Re: [R] lme, nlsList, nlsList.selfStart

Prof Brian Ripley Fri, 17 Feb 2006 09:52:33 -0800

On Fri, 17 Feb 2006, Spencer Graves wrote:

Have you tried making mydata2$Dose the same length as everythingelse?

[<- does that for you: all columns in a data frame must be the samelength. Read on in your inbox for the solution.


          spencer graves

Patrick Giraudoux wrote:

Well, right, Dose was indeed in the global environment and not in thedata.frame. Changing it with


mydata2$Dose<-100 # the real dose at the beginning of the experiment

improves the thing in a sense... but I face a new error:

mymod3<-nlsList(Conc+1 ~ Dose * exp(lKe+lKa-lCl) *(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)) | Organ,

data=mydata2,
start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
)

Error in exp(-exp(lKa) * Conc + 1 ~ Tps) :
       Non-numeric argument to mathematical function
Error in exp(-exp(lKa) * Conc + 1 ~ Tps) :
       Non-numeric argument to mathematical function
Error in exp(-exp(lKa) * Conc + 1 ~ Tps) :
       Non-numeric argument to mathematical function

I have checked the variables in the data.frame with:

 > sapply(mydata2,is.factor)
 Tps  Conc Organ  Dose
FALSE FALSE  TRUE FALSE
 > sapply(mydata2,is.character)
 Tps  Conc Organ  Dose
FALSE FALSE FALSE FALSE

So everything looks OK on this side...

Furthermore, I have still this "old" error intact:

 > mymod4<-nlsList(SSfol,data=mydata2)
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found

I am really sorry for calling help and boring everybody on this likelytrivial issue (this looks like asking a community to participate todebogging line by line, a shame!!!), but I must admit that I am reallylost...


Thanks for your concern,

Kind regards,

Patrick


Prof Brian Ripley a écrit :

We don't have Dose, and I think that is where the error lies. If Dosewere part of mydata2, this is likely to work, but otherwise it is Dosewhich has the wrong length.


?nlsList says

    data: a data frame in which to interpret the variables named in
          'model'.

and it means it: you must get all the variables from there.


On Fri, 17 Feb 2006, Patrick Giraudoux wrote:

Spencer,

Thanks for the hint. I did not dare to bore people with the full data
set and though that this kind of error may have been trivial and often
encountered (so leading to a short answer), even though I did not see
related messages on the r-help list. I already did the checks suggested
before posting, and was aware of the possible confusion between 1 and l
(actually the variable names were not given by myself).

It seems that the trouble comes when the grouping variable "Organ" is
used. The best (?) I can do  is to dump the data.frame here below.

With this example, one can get exactly the same errors:

mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
   data=mydata2,
   start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
   )

... works well!!!

but we get then:

mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)) | Organ,
   data=mydata2,
   start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
   )
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
       variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
       variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
       variable lengths differ


> mymod4<-nlsList(SSfol,data=mydata2)
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found


Sorry and apologise for the inconvenience met,

Kind regards,

Patrick



# data.frame just to copy and past into R

"mydata2" <-
structure(list(Tps = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3,
3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6,
6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9,
9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 14,
14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20, 25, 28, 29,
50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136,
1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4,
4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10,
10, 10, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 17, 17, 17,
17, 17, 20, 20, 20, 20, 25, 28, 29, 50, 50, 50, 136, 136, 136,
136, 136, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 2, 2, 2,
2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5,
6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8,
8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11,
11, 11, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20,
25, 28, 29, 50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136,
136, 136), Conc = c(0, 0, 0, 0, 0, 0, 0, 0.807852503274902,
0.204371494701886,
0.579222129993907, 0.989062273721619, 0, 1.11728297897571,
1.41057428121324,
0.888883702851307, 1.259907624008, 1.45753269675829, 1.07077516747401,
0.843279379, 0, 0.763110069196737, 1.11297791434297, 1.10087763997637,
0.946929594501016, 1.33112168, 0.654041755, 0.694167499, 1.289548703,
1.117139864, 0.807196192, 0.720221376552025, 0.560082823, 0.476583438,

2.590855204, 0.51510972, 1.072946887, 0.537999938614396,0.886684225905255,

0.630178116793598, 1.31534758842196, 1.33333958571746, 0.922032210748255,
0.429930193046174, 1.35881467717335, 0.790045927902363, 1.22484702570724,
0.808104508207897, 1.31185966817903, 1.51837686425553, 1.74105163638734,
1.80365598487402, 1.13240352674377, 1.50086243061644, 2.06355364280445,
0.439350890906039, 1.54692793444949, 1.78758216051046, 1.09043400023239,

