Dear All user,
Hello,

I'm a  student and I have some trouble with the experimental
(columns-experiments) design of my project. I use a randomized block design
with 4 treatments including a control. For each treatment, I use 3
replicates and 3 blocks.

The treatments are:
-T1 = COD (300 mg/Lit)   COD=chemical oxygen demand
-T2 = COD (200 mg/Lit)
-T3 = COD (100 mg/Lit)
-T4 = COD (0 mg/Lit) as a control
The experiment is conducted during three months and a sample is taken each
Week in every experimental unit.
At the first, I irrigated all soil columns (12 columns) with demonize water
for 1 week.


Then during 8 weeks, I irrigated all columns with waste water with different
concentration. Then, gain, I irrigated all columns with demonize water for 4
weeks.
Now I want to know how I can analyses the results in R. For example, I want
to detect the
Effect of waste water on some physical properties of soil, before, during
use waste water and after use waste water (Is there any significant change
in properties of soil.) Time is also important, so I want to know the
interaction between time and some physical properties of soil, like water
content .first comprises between Treatments and then comprise between
weeks).
Questions to be answered:
1)      Theta (water content), before (1 week) and after the COD; is there a
difference?
2)      Theta, during, before and after the COD; is there a difference?
3)      Is there a trend in Theta, during COD (8 weeks)?
4)      Is there a difference in Theta, during COD between the treatments?

I hope somebody can help me to find correct statistical analyses in R. I
sepnt a lot of time, but still , i have problems.

