Re: [R] Generating all possible models from full model

[Frank E Harrell Jr]

On 05/18/2010 11:38 PM, Tim Clark wrote:
Is there a function that will allow me to run all model iterations if I specify 
a full model?  I am using information criteria to choose between possible 
candidate models.  I have been writing out all possible model combinations by 
hand, and I am always worried that I am missing models or have made a mistake 
somewhere.  It is also difficult to alter models if I want to change a term.  
For example, below are the set of models I would like to run.  Is there a way 
to specify the full model and have R generate the rest?  I.e. specify
  
m1234567<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+coslunar+sinlunar+plankton,
 data=mydata))

and have R run all the other models.


library(MASS)

#Intercept only
   m0<-glm.convert(glm.nb(mantas~1,data=mydata))

#One term - 7 models
   #Manta abundance is greater at one of the two sites
   m1<-glm.convert(glm.nb(mantas~site,data=mydata))
   #Manta abundance increases each year as the population increases in size due 
to births or immigration being greater than deaths and emmigration
   m2<-glm.convert(glm.nb(mantas~year,data=mydata))
   #Manta abundances increases during part of the year due to seasonal cycles 
in resources (mates, food)
   m3<-glm.convert(glm.nb(mantas~cosmonth,data=mydata))
   m4<-glm.convert(glm.nb(mantas~sinmonth,data=mydata))
   #Manta abundance decreases with increased lunar phase
   m5<-glm.convert(glm.nb(mantas~coslunar, data=mydata))
   m6<-glm.convert(glm.nb(mantas~sinlunar, data=mydata))
   #Manta abundance increases with increased levels of plankton
   m7<-glm.convert(glm.nb(mantas~plankton,data=mydata))

#Two terms - 21 models
   m12<-glm.convert(glm.nb(mantas~site*year, data=mydata))   #Interaction term 
to account for hotel being closed at Keauhou for some years
   m13<-glm.convert(glm.nb(mantas~site+cosmonth,data=mydata))
   m14<-glm.convert(glm.nb(mantas~site+sinmonth,data=mydata))
   m15<-glm.convert(glm.nb(mantas~site+coslunar,data=mydata))
   m16<-glm.convert(glm.nb(mantas~site+sinlunar,data=mydata))
   m17<-glm.convert(glm.nb(mantas~site+plankton,data=mydata)) #Should this have 
an interaction term?  Plankton may varry by site

   m23<-glm.convert(glm.nb(mantas~year+cosmonth,data=mydata))
   m24<-glm.convert(glm.nb(mantas~year+sinmonth,data=mydata))
   m25<-glm.convert(glm.nb(mantas~year+coslunar,data=mydata))
   m26<-glm.convert(glm.nb(mantas~year+sinlunar,data=mydata))
   m27<-glm.convert(glm.nb(mantas~year+plankton,data=mydata))

   m34<-glm.convert(glm.nb(mantas~cosmonth+sinmonth,data=mydata))
   m35<-glm.convert(glm.nb(mantas~cosmonth+coslunar,data=mydata))
   m36<-glm.convert(glm.nb(mantas~cosmonth+sinlunar,data=mydata))
   m37<-glm.convert(glm.nb(mantas~cosmonth+plankton,data=mydata))  #Interaction 
term?  Plankton may vary by season

   m45<-glm.convert(glm.nb(mantas~sinmonth+coslunar, data=mydata))
   m46<-glm.convert(glm.nb(mantas~sinmonth+sinlunar, data=mydata))
   m47<-glm.convert(glm.nb(mantas~sinmonth+plankton, data=mydata)) #Interaction 
term?  Plankton may vary by season

   m56<-glm.convert(glm.nb(mantas~coslunar+sinlunar, data=mydata))
   m57<-glm.convert(glm.nb(mantas~coslunar+plankton, data=mydata))

   m67<-glm.convert(glm.nb(mantas~sinlunar+plankton, data=mydata)) #Interaction 
term?  Plankton may have lunar cycles

#Three terms - 35 models
   m123<-glm.convert(glm.nb(mantas~site*year+cosmonth, data=mydata))
   m124<-glm.convert(glm.nb(mantas~site*year+sinmonth, data=mydata))
   m125<-glm.convert(glm.nb(mantas~site*year+coslunar, data=mydata))
   m126<-glm.convert(glm.nb(mantas~site*year+sinlunar, data=mydata))
   m127<-glm.convert(glm.nb(mantas~site*year+plankton, data=mydata))

   m134<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth,data=mydata))
   m135<-glm.convert(glm.nb(mantas~site+cosmonth+coslunar,data=mydata))
   m136<-glm.convert(glm.nb(mantas~site+cosmonth+sinlunar,data=mydata))
   m137<-glm.convert(glm.nb(mantas~site+cosmonth+plankton,data=mydata))