0.811328376840514, 0.459192443530981, 0.695333473157298,0.387995007681174,0.784627063444921, 1.02282256375842, 0.382687104107726,0.554290634950242,0.130420456296453, 0.324194753224919, 0.31106140274139,0.513473505828888,

0.878620320248701, 1.18404358659996, 0.136926837896477, 0, 0,

0.835588760032974, 0.558617235576616, 1.21002805866839,0.769381068031404,1.04514254228094, 0.373251847173678, 0.389005898972802,0.183141006154896,

0.223596336820146, 0.315526423315647, 0.0930349732768131,
0.169959185212759,
0.161878841748425, 0, 0.0483041009105874, 0, 0, 0, 0.0777005553478052,
0, 0.153175826795441, 0.0428171049833677, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 26.564295705327, 5.5893744508169, 7.22612934071834,

36.6563989567777, 0, 28.8967184437329, 28.4030370337251,28.0886043901352,

26.1230935842208, 28.8895673910072, 42.6814210131968, 32.3555695551062,
0.76883326657205, 34.6159136622156, 38.329242204291, 56.4476583636484,
26.6249506083603, 31.3001451026823, 23.7339071829084, 23.3702284599355,
36.669903715038, 44.7377244306005, 31.2079335923023, 32.8613384312272,
29.4259634309146, 45.6112405959009, 48.1231689836687, 55.0037961570027,
32.9822316456421, 20.0382768189682, 26.0986380308655, 28.8915584506145,
28.7949023823068, 30.0278417498425, 58.8089779973569, 20.3602570111197,
29.6269605259023, 28.4404986724604, 30.2165182590977, 19.9204461889074,
31.1019196559556, 30.3847467747055, 36.8726911479995, 51.0618036275519,
23.5408013442579, 36.6948355347593, 27.4753860809429, 24.1341667099646,
27.5411488989643, 35.9021799354022, 19.7417897046158, 31.1403887303244,
46.1743622734049, 34.8235854891765, 22.1714704189293, 33.6805966894274,
35.2814908686112, 42.9767437212852, 38.1264997164547, 5.3651357974451,
42.8990434918385, 25.4908883698364, 25.99649502, 36.4958105490917,
40.8004126550705, 5.36867162116895, 0.00898476265269363, 0,
27.6810997945798,
28.7918300045713, 45.7577183830352, 35.9276318604787, 34.9717618087238,
29.620354272564, 24.6537513599869, 13.5363982464958, 25.8289073574818,
12.0090406245759, 4.753436805, 11.849214652228, 8.41410147611612,

0, 1.80855352862552, 1.1987530031681, 1.01148025243171,0.495675369574172,1.62701127228732, 0, 16.6288242287241, 1.23656061354912,0.323708776035328,

0, 0.566916625204436, 0, 0, 0, 0, 0, 0, 0, 2.53578781871283,
3.50083667130797, 0, 0.98049572179098, 0, 3.57129673217304,
2.77298867949388,
2.12302645642669, 4.11923869203499, 4.69069462193674, 2.8698666062651,
2.05079837323067, 0.0602771574448942, 5.96454350250626, 2.26267114439802,
3.06911285674854, 2.04233129537404, 2.62181873844029, 1.51813653072598,
1.46193772981073, 2.69864635755833, 3.44016493913122, 2.50834832469627,
3.48170744166168, 1.00637581555435, 1.67065398473081, 4.18855363095027,
3.39649762611015, 1.72804613460423, 1.40053679329531, 2.37032387724109,
3.19332545080983, 2.49474373894248, 2.17800931288708, 2.7601484443213,
0.91266104095844, 1.93485048639199, 1.19692593420788, 1.79537330666258,
2.14020930767983, 3.0122526724942, 2.81112226980754, 3.54890724398174,
3.01022926452999, 2.38263226710738, 3.53569238341869, 3.47869329713911,
0.679333339820719, 2.4764260756438, 3.82615100065366, 2.20449890383871,
1.371303113329, 1.2427787019995, 1.73319133880954, 0.391268883238408,
1.73610193837913, 2.68494324646718, 1.77065393606844, 1.45079980147062,
0.763775702906329, 0.98566725668627, 0.37838763208699, 0.841811919286804,
1.46436462204795, 1.98409602726, 0.507005887891038, 0.465515668274195,
0, 1.873365675227, 1.69023864630648, 2.65530855919137, 2.34392199908302,
1.61917643594837, 1.05165934333345, 0.564642823436471, 0.121621029620328,

