[R] Odp: multiphasic growth curve analysis

Tue Sep 4 18:59:30 CEST 2007

Although I am not an expert in NLME modelling, looking at your data it 
seems to me that there seems to be no growth pattern in it. Try

library(nlme)
library(reshape)

goat<-read.table("clipboard", header=T)

> str(goat)
'data.frame':   18 obs. of  15 variables:
 $ NoC : int  52 48 54 60 58 42 44 47 50 56 ...
 $ PL1 : int  490 970 1450 620 1370 1200 1200 1000 1300 950 ...
 $ PL2 : int  950 1020 1420 1250 1350 920 1560 1100 1150 1250 ...
 $ PL3 : int  800 980 1430 1100 1200 1150 1650 1000 1200 1200 ...
 $ PL4 : int  900 740 1120 1150 1300 850 1600 870 1030 1280 ...

goat.m <- melt(goat, id="NoC")
levels(goat.m$variable) <- 1:14
goat.m$variable <- as.numeric(as.character(goat.m$variable))
names(goat.m)[2] <- "week"
goat.m$NoC <- ordered(goat.m$NoC)
goat.g <- groupedData(value~week|NoC, data=goat.m)
plot(goat.g)

But maybe I am completely mistaken.

Regards

Petr

r-help-bounces at stat.math.ethz.ch napsal dne 04.09.2007 18:02:09:

> 
> Greetings R Help Group,
> 
> How does one effect a multiphasic logistic growth model with 4 phases 
(e.g. 
> Koops 1986; Weigel, Craig, Bidwell and Bates 1992; Grossman and Koops 
2003) with R.
> 
> Before writing to the group, the R help archives were searched, the web 
was 
> searched with Google, Venables and Ripley 2002 was consulted, Pinheiro 
and 
> Bates 2000 was consulted, Bates and Watts 2007 was bought and consulted, 
ETC. 
> but to no avail.
> 
> I have not written to any other group with respect to this problem.
> 
> The following data are offered as an example of the type of problem I am 

> dealing with and are average daily goat milk production in ml. for 14 
weeks. 
> NoC is the goat number. PL1 is the production during the first week; PL2 
is 
> the production during the second week, etc. 
> 
>  NoC  PL1  PL2  PL3  PL4  PL5  PL6  PL7  PL8  PL9 PL10 PL11 PL12 PL13 
PL14
>   52  490  950  800  900  850  850  750  610  640  900  980  890  890 
910
>   48  970 1020  980  740 1050  970  850  790  900  920 1120 1120 1030 
1300
>   54 1450 1420 1430 1120 1330 1230 1030 1170 1350 1530 1490 1500 1310 
910
>   60  620 1250 1100 1150  780  930  990  940  760  730  790 1050  840 
850
>   58 1370 1350 1200 1300 1350 1310 1070  910 1010 1300 1110 1070  990 
660
>   42 1200  920 1150  850  720  630  630  710  850  810  930  980  820 
1570
>   44 1200 1560 1650 1600 1450 1600 1160 1010 1440 1450 1530 1500 1550 
850
>   47 1000 1100 1000  870  760  900  820  865  910  820  930  900 1130 
1070
>   50 1300 1150 1200 1030 1070  970  860  900  950 1190 1250 1130  800 
1400
>   56  950 1250 1200 1280 1220 1155  840 1016 1370 1220 1570 1520 1500 
1150
>    1  870 1250 1160 1270 1200 1410 1110 1008  970 1130 1490 1330 1320 
820
>    3 1000 1100 1200 1120 1250  980  750  890 1050 1160 1340 1210 1150 
760
>    4  551  760  550  580  540  620  550  520  470  720  680  790  750 
1230
>    5  810 1100  820  950  930  830  850  650  810 1070 1120 1300 1040 
1320
>    6  800 1000  620  850  750  670  660  620  600  610  760  900  758 
1070
>    7  720  830 1120 1050  820  820  850  810  800  750  780  940 1050 
1310
>    8  950 1550 1560 1500 1230 1330 1150 1005 1020 1200 1440 1400 1290 
1080
>   10  660  850 1100  980 1070 1100  870  790  880  950 1000 1210 1050 
1220
> 
> It seems to me that it should be possible to effect the modeling process 
with 
> nlme. Any suggestions and or recommendations would be greatly 
appreciated.
> 
> Peter B.
> 
> 
> 
> Douglas M. Bates and Donald G. Watts. 2007. Nonlinear Regression 
Analysis and 
> Its Applications. Wiley Series in Probability and Statistics. John Wiley 
& 
> Sons, Inc., New York, NY, USA.
> 
> M. Grossman and W.J. Koops. 2003. Modeling Extended Lactation Curves of 
Dairy 
> Cattle: A Biological Basis for the Multiphasic Approach. J. Dairy Sci. 
86:988-998.
> 
> W. J. Koops. 1986. Multiphasic Growth Curve Analysis. Growth 50:169-177.
> 
> Jose C. Pinheiro and Douglas M. Bates 2000. Mixed-Effects Models in S 
and S-
> Plus. Statistics and Computing. Springer-Verlag New York, New York, NY, 
USA.
> 
> W. H. Venables and B. D. Ripley. 2002. Modern Applied Statistics with S. 

> Fourth edition. Statistics and Computing. Springer-Verlag New York, 
Inc., New 
> York, NY, USA.
> 
> K. A. Weigel, B. A. Craig, T. R. Bidwell and D. M. Bates. 1992. 
Comparison of 
> Alternative Diphasic Lactation Curve Models under Bovine Somatotropin 
> Administration. J. Dairy Sci. 75:580-589.
> 
> 
> 
> 
> 
> 
>  Peter B. Mandeville cel:      444 860 3204 tel:  52 444 826 2346-49 ext 
532 
> fax: 52 444 826 2352 P.D. Favor de confirmar la llegada de este correo. 
Gracias.
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