Kind regards,

Alisia
----------------------------------------------------------------------------------------------------------
Week Date BTC timeexp column Block Treatment Condition ThetaV
0 22/jun/08 -4 1 1 T4 DW 0,0962  Irrigation with diminirize water
0 22/jun/08 -4 2 1 T4 DW 0,0935  Irrigation with diminirize water
0 22/jun/08 -4 3 1 T4 DW 0,1181  Irrigation with diminirize water
0 22/jun/08 -4 4 1 T4 DW 0,0752  Irrigation with diminirize water
0 22/jun/08 -4 5 2 T4 DW 0,0761  Irrigation with diminirize water
0 22/jun/08 -4 6 2 T4 DW 0,0729  Irrigation with diminirize water
0 25/jun/08 -1 7 2 T4 DW 0,076  Irrigation with diminirize water
0 25/jun/08 -1 8 2 T4 DW 0,0766  Irrigation with diminirize water
0 25/jun/08 -1 9 3 T4 DW 0,0981  Irrigation with diminirize water
0 25/jun/08 -1 10 3 T4 DW 0,0628  Irrigation with diminirize water
0 25/jun/08 -1 11 3 T4 DW 0,0867  Irrigation with diminirize water
0 25/jun/08 -1 12 3 T4 DW 0,0657  Irrigation with diminirize water
1 27/jun/08 1 1 1 T3 WW 0,0903  Irrigation with wastewater
1 27/jun/08 1 2 1 T2 WW 0,0864  Irrigation with wastewater
1 27/jun/08 1 3 1 T4 WW 0,1101  Irrigation with wastewater
1 27/jun/08 1 4 1 T1 WW 0,0665  Irrigation with wastewater
1 27/jun/08 1 5 2 T1 WW 0,0675  Irrigation with wastewater
1 27/jun/08 1 6 2 T2 WW 0,0668  Irrigation with wastewater
1 3/jul/08 7 7 2 T3 WW 0,0718  Irrigation with wastewater
1 3/jul/08 7 8 2 T4 WW 0,0777  Irrigation with wastewater
1 3/jul/08 7 9 3 T4 WW 0,0982  Irrigation with wastewater
1 3/jul/08 7 10 3 T1 WW 0,065  Irrigation with wastewater
1 3/jul/08 7 11 3 T2 WW 0,081  Irrigation with wastewater
1 3/jul/08 7 12 3 T3 WW 0,0661  Irrigation with wastewater
2 7/jul/08 11 1 1 T3 WW 0,0935  Irrigation with wastewater
2 7/jul/08 11 2 1 T2 WW 0,0874  Irrigation with wastewater
2 7/jul/08 11 3 1 T4 WW 0,1273  Irrigation with wastewater
2 7/jul/08 11 4 1 T1 WW 0,0688  Irrigation with wastewater
2 7/jul/08 11 5 2 T1 WW 0,07  Irrigation with wastewater
2 7/jul/08 11 6 2 T2 WW 0,0686  Irrigation with wastewater
2 10/jul/08 14 7 2 T3 WW 0,0743  Irrigation with wastewater
2 10/jul/08 14 8 2 T4 WW 0,0774  Irrigation with wastewater
2 10/jul/08 14 9 3 T4 WW 0,0996  Irrigation with wastewater
2 10/jul/08 14 10 3 T1 WW 0,0593  Irrigation with wastewater
2 10/jul/08 14 11 3 T2 WW 0,0818  Irrigation with wastewater
2 10/jul/08 14 12 3 T3 WW 0,0658  Irrigation with wastewater
3 12/jul/08 16 1 1 T3 WW 0,0939  Irrigation with wastewater
3 12/jul/08 16 2 1 T2 WW 0,0884  Irrigation with wastewater
3 12/jul/08 16 3 1 T4 WW 0,1077  Irrigation with wastewater
3 12/jul/08 16 4 1 T1 WW 0,068  Irrigation with wastewater
3 12/jul/08 16 5 2 T1 WW 0,0683  Irrigation with wastewater
3 12/jul/08 16 6 2 T2 WW 0,0666  Irrigation with wastewater
3 12/jul/08 16 7 2 T3 WW 0,068  Irrigation with wastewater
3 16/jul/08 20 8 2 T4 WW 0,0739  Irrigation with wastewater
3 16/jul/08 20 9 3 T4 WW 0,1033  Irrigation with wastewater
3 16/jul/08 20 10 3 T1 WW 0,0594  Irrigation with wastewater
3 16/jul/08 20 11 3 T2 WW 0,0799  Irrigation with wastewater
3 16/jul/08 20 12 3 T3 WW 0,0623  Irrigation with wastewater
3,5 18/jul/08 22 1 1 T3 WW 0,0961  Irrigation with wastewater
3,5 18/jul/08 22 2 1 T2 WW 0,0911  Irrigation with wastewater
3,5 18/jul/08 22 3 1 T4 WW 0,1066  Irrigation with wastewater
3,5 18/jul/08 22 4 1 T1 WW 0,0715  Irrigation with wastewater
3,5 18/jul/08 22 5 2 T1 WW 0,0704  Irrigation with wastewater
3,5 18/jul/08 22 6 2 T2 WW 0,0685  Irrigation with wastewater
3,5 20/jul/08 24 7 2 T3 WW 0,068  Irrigation with wastewater
3,5 20/jul/08 24 8 2 T4 WW 0,0739  Irrigation with wastewater
3,5 20/jul/08 24 9 3 T4 WW 0,1033  Irrigation with wastewater
3,5 20/jul/08 24 10 3 T1 WW 0,0594  Irrigation with wastewater
3,5 20/jul/08 24 11 3 T2 WW 0,0799  Irrigation with wastewater
3,5 20/jul/08 24 12 3 T3 WW 0,0623  Irrigation with wastewater
4 23/jul/08 27 1 1 T3 WW 0,0767  Irrigation with wastewater
4 23/jul/08 27 2 1 T2 WW 0,0877  Irrigation with wastewater
4 23/jul/08 27 3 1 T4 WW 0,104  Irrigation with wastewater
4 23/jul/08 27 4 1 T1 WW 0,0593  Irrigation with wastewater
4 23/jul/08 27 5 2 T1 WW 0,0646  Irrigation with wastewater
4 23/jul/08 27 6 2 T2 WW 0,0668  Irrigation with wastewater
4 26/jul/08 30 7 2 T3 WW 0,0645  Irrigation with wastewater
