[R] offset in nlme

Wed Dec 28 11:02:50 CET 2016

Hi

> -----Original Message-----
> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
> Sent: Wednesday, December 28, 2016 10:13 AM
> To: PIKAL Petr <petr.pikal at precheza.cz>; r-help mailing list <r-help at r-
> project.org>
> Subject: RE: [R] offset in nlme
>
> You don't need to post WORKING code... just code that leads to the problem
> you want help with. The ability to create the error and then eliminate the
> error greatly reduces guessing on both sides of the conversation about the
> nature of the question. (Things the asker did not know were important
> become clear to the answerer and can be highlighted.)
>
> I think you can also forgo the little function definition if you simply remove R0
> from the start list in your original call to nlme and put a zero in the function
> call.

Yes, you are correct. I am not sure if it is intended but I did not find any mention about this feature in help pages nor in Pinheiro, Bates book.

fit<-nlsList(rutrtg ~ SSasymp(doba, Asym, R0=5, lrc), data=rutil.g, start=c(Asym=100, lrc=-3))
fit1<-nlme(fit, random=Asym+lrc~1)
fixef(fit1)
    Asym      lrc
73.77617 -3.31942

Cheers
Petr

For completeness, here are the data.
dput(rutil.g)
structure(list(vzorek = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 5L, 7L, 9L, 11L, 13L,
6L, 8L, 10L, 12L, 14L), .Label = c("01.I", "02.I", "1", "2",
"2/1*A/900C", "2/1*A/950C", "2/1*B/900C", "2/1*B/950C", "2/1*C/900C",
"2/1*C/950C", "2/1*D/900C", "2/1*D/950C", "2/1*E/900C", "2/1*E/950C",
"3", "4"), class = "factor"), promot = 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, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L), teplota = c(875L, 875L, 875L, 875L, 875L, 925L, 925L, 925L,
925L, 925L, 875L, 875L, 875L, 875L, 875L, 925L, 925L, 925L, 925L,
925L, 875L, 875L, 875L, 875L, 875L, 925L, 925L, 925L, 925L, 925L,
875L, 875L, 875L, 875L, 875L, 925L, 925L, 925L, 925L, 925L, 875L,
875L, 875L, 875L, 875L, 925L, 925L, 925L, 925L, 925L, 875L, 875L,
875L, 875L, 875L, 925L, 925L, 925L, 925L, 925L, 875L, 875L, 875L,
875L, 875L, 925L, 925L, 925L, 925L, 925L), k2oteor = c(0.2, 0.2,
0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.2,
0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4), p2o5teor = c(0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17, 0.17), k2omer = c(0.104,
0.104, 0.104, 0.104, 0.104, 0.104, 0.104, 0.104, 0.104, 0.104,
0.102, 0.102, 0.102, 0.102, 0.102, 0.102, 0.102, 0.102, 0.102,
0.102, 0.384, 0.384, 0.384, 0.384, 0.384, 0.384, 0.384, 0.384,
0.384, 0.384, 0.211, 0.211, 0.211, 0.211, 0.211, 0.211, 0.211,
0.211, 0.211, 0.211, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18, 0.18,
0.18, 0.18, 0.18, 0.266, 0.266, 0.266, 0.266, 0.266, 0.266, 0.266,
0.266, 0.266, 0.266, 0.26, 0.26, 0.26, 0.26, 0.26, 0.26, 0.26,
0.26, 0.26, 0.26), p2o5mer = c(0.167, 0.167, 0.167, 0.167, 0.167,
0.167, 0.167, 0.167, 0.167, 0.167, 0.165, 0.165, 0.165, 0.165,
0.165, 0.165, 0.165, 0.165, 0.165, 0.165, 0.171, 0.171, 0.171,
0.171, 0.171, 0.171, 0.171, 0.171, 0.171, 0.171, 0.16, 0.16,
0.16, 0.16, 0.16, 0.16, 0.16, 0.16, 0.16, 0.16, 0.164, 0.164,
0.164, 0.164, 0.164, 0.164, 0.164, 0.164, 0.164, 0.164, 0.162,
