[R] structural equation modeling in sem, error, The model has negative degrees of freedom = -3, and The model is almost surely misspecified...

[John Fox]

Dear Michele,

It's impossible to know without the data, since that's the only way to determine which variables in the model are observed and which are latent variables, but if there are negative df, then you're trying to estimate a model with more free parameters than there are moments (typically, covariances) among the observed variables. Clearly, such a model is necessarily underidentified.

Additionally, I suggest that you use specifyEquations() in preference to specifyModel() to describe the model. That should prove simpler (but of course won't allow you to estimate an underidentified model).

I hope this helps,
 John

-----------------------------------------------
John Fox, Professor
Chair, Sociology Graduate Programme
McMaster University
Hamilton, Ontario, Canada
http://socserv.socsci.mcmaster.ca/jfox/


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Michele Silva
> Sent: Thursday, September 04, 2014 2:58 PM
> To: r-help at r-project.org
> Subject: Re: [R] structural equation modeling in sem, error, The model
> has negative degrees of freedom = -3, and The model is almost surely
> misspecified...
> 
> Dear Prof. John,
> 
> I'm trying to solve the following model in R, but I getting error about
> the degree of freedom. As I don't have much experience, could you
> please
> explain to me what is the problem? I'm studying the influence of
> several
> soil parameters (pH, NH4, OM, Moisture) on the abundance of some
> microbial groups (Nitrosotalea, Nitrosos_Cl1, Nitrosos_Cl3,
> Nitrosos_Cl4
> e Nitrosos_Cl7), and on enzyme activity (PNA).
> 
> Thanks in advance,
> 
> Best regards
> 
> Michele
> 
> 
> 
> mod.pnr1 <- specifyModel()
> PD_AOA -> PNA, B1, NA
> Nitrosotalea -> PNA, B2, NA
> Nitrosos_Cl1 -> PNA, B3, NA
> Nitrosos_Cl3 -> PNA, B4, NA
> Nitrosos_Cl4 -> PNA, B5, NA
> Nitrosos_Cl7 -> PNA, B6, NA
> pH -> PNA, B9, NA
> NH4 -> PNA, B10, NA
> OM -> PNA, B11, NA
> Moisture -> PNA, B12, NA
> pH -> PD_AOA, B18, NA
> NH4 -> PD_AOA, B19, NA
> OM -> PD_AOA, B20, NA
> Moisture -> PD_AOA, B21, NA
> pH -> Nitrosotalea, B22, NA
> NH4 -> Nitrosotalea, B23, NA
> OM -> Nitrosotalea, B24, NA
> Moisture -> Nitrosotalea, B25, NA
> pH -> Nitrosos_Cl1, B26, NA
> NH4 -> Nitrosos_Cl1, B27, NA
> OM -> Nitrosos_Cl1, B28, NA
> Moisture -> Nitrosos_Cl1, B29, NA
> pH -> Nitrosos_Cl3, B30, NA
> NH4 -> Nitrosos_Cl3, B31, NA
> OM -> Nitrosos_Cl3, B32, NA
> Moisture -> Nitrosos_Cl3, B33, NA
> pH -> Nitrosos_Cl4, B34, NA
> NH4 -> Nitrosos_Cl4, B35, NA
> OM -> Nitrosos_Cl4, B36, NA
> Moisture -> Nitrosos_Cl4, B37, NA
> pH -> Nitrosos_Cl7, B38, NA
> NH4 -> Nitrosos_Cl7, B39, NA
> OM -> Nitrosos_Cl7, B40, NA
> Moisture -> Nitrosos_Cl7, B41, NA
> Nitrosotalea -> Nitrosos_Cl1, B53, NA
> Nitrosotalea -> Nitrosos_Cl3, B54, NA
> Nitrosotalea -> Nitrosos_Cl4, B55, NA
> Nitrosotalea -> Nitrosos_Cl7, B56, NA
> Nitrosos_Cl1 -> Nitrosotalea, B57, NA
> Nitrosos_Cl1 -> Nitrosos_Cl3, B58, NA
> Nitrosos_Cl1 -> Nitrosos_Cl4, B59, NA
> Nitrosos_Cl1 -> Nitrosos_Cl7, B60, NA
> Nitrosos_Cl3 -> Nitrosotalea, B61, NA
> Nitrosos_Cl3 -> Nitrosos_Cl1, B62, NA
> Nitrosos_Cl3 -> Nitrosos_Cl4, B63, NA
> Nitrosos_Cl3 -> Nitrosos_Cl7, B64, NA
> Nitrosos_Cl4 -> Nitrosotalea, B65, NA
> Nitrosos_Cl4 -> Nitrosos_Cl1, B66, NA
> Nitrosos_Cl4 -> Nitrosos_Cl3, B67, NA
> Nitrosos_Cl4 -> Nitrosos_Cl7, B68, NA
> Nitrosos_Cl7 -> Nitrosotalea, B69, NA
> Nitrosos_Cl7 -> Nitrosos_Cl1, B70, NA
> Nitrosos_Cl7 -> Nitrosos_Cl4, B71, NA
> Nitrosos_Cl7 -> Nitrosos_Cl3, B72, NA
> pH -> NH4, B42, NA
> pH -> OM, B43, NA
> NH4 -> OM, B45, NA
> NH4 -> pH, B46, NA
> OM -> NH4, B47, NA
> OM -> Moisture, B48, NA
> OM -> pH, B52, NA
> Moisture -> OM, B70, NA
> PNA <-> PNA, e12, NA
> PD_AOA <-> PD_AOA, NA, 1
> Nitrosotalea <-> Nitrosotalea, e5, NA
> Nitrosos_Cl1 <-> Nitrosos_Cl1, e6, NA
> Nitrosos_Cl3 <-> Nitrosos_Cl3, e7, NA
> Nitrosos_Cl4 <-> Nitrosos_Cl4, e8, NA
> Nitrosos_Cl7 <-> Nitrosos_Cl7, e9, NA
> NH4 <-> NH4, e6, NA
> OM <-> OM, e5, NA
> Moisture <-> Moisture, e7, NA
> pH <-> pH, NA, 1
> 
> 
> 
> 
> --
> Dra. Michele de C�ssia Pereira e Silva
> Escola Superior de Agricultura Luiz de Queiroz (ESALQ)/ USP
> Departamento de Ci�ncia do Solo e Nutri��o de Plantas
> Laborat�rio de Microbiologia do Solo
> Av P�dua Dias, 11 CP 09 CEP-13400-970
> Piracicaba - S�o Paulo
> 
> 
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