4 26/jul/08 30 8 2 T4 WW 0,0705  Irrigation with wastewater
4 26/jul/08 30 9 3 T4 WW 0,0942  Irrigation with wastewater
4 26/jul/08 30 10 3 T1 WW 0,0553  Irrigation with wastewater
4 26/jul/08 30 11 3 T2 WW 0,0744  Irrigation with wastewater
4 26/jul/08 30 12 3 T3 WW 0,06  Irrigation with wastewater
4,5 30/jul/08 34 1 1 T3 WW 0,0764  Irrigation with wastewater
4,5 30/jul/08 34 2 1 T2 WW 0,0812  Irrigation with wastewater
4,5 30/jul/08 34 3 1 T4 WW 0,1011  Irrigation with wastewater
4,5 30/jul/08 34 4 1 T1 WW 0,0643  Irrigation with wastewater
4,5 30/jul/08 34 5 2 T1 WW 0,0673  Irrigation with wastewater
4,5 30/jul/08 34 6 2 T2 WW 0,064  Irrigation with wastewater
4,5 1/aug/08 36 7 2 T3 WW 0,0623  Irrigation with wastewater
4,5 1/aug/08 36 8 2 T4 WW 0,0646  Irrigation with wastewater
4,5 1/aug/08 36 9 3 T4 WW 0,0702  Irrigation with wastewater
4,5 1/aug/08 36 10 3 T1 WW 0,0531  Irrigation with wastewater
4,5 1/aug/08 36 11 3 T2 WW 0,0707  Irrigation with wastewater
4,5 1/aug/08 36 12 3 T3 WW 0,0619  Irrigation with wastewater
5 6/aug/08 41 1 1 T3 WW 0,0766  Irrigation with wastewater
5 6/aug/08 41 2 1 T2 WW 0,077  Irrigation with wastewater
5 6/aug/08 41 3 1 T4 WW 0,1022  Irrigation with wastewater
5 6/aug/08 41 4 1 T1 WW 0,0624  Irrigation with wastewater
5 6/aug/08 41 5 2 T1 WW 0,0615  Irrigation with wastewater
5 6/aug/08 41 6 2 T2 WW 0,061  Irrigation with wastewater
5 9/aug/08 44 7 2 T3 WW 0,0594  Irrigation with wastewater
5 9/aug/08 44 8 2 T4 WW 0,0709  Irrigation with wastewater
5 9/aug/08 44 9 3 T4 WW 0,0787  Irrigation with wastewater
5 9/aug/08 44 10 3 T1 WW 0,0523  Irrigation with wastewater
5 9/aug/08 44 11 3 T2 WW 0,0778  Irrigation with wastewater
5 9/aug/08 44 12 3 T3 WW 0,0626  Irrigation with wastewater
6 11/aug/08 46 1 1 T3 WW 0,0702  Irrigation with wastewater
6 11/aug/08 46 2 1 T2 WW 0,0787  Irrigation with wastewater
6 11/aug/08 46 3 1 T4 WW 0,1035  Irrigation with wastewater
6 11/aug/08 46 4 1 T1 WW 0,0607  Irrigation with wastewater
6 11/aug/08 46 5 2 T1 WW 0,0617  Irrigation with wastewater
6 11/aug/08 46 6 2 T2 WW 0,0613  Irrigation with wastewater
6 13/aug/08 48 7 2 T3 WW 0,0616  Irrigation with wastewater
6 13/aug/08 48 8 2 T4 WW 0,0649  Irrigation with wastewater
6 13/aug/08 48 9 3 T4 WW 0,0737  Irrigation with wastewater
6 13/aug/08 48 10 3 T1 WW 0,0534  Irrigation with wastewater
6 13/aug/08 48 11 3 T2 WW 0,0777  Irrigation with wastewater
6 13/aug/08 48 12 3 T3 WW 0,0675  Irrigation with wastewater
6,5 15/aug/08 50 1 1 T3 WW 0,0728  Irrigation with wastewater
6,5 15/aug/08 50 2 1 T2 WW 0,074  Irrigation with wastewater
6,5 15/aug/08 50 3 1 T4 WW 0,0968  Irrigation with wastewater
6,5 15/aug/08 50 4 1 T1 WW 0,0629  Irrigation with wastewater
6,5 15/aug/08 50 5 2 T1 WW 0,0602  Irrigation with wastewater
6,5 15/aug/08 50 6 2 T2 WW 0,0596  Irrigation with wastewater
6,5 16/aug/08 51 7 2 T3 WW 0,0633  Irrigation with wastewater
6,5 16/aug/08 51 8 2 T4 WW 0,0678  Irrigation with wastewater
6,5 16/aug/08 51 9 3 T4 WW 0,09  Irrigation with wastewater
6,5 16/aug/08 51 10 3 T1 WW 0,0545  Irrigation with wastewater
6,5 16/aug/08 51 11 3 T2 WW 0,0745  Irrigation with wastewater
6,5 16/aug/08 51 12 3 T3 WW 0,0673  Irrigation with wastewater
7 20/aug/08 55 1 1 T3 WW 0,079  Irrigation with wastewater
7 20/aug/08 55 2 1 T2 WW 0,0802  Irrigation with wastewater
7 20/aug/08 55 3 1 T4 WW 0,0995  Irrigation with wastewater
7 20/aug/08 55 4 1 T1 WW 0,0596  Irrigation with wastewater
7 20/aug/08 55 5 2 T1 WW 0,0662  Irrigation with wastewater
7 20/aug/08 55 6 2 T2 WW 0,0606  Irrigation with wastewater
7 23/aug/08 58 7 2 T3 WW 0,0617  Irrigation with wastewater
7 23/aug/08 58 8 2 T4 WW 0,0684  Irrigation with wastewater
7 23/aug/08 58 9 3 T4 WW 0,09  Irrigation with wastewater
7 23/aug/08 58 10 3 T1 WW 0,054  Irrigation with wastewater
7 23/aug/08 58 11 3 T2 WW 0,0782  Irrigation with wastewater
7 23/aug/08 58 12 3 T3 WW 0,0548  Irrigation with wastewater
7,5 26/aug/08 61 1 1 T3 WW 0,0775  Irrigation with wastewater
7,5 26/aug/08 61 2 1 T2 WW 0,0767  Irrigation with wastewater
7,5 26/aug/08 61 3 1 T4 WW 0,1102  Irrigation with wastewater
7,5 26/aug/08 61 4 1 T1 WW 0,0691  Irrigation with wastewater
7,5 26/aug/08 61 5 2 T1 WW 0,0654  Irrigation with wastewater
7,5 26/aug/08 61 6 2 T2 WW 0,0662  Irrigation with wastewater
