166.8327 79.2474 80.92576 6 2007 1.742629 0.6891045 228.0253 7.130082 162.6692 71.91434 77.22507 7 2008 0.8382246 0.3612176 110.9079 2.024197 86.60459 25.46127 32.9733 #which looks lika a data frame #And if I type is.data.frame(carichi.annui) # I get this: [1] TRUE #but if I try write.table(carichi.annui, carichi.annui.lav) #It doesn't work?!?!?! Does someone have an explanation? Thanks a lot for any help!! Laura Laura, What do you mean by It doesn't work? Do you get error messages? Or, do you just not get what you want? And if so, what is that you want? Dan Daniel Nordlund Bothell, WA USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list
Re: [R] read.table : how to condition on error while opening file?
Hello Stephane,
here is something you could try,
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
tmpList-try(read.table(filelist[[i]]), silent=TRUE)
if(inherits(tmpList, try-error))
{print(paste(error opening file , filelist[[i]]))
} else {
tmp-read.table(filelist[[i]])-namelist[[i]]
}
}
There is though a problem that I didnt manage to fix, that is: if , suppose,
file1.txt exists, file2 doesn't exist
and file 3 exists,
the dataframe in file 1 will at first be called tmp, but then it will be
substituted by the data.frame in file 3...
It is as if you would do:
c(1,2,3,4)-tmp
and then do
c(1,6,7,8)-tmp
the second tmp will substitute the first one...
Hope this helps
Laura
Messaggio originale
Da: e.vettora...@uke.uni-hamburg.de
Data: 19.02.2009 17.23
A: Stephane Bourgeoiss...@sanger.ac.uk
Copia: r-help@r-project.org
Oggetto: Re: [R] read.table : how to condition on error while opening file?
Hi Stephane,
see ?try
hth.
Stephane Bourgeois schrieb:
Hi,
I'm using read.table in a loop, to read in multiple files. The problem
is that when a file is missing there is an error message and the loop is
broken; what I'd like to do is to test for the error and simply do
next instead of breaking the loop. Anybody knows how to do that?
Example:
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
if (read.table(filelist[i]) == ERROR LOADING FILE) {
# this is where I do not know how to write the condition
print(paste(error opening file , filelist[i], sep=))
next
} else {
tmp - read.table(filelist[i])
}
}
Cheers,
Stephane
--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
T ++49/40/42803-8243
F ++49/40/42803-7790
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] write.table
Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done: as.vector(c(unique(portate$Anno)))-anno as.vector(loadListPO4)-loadPO4 as.vector(loadListPTG)-loadPTG as.vector(loadListNT)-loadNT as.vector(loadListNH4)-loadNH4 as.vector(loadListNO3)-loadNO3 as.vector(loadListBOD5)-loadBOD5 as.vector(loadListSiO2)-loadSiO2 cbind(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2)-carichi as.data.frame(carichi)-carichi.annui #if I type carichi.annui #I get anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 1 2002 3.399518 1.382235 390.6959 22.07992 256.2244 492.9177 150.6505 2 2003 1.559606 0.6271712 202.9181 6.198592 145.9498 63.07578 68.08632 3 2004 2.363862 0.9493779 292.0841 12.21207 200.2545 141.0533 105.2409 4 2005 1.64 0.6570313 217.2192 6.58045 155.7393 66.44154 73.0394 5 2006 1.827174 0.7290634 235.7914 7.858396 166.8327 79.2474 80.92576 6 2007 1.742629 0.6891045 228.0253 7.130082 162.6692 71.91434 77.22507 7 2008 0.8382246 0.3612176 110.9079 2.024197 86.60459 25.46127 32.9733 #which looks lika a data frame #And if I type is.data.frame(carichi.annui) # I get this: [1] TRUE #but if I try write.table(carichi.annui, carichi.annui.lav) #It doesn't work?!?!?! Does someone have an explanation? Thanks a lot for any help!! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] summary of a list
Hello Dieter and everyone,
Thank you for your advice... but I didn't manage to solve my problem... :-(
I actually like the fact that R tells me which ones of my regressions didn't
achieve convergence and gives me a
warning saying that there was a false or singular convergence...
the problem is that out of 35 regressions I do with my loop, only 5 don't
achieve convergence and I would like to be
able to get the summaries(or sigma, or coef, ...)
of the 30 regressions that did achieve convergence... (I know from the start
that some regression functions will work
for some variable and not necessarily for others)
At the moment I check which ones reach convergence by doing
print(resultList)
and then I extract the summary by doing the following loop:
summaryList-list()
for (i in c(1:8, 11:14, 16:24, 26:34))
{
summaryList[[i]]-summary(resultList[[i]])
}
But this is quite tedious, since I will have to repeat it for other rivers and
also in the next years...