0.162, 0.162, 0.162, 0.162, 0.162, 0.162, 0.162, 0.162, 0.162,
0.165, 0.165, 0.165, 0.165, 0.165, 0.165, 0.165, 0.165, 0.165,
0.165), al2o3 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.017, 0.017,
0.017, 0.017, 0.017, 0.017, 0.017, 0.017, 0.017, 0.017, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.006, 0.006, 0.006, 0.006, 0.006, 0.006,
0.006, 0.006, 0.006, 0.006, 0.025, 0.025, 0.025, 0.025, 0.025,
0.025, 0.025, 0.025, 0.025, 0.025, 0.019, 0.019, 0.019, 0.019,
0.019, 0.019, 0.019, 0.019, 0.019, 0.019, 0.016, 0.016, 0.016,
0.016, 0.016, 0.016, 0.016, 0.016, 0.016, 0.016), tskut = c(900L,
900L, 900L, 900L, 900L, 950L, 950L, 950L, 950L, 950L, 900L, 900L,
900L, 900L, 900L, 950L, 950L, 950L, 950L, 950L, 900L, 900L, 900L,
900L, 900L, 950L, 950L, 950L, 950L, 950L, 900L, 900L, 900L, 900L,
900L, 950L, 950L, 950L, 950L, 950L, 900L, 900L, 900L, 900L, 900L,
950L, 950L, 950L, 950L, 950L, 900L, 900L, 900L, 900L, 900L, 950L,
950L, 950L, 950L, 950L, 900L, 900L, 900L, 900L, 900L, 950L, 950L,
950L, 950L, 950L), doba = c(15L, 30L, 60L, 120L, 240L, 15L, 30L,
60L, 120L, 240L, 15L, 30L, 60L, 120L, 240L, 15L, 30L, 60L, 120L,
240L, 15L, 30L, 60L, 120L, 240L, 15L, 30L, 60L, 120L, 240L, 15L,
30L, 60L, 120L, 240L, 15L, 30L, 60L, 120L, 240L, 15L, 30L, 60L,
120L, 240L, 15L, 30L, 60L, 120L, 240L, 15L, 30L, 60L, 120L, 240L,
15L, 30L, 60L, 120L, 240L, 15L, 30L, 60L, 120L, 240L, 15L, 30L,
60L, 120L, 240L), rutrtg = c(16.4, 87.1, 96.6, 95, 96.5, 34.9,
98.5, 98.3, 99.3, 99.8, 25.9, 71.3, 79.8, 84.9, 89.6, 43.3, 83.2,
87.2, 93.4, 93.5, 10.1, 33, 53.8, 30.5, 34.2, 17.7, 50.9, 69.1,
86.6, 92.4, 20.3, 76.1, 87.6, 89.7, 94.7, 17, 44.6, 43.4, 46.7,
54.7, 10, 42.6, 76.9, 54.2, 75.6, 29, 80.8, 96.2, 84.2, 85.7,
8.9, 41.3, 56.9, 43.9, 46.5, 36.6, 71.8, 83.5, 75.5, 80.4, 9.1,
26.6, 40.7, 36, 56.3, 34.5, 69.2, 73.3, 74.7, 79.5), barvivost = c(888,
1611, 1663, 1681, 1706, 1287, 1341, 1519, 1645, 1689, 1176, 1562,
1665, 1669, 1731, 1375, 1694, 1718, 1769, 1783, 954, 1428, 1568,
1476, 1521, 927, 1641, 1717, 1796, 1848, 1158, 1629, 1746, 1743,
1792, 1090, 1508, 1620, 1636, 1689, 932, 1442, 1689, 1538, 1731,
1139, 1760, 1822, 1864, 1868, 894, 1443, 1629, 1594, 1666, 1572,
1705, 1811, 1774, 1806, 796, 1371, 1512, 1515, 1636, 1352, 1690,
1771, 1778, 1849), podton = c(10L, 6L, 5L, 7L, 7L, 9L, -7L, -3L,
3L, 3L, 12L, 10L, 12L, 11L, 10L, 10L, 11L, 8L, 10L, 8L, 15L,
15L, 16L, 16L, 16L, 10L, 14L, 12L, 13L, 9L, 15L, 14L, 15L, 15L,
13L, 12L, 12L, 12L, 12L, 10L, 13L, 12L, 13L, 15L, 12L, 14L, 13L,
8L, 7L, 6L, 14L, 16L, 15L, 15L, 13L, 15L, 13L, 8L, 9L, 7L, 13L,
16L, 16L, 16L, 13L, 14L, 13L, 8L, 8L, 5L), lpas = c(45.21, 52.42,
52.94, 53.12, 53.37, 49.19, 49.73, 51.5, 52.76, 53.2, 48.08,
51.93, 52.96, 53, 53.62, 50.07, 53.25, 53.49, 54, 54.13, 45.87,
50.6, 51.99, 51.07, 51.52, 45.6, 52.72, 53.48, 54.26, 54.78,
47.9, 52.6, 53.77, 53.74, 54.22, 47.23, 51.39, 52.51, 52.67,
53.2, 45.65, 50.74, 53.2, 51.69, 53.62, 47.71, 53.91, 54.52,
54.94, 54.98, 45.27, 50.75, 52.6, 52.25, 52.97, 52.03, 53.36,
54.41, 54.04, 54.36, 44.3, 50.03, 51.43, 51.46, 52.67, 49.84,
53.21, 54.02, 54.08, 54.79), apas = c(1.05, 0.46, 0.48, 0.45,
0.39, 0.6, 0.82, 0.59, 0.4, 0.33, 0.7, 0.47, 0.27, 0.31, 0.18,