7,5 28/aug/08 63 7 2 T3 WW 0,0684  Irrigation with wastewater
7,5 28/aug/08 63 8 2 T4 WW 0,0674  Irrigation with wastewater
7,5 28/aug/08 63 9 3 T4 WW 0,0936  Irrigation with wastewater
7,5 28/aug/08 63 10 3 T1 WW 0,055  Irrigation with wastewater
7,5 28/aug/08 63 11 3 T2 WW 0,0751  Irrigation with wastewater
7,5 28/aug/08 63 12 3 T3 WW 0,0651  Irrigation with wastewater
8 4/sep/08 70 1 1 T3 WW 0,0839  Irrigation with wastewater
8 4/sep/08 70 2 1 T2 WW 0,0841  Irrigation with wastewater
8 4/sep/08 70 3 1 T4 WW 0,1073  Irrigation with wastewater
8 4/sep/08 70 4 1 T1 WW 0,0661  Irrigation with wastewater
8 4/sep/08 70 5 2 T1 WW 0,0668  Irrigation with wastewater
8 4/sep/08 70 6 2 T2 WW 0,0734  Irrigation with wastewater
8 9/sep/08 75 7 2 T3 WW 0,0699  Irrigation with wastewater
8 9/sep/08 75 8 2 T4 WW 0,0729  Irrigation with wastewater
8 9/sep/08 75 9 3 T4 WW 0,1004  Irrigation with wastewater
8 9/sep/08 75 10 3 T1 WW 0,0569  Irrigation with wastewater
8 9/sep/08 75 11 3 T2 WW 0,0748  Irrigation with wastewater
8 9/sep/08 75 12 3 T3 WW 0,0636  Irrigation with wastewater
9 15/sep/08 81 1 1 T3 DW 0,091  Irrigation with diminirize water
9 15/sep/08 81 2 1 T2 DW 0,0952  Irrigation with diminirize water
9 15/sep/08 81 3 1 T4 DW 0,1135  Irrigation with diminirize water
9 15/sep/08 81 4 1 T1 DW 0,0839  Irrigation with diminirize water
9 15/sep/08 81 5 2 T1 DW 0,0758  Irrigation with diminirize water
9 15/sep/08 81 6 2 T2 DW 0,0684  Irrigation with diminirize water
9 21/sep/08 87 7 2 T3 DW 0,0965  Irrigation with diminirize water
9 21/sep/08 87 8 2 T4 DW 0,0887  Irrigation with diminirize water
9 21/sep/08 87 9 3 T4 DW 0,1028  Irrigation with diminirize water
9 21/sep/08 87 10 3 T1 DW 0,071  Irrigation with diminirize water
9 21/sep/08 87 11 3 T2 DW 0,0712  Irrigation with diminirize water
9 21/sep/08 87 12 3 T3 DW 0,0639  Irrigation with diminirize water
10 2/okt/08 98 1 1 T3 DW 0,092  Irrigation with diminirize water
10 2/okt/08 98 2 1 T2 DW 0,0895  Irrigation with diminirize water
10 2/okt/08 98 3 1 T4 DW 0,1051  Irrigation with diminirize water
10 2/okt/08 98 4 1 T1 DW 0,0768  Irrigation with diminirize water
10 2/okt/08 98 5 2 T1 DW 0,0732  Irrigation with diminirize water
10 2/okt/08 98 6 2 T2 DW 0,072  Irrigation with diminirize water
10 7/okt/08 103 7 2 T3 DW 0,079  Irrigation with diminirize water
10 7/okt/08 103 8 2 T4 DW 0,0684  Irrigation with diminirize water
10 7/okt/08 103 9 3 T4 DW 0,1038  Irrigation with diminirize water
10 7/okt/08 103 10 3 T1 DW 0,074  Irrigation with diminirize water
10 7/okt/08 103 11 3 T2 DW 0,0699  Irrigation with diminirize water
10 7/okt/08 103 12 3 T3 DW 0,0659  Irrigation with diminirize water
11 10/okt/08 106 1 1 T3 DW 0,091  Irrigation with diminirize water
11 10/okt/08 106 2 1 T2 DW 0,087  Irrigation with diminirize water
11 10/okt/08 106 3 1 T4 DW 0,105  Irrigation with diminirize water
11 10/okt/08 106 4 1 T1 DW 0,0776  Irrigation with diminirize water
11 10/okt/08 106 5 2 T1 DW 0,071  Irrigation with diminirize water
11 10/okt/08 106 6 2 T2 DW 0,0692  Irrigation with diminirize water
11 14/okt/08 110 7 2 T3 DW 0,08  Irrigation with diminirize water
11 14/okt/08 110 8 2 T4 DW 0,0514  Irrigation with diminirize water
11 14/okt/08 110 9 3 T4 DW 0,1012  Irrigation with diminirize water
11 14/okt/08 110 10 3 T1 DW 0,0625  Irrigation with diminirize water
11 14/okt/08 110 11 3 T2 DW 0,0689  Irrigation with diminirize water
11 14/okt/08 110 12 3 T3 DW 0,0649  Irrigation with diminirize water
12 18/okt/08 114 1 1 T3 DW 0,096  Irrigation with diminirize water
12 18/okt/08 114 2 1 T2 DW 0,093  Irrigation with diminirize water
12 18/okt/08 114 3 1 T4 DW 0,1084  Irrigation with diminirize water
12 18/okt/08 114 4 1 T1 DW 0,0756  Irrigation with diminirize water
12 18/okt/08 114 5 2 T1 DW 0,0681  Irrigation with diminirize water
12 18/okt/08 114 6 2 T2 DW 0,0689  Irrigation with diminirize water
12 23/okt/08 119 7 2 T3 DW 0,077  Irrigation with diminirize water
12 23/okt/08 119 8 2 T4 DW 0,0614  Irrigation with diminirize water
12 23/okt/08 119 9 3 T4 DW 0,0999  Irrigation with diminirize water
12 23/okt/08 119 10 3 T1 DW 0,0585  Irrigation with diminirize water
12 23/okt/08 119 11 3 T2 DW 0,0681  Irrigation with diminirize water
12 23/okt/08 119 12 3 T3 DW 0,0629  Irrigation with diminirize water



