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

[PIKAL Petr]

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
>
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> and provide commented, minimal, self-contained, reproducible code.

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