[R] nls, convergence and starting values

[Bert Gunter]

Based on a simple scatterplot of pourcma vs  transat, a 4 parameter logistic
looks like wild overfitting, and that may be the source of your problems.
Given the huge scatter, a straight line is about as much as would seem
sensible. I think this falls into the "Why ever would you want to do such a
thing?" category.

-- Bert


Bert Gunter
Genentech Nonclinical Biostatistics
650-467-7374

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Patrick Giraudoux
Sent: Friday, March 27, 2009 12:39 PM
To: r-help at stat.math.ethz.ch
Cc: Francis Raoul
Subject: [R] nls, convergence and starting values

"in non linear modelling finding appropriate starting values is
something like an art"... (maybe from somewhere in Crawley , 2007)  Here
a colleague and I just want to compare different response models to a
null model. This has worked OK for almost all the other data sets except
that one (dumped below). Whatever our trials and algorithms, even
subsetting data (to check if some singular point was the cause of the
mess), we do not reach convergence... or screw up with singular
gradients (?) etc...

eg:

nls(pourcma~SSlogis(transat, Asym, xmid, scal), start=c(Asym=30,
xmid=0.07, scal=0.02),data=bdd, weights=sqrt(nbfeces),trace=T,alg="plinear")

As anyone a hint about an alternate approach to fit a model ? Or an idea
to get evidence that such model cannot be fitted to the data....


bdd <-
structure(list(transat = c(0.0697, 0.13079, 0.314265, 0.241613,
0.039319, 0, 0, 0, 0, 0, 0.0805, 0.41, 0.30585, 0.27465, 0.06085,
0.09114, 0.05766, 0.036983, 0.093186, 0.046624, 0, 0, 0, 0, 0.000616,
0, 0.0025, 0.0325, 0.03125, 0.04599, 0.38398, 0.524505, 0.450337,
0.061831, 0.133926, 0.091806, 0.00928, 0.25114, 0.3074, 0.431056,
0.026158), transma = c(0.04141, 0.01599, 0.101803, 0.002378,
0.039319, 0.00472459016393443, 0.0031016393442623, 0.000178524590163934,
0.00255704918032787, 0.000346229508196721, 0.0665, 0.012, 0.0553,
0.0045, 0.0056, 0.00155, 0.00124, 0.011966, 0.001736, 0.004712,
3.62903225806452e-05, 9.79838709677419e-05, 2.20161290322581e-05,
0.00462, 0.0100644444444444, 0.00213111111111111, 0.046, 0.005,
0.01195, 0.07154, 0.08468, 0.141182, 0.086578, 0.027959, 0.003159,
0.003081, 0.13862, 0.00754, 0.078648, 0.068324, 0.025288), nbfeces = c(22L,
26L, 43L, 30L, 35L, 25L, 21L, 36L, 34L, 37L, 23L, 32L, 40L, 35L,
30L, 16L, 25L, 37L, 37L, 34L, 31L, 35L, 41L, 31L, 34L, 39L, 5L,
14L, 31L, 13L, 21L, 34L, 32L, 36L, 36L, 40L, 31L, 35L, 39L, 29L,
32L), pourcma = c(50, 34.6153846153846, 27.9069767441860, 43.3333333333333,
65.7142857142857, 32, 28.5714285714286, 22.2222222222222, 50,
10.8108108108108, 26.0869565217391, 40.625, 12.5, 22.8571428571429,
43.3333333333333, 6.25, 4, 10.8108108108108, 16.2162162162162,
23.5294117647059, 25.8064516129032, 45.7142857142857, 39.0243902439024,
25.8064516129032, 41.6666666666667, 27.5, 20, 14.2857142857143,
22.5806451612903, 15.3846153846154, 38.0952380952381, 17.6470588235294,
78.125, 61.1111111111111, 25, 37.5, 22.5806451612903, 40, 17.9487179487179,
41.3793103448276, 50), pourcat = c(22.7272727272727, 30.7692307692308,
41.8604651162791, 56.6666666666667, 5.71428571428571, 0, 0, 0,
0, 0, 30.4347826086957, 15.625, 45, 74.2857142857143, 13.3333333333333,
50, 12, 18.9189189189189, 27.0270270270270, 20.5882352941176,
0, 0, 0, 0, 0, 5, 40, 0, 0, 7.69230769230769, 9.52380952380952,
38.2352941176471, 59.375, 5.55555555555556, 41.6666666666667,
42.5, 9.67741935483871, 14.2857142857143, 51.2820512820513,
79.3103448275862,
6.25)), .Names = c("transat", "transma", "nbfeces", "pourcma",
"pourcat"), class = "data.frame", row.names = c(NA, -41L))

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