----------------------------------------------------------------------------------------------

> mod <- aov(ThetaV ~ factor(Block) + Treatmen:factor(Week))
> anova(mod)
Analysis of Variance Table

Response: ThetaV
                      Df    Sum Sq   Mean Sq F value    Pr(>F)
factor(Block)          2 0.0073713 0.0036856 49.4955 2.074e-15 ***
Treatmen:factor(Week) 47 0.0168852 0.0003593  4.8246 4.606e-11 ***
Residuals             94 0.0069996 0.0000745
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> mod <- aov(ThetaV ~ factor(Block) + Treatmen*factor(Week))
> anova(mod)
Analysis of Variance Table

Response: ThetaV
                      Df    Sum Sq   Mean Sq F value    Pr(>F)
factor(Block)          2 0.0073713 0.0036856 49.4955 2.074e-15 ***
Treatmen               3 0.0139313 0.0046438 62.3627 < 2.2e-16 ***
factor(Week)          11 0.0024297 0.0002209  2.9663  0.002038 **
Treatmen:factor(Week) 33 0.0005242 0.0000159  0.2133  0.999998
Residuals             94 0.0069996 0.0000745
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> TukeyHSD(mod,"Treatmen")
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = ThetaV ~ factor(Block) + Treatmen * factor(Week))

$Treatmen
              diff          lwr          upr     p adj
T2-T1  0.012650000  0.007330061 0.0179699388 0.0000001
T3-T1  0.008130556  0.002810617 0.0134504943 0.0007251
T4-T1  0.027086111  0.021766172 0.0324060499 0.0000000
T3-T2 -0.004519444 -0.009839383 0.0008004943 0.1247735
T4-T2  0.014436111  0.009116172 0.0197560499 0.0000000
T4-T3  0.018955556  0.013635617 0.0242754943 0.0000000

> tapply(ThetaV,Treatmen,mean)
        T1         T2         T3         T4
0.06240833 0.07505833 0.07053889 0.08949444
> tapply(NoThetaV,Week,mean)
         1          2          3          4          5          6          7

0.07895000 0.08115000 0.07830833 0.07925000 0.07316667 0.06975833 0.07020000

         8          9         10         11         12
0.06957500 0.07030833 0.07101667 0.07414167 0.07667500
> tapply(ThetaV,list(Week,Treatmen),mean)
           T1         T2         T3         T4
1  0.06633333 0.07806667 0.07606667 0.09533333
2  0.06603333 0.07926667 0.07786667 0.10143333
3  0.06523333 0.07830000 0.07473333 0.09496667
4  0.06710000 0.07983333 0.07546667 0.09460000
5  0.05973333 0.07630000 0.06706667 0.08956667
6  0.06156667 0.07196667 0.06686667 0.07863333
7  0.05873333 0.07193333 0.06620000 0.08393333
8  0.05860000 0.07256667 0.06643333 0.08070000
9  0.05920000 0.06936667 0.06780000 0.08486667
10 0.05993333 0.07300000 0.06516667 0.08596667
11 0.06316667 0.07266667 0.07033333 0.09040000
12 0.06326667 0.07743333 0.07246667 0.09353333
>
_____________________________________________________________________________________________



> RBF <- aov(ThetaExpT$ThetaV ~ factor(ThetaExpT$Block) +
factor(ThetaExpT$Week):factor(ThetaExpT$Treatment) )
> anova(RBF)
Analysis of Variance Table