   m145<-glm.convert(glm.nb(mantas~site+sinmonth+coslunar,data=mydata))
   m146<-glm.convert(glm.nb(mantas~site+sinmonth+sinlunar,data=mydata))
   m147<-glm.convert(glm.nb(mantas~site+sinmonth+plankton,data=mydata))

   m156<-glm.convert(glm.nb(mantas~site+coslunar+sinlunar,data=mydata))
   m157<-glm.convert(glm.nb(mantas~site+coslunar+plankton,data=mydata))

   m167<-glm.convert(glm.nb(mantas~site+sinlunar+plankton,data=mydata))

   m234<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth,data=mydata))
   m235<-glm.convert(glm.nb(mantas~year+cosmonth+coslunar,data=mydata))
   m236<-glm.convert(glm.nb(mantas~year+cosmonth+sinlunar,data=mydata))
   m237<-glm.convert(glm.nb(mantas~year+cosmonth+plankton,data=mydata))

   m245<-glm.convert(glm.nb(mantas~year+sinmonth+coslunar,data=mydata))
   m246<-glm.convert(glm.nb(mantas~year+sinmonth+sinlunar,data=mydata))
   m247<-glm.convert(glm.nb(mantas~year+sinmonth+plankton,data=mydata))

   m256<-glm.convert(glm.nb(mantas~year+coslunar+sinlunar,data=mydata))
   m257<-glm.convert(glm.nb(mantas~year+coslunar+plankton,data=mydata))

   m267<-glm.convert(glm.nb(mantas~year+sinlunar+plankton,data=mydata))

   m345<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+coslunar,data=mydata))
   m346<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+sinlunar,data=mydata))
   m347<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+plankton,data=mydata))

   m356<-glm.convert(glm.nb(mantas~cosmonth+coslunar+sinlunar,data=mydata))
   m357<-glm.convert(glm.nb(mantas~cosmonth+coslunar+plankton,data=mydata))

   m367<-glm.convert(glm.nb(mantas~cosmonth+sinlunar+plankton,data=mydata))

   m456<-glm.convert(glm.nb(mantas~sinmonth+coslunar+sinlunar,data=mydata))
   m457<-glm.convert(glm.nb(mantas~sinmonth+coslunar+plankton,data=mydata))

   m467<-glm.convert(glm.nb(mantas~sinmonth+sinlunar+plankton,data=mydata))

   m567<-glm.convert(glm.nb(mantas~coslunar+sinlunar+plankton,data=mydata))

#Four terms - 34 models
   m1234<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth, data=mydata))
   m1235<-glm.convert(glm.nb(mantas~site*year+cosmonth+coslunar, data=mydata))
   m1236<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinlunar, data=mydata))
   m1237<-glm.convert(glm.nb(mantas~site*year+cosmonth+plankton, data=mydata))

   m1245<-glm.convert(glm.nb(mantas~site*year+sinmonth+coslunar, data=mydata))
   m1246<-glm.convert(glm.nb(mantas~site*year+sinmonth+sinlunar, data=mydata))
   m1247<-glm.convert(glm.nb(mantas~site*year+sinmonth+plankton, data=mydata))

   m1256<-glm.convert(glm.nb(mantas~site*year+coslunar+sinlunar, data=mydata))
   m1257<-glm.convert(glm.nb(mantas~site*year+coslunar+plankton, data=mydata))

   m1267<-glm.convert(glm.nb(mantas~site*year+sinlunar+plankton, data=mydata))

   
m1345<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+coslunar,data=mydata))
   
m1346<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+sinlunar,data=mydata))
   
m1347<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+plankton,data=mydata))

   
m1356<-glm.convert(glm.nb(mantas~site+cosmonth+coslunar+sinlunar,data=mydata))
   
m1357<-glm.convert(glm.nb(mantas~site+cosmonth+coslunar+plankton,data=mydata))

   
m1367<-glm.convert(glm.nb(mantas~site+cosmonth+sinlunar+plankton,data=mydata))

   
m1456<-glm.convert(glm.nb(mantas~site+sinmonth+coslunar+sinlunar,data=mydata))
   
m1457<-glm.convert(glm.nb(mantas~site+sinmonth+coslunar+plankton,data=mydata))

   
m1467<-glm.convert(glm.nb(mantas~site+sinmonth+sinlunar+plankton,data=mydata))

   
m1567<-glm.convert(glm.nb(mantas~site+coslunar+sinlunar+plankton,data=mydata))

   
m2345<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+coslunar,data=mydata))
   
m2346<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+sinlunar,data=mydata))
   
