Wall, Wade A ERDC-RDE-CERL-IL CIV
2017-Oct-18 15:58 UTC
[R] Error messages using nonlinear regression function (nls)
Hi all,
I am trying to use nonlinear regression (nls) to analyze some seed germination
data, but am having problems with error codes.
The data that I have closely matches the germination dataset included in the drc
package.
Here is the head of the data
temp species start end germinated TotSeeds TotGerminated Prop
1 10 wheat 0 1 0 20 0 0.0
2 10 wheat 1 2 0 20 0 0.0
3 10 wheat 2 3 0 20 0 0.0
4 10 wheat 3 4 0 20 0 0.0
5 10 wheat 4 5 0 20 0 0.0
6 10 wheat 5 6 4 20 4 0.2
temp is the temperature under which the seeds were germinated, species denotes
the species (wheat, mungbean, or rice)
Start and end denote the beginning and end of a period of time and germinated
denotes how many seeds germinated during
that period of time. Prop represents the proportion of seeds that have
germinated.
I have attempted to mimic Fox and Weisberg's appendix to Nonlinear
Regression found here.
https://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendix/Appendix-Nonlinear-Regression.pdf
My first step is to look at a single species, wheat, and use nls on the
individual temperatures.
I have tried to use both the nlsList function and to attempt to estimate the
parameters using lm(), but I
receive error messages on both. Here is the code.
library(drc) ### for germination dataset
data(germination)
wheat = germination[germination$species == "wheat",] ### subset by
wheat
scatterplot(Prop ~ end|temp,data=wheat,box=FALSE,reg=FALSE) ### view the data
wheat$temp = as.factor(wheat$temp) ### convert to factor
### First, try to use nlsList
wheat.list <- nlsList(Prop ~ SSlogis(end,phi1,phi2,phi3)|
temp,pool=FALSE,data=wheat) ###
### next, try to use lm to estimate starting parameters.
wheat.list = list()
for (i in 1:length(levels(wheat$temp))){
tmpDat = wheat[wheat$temp == levels(wheat$temp)[i],]
tmp.lm <- lm(Prop ~ end,data = tmpDat)
tmp.nls <- nls(Prop ~ theta1 / (1 + exp(-(theta2 + theta3*end))),
start = list(theta1 = .5,theta2=coef(tmp.lm)[1],theta3 = coef(tmp.lm)[2]),
data = tmpDat,trace=TRUE)
tmp2.nls <- nls(Prop ~ SSlogis(end,phi1,phi2,phi3),data=tmpDat)
wheat.list[i] <- tmp.nls
}
#### End code
nlsList just returns an empty list.
When I try to loop through the individual temperatures, for the first
temperature, nls converges when I provide
starting values, but when I try to use SSlogis(), I get the error messsage
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
NA/NaN/Inf in 'x'
For the second temperature (16), I get the following error message when provided
initial values using lm:
Error in nls(Prop ~ theta1/(1 + exp(-(theta2 + theta3 * end))), start =
list(theta1 = 0.5, :
singular gradient
I have tried to read through posts, but none of them seem to apply to this case.
The data seem relatively simply and
I am not sure what I am doing wrong. Any help would be appreciated.