Response: ThetaExpT$ThetaV
                                                    Df    Sum Sq   Mean Sq
factor(ThetaExpT$Block)                              2 0.0108151 0.0054075
factor(ThetaExpT$Week):factor(ThetaExpT$Treatment)  63 0.0215197 0.0003416
Residuals                                          126 0.0112558 0.0000893
                                                   F value    Pr(>F)
factor(ThetaExpT$Block)                            60.5330 < 2.2e-16 ***
factor(ThetaExpT$Week):factor(ThetaExpT$Treatment)  3.8237 7.783e-11 ***
Residuals
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> RBF <- aov(ThetaExpT$ThetaV ~ factor(ThetaExpT$Block) +
factor(ThetaExpT$Week)*factor(ThetaExpT$Treatment) )
> anova(RBF)
Analysis of Variance Table

Response: ThetaExpT$ThetaV
                                                    Df    Sum Sq   Mean Sq
factor(ThetaExpT$Block)                              2 0.0108151 0.0054075
factor(ThetaExpT$Week)                              15 0.0041717 0.0002781
factor(ThetaExpT$Treatment)                          3 0.0161244 0.0053748
factor(ThetaExpT$Week):factor(ThetaExpT$Treatment)  45 0.0012236 0.0000272
Residuals                                          126 0.0112558 0.0000893
                                                   F value    Pr(>F)
factor(ThetaExpT$Block)                            60.5330 < 2.2e-16 ***
factor(ThetaExpT$Week)                              3.1133 0.0002501 ***
factor(ThetaExpT$Treatment)                        60.1665 < 2.2e-16 ***
factor(ThetaExpT$Week):factor(ThetaExpT$Treatment)  0.3044 0.9999915
Residuals
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> TukeyHSD(RBF,"Treatment")
Error in TukeyHSD.aov(RBF, "Treatment") : 'which' specified no factors
> TukeyHSD(RBF,"factor(ThetaExpT$Treatment)")
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = ThetaExpT$ThetaV ~ factor(ThetaExpT$Block) +
factor(ThetaExpT$Week) * factor(ThetaExpT$Treatment))

$`factor(ThetaExpT$Treatment)`
              diff          lwr         upr     p adj
T2-T1  0.010597917  0.005574723 0.015621111 0.0000012
T3-T1  0.008016667  0.002993473 0.013039861 0.0003436
T4-T1  0.025347917  0.020324723 0.030371111 0.0000000
T3-T2 -0.002581250 -0.007604444 0.002441944 0.5406528
T4-T2  0.014750000  0.009726806 0.019773194 0.0000000
T4-T3  0.017331250  0.012308056 0.022354444 0.0000000

> TukeyHSD(RBF,"factor(ThetaExpT$Week)")
  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = ThetaExpT$ThetaV ~ factor(ThetaExpT$Block) +
factor(ThetaExpT$Week) * factor(ThetaExpT$Treatment))

