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R: how to extract information from a master model

library(nlme)
fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
            data = Loblolly,
            fixed = Asym + R0 + lrc ~ 1,
            random = Asym ~ 1,
            start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
> summary(fm1)
Nonlinear mixed-effects model fit by maximum likelihood
  Model: height ~ SSasymp(age, Asym, R0, lrc) 
 Data: Loblolly 
       AIC      BIC    logLik
  239.4856 251.6397 -114.7428

Random effects:
 Formula: Asym ~ 1 | Seed
            Asym  Residual
StdDev: 3.650642 0.7188625

Fixed effects: Asym + R0 + lrc ~ 1 
         Value Std.Error DF   t-value p-value
Asym 101.44960 2.4616951 68  41.21128       0
R0    -8.62733 0.3179505 68 -27.13420       0
lrc   -3.23375 0.0342702 68 -94.36052       0
 Correlation: 
    Asym   R0    
R0   0.704       
lrc -0.908 -0.827

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-2.23601930 -0.62380854  0.05917466  0.65727206  1.95794425 

Number of Observations: 84
Number of Groups: 14

I am interested in extracting information from the final output of NLME compliance.

I would like to extract

  • StdDev random effects (i.e. StdDev from Asym, which = 3.65) For this I tried fm1$apVar, but no luck.
  • Estimation of parameters of fixed effects (i.e.Asym = 101.44960, R0 = -8.62733, etc.), which can be extracted using fixef(fm1)
  • Std.Error of fixed effects (i.e. 2.46, 0.317, 0.034). For this I tried sqrt(diag(fm1$varFix)), but these values ​​do not exactly match the columns of Std.Error with fixed effects?
  • logLikelihood (i.e. -114.7428, which can be retrieved with fm1$logLik)
  • Residual (i.e. 0.7188625, which can be extracted using fm1$Residuals)

- data.frame.

fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
            data = Loblolly,
            fixed = Asym + R0 + lrc ~ 1,
            random = Asym ~ 1,
            start = c(Asym = 103, R0 = -8.5, lrc = -3.3))

fm2 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
            data = Loblolly,
            fixed = Asym + R0 + lrc ~ 1,
            random = Asym ~ 1,
            start = c(Asym = 103, R0 = -5.4, lrc = -3.3))

summary(fm1)
summary(fm2)

mylist = list(NULL, summary(fm1), NULL, summary(fm2), NULL, NULL)

, mylist. data.frame, :

model    FixedAsym    FixedAsymStdError   FixedR0      ...     Residual
 1       101.44960        2.4616951       -8.62733            0.7188625
 2       101.44934        2.4616788       -8.62736     ...    0.7188625

data.frame( , mylist), ( 1-5) .

+4
1

...

as.numeric(VarCorr(fm1)[,2])
# [1] 3.6506418 0.7188625

summary(fm1)$tTable[,2]
#       Asym         R0        lrc 
# 2.46169512 0.31795045 0.03427017 

# looks like you don't need this one anymore, but here a way of getting it
summary(fm1)$corFixed
#            Asym         R0        lrc
# Asym  1.0000000  0.7039498 -0.9077793
# R0    0.7039498  1.0000000 -0.8271022
# lrc  -0.9077793 -0.8271022  1.0000000

, . , , , .

0

Source: https://habr.com/ru/post/1679826/

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