m2347<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+plankton,data=mydata))

   
m2356<-glm.convert(glm.nb(mantas~year+cosmonth+coslunar+sinlunar,data=mydata))
   
m2357<-glm.convert(glm.nb(mantas~year+cosmonth+coslunar+plankton,data=mydata))

   
m2367<-glm.convert(glm.nb(mantas~year+cosmonth+sinlunar+plankton,data=mydata))

   
m2456<-glm.convert(glm.nb(mantas~year+sinmonth+coslunar+sinlunar,data=mydata))
   
m2457<-glm.convert(glm.nb(mantas~year+sinmonth+coslunar+plankton,data=mydata))

   
m2467<-glm.convert(glm.nb(mantas~year+sinmonth+sinlunar+plankton,data=mydata))

   
m2567<-glm.convert(glm.nb(mantas~year+coslunar+sinlunar+plankton,data=mydata))

   
m3456<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+coslunar+sinlunar,data=mydata))
   
m3457<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+coslunar+plankton,data=mydata))

   
m3567<-glm.convert(glm.nb(mantas~cosmonth+coslunar+sinlunar+plankton,data=mydata))

   
m4567<-glm.convert(glm.nb(mantas~sinmonth+coslunar+sinlunar+plankton,data=mydata))

#Five terms - 21 models
   m12345<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+coslunar, 
data=mydata))
   m12346<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+sinlunar, 
data=mydata))
   m12347<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+plankton, 
data=mydata))

   m12356<-glm.convert(glm.nb(mantas~site*year+cosmonth+coslunar+sinlunar, 
data=mydata))
   m12357<-glm.convert(glm.nb(mantas~site*year+cosmonth+coslunar+plankton, 
data=mydata))

   m12367<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinlunar+plankton, 
data=mydata))

   m12456<-glm.convert(glm.nb(mantas~site*year+sinmonth+coslunar+sinlunar, 
data=mydata))
   m12457<-glm.convert(glm.nb(mantas~site*year+sinmonth+coslunar+plankton, 
data=mydata))

   m12467<-glm.convert(glm.nb(mantas~site*year+sinmonth+sinlunar+plankton, 
data=mydata))

   m12567<-glm.convert(glm.nb(mantas~site*year+coslunar+sinlunar+plankton, 
data=mydata))

   m13456<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+coslunar+sinlunar, 
data=mydata))
   m13457<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+coslunar+plankton, 
data=mydata))

   m13467<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+sinlunar+plankton, 
data=mydata))

   m13567<-glm.convert(glm.nb(mantas~site+cosmonth+coslunar+sinlunar+plankton, 
data=mydata))

   m14567<-glm.convert(glm.nb(mantas~site+sinmonth+coslunar+sinlunar+plankton, 
data=mydata))

   m23456<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+coslunar+sinlunar, 
data=mydata))
   m23457<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+coslunar+plankton, 
data=mydata))

   m23467<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+sinlunar+plankton, 
data=mydata))

   m23567<-glm.convert(glm.nb(mantas~year+cosmonth+coslunar+sinlunar+plankton, 
data=mydata))

   m24567<-glm.convert(glm.nb(mantas~year+sinmonth+coslunar+sinlunar+plankton, 
data=mydata))

   
m34567<-glm.convert(glm.nb(mantas~cosmonth+sinmonth+coslunar+sinlunar+plankton, 
data=mydata))

#Six terms - 7 models
   
m123456<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+coslunar+sinlunar,
 data=mydata))
   
m123457<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+coslunar+plankton,
 data=mydata))

   
m123467<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+sinlunar+plankton,
 data=mydata))

   
m123567<-glm.convert(glm.nb(mantas~site*year+cosmonth+coslunar+sinlunar+plankton,
 data=mydata))

   
m124567<-glm.convert(glm.nb(mantas~site*year+sinmonth+coslunar+sinlunar+plankton,
 data=mydata))

   
m134567<-glm.convert(glm.nb(mantas~site+cosmonth+sinmonth+coslunar+sinlunar+plankton,
 data=mydata))

   
m234567<-glm.convert(glm.nb(mantas~year+cosmonth+sinmonth+coslunar+sinlunar+plankton,
 data=mydata))

#Seven terms - 1 model
   
m1234567<-glm.convert(glm.nb(mantas~site*year+cosmonth+sinmonth+coslunar+sinlunar+plankton,
 data=mydata))


Tim Clark
Department of Zoology
University of Hawaii

Please read the large number of notes in the e-mail archive about the 
invalidity of such modeling procedures.

Frank

--
Frank E Harrell Jr   Professor and Chairman        School of Medicine
                     Department of Biostatistics   Vanderbilt University

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