[R] Post-hoc test on split-plot design

[Md Newaz]

Hi Richard,
Thank you very much for your cooperation. I installed the packages "HH" and
run the following model:

Bud.aov<-aov(terms(Budburst~CO2*SoilTemp*Photoperiod+Greenhouse/(SoilTemp*Photoperiod),keep.order=TRUE),data=data)

> summary(Bud.aov)

                                                  Df   Sum Sq   Mean Sq
   F value    Pr(>F)

CO2                                            1    1465.2    1465.2
      109.612   < 2e-16 ***

SoilTemp                                     1    238.0      238.0
       17.805      3.60e-05 ***

CO2:SoilTemp                              1    145.7      145.7
        10.900     0.001125 **

Photoperiod                                  2    986.9      493.4
        36.914     1.62e-14 ***

CO2:Photoperiod                           2     0.2          0.1
 0.006        0.994095

SoilTemp:Photoperiod                    2     14.6        7.3
 0.545        0.580893

CO2:SoilTemp:Photoperiod             2    186.3      93.2           6.969
       0.001167 **

Greenhouse                                   2    75.5        37.8
  2.824        0.061538 .

SoilTemp:Greenhouse                     2     5.9          3.0
  0.221        0.801896

Photoperiod:Greenhouse                  4    283.4      70.8
  5.300       0.000433 ***

SoilTemp:Photoperiod:Greenhouse   4    56.7        14.2          1.060
       0.377363

Residuals                                       216 2887.3    13.4


The results that I got don't look like the results for the split-plot
design which I got using the model below:

mod<-aov(Budburst~CO2*SoilTemp*Photoperiod+Error(Greenhouse/(SoilTemp*Photoperiod)),data=data)

> summary(mod)

Error: Greenhouse

              Df Sum Sq Mean Sq F value Pr(>F)

CO2        1 1465.2  1465.2      38.81    0.0248 *

Residuals  2   75.5    37.8

Error: Greenhouse:SoilTemp

                      Df Sum Sq Mean Sq F value Pr(>F)

SoilTemp         1 238.00  238.00   80.57       0.0122 *

CO2:SoilTemp  1 145.70  145.70   49.32       0.0197 *

Residuals         2   5.91    2.95

Error: Greenhouse:Photoperiod

                          Df Sum Sq Mean Sq F value Pr(>F)

Photoperiod         2  986.9   493.4        6.965    0.0498 *

CO2:Photoperiod  2    0.2     0.1          0.001     0.9989

Residuals            4  283.4    70.8

Error: Greenhouse:SoilTemp:Photoperiod

                                        Df Sum Sq Mean Sq F value Pr(>F)

SoilTemp:Photoperiod         2  14.56    7.28        0.514    0.6330

CO2:SoilTemp:Photoperiod  2 186.31   93.15      6.576    0.0544 .

Residuals                           4  56.67   14.17

Error: Within

                Df   Sum Sq Mean Sq F value Pr(>F)

Residuals 216   2887     13.37

The F and P values are quite different. Moreover, I could not run the
post-hoc tests as well. At this stage I shall highly appreciate your
further cooperation.

Thanks.

Shah

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