$`factor(ThetaExpT$Week)`
                 diff           lwr         upr     p adj
2-1      0.0022000000 -0.0112915964 0.015691596 0.9999999
3-1     -0.0006416667 -0.0141332631 0.012849930 1.0000000
3.5-1    0.0003000000 -0.0131915964 0.013791596 1.0000000
4-1     -0.0057833333 -0.0192749297 0.007708263 0.9807680
4.5-1   -0.0091916667 -0.0226832631 0.004299930 0.5643712
5-1     -0.0087500000 -0.0222415964 0.004741596 0.6477289
6-1     -0.0093750000 -0.0228665964 0.004116596 0.5295103
6.5-1   -0.0086416667 -0.0221332631 0.004849930 0.6677096
7-1     -0.0079333333 -0.0214249297 0.005558263 0.7884928
7.5-1   -0.0048083333 -0.0182999297 0.008683263 0.9969774
8-1     -0.0022750000 -0.0157665964 0.011216596 0.9999998
9-1      0.0062083333 -0.0072832631 0.019699930 0.9638857
10-1     0.0018500000 -0.0116415964 0.015341596 1.0000000
11-1    -0.0014750000 -0.0149665964 0.012016596 1.0000000
12-1    -0.0008000000 -0.0142915964 0.012691596 1.0000000
3-2     -0.0028416667 -0.0163332631 0.010649930 0.9999952
3.5-2   -0.0019000000 -0.0153915964 0.011591596 1.0000000
4-2     -0.0079833333 -0.0214749297 0.005508263 0.7806960
4.5-2   -0.0113916667 -0.0248832631 0.002099930 0.2052535
5-2     -0.0109500000 -0.0244415964 0.002541596 0.2621502
6-2     -0.0115750000 -0.0250665964 0.001916596 0.1843734
6.5-2   -0.0108416667 -0.0243332631 0.002649930 0.2775172
7-2     -0.0101333333 -0.0236249297 0.003358263 0.3905650
7.5-2   -0.0070083333 -0.0204999297 0.006483263 0.9058749
8-2     -0.0044750000 -0.0179665964 0.009016596 0.9986299
9-2      0.0040083333 -0.0094832631 0.017499930 0.9996182
10-2    -0.0003500000 -0.0138415964 0.013141596 1.0000000
11-2    -0.0036750000 -0.0171665964 0.009816596 0.9998671
12-2    -0.0030000000 -0.0164915964 0.010491596 0.9999901
3.5-3    0.0009416667 -0.0125499297 0.014433263 1.0000000
4-3     -0.0051416667 -0.0186332631 0.008349930 0.9938879
4.5-3   -0.0085500000 -0.0220415964 0.004941596 0.6843839
5-3     -0.0081083333 -0.0215999297 0.005383263 0.7606483
6-3     -0.0087333333 -0.0222249297 0.004758263 0.6508201
6.5-3   -0.0080000000 -0.0214915964 0.005491596 0.7780682
7-3     -0.0072916667 -0.0207832631 0.006199930 0.8756776
7.5-3   -0.0041666667 -0.0176582631 0.009324930 0.9993965
8-3     -0.0016333333 -0.0151249297 0.011858263 1.0000000
9-3      0.0068500000 -0.0066415964 0.020341596 0.9204690
10-3     0.0024916667 -0.0109999297 0.015983263 0.9999992
11-3    -0.0008333333 -0.0143249297 0.012658263 1.0000000
12-3    -0.0001583333 -0.0136499297 0.013333263 1.0000000
4-3.5   -0.0060833333 -0.0195749297 0.007408263 0.9697055
4.5-3.5 -0.0094916667 -0.0229832631 0.003999930 0.5074372
5-3.5   -0.0090500000 -0.0225415964 0.004441596 0.5913084
6-3.5   -0.0096750000 -0.0231665964 0.003816596 0.4731081
6.5-3.5 -0.0089416667 -0.0224332631 0.004549930 0.6118196
7-3.5   -0.0082333333 -0.0217249297 0.005258263 0.7398602
7.5-3.5 -0.0051083333 -0.0185999297 0.008383263 0.9942829
8-3.5   -0.0025750000 -0.0160665964 0.010916596 0.9999987
9-3.5    0.0059083333 -0.0075832631 0.019399930 0.9766245
10-3.5   0.0015500000 -0.0119415964 0.015041596 1.0000000
11-3.5  -0.0017750000 -0.0152665964 0.011716596 1.0000000
12-3.5  -0.0011000000 -0.0145915964 0.012391596 1.0000000
4.5-4   -0.0034083333 -0.0168999297 0.010083263 0.9999484
5-4     -0.0029666667 -0.0164582631 0.010524930 0.9999915
6-4     -0.0035916667 -0.0170832631 0.009899930 0.9999001
6.5-4   -0.0028583333 -0.0163499297 0.010633263 0.9999948
7-4     -0.0021500000 -0.0156415964 0.011341596 0.9999999
7.5-4    0.0009750000 -0.0125165964 0.014466596 1.0000000
8-4      0.0035083333 -0.0099832631 0.016999930 0.9999255
9-4      0.0119916667 -0.0014999297 0.025483263 0.1427516
10-4     0.0076333333 -0.0058582631 0.021124930 0.8323616
11-4     0.0043083333 -0.0091832631 0.017799930 0.9991104
12-4     0.0049833333 -0.0085082631 0.018474930 0.9955808
5-4.5    0.0004416667 -0.0130499297 0.013933263 1.0000000
6-4.5   -0.0001833333 -0.0136749297 0.013308263 1.0000000
6.5-4.5  0.0005500000 -0.0129415964 0.014041596 1.0000000
7-4.5    0.0012583333 -0.0122332631 0.014749930 1.0000000
7.5-4.5  0.0043833333 -0.0091082631 0.017874930 0.9989162
8-4.5    0.0069166667 -0.0065749297 0.020408263 0.9145216
9-4.5    0.0154000000  0.0019084036 0.028891596 0.0102437
10-4.5   0.0110416667 -0.0024499297 0.024533263 0.2495770
11-4.5   0.0077166667 -0.0057749297 0.021208263 0.8206976
12-4.5   0.0083916667 -0.0050999297 0.021883263 0.7125787
6-5     -0.0006250000 -0.0141165964 0.012866596 1.0000000
6.5-5    0.0001083333 -0.0133832631 0.013599930 1.0000000
7-5      0.0008166667 -0.0126749297 0.014308263 1.0000000
7.5-5    0.0039416667 -0.0095499297 0.017433263 0.9996876
8-5      0.0064750000 -0.0070165964 0.019966596 0.9487494
9-5      0.0149583333  0.0014667369 0.028449930 0.0151166
10-5     0.0106000000 -0.0028915964 0.024091596 0.3137269
11-5     0.0072750000 -0.0062165964 0.020766596 0.8775993
12-5     0.0079500000 -0.0055415964 0.021441596 0.7859085
6.5-6    0.0007333333 -0.0127582631 0.014224930 1.0000000
7-6      0.0014416667 -0.0120499297 0.014933263 1.0000000
7.5-6    0.0045666667 -0.0089249297 0.018058263 0.9982809
8-6      0.0071000000 -0.0063915964 0.020591596 0.8966805
9-6      0.0155833333  0.0020917369 0.029074930 0.0086842
10-6     0.0112250000 -0.0022665964 0.024716596 0.2256286
11-6     0.0079000000 -0.0055915964 0.021391596 0.7936171
12-6     0.0085750000 -0.0049165964 0.022066596 0.6798597
7-6.5    0.0007083333 -0.0127832631 0.014199930 1.0000000
7.5-6.5  0.0038333333 -0.0096582631 0.017324930 0.9997770
8-6.5    0.0063666667 -0.0071249297 0.019858263 0.9553666
9-6.5    0.0148500000  0.0013584036 0.028341596 0.0165983
10-6.5   0.0104916667 -0.0029999297 0.023983263 0.3307898
11-6.5   0.0071666667 -0.0063249297 0.020658263 0.8896480
12-6.5   0.0078416667 -0.0056499297 0.021333263 0.8024391
7.5-7    0.0031250000 -0.0103665964 0.016616596 0.9999831
8-7      0.0056583333 -0.0078332631 0.019149930 0.9843135
9-7      0.0141416667  0.0006500703 0.027633263 0.0299922
10-7     0.0097833333 -0.0037082631 0.023274930 0.4531110
11-7     0.0064583333 -0.0070332631 0.019949930 0.9498107
12-7     0.0071333333 -0.0063582631 0.020624930 0.8932006
8-7.5    0.0025333333 -0.0109582631 0.016024930 0.9999990
9-7.5    0.0110166667 -0.0024749297 0.024508263 0.2529667
10-7.5   0.0066583333 -0.0068332631 0.020149930 0.9359982
11-7.5   0.0033333333 -0.0101582631 0.016824930 0.9999611
12-7.5   0.0040083333 -0.0094832631 0.017499930 0.9996182
9-8      0.0084833333 -0.0050082631 0.021974930 0.6963560
10-8     0.0041250000 -0.0093665964 0.017616596 0.9994636
11-8     0.0008000000 -0.0126915964 0.014291596 1.0000000
12-8     0.0014750000 -0.0120165964 0.014966596 1.0000000
10-9    -0.0043583333 -0.0178499297 0.009133263 0.9989846
11-9    -0.0076833333 -0.0211749297 0.005808263 0.8254130
12-9    -0.0070083333 -0.0204999297 0.006483263 0.9058749
11-10   -0.0033250000 -0.0168165964 0.010166596 0.9999624
12-10   -0.0026500000 -0.0161415964 0.010841596 0.9999981
12-11    0.0006750000 -0.0128165964 0.014166596 1.0000000