0.54, 0.28, 0.22, 0.1, 0.07, 0.89, 0.57, 0.43, 0.47, 0.38, 0.94,
0.3, 0.14, -0.03, -0.01, 0.67, 0.4, 0.12, 0.17, -0.02, 0.82,
0.46, 0.33, 0.31, 0.26, 0.93, 0.5, 0.24, 0.35, 0.15, 0.72, 0.15,
0.17, 0.12, 0.16, 0.96, 0.54, 0.24, 0.28, 0.27, 0.38, 0.18, 0.16,
0.21, 0.22, 1.13, 0.66, 0.41, 0.41, 0.31, 0.54, 0.18, 0.22, 0.23,
0.19), bpas = c(-0.02, 0.87, 0.91, 0.51, 0.59, 0.13, 3.45, 2.53,
1.45, 1.36, -0.31, 0.03, -0.42, -0.13, 0.03, -0.04, -0.28, 0.46,
0.09, 0.47, -0.92, -0.95, -1.11, -1.1, -1.11, 0.02, -0.7, -0.39,
-0.5, 0.18, -1, -0.81, -0.9, -0.95, -0.68, -0.44, -0.44, -0.33,
-0.33, -0.02, -0.63, -0.48, -0.68, -0.92, -0.36, -0.84, -0.53,
0.43, 0.61, 0.83, -0.72, -1.11, -0.97, -1.06, -0.62, -0.9, -0.56,
0.35, 0.14, 0.64, -0.59, -1.24, -1.13, -1.28, -0.52, -0.83, -0.51,
0.47, 0.4, 0.97), vodivost = c(868, 185.3, 95.5, 106.3, 87.8,
514, 86.4, 95.3, 62.2, 56.4, 1192, 570, 497, 484, 448, 930, 571,
503, 453, 832, 1966, 969, 661, 1288, 678, 3054, 597, 477, 431,
347, 1095, 430, 401, 371, 332, 2250, 1392, 1205, 1173, 1142,
1508, 710, 479, 686, 529, 1017, 520, 417, 466, 488, 2240, 908,
692, 808, 784, 724, 698, 557, 773, 698, 1784, 848, 800, 777,
644, 883, 609, 702, 628, 716), zaverage = c(311.7, 348.1, 336,
321, 325.2, 327.6, 518.3, 415, 353.1, 355.4, 258.3, 286.2, 265.1,
288.7, 308.5, 258.5, 271.6, 311.8, 283.7, 298.3, 209.5, 227,
231, 219.9, 228.1, 245.1, 254.9, 270.6, 265.6, 297.6, 231.8,
256.9, 247.5, 246.7, 258.1, 223.3, 246.2, 253.2, 255.6, 275.8,
250.4, 256.6, 248.6, 223.5, 254.2, 254, 293.8, 296.6, 299.6,
310.1, 225.4, 228.6, 237.4, 228.7, 238, 239.5, 250.5, 288.4,
303.7, 301.1, 230.1, 222, 225.8, 222.9, 255.4, 236.8, 261.6,
292.9, 295.7, 318.7), k2o.f = structure(c(1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 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, 3L, 3L, 3L, 3L,
3L), .Label = c("low", "standard", "high", "extreme"), class = "factor"),
    int = structure(c(1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L,
    1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L,
    8L, 8L, 8L, 8L, 8L, 2L, 2L, 2L, 2L, 2L, 6L, 6L, 6L, 6L, 6L,
    9L, 9L, 9L, 9L, 9L, 11L, 11L, 11L, 11L, 11L, 10L, 10L, 10L,
    10L, 10L, 12L, 12L, 12L, 12L, 12L, 3L, 3L, 3L, 3L, 3L, 7L,
    7L, 7L, 7L, 7L), .Label = c("low/900/3", "standard/900/3",
    "high/900/3", "extreme/900/3", "low/950/3", "standard/950/3",
    "high/950/3", "extreme/950/3", "standard/900/6", "high/900/6",
    "standard/950/6", "high/950/6"), class = c("ordered", "factor"
    ), scores = structure(c(3, 6, 3, 3, 6, 3, 3, 6, 3, 3, 6,
    3), .Dim = 12L, .Dimnames = list(c("low/900/3", "standard/900/6",
    "standard/900/3", "high/900/3", "high/900/6", "extreme/900/3",
    "low/950/3", "standard/950/6", "standard/950/3", "high/950/3",
    "high/950/6", "extreme/950/3"))))), .Names = c("vzorek",
"promot", "teplota", "k2oteor", "p2o5teor", "k2omer", "p2o5mer",
"al2o3", "tskut", "doba", "rutrtg", "barvivost", "podton", "lpas",
"apas", "bpas", "vodivost", "zaverage", "k2o.f", "int"), class = c("nfnGroupedData",
"nfGroupedData", "groupedData", "data.frame"), row.names = c(NA,
70L), formula = rutrtg ~ doba | int, FUN = function (x)
max(x, na.rm = TRUE), order.groups = TRUE)