Wade
PIKAL Petr
2017-Oct-19 06:21 UTC
[R] Error messages using nonlinear regression function (nls)
Hi Thanks for the code but where is Prop? It is not a variable in germination data set so we do not know how you did the computation. My wild guess is, that your Prop do not follow logistic curve and therefore no results from nlsList Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Wall, Wade A > ERDC-RDE-CERL-IL CIV > Sent: Wednesday, October 18, 2017 5:58 PM > To: r-help at r-project.org > Subject: [R] Error messages using nonlinear regression function (nls) > > Hi all, > > I am trying to use nonlinear regression (nls) to analyze some seed germination > data, but am having problems with error codes. > > The data that I have closely matches the germination dataset included in the > drc package. > > Here is the head of the data > > temp species start end germinated TotSeeds TotGerminated Prop > 1 10 wheat 0 1 0 20 0 0.0 > 2 10 wheat 1 2 0 20 0 0.0 > 3 10 wheat 2 3 0 20 0 0.0 > 4 10 wheat 3 4 0 20 0 0.0 > 5 10 wheat 4 5 0 20 0 0.0 > 6 10 wheat 5 6 4 20 4 0.2 > > temp is the temperature under which the seeds were germinated, species > denotes the species (wheat, mungbean, or rice) > Start and end denote the beginning and end of a period of time and > germinated denotes how many seeds germinated during > that period of time. Prop represents the proportion of seeds that have > germinated. > > I have attempted to mimic Fox and Weisberg's appendix to Nonlinear > Regression found here. > https://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendix/Appendix > -Nonlinear-Regression.pdf > > My first step is to look at a single species, wheat, and use nls on the individual > temperatures. > > I have tried to use both the nlsList function and to attempt to estimate the > parameters using lm(), but I > receive error messages on both. Here is the code. > > library(drc) ### for germination dataset > data(germination) > > wheat = germination[germination$species == "wheat",] ### subset by wheat > scatterplot(Prop ~ end|temp,data=wheat,box=FALSE,reg=FALSE) ### view the > data > wheat$temp = as.factor(wheat$temp) ### convert to factor > > ### First, try to use nlsList > wheat.list <- nlsList(Prop ~ SSlogis(end,phi1,phi2,phi3)| > temp,pool=FALSE,data=wheat) ### > > ### next, try to use lm to estimate starting parameters. > wheat.list = list() > > for (i in 1:length(levels(wheat$temp))){ > tmpDat = wheat[wheat$temp == levels(wheat$temp)[i],] > tmp.lm <- lm(Prop ~ end,data = tmpDat) > tmp.nls <- nls(Prop ~ theta1 / (1 + exp(-(theta2 + theta3*end))), > start = list(theta1 = .5,theta2=coef(tmp.lm)[1],theta3 = coef(tmp.lm)[2]), > data = tmpDat,trace=TRUE) > tmp2.nls <- nls(Prop ~ SSlogis(end,phi1,phi2,phi3),data=tmpDat) > wheat.list[i] <- tmp.nls > } > #### End code > nlsList just returns an empty list. > > When I try to loop through the individual temperatures, for the first > temperature, nls converges when I provide > starting values, but when I try to use SSlogis(), I get the error messsage > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : > NA/NaN/Inf in 'x' > > For the second temperature (16), I get the following error message when > provided initial values using lm: > > Error in nls(Prop ~ theta1/(1 + exp(-(theta2 + theta3 * end))), start = list(theta1 > = 0.5, : > singular gradient > > I have tried to read through posts, but none of them seem to apply to this case. > The data seem relatively simply and > I am not sure what I am doing wrong. Any help would be appreciated. > > Wade > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. 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PIKAL Petr
2017-Oct-20 06:33 UTC
[R] Error messages using nonlinear regression function (nls)
