[R] nested model and post hoc?

a_wohl
Wed, 05 Aug 2015 14:40:22 -0000

Hi :-) i am really looking forward to get some help... Since I am a
R-beginner I need it.

I have a model consisting of the factors: dpi, infection, dissection day and
plate. My reskponse variable is cells/mg. dpi is nested in dissection day.
They are all fixed variables.
I produced this nested model (best AIC index)
glm.3<-cm.2~infect.f+dpi.f+dpi.f/diss.f, na.action=na.omit)

summary(glm.3)
Call:
glm(formula = cm.2 ~ infect.f + dpi.f + dpi.f %in% diss.f, family gaussian,
    na.action = na.omit)

Deviance Residuals:
    Min       1Q   Median       3Q      Max
-2.7746  -0.3625   0.0080   0.3628   1.9031

Coefficients: (18 not defined because of singularities)
                Estimate Std. Error t value Pr(>|t|)
(Intercept)      7.01887    0.15278  45.941  < 2e-16 ***
infect.finf      0.05544    0.08107   0.684   0.4946
infect.fsha     -0.15563    0.08831  -1.762   0.0791 .
dpi.f2           0.08924    0.20459   0.436   0.6630
dpi.f4          -0.40167    0.21082  -1.905   0.0577 .
dpi.f8           0.01961    0.20789   0.094   0.9249
dpi.f16          0.82210    0.20469   4.016 7.54e-05 ***
dpi.f32          0.99639    0.21435   4.648 5.09e-06 ***
dpi.f1:diss.f2   0.13276    0.21077   0.630   0.5293
dpi.f2:diss.f2        NA         NA      NA       NA
dpi.f4:diss.f2   0.46749    0.20784   2.249   0.0253 *
dpi.f8:diss.f2  -0.06555    0.20205  -0.324   0.7459
dpi.f16:diss.f2       NA         NA      NA       NA
dpi.f32:diss.f2       NA         NA      NA       NA
dpi.f1:diss.f3        NA         NA      NA       NA
dpi.f2:diss.f3  -0.15794    0.20186  -0.782   0.4346
dpi.f4:diss.f3   0.20921    0.21081   0.992   0.3218
dpi.f8:diss.f3        NA         NA      NA       NA
dpi.f16:diss.f3 -0.03611    0.20178  -0.179   0.8581
dpi.f32:diss.f3       NA         NA      NA       NA
dpi.f1:diss.f4   0.14040    0.20459   0.686   0.4931
dpi.f2:diss.f4  -0.01701    0.21152  -0.080   0.9360
dpi.f4:diss.f4        NA         NA      NA       NA
dpi.f8:diss.f4        NA         NA      NA       NA
dpi.f16:diss.f4 -0.19082    0.20168  -0.946   0.3449
dpi.f32:diss.f4       NA         NA      NA       NA
dpi.f1:diss.f5        NA         NA      NA       NA
dpi.f2:diss.f5        NA         NA      NA       NA

........and so forth.
Since i decided for a nested modul, I wonder where the NAs are coming from?
Since I want to perform a post hoc test, I was trysing the glht fuinction
form the multcomp package.
I always get this error
Error in modelparm.default(model, ...) :
  dimensions of coefficients and covariance matrix don't match

I think this is due to my NAs in the summary(glm.3).
Can anyone help me, how I can perform a post hoc test (Bonferroni) on my
data?

thank you
a_wohl



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