[R] df pseudoreplication in lme model
Lauren Meyer
lauren.meyer90 at gmail.com
Fri Jan 30 00:09:24 CET 2015
Hello, I am trying to assess weather or not my df are pseudoreplicated in my
lme model.
my study was undertaken on five fish (labeled PC) each tested in two
replicates(REP), across each combination of three treatments HOM, C18 and
CU, each of which had two levels; HOM(SON, BLD),C18 SML, BIG), CU (YES, NO).
The variable we are assessing is the amount of toxin extracted (TOX1). Also,
some data is missing, and has already been removed.
Here is the model I am using and output:
model<- lme(TOX1~HOM*C18*CU, random=~1|PC/REP, data=Data4, method="ML")
Linear mixed-effects model fit by maximum likelihood
Data: Data4
AIC BIC logLik
220.603 244.5213 -99.30151
Random effects:
Formula: ~1 | PC
(Intercept)
StdDev: 1.574392
Formula: ~1 | REP %in% PC
(Intercept) Residual
StdDev: 0.0001356862 0.9724221
Fixed effects: TOX1 ~ HOM * C18 * CU
Value Std.Error DF t-value p-value
(Intercept) 3.729044 0.8204586 48 4.545073 0.0000
HOMSON 0.423330 0.5175211 48 0.817995 0.4174
C18SML -1.160060 0.5475120 48 -2.118784 0.0393
CUYES 0.419067 0.4643966 48 0.902391 0.3714
HOMSON:C18SML -0.645514 1.0385203 48 -0.621571 0.5372
HOMSON:CUYES -0.436996 0.6953361 48 -0.628467 0.5327
C18SML:CUYES -0.137128 0.7179371 48 -0.191003 0.8493
HOMSON:C18SML:CUYES 0.313720 1.2287607 48 0.255314 0.7996
Correlation:
(Intr) HOMSON C18SML CUYES HOMSON:C18SML HOMSON:CU
C18SML:
HOMSON -0.254
C18SML -0.240 0.361
CUYES -0.283 0.449 0.424
HOMSON:C18SML 0.127 -0.472 -0.550 -0.224
HOMSON:CUYES 0.189 -0.744 -0.268 -0.668 0.351
C18SML:CUYES 0.183 -0.275 -0.763 -0.647 0.419 0.421
HOMSON:C18SML:CUYES -0.107 0.399 0.464 0.378 -0.845 -0.549
-0.599
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-4.090875567 -0.433368736 -0.007582723 0.498944076 2.603341469
Number of Observations: 65
Number of Groups:
PC REP %in% PC
5 10
As the three way interaction as well as all of the two way interactions were
deemed non-significant, I simplified the model, removing first the three way
interaction, then each two way interaction in turn, comparing each
subsequent model with the previous one using an ANOVA as per the example in
the R book on pg. 632. I have a final model of:
> model5<- lme(TOX1~HOM+C18+CU, random=~1|PC/REP, data=Data4, method="ML")
> summary(model5)
Linear mixed-effects model fit by maximum likelihood
Data: Data4
AIC BIC logLik
214.0699 229.2906 -100.035
Random effects:
Formula: ~1 | PC
(Intercept)
StdDev: 1.567082
Formula: ~1 | REP %in% PC
(Intercept) Residual
StdDev: 0.0005730032 0.9847228
Fixed effects: TOX1 ~ HOM + C18 + CU
Value Std.Error DF t-value p-value
(Intercept) 3.927801 0.7623505 52 5.152225 0.0000
HOMSON -0.028203 0.2603204 52 -0.108341 0.9141
C18SML -1.437095 0.2605651 52 -5.515302 0.0000
CUYES 0.214583 0.2675196 52 0.802122 0.4261
Correlation:
(Intr) HOMSON C18SML
HOMSON -0.125
C18SML -0.114 0.047
CUYES -0.167 -0.152 -0.184
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-4.212407492 -0.433128656 0.003244622 0.618291014 2.578288257
Number of Observations: 65
Number of Groups:
PC REP %in% PC
5 10
However, I am unsure if these Df are pseudoreplicated and would like some
help in how to determine if this is the case. Thank you
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