Hi Keep your messages in the list, you increase your chance to get some answer. I changed your data to groupedData object (see below), but I did not find any problem in it. plot(wlg) gives reasonable picture and I am not such expert to see any problem with data. Seems to me, that something has to be wrong with nlsList function.> wheat.list <- nlsList(Prop ~ SSlogis(end,Asym, xmid, scal), data=wlg)Warning message: 6 times caught the same error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...): NA/NaN/Inf in 'x' produces empty list. So maybe others could find some problem. Cheers Petr> dput(wlg)structure(list(temp = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("40", "10", "16", "22", "28", "34"), class = c("ordered", "factor")), species = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("mungbean", "rice", "wheat"), class = "factor"), start = c(0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17), end = c(1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18), germinated = c(0L, 0L, 0L, 0L, 0L, 4L, 6L, 8L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 11L, 7L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 12L, 3L, 0L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 8L, 0L, 8L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 11L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 2L, 0L, 0L, 0L, 0L, 0L, 0L), TotSeeds = c(20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20), TotGerminated = c(0, 0, 0, 0, 0, 4, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 0, 0, 11, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 0, 1, 13, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 0, 0, 0, 8, 8, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 0, 5, 16, 17, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 3, 3, 3, 3, 3, 3), Prop = c(0, 0, 0, 0, 0, 0.2, 0.5, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0, 0, 0.55, 0.9, 0.9, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0.05, 0.65, 0.8, 0.8, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0, 0, 0.4, 0.4, 0.8, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0.25, 0.8, 0.85, 0.9, 0.9, 0.9, 0.9, 0.9, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0, 0, 0, 0, 0, 0, 0, 0.05, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15)), .Names = c("temp", "species", "start", "end", "germinated", "TotSeeds", "TotGerminated", "Prop"), row.names = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 159L, 160L, 161L, 162L, 163L, 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L ), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = Prop ~ end | temp, FUN = function (x) max(x, na.rm = TRUE), order.groups = TRUE)>> sessionInfo()R Under development (unstable) (2017-07-31 r73003) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393) Matrix products: default locale: [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech Republic.1250 [3] LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C [5] LC_TIME=Czech_Czech Republic.1250 attached base packages: [1] stats datasets utils grDevices graphics methods base other attached packages: [1] nlme_3.1-131 lattice_0.20-35 fun_0.1 loaded via a namespace (and not attached): [1] compiler_3.5.0 colorspace_1.3-2 scales_0.4.1 lazyeval_0.2.0 [5] plyr_1.8.4 tools_3.5.0 gtable_0.2.0 tibble_1.3.3 [9] Rcpp_0.12.12 ggplot2_2.2.1 grid_3.5.0 rlang_0.1.1 [13] munsell_0.4.3>> -----Original Message----- > From: Wall, Wade A ERDC-RDE-CERL-IL CIV > [mailto:Wade.A.Wall at erdc.dren.mil] > Sent: Thursday, October 19, 2017 3:18 PM > To: PIKAL Petr <petr.pikal at precheza.cz> > Subject: RE: Error messages using nonlinear regression function (nls) > > "Prop" is the proportion of seeds that have germinated from the total. Here is > the code I used to transform the germination data set. When graphed, the > logistic curve provides a reasonable fit. > > data(germination) > germination$TotSeeds = 20 > germination$TotGerminated = 0 > tmpCount = 0 > > for(i in 2:nrow(germination)){ > if((germination$temp[i]!=germination$temp[i-1]) | (germination$species[i] !> germination$species[i-1])) {tmpCount = 0} > if((germination$temp[i]==germination$temp[i-1]) & (germination$species[i] > == germination$species[i-1])) > {tmpCount = tmpCount + germination$germinated[i]; > germination$TotGerminated[i]=tmpCount} > } > germination$Prop = germination$TotGerminated/germination$TotSeeds > germination = germination[germination$end != Inf,] > > Wade > > -----Original Message----- > From: PIKAL Petr [mailto:petr.pikal at precheza.cz] > Sent: Thursday, October 19, 2017 1:21 AM > To: Wall, Wade A ERDC-RDE-CERL-IL CIV <Wade.A.Wall at erdc.dren.mil>; r- > help at r-project.org > Subject: RE: Error messages using nonlinear regression function (nls) > > Hi > > Thanks for the code but where is Prop? > > It is not a variable in germination data set so we do not know how you did the > computation. > > My wild guess is, that your Prop do not follow