Is there a way to tell R to show me the summary of all the results anyway?
Cause right now if I do:
summaryList-list()
for (i in length(resultList))
{
summaryList[[i]]-summary(resultList[[i]])
}
R only shows me the first 8 summaries and then stops because the ninth didn't
reach convergence...
Any suggestion?
P.S. I tried to use nls2 but I have the same problems...
lauramorgana at bluewin.ch lauramorgana at bluewin.ch writes:
Hello,
I'm using the following for loop to find regression curves using a list of
functions (formList), a list of
.. long non-reproducible code removed
And I got the following error message:
Error in chol2inv(object$m$Rmat()) : l'elemento (3, 3) è zero, quindi
l'inversa non può essere calcolata
Which translated should be: Error in chol2inv(object$m$Rmat()): the element
(3, 3) is zero (NULL?),
that's why the
inverse (inverse function?) can not be computed
nls is rather nasty or nice in telling you when the result should not
be trusted. Other software gives nonsense result without blinking.
In package nlme, there is a function nlsList which does directly what you
want, but there is little help besides revising the model for the cases
without convergence.
Also try check Gabor Grothendieks package nls2 which could help you
finding better start values.
Dieter
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[R] odfWeave prettyR
Hello,
I've been trying to use odfWeave and prettyR packages to create documents with
both text and graphs, but so far I
haven't been very lucky...
With the function R2html () in prettyR package, when I try to use a source
file, which works perfectly if I run it
directly form R using source(file),
it works for the first part and then it makes a mess, i guess something might
be wrong in my formatting or the
function R2html doesnt recognize the function if()
because i get errors like this one
Error in parse(cmdcon) : unexpected 'if' at
1: for (i in 1:length(resultList)){tempSummary -
try(summary(resultList[[i]]), silent = TRUE)if
everytime there is a if.
I tried with the function htmlize and it works for the text (like summaries)
but I didn't manage to get the plots on
the html file
I tried to use the funcion HTMLgraph but I couldn't understand what it does and
what its arguments are (listfile,
graphfile)
With odfWeave I tried to download it, and saw that it depends on XML package.
If I try to load the odfWeave package
with
library(odfWeave) I get this message:
Loading: XML
Error: package 'XML' not loaded
Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no 'XML' package
The problem is that on the CRAN web site the XML package is not available for
windows...
Any suggestions?
Thanks and sorry for bothering you all again with this subject...
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Re: [R] plotting the result of a nonlinear regression
Thank you for the suggestion of using predict!
If someone is interested here is the loop I used:
seq(0,max(subset(dati, Fiume==Laveggio)$Portata), length=100)-seqQ
for(i in 1:35)
{
jpeg(paste(result,i,.jpg))
plot(subset(dati,Fiume==Laveggio)$PTG.P~subset(dati,Fiume==Laveggio)$Portata,
main=print(formList[[i]]), sub=print(summary(resultList[[i]])$sigma))
lines(seqQ, predict(resultList[[i]], list(Portata = seqQ)))
dev.off()
}
Messaggio originale
Da: ssef...@gmail.com
Data: 10.02.2009 18.15
A: lauramorg...@bluewin.ch
Copia: r-help@r-project.org
Oggetto: Re: [R] plotting the result of a nonlinear regression
?predict
On Tue, Feb 10, 2009 at 11:06 AM, lauramorg...@bluewin.ch
lauramorg...@bluewin.ch wrote:
Hello,
to plot the result of a singular non linear regression (using nls) I usually
use the function plotfit, for
example:
r.PTG.V-nls(PTG.P~ fz1(Portata, a,b), data=dati, start=list(a=10, b=10),
nls.control(maxiter=200),
algorithm='port',
trace=TRUE, na.action=na.omit, lower=list(a=0, b=10), upper=list(a=100,
b=100))
plotfit(r.PTG.V)
I tried to use the function plotfit on the result of the following for loop
but I got an error message:
for (i in 1:length(formList))
{
resultList[[i]] - nls(formList[[i]], data=subset(dati,
Fiume==Laveggio), start=startList7[[i]],
nls.control(maxiter=1000, warnOnly=TRUE), algorithm='port',
na.action=na.omit,lower=lowerList7[[i]],
upper=upperList7[[i]])
}
plotfit(resultList[[1]]
Error in diff(as.numeric(y[ord])) :
(list) object cannot be coerced to type 'double'
Could somebody tell me what this error means? how can I fix this problem?