0.515007625737071, 0.524345809084086, 0.130898614090571,0.332427740242623,0.110214989555118, 0, 0.128642193589, 0.119407067173878,0.128926224027295,

0.0622331866694357, 0.215645168287442, 0, 0.859343941945178,
0.0500810300696456, 0, 0, 0.0628746592609754), Organ =
structure(as.integer(c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2)), .Label = c("Carc", "TD", "Foie"), class = c("ordered",
"factor"))), .Names = c("Tps", "Conc", "Organ"), row.names = c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
"80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90",
"91", "92", "93", "94", "95", "96", "97", "98", "99", "100",
"101", "102", "103", "104", "105", "106", "107", "108", "109",
"110", "111", "112", "113", "114", "115", "116", "117", "118",
"119", "120", "121", "122", "123", "124", "125", "126", "127",
"128", "129", "130", "131", "132", "133", "134", "135", "136",
"137", "138", "139", "140", "141", "142", "143", "144", "145",
"146", "147", "148", "149", "150", "151", "152", "153", "154",
"155", "156", "157", "158", "159", "160", "161", "162", "163",
"164", "165", "166", "167", "168", "169", "170", "171", "172",
"173", "174", "175", "176", "177", "178", "179", "180", "181",
"182", "183", "184", "185", "186", "187", "188", "189", "190",
"191", "192", "193", "194", "195", "196", "197", "198", "199",
"200", "201", "202", "203", "204", "205", "206", "207", "208",
"209", "210", "211", "212", "213", "214", "215", "216", "217",
"218", "219", "220", "221", "222", "223", "224", "225", "226",
"227", "228", "229", "230", "231", "232", "233", "234", "235",
"236", "237", "238", "239", "240", "241", "242", "243", "244",
"245", "246", "247", "248", "249", "250", "251", "252", "253",
"254", "255", "256", "257", "258", "259", "260", "261", "262",
"263", "264", "265", "266", "267", "268", "269", "270", "271",
"272", "273", "274", "275", "276", "277", "278", "279", "280",
"281", "282", "283", "284", "285", "286", "287", "288", "289",
"290", "291", "292", "293", "294", "295", "296", "297", "298",

"299", "300"), class = c("nfnGroupedData", "nfGroupedData","groupedData",

"data.frame"), formula = quote(Conc ~ Tps | Organ), FUN = function (x)
max(x, na.rm = TRUE), order.groups = TRUE)




Spencer Graves a écrit :

      Regarding the following:

mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
     data=mydata,
     start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ



      This example is NOT self contained and is entirely too
complicated for me to try to replicate it myself in a reasonable
period of time.  I will therefore ask one short question:  Are all the
variable names in the "nlsList" call either columns of "mydata" or
parameters to be estimated and therefore spelled out in "start"?  If I
were you, I'd check this all very carefully, being especially careful
about the distinction between "lCl" and "lC1", in particular.

      If you'd like further help with this, I suggest you try to find
the simplest possible example that generates problem you don't
understand, then try to recast that example into one that is
completely self contained, either a data set in the standard R or nlme
distribution  or numbers that one can generate with a very few lines
of code.  If you use random numbers, please "set.seed", to increase
your confidence that someone else will see what you see.  (And please
review the posting guide! "www.R-project.org/posting-guide.html".
Doing so may increase your chances of getting more useful information
more quickly.)

      spencer graves

Patrick Giraudoux wrote:

Dear listers,

I am trying to fit a model using nlsList() using alternately a
SSfol() selfstart function or its developped equivalent formulae.

This preliminary trial works well

mydata<-groupedData(Conc~Tps|Organ,data=mydata)
mymod1<-nls(Conc~SSfol(Dose,Tps,lKe,lKa,lCl),data=mydata)

as well as a developped form:

mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
    data=mydata,
    start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
    )

However when trying to fit the model with nlsList, I get:

mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
     data=mydata,
     start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
     )
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ

Or specifying  the grouping factor explicitely:

mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
(exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe))|Organ,
     data=mydata,
     start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
     )

Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ


I cannot find out why the grouping factor cannot be used (it has the
same length as the other variables...)

Another strange thing occurs: in the example given in the help of
nlsList.selfstart, the following command works  well:

 fm1 <- nlsList(SSasympOff, CO2)

However its seemingly equivalent applied to the case above fails:

mymod4<-nlsList(SSfol,data=mydata)
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found
Error in eval(expr, envir, enclos) : object "input" not found


Any hint/suggestion appreciated.

Kind regards,

Patrick Giraudoux

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--
Brian D. Ripley,                  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: [R] lme, nlsList, nlsList.selfStart

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