>
___________________________________________________________________________________________

library(RODBC)
canal <- odbcConnectExcel("final_results_Oxct08")
A<- sqlFetch(canal,"A")
odbcCloseAll()
str(A)
model <- lm(ThetaV ~ Block + Treatment + condition, data = A)
residual<-residuals(model)
# Only efect time
model2 <- lm(residual ~ DateBTC, data=A)
summary(model2)
# Other case
model3 <- lm(ThetaV ~ Treatment, data = A)
summary(model3)
model4 <- lm(ThetaV ~ condition+DateBTC, data = A)
summary(model4)
model5 <- lm(ThetaV ~ condition, data = A)
summary(model5)

--------------------------------------------------------------------------------------------------

In this particular case, the fixed-effect model and the RCB
design will give the same p-values:


bad.aov <- aov(ThetaV ~ Treatment + Block, data=table)
summary(bad.aov)


------------------------------------------------------------------




library(nlme)
m2 = lme(ThetaV ~ Treatment, random = ~1|Block, data=table)
anova(m2)


detach("package:nlme")
library(lme4)
m3 = lmer(ThetaV ~ Treatment+(1|Block), data=table)
anova(m3)

--------------------------------------------------------------------------------------------------

library(lme4)
water<-read.csv("locationofattachedfile",header=T)
attach(water)
model<-lmer(ThetaV~trt+(block|trt)+week+condition,data=water)
model
anova(model)

------------------------------------------------------------------------------------------------


alis.lme=lme(fixed=response~treatment-1 + time +
time*treatment,data=alis.grDat,random=~1|Block)
summary(alis.lme)

--------------------------------------------------------------------------------------------------------

	[[alternative HTML version deleted]]


