[R] Optimization problem
Gabor Grothendieck
ggrothendieck at gmail.com
Tue Aug 21 21:38:42 CEST 2007
Lac and Lacfac are the same.
On 8/21/07, Alan Harrison <tharrison01 at qub.ac.uk> wrote:
> Hello Folks,
>
> Very new to R so bear with me, running 5.2 on XP. Trying to do a zero-inflated negative binomial regression on placental scar data as dependent. Lactation, location, number of tick larvae present and mass of mouse are independents. Dataframe and attributes below:
>
>
> Location Lac Scars Lar Mass Lacfac
> 1 Tullychurry 0 0 15 13.87 0
> 2 Somerset 0 0 0 15.60 0
> 3 Tollymore 0 0 3 16.43 0
> 4 Tollymore 0 0 0 16.55 0
> 5 Caledon 0 0 0 17.47 0
> 6 Hillsborough 1 5 0 18.18 1
> 7 Caledon 0 0 1 19.06 0
> 8 Portglenone 0 4 0 19.10 0
> 9 Portglenone 0 5 0 19.13 0
> 10 Tollymore 0 5 3 19.50 0
> 11 Hillsborough 1 5 0 19.58 1
> 12 Portglenone 0 4 0 19.76 0
> 13 Caledon 0 8 0 19.97 0
> 14 Hillsborough 1 4 0 20.02 1
> 15 Tullychurry 0 3 3 20.13 0
> 16 Hillsborough 1 5 0 20.18 1
> 17 LoughNavar 1 5 0 20.20 1
> 18 Tollymore 0 0 1 20.24 0
> 19 Hillsborough 1 5 0 20.48 1
> 20 Caledon 0 4 1 20.56 0
> 21 Caledon 0 3 2 20.58 0
> 22 Tollymore 0 4 3 20.58 0
> 23 Tollymore 0 0 2 20.88 0
> 24 Hillsborough 1 0 0 21.01 1
> 25 Portglenone 0 5 0 21.08 0
> 26 Tullychurry 0 2 5 21.28 0
> 27 Ballysallagh 1 4 0 21.59 1
> 28 Caledon 0 0 1 21.68 0
> 29 Hillsborough 1 5 0 22.09 1
> 30 Tullychurry 0 5 5 22.28 0
> 31 Tullychurry 1 6 75 22.43 1
> 32 Ballysallagh 1 5 0 22.57 1
> 33 Ballysallagh 1 4 0 22.67 1
> 34 LoughNavar 1 5 3 22.71 1
> 35 Hillsborough 1 4 0 23.01 1
> 36 Caledon 0 0 3 23.08 0
> 37 LoughNavar 1 5 0 23.53 1
> 38 Ballysallagh 1 4 0 23.55 1
> 39 Portglenone 1 6 0 23.61 1
> 40 Mt.Stewart 0 3 0 23.70 0
> 41 Somerset 0 5 0 23.83 0
> 42 Ballysallagh 1 5 0 23.93 1
> 43 Ballysallagh 1 5 0 24.01 1
> 44 Caledon 0 0 3 24.14 0
> 45 LoughNavar 0 6 0 24.30 0
> 46 LoughNavar 1 5 0 24.34 1
> 47 Hillsborough 1 4 0 24.45 1
> 48 Caledon 0 3 2 24.55 0
> 49 Tullychurry 0 5 44 24.83 0
> 50 Hillsborough 1 5 0 24.86 1
> 51 Ballysallagh 1 5 0 25.02 1
> 52 Tullychurry 0 0 9 25.27 0
> 53 Mt.Stewart 0 5 0 25.31 0
> 54 LoughNavar 1 4 8 25.43 1
> 55 Somerset 1 0 0 25.58 1
> 56 Hillsborough 1 5 0 25.82 1
> 57 Portglenone 1 2 0 26.02 1
> 58 Ballysallagh 1 5 0 26.19 1
> 59 Mt.Stewart 1 0 0 26.66 1
> 60 Randalstown 1 0 1 26.70 1
> 61 Somerset 0 4 0 27.01 0
> 62 Mt.Stewart 0 4 0 27.05 0
> 63 Somerset 0 3 0 27.10 0
> 64 Somerset 0 6 0 27.34 0
> 65 Somerset 0 0 0 27.87 0
> 66 LoughNavar 1 5 1 28.01 1
> 67 Tullychurry 1 6 42 28.55 1
> 68 Hillsborough 1 5 0 28.84 1
> 69 Portglenone 1 4 0 29.00 1
> 70 Somerset 1 4 0 31.87 1
> 71 Ballysallagh 1 5 0 33.06 1
> 72 LoughNavar 1 4 0 33.24 1
> 73 Somerset 1 4 0 33.36 1
>
> alan : 'data.frame': 73 obs. of 6 variables:
> $ Location: Factor w/ 10 levels "Ballysallagh",..: 10 8 9 9 2 3 2 6 6 9 ...
> $ Lac : int 0 0 0 0 0 1 0 0 0 0 ...
> $ Scars : int 0 0 0 0 0 5 0 4 5 5 ...
> $ Lar : int 15 0 3 0 0 0 1 0 0 3 ...
> $ Mass : num 13.9 15.6 16.4 16.6 17.5 ...
> $ Lacfac : Factor w/ 2 levels "0","1": 1 1 1 1 1 2 1 1 1 1 ...
>
> The syntax I used to create the model is:
>
> zinb.zc <- zicounts(resp=Scars~.,x =~Location + Lar + Mass + Lar:Mass + Location:Mass,z =~Location + Lar + Mass + Lar:Mass + Location:Mass, data=alan)
>
> The error given is:
>
> Error in optim(par = parm, fn = neg.like, gr = neg.grad, hessian = TRUE, :
> non-finite value supplied by optim
> In addition: Warning message:
> fitted probabilities numerically 0 or 1 occurred in: glm.fit(zz, 1 - pmin(y, 1), family = binomial())
>
> I understand this is a problem with the model I specified, could anyone help out??
>
> Many thanks
>
> Alan Harrison
>
> Quercus
> Queen's University Belfast
> MBC, 97 Lisburn Road
> Belfast
>
> BT9 7BL
>
> T: 02890 972219
> M: 07798615682
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
More information about the R-help
mailing list