[R] Error messages using nonlinear regression function (nls)

PIKAL Petr
Fri, 20 Oct 2017 06:33:36 -0000

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
> >

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