logistic curve and therefore no > results from nlsList > > Cheers > Petr > > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Wall, > > Wade A ERDC-RDE-CERL-IL CIV > > Sent: Wednesday, October 18, 2017 5:58 PM > > To: r-help at r-project.org > > Subject: [R] Error messages using nonlinear regression function (nls) > > > > Hi all, > > > > I am trying to use nonlinear regression (nls) to analyze some seed > > germination data, but am having problems with error codes. > > > > The data that I have closely matches the germination dataset included > > in the drc package. > > > > Here is the head of the data > > > > temp species start end germinated TotSeeds TotGerminated Prop > > 1 10 wheat 0 1 0 20 0 0.0 > > 2 10 wheat 1 2 0 20 0 0.0 > > 3 10 wheat 2 3 0 20 0 0.0 > > 4 10 wheat 3 4 0 20 0 0.0 > > 5 10 wheat 4 5 0 20 0 0.0 > > 6 10 wheat 5 6 4 20 4 0.2 > > > > temp is the temperature under which the seeds were germinated, species > > denotes the species (wheat, mungbean, or rice) Start and end denote > > the beginning and end of a period of time and germinated denotes how > > many seeds germinated during that period of time. Prop represents the > > proportion of seeds that have germinated. > > > > I have attempted to mimic Fox and Weisberg's appendix to Nonlinear > > Regression found here. > > Blockedhttps://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendi > > x/AppendixBlocked > > -Nonlinear-Regression.pdf > > > > My first step is to look at a single species, wheat, and use nls on > > the individual temperatures. > > > > I have tried to use both the nlsList function and to attempt to > > estimate the parameters using lm(), but I receive error messages on > > both. Here is the code. > > > > library(drc) ### for germination dataset > > data(germination) > > > > wheat = germination[germination$species == "wheat",] ### subset by > > wheat scatterplot(Prop ~ end|temp,data=wheat,box=FALSE,reg=FALSE) ### > > view the data wheat$temp = as.factor(wheat$temp) ### convert to factor > > > > ### First, try to use nlsList > > wheat.list <- nlsList(Prop ~ SSlogis(end,phi1,phi2,phi3)| > > temp,pool=FALSE,data=wheat) ### > > > > ### next, try to use lm to estimate starting parameters. > > wheat.list = list() > > > > for (i in 1:length(levels(wheat$temp))){ > > tmpDat = wheat[wheat$temp == levels(wheat$temp)[i],] > > tmp.lm <- lm(Prop ~ end,data = tmpDat) > > tmp.nls <- nls(Prop ~ theta1 / (1 + exp(-(theta2 + theta3*end))), > > start = list(theta1 = .5,theta2=coef(tmp.lm)[1],theta3 = coef(tmp.lm)[2]), > > data = tmpDat,trace=TRUE) > > tmp2.nls <- nls(Prop ~ SSlogis(end,phi1,phi2,phi3),data=tmpDat) > > wheat.list[i] <- tmp.nls > > } > > #### End code > > nlsList just returns an empty list. > > > > When I try to loop through the individual temperatures, for the first > > temperature, nls converges when I provide starting values, but when I > > try to use SSlogis(), I get the error messsage > > > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : > > NA/NaN/Inf in 'x' > > > > For the second temperature (16), I get the following error message > > when provided initial values using lm: > > > > Error in nls(Prop ~ theta1/(1 + exp(-(theta2 + theta3 * end))), start > > = list(theta1 = 0.5, : > > singular gradient > > > > I have tried to read through posts, but none of them seem to apply to this > case. > > The data seem relatively simply and > > I am not sure what I am doing wrong. Any help would be appreciated. > > > > Wade > >________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. 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Martin Maechler
2017-Oct-20 11:03 UTC
[R] Error messages using nonlinear regression function (nls)
>>>>> PIKAL Petr <petr.pikal at precheza.cz> >>>>> on Fri, 20 Oct 2017 06:33:36 +0000 writes:> Hi > Keep your messages in the list, you increase your chance to get some answer. > I changed your data to groupedData object (see below), but I did not find any problem in it. > plot(wlg) > gives reasonable picture and I am not such expert to see any problem with data. Seems to me, that something has to be wrong with nlsList function. >> wheat.list <- nlsList(Prop ~ SSlogis(end,Asym, xmid, scal), data=wlg) > Warning message: > 6 times caught the same error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...): NA/NaN/Inf in 'x' > produces empty list. So