Any suggestion appreciated!!
Thanks,
Laura
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--
Stephen Sefick
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
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[R] plotting the result of a nonlinear regression
Hello,
to plot the result of a singular non linear regression (using nls) I usually
use the function plotfit, for example:
r.PTG.V-nls(PTG.P~ fz1(Portata, a,b), data=dati, start=list(a=10, b=10),
nls.control(maxiter=200), algorithm='port',
trace=TRUE, na.action=na.omit, lower=list(a=0, b=10), upper=list(a=100, b=100))
plotfit(r.PTG.V)
I tried to use the function plotfit on the result of the following for loop but
I got an error message:
for (i in 1:length(formList))
{
resultList[[i]] - nls(formList[[i]], data=subset(dati, Fiume==Laveggio),
start=startList7[[i]],
nls.control(maxiter=1000, warnOnly=TRUE), algorithm='port',
na.action=na.omit,lower=lowerList7[[i]],
upper=upperList7[[i]])
}
plotfit(resultList[[1]]
Error in diff(as.numeric(y[ord])) :
(list) object cannot be coerced to type 'double'
Could somebody tell me what this error means? how can I fix this problem?
Any suggestion appreciated!!
Thanks,
Laura
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[R] summary of a list
Hello,
I'm using the following for loop to find regression curves using a list of
functions (formList), a list of starting
values (startList), uppervalues (upperList) and lower values (lowerList).
A sample of the list of function I use in the loop is the following:
FormList - list(PTG.P ~ fz1(Portata, a, b), PTG.P ~ fz2(Portata, a, b), PTG.P
~ fz3(Portata,a, b, d, e),
PTG.P ~ fz4(Portata, a, b), PTG.P ~ fz5(Portata, a, b, d), PO4.P ~ fz1(Portata,
a, b),
PO4.P ~ fz2(Portata, a, b), ...
And the loop I use is:
resultList - list()
for (i in 1:length(formList))
{
resultList[[i]] - nls(formList[[i]], data=subset(dati, Fiume==Laveggio),
start=startList[[i]],
nls.control(maxiter=1000, warnOnly=TRUE), algorithm='port',
na.action=na.omit,lower=lowerList[[i]],
upper=upperList[[i]])
}
When the computation ends I get 5 warning messages (one of false convergence, 4
of singular convergence:
In nls(formList[[i]], data = subset(dati, Fiume == Laveggio), : Convergence
failure: false convergence (8)
2: In nls(formList[[i]], data = subset(dati, Fiume == Laveggio), :
Convergence failure: singular convergence (7)
If I want to get the summary of the first object of the resultList I do:
summary(resultList[[1]])
And I get a result with no problem:
Formula: PTG.P ~ fz1(Portata, a, b)
Parameters:
Estimate Std. Error t value Pr(|t|)
a 61.158 18.591 3.290 0.00140 **
b7.616 8.720 0.873 0.38464
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 91.32 on 96 degrees of freedom
Algorithm port, convergence message: both X-convergence and relative
convergence (5)
It also works if I try to get the summary of the first 5 object of the
resultList with:
summaryList-list()
for (i in 1:5)
{
summaryList[[i]]-summary(resultList[[i]])
}
But if I try to get the summary of all the objects of the resultList (there are
35 objects) it doesn't work...
I tried:
summaryList-list()
for (i in 1:length(resultList))
+ {
+ summaryList[[i]]-summary(resultList[[i]])
+ }
And I got the following error message:
Error in chol2inv(object$m$Rmat()) : l'elemento (3, 3) è zero, quindi l'inversa
non può essere calcolata
Which translated should be: Error in chol2inv(object$m$Rmat()): the element (3,
3) is zero (NULL?), that's why the
inverse (inverse function?) can not be computed
Does somebody have an idea on how to fix this?
