# [R] trouble with step() and stepAIC() selecting the best model

From: natalia norden <norden_at_cict.fr>
Date: Fri 05 May 2006 - 19:14:18 EST

The model is

model=glm.nb(sdg.cens1 ~ seed.cens1 + log(in.lit+1) + log(trans.dir+1)+ log(trans.dif+1) + slope +log(pH+1) + log(CN+1) + site,

data=data)

For example, for species A using stepAIC() I get:

Call:
glm.nb(formula = tot.rec ~ slope + log(pH + 1) + log(CN + 1),

data = data, init.theta = 0.0575099635396228, link = log)

Deviance Residuals:

Min 1Q Median 3Q Max -7.591e-01 -3.688e-01 -1.828e-01 -8.494e-08 1.520e+00

Coefficients:

```               Estimate Std. Error   z value Pr(>|z|)

(Intercept)    110.729     47.643     2.324  0.02012 *

slope2         -34.202 972079.452 -3.52e-05  0.99997
slope3          -1.423      1.371    -1.038  0.29928
log(pH + 1)    -51.244     19.544    -2.622  0.00874 **
log(CN + 1)     -9.132      6.906    -1.322  0.18602
```
```---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for Negative Binomial(0.0575) family taken to be 1)

Null deviance: 34.068  on 156  degrees of freedom
Residual deviance: 19.602  on 152  degrees of freedom
AIC: 90.357

But using step() I get:

Step:  AIC= 138.4
tot.rec ~ log(mean.lit.rec + 1) + log(trans.dir + 1) + log(trans.dif +
1) + slope + log(pH + 1) + log(CN + 1) + site

Call:
glm.nb(formula = tot.rec ~ log(mean.lit.rec + 1) + log(trans.dir +
1) + log(trans.dif + 1) + slope + log(pH + 1) + log(CN +
1) + site, data = data, init.theta = 74070.0501196965, link = log)

Deviance Residuals:
Min       1Q   Median       3Q      Max
-2.3110  -0.5450  -0.3179   0.0000   3.8755

Coefficients:
Estimate Std. Error   z value Pr(>|z|)

(Intercept)            6.809e+01  1.905e+01     3.574 0.000351 ***

log(mean.lit.rec + 1) -1.238e+00  1.083e+00    -1.143 0.252987
log(trans.dir + 1)     2.069e-01  1.227e+00     0.169 0.866120
log(trans.dif + 1)    -6.978e-01  1.578e+00    -0.442 0.658327
slope2                -3.730e+01  1.022e+07 -3.65e-06 0.999997
slope3                -9.195e-01  6.269e-01    -1.467 0.142488
log(pH + 1)           -3.152e+01  6.918e+00    -4.556 5.22e-06 ***
log(CN + 1)           -5.053e+00  3.404e+00    -1.485 0.137643
site1                  1.379e-01  4.618e-01     0.299 0.765278
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for Negative Binomial(91071.54) family taken to be 1)

Null deviance: 145.586  on 156  degrees of freedom
Residual deviance:  99.166  on 148  degrees of freedom
AIC: 140.40

However, for species B I get the opposite, it works with step() but not
with stepAIC().

Using step() AIC =414.28 and using stepAIC(), AIC=424.15 and the results
are totally different.

I would appreciate any help!!
Thank you

Natalia Norden

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