> --
> Sent from my phone. Please excuse my brevity.
>
> On December 27, 2016 11:39:29 PM PST, PIKAL Petr
> <petr.pikal at precheza.cz> wrote:
> >Hi Jeff.
> >
> >Yes, if it had been reproducible I would not post it as I had known
> >solution myself. (Uff, I hope I used this conditional clause
> >correctly).
> >
> >OTOH your suggestion works and seems to arrive to desired result even
> >that you said you do not know what I am talking about. R (and this
> >smart community) sometimes surprise me even after quite a long time
> >experience.
> >
> >Thanks.
> >Petr
> >
> >> -----Original Message-----
> >> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
> >> Sent: Tuesday, December 27, 2016 4:21 PM
> >> To: PIKAL Petr <petr.pikal at precheza.cz>; r-help mailing list
> ><r-help at r-
> >> project.org>
> >> Subject: Re: [R] offset in nlme
> >>
> >> Not reproducible. Tsk!
> >>
> >> I really don't know what you are taking about,  but some ideas are:
> >>
> >> mySSasymp <- function( doba, Asym, lrc ) {
> >>   SSasymp(doba, Asym, 0, lrc)
> >> }
> >>
> >> Another idea is to use log( time ) rather than time.
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On December 27, 2016 6:47:12 AM PST, PIKAL Petr
> ><petr.pikal at precheza.cz>
> >> wrote:
> >> >Dear all
> >> >
> >> >I would like to fit SSasymp model to some data by nlme. I did not
> >find
> >> >any clue how to set one of parameters to fixed constant value
> >(R0=0).
> >> >
> >> >One suitable way could be to use SSlogis as it has one parameter
> >zero,
> >> >however it is not correct AFAIK logistics is defined from -Inf to
> >Inf
> >> >and my x value is time, starting from 0.
> >> >
> >> >The only option I found is to define my own growth function which is
> >> >constrained by some fixed starting point. Does anybody know other
> >way
> >> >around? Like persuading nlme not optimize R0 and be happy with the
> >> >value set in the function call.
> >> >
> >> >something like
> >> >
> >> >nlsList(rutrtg ~ SSasymp(doba, Asym, R0, lrc), data=rutil.g,
> >> >start=c(Asym=100, R0= 10, lrc=-2), offset=c(R0=10))
> >> >
> >> >which obviously does not work.
> >> >
> >> >I could put some data but it is more a matter of nlme or other R
> >> >functions then real data.
> >> >
> >> >Looking forward to some answer.
> >> >Happy New year 2017
> >> >
> >> >Petr Pikal
> >> >

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- 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.