Thanks
Laura
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Re: [R] non linear regression with nls
Thank you! It worked perfectly, also for the other variables! Messaggio originale Da: r...@life.ku.dk Data: 06.02.2009 13.29 A: lauramorg...@bluewin.ch Oggetto: Re: [R] non linear regression with nls Hi Laura, I think you have to make a list formulas: formList - list(NT.N ~ fz1(Portata, a, b), NT.N ~ fz2(Portata, a, b), NT.N ~ fz3(Portata, a, b, d, e), NT.N ~ fz4(Portata, a, b), NT.N ~ fz5(Portata, a, b, d)) and then in the loop: resultList[[i]] - nls(formList[[i]], ... Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] non linear regression with nls
Thank you a lot Mr. Ritz!
I've tried the loop you suggested and I added a list for lower and upper limits
of the parameters, but there is still
a problem...
I have a list of functions, which works...
fz1-function(Portata, a, b){a+(b/Portata)}
fz2-function(Portata, a, b){a*exp(b*Portata)}
fz3-function(Portata, a, b, d, e){a+(b/Portata)+d*(Portata^e)}
fz4-function(Portata, a, b){a*Portata^b}
fz5-function(Portata, a, b, d){a+b*(Portata^d)}
fctList - list(fz1, fz2, fz3, fz4, fz5)
as well as lists for starting values, upper and lower values, which work as
well:
startList - list(list(a=10, b=10), list(a=10, b=1), list(a=10, b=10, d=10,
e=1), list(a=10, b=1), list(a=10, b=10,
d=1))
lowerList-list(list(a=0,b=0),list(a=0,b=0), list(a=0,b=0,d=0,e=-50),list(a=0,
b=-50), list(a=0, b=0, d=-50))
upperList-list(list(a=1000, b=1000), list(a=1000, b=1000),
list(a=1000,b=1000,d=1000,e=50), list(a=1000,b=50), list
(a=1000, b=1000, d=50))
but if I try to run this for loop
resultList - list()
for (i in 1:5)
{
resultList[[i]] - nls(NT.N ~ fctList[[i]](Portata, a,b), data=subset(dati,
Fiume==Laveggio), start=startList[[i]],
nls.control(maxiter=200), algorithm='port', trace=TRUE, na.action=na.omit,
upper=upperList[[i]], lower=lowerList[[i]])
}
I get the following error message:
Error in fctList[[i]](Portata, a, b) : element 1 is empty;
the part of the args list of '*' being evaluated was:
(d, (Portata^e))
I realized that the problem is the element after the function, i.e. (Portata,
a, b), since fct 3 and 5 have more
parameters (Portata,a,b,d,e).
So I tried to make a list (parList) for this too, i tried 2 versions:
#version1
list(Portata,a, b)-pf1.2.4
list(Portata,a,b,d,e)-pf3
list(Portata,a,b,d)-pf5
parList-list(pf1.2.4, pf1.2.4,pf3,pf1.2.4,pf5)
#version 2
parList-list(Portata,a,b,Portata,a,b,Portata,a,b,d,e,
Portata,a,b,Portata,a,b,d)
and then I tried them (one at a time) in the loop:
resultList - list()
for (i in 1:5)
{
resultList[[i]] - nls(NT.N ~ fctList[[i]](parList[[i]]), data=subset(dati,
Fiume==Laveggio), start=startList
[[i]], nls.control(maxiter=200), algorithm='port', trace=TRUE,
na.action=na.omit,upper=upperList[[i]], lower=lowerList
[[i]])
}
but I got this error message: Error in fctList[[i]](parList[i]) : element 1
is empty;
the part of the args list of '+' being evaluated was:
(a, (b/Portata))
What can I do to fix it?
I'm also wondering which kind of function (maybe another loop?) I could use to
automize the regression not only for
the variable NT.N but for every variable (PTG.P, PO4.P,. ..)