maybe others could find some problem. > Cheers > Petr Thank you, Petr, for the reproducible example. This indeed can be traced back to a bug in SSlogis() that has been there since Doug Bates added the 'nls' package on Martin's day 1999 (==> before R version 1.0.0 !) to R (svn rev 6455). It's this part which does contain a thinko (by whomever, only Doug may be able to remember/recall, but I guess it would have been Jos? Pinheiro, then the grad student doing the nitty gritty), I have added 2 '----------' below to make the 2 important lines stand out : z <- xy[["y"]] --------------------------------------------------------------------- if (min(z) <= 0) { z <- z - 1.05 * min(z) } # avoid zeroes z <- z/(1.05 * max(z)) # scale to within unit height --------------------------------------------------------------------- xy[["z"]] <- log(z/(1 - z)) # logit transformation aux <- coef(lm(x ~ z, xy)) the first of the 2 lines, commented "avoid zeroes" is obviously *not* avoiding zeroes in the case min(z) == 0 , and even though the 2 lines should rescale an interval [0, M] to [eps, 1 - eps] they don't in this case. Consequently, the next line log(z/(1 - z)) transforms the 0s into -Inf and these lead to the warning (or error in nls()) " NA/NaN/Inf in 'x' " One could fix this up by replacing min(z) by min(z, -1e-7) which may be best for pure back compatibility, but I really don't like it either : The famous logit - transform log( z / (1-z)) is really anti-symmetric around z = 1/2 , in particular should treat 0 and 1 "symmetrically" and I find it ugly that the previous fixup (our two ominous lines) is not at all symmetric wrt 1/2, notably the 2nd transformation is made unconditionally but the first one not. Fortunately, the same source file, <R>/src/library/stats/R/zzzModels.R also defines the SSfpl() == 4-parameter logistic model and there, the 'init' function needs to do the same scaling to (0, 1) and does it much nicer, indeed (anti)symmetrically. I'm looking into using that in SSlogis() as well, fixing this bug. Martin Maechler ETH Zurich and R Core Team
William Dunlap
2017-Oct-20 14:54 UTC
[R] Error messages using nonlinear regression function (nls)
The Logistic link does not work well with zero or unit proportions. Try pulling it away from the edges with wlg$Prop <- pmin( 1-1e-10, pmax( 1e-10, w1g$Prop )) Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Oct 19, 2017 at 11:33 PM, PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi > > Keep your messages in the list, you increase your chance to get some > answer. > > I changed your data to groupedData object (see below), but I did not find > any problem in it. > > plot(wlg) > gives reasonable picture and I am not such expert to see any problem with > data. Seems to me, that something has to be wrong with nlsList function. > > > wheat.list <- nlsList(Prop ~ SSlogis(end,Asym, xmid, scal), data=wlg) > Warning message: > 6 times caught the same error in lm.fit(x, y, offset = offset, singular.ok > = singular.ok, ...): NA/NaN/Inf in 'x' > > produces empty list. So maybe others could find some problem. > > Cheers > Petr > > > dput(wlg) > structure(list(temp = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, > 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, > 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, > 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, > 6L, 6L, 6L, 6L, 6L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, > 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("40", "10", "16", "22", "28", > "34"), class = c("ordered", "factor")), species = structure(c(3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("mungbean", > "rice", "wheat"), class = "factor"), start = c(0, 1, 2, 3, 4, > 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, > 9, 10, 11, 12, 13, 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, > 12, 13, 14, 16, 17, 0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, > 14, 16, 17, 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, > 0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17), end = c(1, > 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, > 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, > 9, 10, 11, 12, 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, > 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, > 