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.name" "Portata" "PTG.P" "PO4.P" "NT.N" "NH4.N" "NO3.N" "BOD5" "SiO2" 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.
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
1 Vedeggio 10 1 1995 0.981 218.40 118.000 9.196 6.5700 2.06 6.080
4.33 34709
2 Vedeggio 7 2 1995 0.965 125.84 54.000 8.701 5.2600 2.31 16.480
4.43 34737
3 Vedeggio 7 3 1995 1.536 37.44 12.000 7.271 5.5600 1.88 5.240
4.15 34765
...
190 Cassarate 29 9 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 0.0500 NA 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 15 1 2002 0.347 77.00 30.000 9.690 0.4300 7.23 1.950
4.17 37271
280 Laveggio 11 2 2002 0.527 54.00 17.000 7.520 0.8800 5.87 2.410
3.58 37298
281 Laveggio 13 3 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: ritz at life.ku.dk
Data: 03.02.2009 19.00
A: <lauramorgana at 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 ~ fctList[[i]](Portata, a,b),
data=subset(dati, river.name=="Laveggio"), start=startList[[i]],
nls.control(maxiter=200), algorithm='port', trace=TRUE,
na.action=na.omit)
}
summary(resultList[[1]])
plotfit(resultList[[1]])
summary(resultList[[2]])
plotfit(resultList[[2]])
...
I hope you can make it work?
Christian
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: kfrost at wisc.edu Data: 03.02.2009 15.36 A: <lauramorgana at bluewin.ch> Oggetto: Re: [R] non linear regression with nls Hi, Laura- You might have a look at ?nlsList(). Ken ----- Original Message ----- From: "lauramorgana at bluewin.ch" <lauramorgana at bluewin.ch> Date: Tuesday, February 3, 2009 4:38 am Subject: [R] non linear regression with nls To: r-help at 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.name" "Portata" "PTG.P" "PO4.P" "NT.N" "NH4.N" > "NO3.N" "BOD5" "SiO2" > 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. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Thank you! It worked perfectly, also for the other variables! ----Messaggio originale---- Da: ritz at life.ku.dk Data: 06.02.2009 13.29 A: <lauramorgana at 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