My dataframe look like this (a sample):
Fiume giorno mese anno Portata PTG.P PO4.P NT.N NH4.N NO3.N
BOD5 SiO2 data
1Vedeggio 101 1995 0.981 218.40 118.000 9.196 6.5700 2.06
6.080 4.33 34709
2Vedeggio 72 1995 0.965 125.84 54.000 8.701 5.2600 2.31
16.480 4.43 34737
3Vedeggio 73 1995 1.536 37.44 12.000 7.271 5.5600 1.88
5.240 4.15 34765
...
190 Cassarate 299 2008 1.240 26.00 20.000 2.480 0.1200 1.79
1.700 4.03 39720
191 Cassarate 13 10 2008 0.860 23.00 16.000 2.720 0.0200 2.13
1.780 3.71 39734
192 Cassarate 10 11 2008 8.840 26.00 14.000 2.900 0.0500NA
1.400 3.62 39762
193 Cassarate 9 12 2008 2.030 35.00 23.000 2.190 0.0700 1.79
1.950 3.74 39791
...
279 Laveggio 151 2002 0.347 77.00 30.000 9.690 0.4300 7.23
1.950 4.17 37271
280 Laveggio 112 2002 0.527 54.00 17.000 7.520 0.8800 5.87
2.410 3.58 37298
281 Laveggio 133 2002 0.900 34.00 15.000 7.520 0.7100 6.17
6.550 3.03 37328
...
Thanks to anyone that could give me any hint!!
Laura
## a for loop
resultList - list()
for (i in 1:5)
{
## storing the result as the i'th list component
## notice that the i'th list components in fctList and startList
## are used for the i'th fit
resultList[[i]] - nls(NT.N ~ fctList[[i]](parList[[i]]), data=subset(dati,
Fiume==Laveggio), start=startList
[[i]], nls.control(maxiter=200), algorithm='port', trace=TRUE,
na.action=na.omit)
}
Messaggio originale
Da: r...@life.ku.dk
Data: 03.02.2009 19.00
A: lauramorg...@bluewin.ch
Oggetto: Re: [R] non linear regression with nls
Hi Laura,
I've the following suggestion for you using several lists and a for loop:
fz1-function(Portata, a, b){a+b/Portata}
fz2-function(Portata, a, b){a*exp(b*Portata)}
fz3-function(Portata, a, b, d, e){a+b/Portata+d*(Portata^e)}
fz4-function(Portata, b, d){b*Portata^d}
fz5-function(Portata, a, b, d){a+b*(Portata^d)}
fctList - list(fz1, fz2, fz3, fz4, fz5)
startList - list(list(a=10, b=10), list(a=10, b=1), start=list(a=10, b=10,
d=10, e=10),
list(a=10, b=1), list(a=10, b=10, d=1))
## a for loop
resultList - list()
for (i in 1:5)
{
## storing the result as the i'th list component
## notice that the i'th list components in fctList and startList
## are used for the i'th fit
resultList[[i]] - nls(NT.N
Re: [R] non linear regression with nls
Hello, thanks for the advice of nlsList!
I tried to look at the help page of nlsList, but I didnt understand how to use
the subset argument of the function
and it's not clear to
me if this only allows you to choose one subset or if it run the regression for
every given subset, in this case how
can someone specify the groups/subset?
Thanks a lot!
Laura
Messaggio originale
Da: kfr...@wisc.edu
Data: 03.02.2009 15.36
A: lauramorg...@bluewin.ch
Oggetto: Re: [R] non linear regression with nls
Hi, Laura-
You might have a look at ?nlsList().
Ken
- Original Message -
From: lauramorg...@bluewin.ch lauramorg...@bluewin.ch
Date: Tuesday, February 3, 2009 4:38 am
Subject: [R] non linear regression with nls
To: r-help@r-project.org
Hello,
I'm a beginner with R and it's the first time I'm using the R-help
list... I hope I'm in the right place, if not:
Sorry!!