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, > 16, 17, 18), germinated = c(0L, 0L, 0L, 0L, 0L, 4L, 6L, 8L, 0L, > 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 11L, 7L, 0L, 1L, 0L, 0L, > 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 12L, 3L, 0L, 3L, 0L, 0L, > 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 8L, 0L, 8L, 3L, 0L, 0L, > 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 11L, 1L, 1L, 0L, 0L, 0L, > 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, > 2L, 0L, 0L, 0L, 0L, 0L, 0L), TotSeeds = c(20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, > 20, 20, 20, 20, 20, 20, 20, 20), TotGerminated = c(0, 0, 0, 0, > 0, 4, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 0, 0, 11, 18, 18, > 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 0, 1, 13, 16, 16, 19, > 19, 19, 19, 19, 19, 19, 19, 19, 19, 0, 0, 0, 8, 8, 16, 19, 19, > 19, 19, 19, 19, 19, 19, 19, 19, 0, 5, 16, 17, 18, 18, 18, 18, > 18, 19, 19, 19, 19, 19, 19, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 3, > 3, 3, 3, 3, 3), Prop = c(0, 0, 0, 0, 0, 0.2, 0.5, 0.9, 0.9, 0.9, > 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0, 0, 0.55, 0.9, 0.9, 0.95, 0.95, > 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0.05, 0.65, > 0.8, 0.8, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, > 0.95, 0, 0, 0, 0.4, 0.4, 0.8, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, > 0.95, 0.95, 0.95, 0.95, 0, 0.25, 0.8, 0.85, 0.9, 0.9, 0.9, 0.9, > 0.9, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0, 0, 0, 0, 0, 0, 0, > 0, 0.05, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15)), .Names = c("temp", > "species", "start", "end", "germinated", "TotSeeds", "TotGerminated", > "Prop"), row.names = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, > 11L, 12L, 13L, 14L, 15L, 16L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, > 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 63L, 64L, 65L, 66L, 67L, > 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 95L, 96L, 97L, > 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, > 109L, 110L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, > 136L, 137L, 138L, 139L, 140L, 141L, 159L, 160L, 161L, 162L, 163L, > 164L, 165L, 166L, 167L, 168L, 169L, 170L, 171L, 172L, 173L, 174L > ), class = c("nfnGroupedData", "nfGroupedData", "groupedData", > "data.frame"), formula = Prop ~ end | temp, FUN = function (x) > max(x, na.rm = TRUE), order.groups = TRUE) > > > > > sessionInfo() > R Under development (unstable) (2017-07-31 r73003) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 10 x64 (build 14393) > > Matrix products: default > > locale: > [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech > Republic.1250 > [3] LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C > [5] LC_TIME=Czech_Czech Republic.1250 > > attached base packages: > [1] stats datasets utils grDevices graphics methods base > > other attached packages: > [1] nlme_3.1-131 lattice_0.20-35 fun_0.1 > > loaded via a namespace (and not attached): > [1] compiler_3.5.0 colorspace_1.3-2 scales_0.4.1 lazyeval_0.2.0 > [5] plyr_1.8.4 tools_3.5.0 gtable_0.2.0 tibble_1.3.3 > [9] Rcpp_0.12.12 ggplot2_2.2.1 grid_3.5.0 rlang_0.1.1 > [13] munsell_0.4.3 > > > > > -----Original Message----- > > From: Wall, Wade A ERDC-RDE-CERL-IL CIV > > [mailto:Wade.A.Wall at erdc.dren.mil] > > Sent: Thursday, October 19, 2017 3:18 PM > > To: PIKAL Petr <petr.pikal at precheza.cz> > > Subject: RE: Error messages using nonlinear regression function (nls) > > > > "Prop" is the proportion of seeds that have germinated from the total. > Here is > > the code I used to transform the germination data set. When graphed, the > > logistic curve provides a reasonable fit. > > > > data(germination) > > germination$TotSeeds = 20 > > germination$TotGerminated = 0 > > tmpCount = 0 > > > > for(i in 2:nrow(germination)){ > > if((germination$temp[i]!=germination$temp[i-1]) | > (germination$species[i] !