I need to do non linear regressions on a data set which columns are:
river.namePortata PTG.P PO4.P NT.NNH4.N
NO3.N BOD5SiO2
I need to predict every variable (PTG, PO4, NT, ..., which are
concentration of substances in water) starting from
the Portata variable (which is the water flow)
The functions that I'm using are:
fz1-function(Portata, a, b){a+b/Portata}
fz2-function(Portata, a, b){a*exp(b*Portata)}
fz3-function(Portata, a, b, d, e){a+b/Portata+d*(Portata^e)}
fz4-function(Portata, b, d){b*Portata^d}
fz5-function(Portata, a, b, d){a+b*(Portata^d)}
I've made a list of the functions with list(fz1, fz2, fz3, fz4, fz5)
and the starting , lower and upper parameters for each function are:
fz1: start=list(a=10, b=10), lower=list(a=0, b=0), upper=list(a=1000,
b=1000)
fz2: start=list(a=10, b=1), lower=list(a=0, b=0), upper=list(a=1000, b=1000)
fz3: start=list(a=10, b=10, d=10, e=10), lower=list(a=0, b=0, d=0,
e=-50), upper=list(a=1000, b=1000, d=1000, e=50)
fz4: start=list (a=10, b=1), lower=list(a=0, b=-50),
upper=list(a=1000, b=50)
fz5: start=list(a=10, b=10, d=1), lower=list(a=0, b=0, d=-50),
upper=list(a=1000, b=1000, d=50)
so far i manage to do non linear regression one at a time that is,
using one function for one river) using nls(), for
example:
r.NT.lav-nls(NT.N~ fz1(Portata, a,b),
data=subset(dati,river.name==Laveggio), start=list(a=10, b=10), nls.control
(maxiter=200), algorithm='port', trace=TRUE, na.action=na.omit,
lower=list(a=0, b=0), upper=list(a=1000, b=1000))
and then I get the results with summary() and the graph using plotfit()
but this will get extremly long since I have 12 rivers to analize for
every variable and then compare the results, so
I'd like to use a loop (cycle for??) but I can't figure out how it
works. I've tried to look on the help page on ?
Control (control flow) but I didn't understand it...
Can somebody help me (give me a hint or an example of a loop) to
automize the regression and save the results
Please consider that my knowledge of computer programming is
practically non-existent!!
Thanks a lot!
Laura F.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] non linear regression with nls
Hello,
I'm a beginner with R and it's the first time I'm using the R-help list... I
hope I'm in the right place, if not:
Sorry!!
I need to do non linear regressions on a data set which columns are:
river.namePortata PTG.P PO4.P NT.NNH4.N NO3.N
BOD5SiO2
I need to predict every variable (PTG, PO4, NT, ..., which are concentration of
substances in water) starting from
the Portata variable (which is the water flow)
The functions that I'm using are:
fz1-function(Portata, a, b){a+b/Portata}
fz2-function(Portata, a, b){a*exp(b*Portata)}
fz3-function(Portata, a, b, d, e){a+b/Portata+d*(Portata^e)}
fz4-function(Portata, b, d){b*Portata^d}
fz5-function(Portata, a, b, d){a+b*(Portata^d)}
I've made a list of the functions with list(fz1, fz2, fz3, fz4, fz5)
and the starting , lower and upper parameters for each function are:
fz1: start=list(a=10, b=10), lower=list(a=0, b=0), upper=list(a=1000, b=1000)
fz2: start=list(a=10, b=1), lower=list(a=0, b=0), upper=list(a=1000, b=1000)
fz3: start=list(a=10, b=10, d=10, e=10), lower=list(a=0, b=0, d=0, e=-50),
upper=list(a=1000, b=1000, d=1000, e=50)
fz4: start=list (a=10, b=1), lower=list(a=0, b=-50), upper=list(a=1000, b=50)
fz5: start=list(a=10, b=10, d=1), lower=list(a=0, b=0, d=-50),
upper=list(a=1000, b=1000, d=50)
so far i manage to do non linear regression one at a time that is, using one
function for one river) using nls(), for
example:
r.NT.lav-nls(NT.N~ fz1(Portata, a,b),
data=subset(dati,river.name==Laveggio), start=list(a=10, b=10), nls.control
(maxiter=200), algorithm='port', trace=TRUE, na.action=na.omit, lower=list(a=0,
b=0), upper=list(a=1000, b=1000))
and then I get the results with summary() and the graph using plotfit()
but this will get extremly long since I have 12 rivers to analize for every
variable and then compare the results, so
I'd like to use a loop (cycle for??) but I can't figure out how it works. I've
tried to look on the help page on ?
Control (control flow) but I didn't understand it...
Can somebody help me (give me a hint or an example of a loop) to automize the
regression and save the results
Please consider that my knowledge of computer programming is practically
non-existent!!
Thanks a lot!
Laura F.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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