> > germination$species[i-1])) {tmpCount = 0} > > if((germination$temp[i]==germination$temp[i-1]) & > (germination$species[i] > > == germination$species[i-1])) > > {tmpCount = tmpCount + germination$germinated[i]; > > germination$TotGerminated[i]=tmpCount} > > } > > germination$Prop = germination$TotGerminated/germination$TotSeeds > > germination = germination[germination$end != Inf,] > > > > Wade > > > > -----Original Message----- > > From: PIKAL Petr [mailto:petr.pikal at precheza.cz] > > Sent: Thursday, October 19, 2017 1:21 AM > > To: Wall, Wade A ERDC-RDE-CERL-IL CIV <Wade.A.Wall at erdc.dren.mil>; r- > > help at r-project.org > > Subject: RE: Error messages using nonlinear regression function (nls) > > > > Hi > > > > Thanks for the code but where is Prop? > > > > It is not a variable in germination data set so we do not know how you > did the > > computation. > > > > My wild guess is, that your Prop do not follow logistic curve and > therefore no > > results from nlsList > > > > Cheers > > Petr > > > > > > > -----Original Message----- > > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Wall, > > > Wade A ERDC-RDE-CERL-IL CIV > > > Sent: Wednesday, October 18, 2017 5:58 PM > > > To: r-help at r-project.org > > > Subject: [R] Error messages using nonlinear regression function (nls) > > > > > > Hi all, > > > > > > I am trying to use nonlinear regression (nls) to analyze some seed > > > germination data, but am having problems with error codes. > > > > > > The data that I have closely matches the germination dataset included > > > in the drc package. > > > > > > Here is the head of the data > > > > > > temp species start end germinated TotSeeds TotGerminated Prop > > > 1 10 wheat 0 1 0 20 0 0.0 > > > 2 10 wheat 1 2 0 20 0 0.0 > > > 3 10 wheat 2 3 0 20 0 0.0 > > > 4 10 wheat 3 4 0 20 0 0.0 > > > 5 10 wheat 4 5 0 20 0 0.0 > > > 6 10 wheat 5 6 4 20 4 0.2 > > > > > > temp is the temperature under which the seeds were germinated, species > > > denotes the species (wheat, mungbean, or rice) Start and end denote > > > the beginning and end of a period of time and germinated denotes how > > > many seeds germinated during that period of time. Prop represents the > > > proportion of seeds that have germinated. > > > > > > I have attempted to mimic Fox and Weisberg's appendix to Nonlinear > > > Regression found here. > > > Blockedhttps://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendi > > > x/AppendixBlocked > > > -Nonlinear-Regression.pdf > > > > > > My first step is to look at a single species, wheat, and use nls on > > > the individual temperatures. > > > > > > I have tried to use both the nlsList function and to attempt to > > > estimate the parameters using lm(), but I receive error messages on > > > both. Here is the code. > > > > > > library(drc) ### for germination dataset > > > data(germination) > > > > > > wheat = germination[germination$species == "wheat",] ### subset by > > > wheat scatterplot(Prop ~ end|temp,data=wheat,box=FALSE,reg=FALSE) ### > > > view the data wheat$temp = as.factor(wheat$temp) ### convert to factor > > > > > > ### First, try to use nlsList > > > wheat.list <- nlsList(Prop ~ SSlogis(end,phi1,phi2,phi3)| > > > temp,pool=FALSE,data=wheat) ### > > > > > > ### next, try to use lm to estimate starting parameters. > > > wheat.list = list() > > > > > > for (i in 1:length(levels(wheat$temp))){ > > > tmpDat = wheat[wheat$temp == levels(wheat$temp)[i],] > > > tmp.lm <- lm(Prop ~ end,data = tmpDat) > > > tmp.nls <- nls(Prop ~ theta1 / (1 + exp(-(theta2 + theta3*end))), > > > start = list(theta1 = .5,theta2=coef(tmp.lm)[1],theta3 > coef(tmp.lm)[2]), > > > data = tmpDat,trace=TRUE) > > > tmp2.nls <- nls(Prop ~ SSlogis(end,phi1,phi2,phi3),data=tmpDat) > > > wheat.list[i] <- tmp.nls > > > } > > > #### End code > > > nlsList just returns an empty list. > > > > > > When I try to loop through the individual temperatures, for the first > > > temperature, nls converges when I provide starting values, but when I > > > try to use SSlogis(), I get the error messsage > > > > > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) > : > > > NA/NaN/Inf in 'x' > > > > > > For the second temperature (16), I get the following error message > > > when provided initial values using lm: > > > > > > Error in nls(Prop ~ theta1/(1 + exp(-(theta2 + theta3 * end))), start > > > = list(theta1 = 0.5, : > > > singular gradient > > > > > > I have tried to read through posts, but none of them seem to apply to > this > > case. > > > The data seem relatively simply and > > > I am not sure what I am doing wrong. Any help would be appreciated. > > > > > > Wade > > > > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code.[[alternative HTML version deleted]]