library(nlme)
library(multcomp)
## Loading required package: mvtnorm
## Loading required package: survival
## Loading required package: TH.data
## Loading required package: MASS
##
## Attaching package: 'TH.data'
## The following object is masked from 'package:MASS':
##
## geyser
setwd("/home/michael/Dropbox/BGU/1_Other/Ilan_Stavi/")
# Read
dat = read.csv("data/Sde Zin_all data_170703+correlations.csv", stringsAsFactors = FALSE, check.names = TRUE)
# Factors
# Variables
vars = setdiff(colnames(dat), c("X.", "Block", "Treatment", "Spot", "Depth"))
# Fit model
for(i in vars) {
print("#############################################")
print(i)
print("#############################################")
tmp = dat[, c(i, c("Block", "Treatment", "Depth"))]
tmp = tmp[complete.cases(tmp), ]
tmp$Treatment = factor(tmp$Treatment)
tmp$Depth = factor(tmp$Depth)
if(length(unique(tmp$Depth)) == 1) {
f = as.formula(paste0(i, " ~ Treatment"))
} else {
f = as.formula(paste0(i, " ~ Treatment * Depth"))
}
fit = lme(f, random = ~ 1|Block, tmp)
s = summary(fit)
print(s)
}
## [1] "#############################################"
## [1] "PR..penetration.resistance..MPa."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 143.8841 161.4014 -63.94207
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.1079614 0.5629206
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 1.2571058 0.1712324 63 7.341518
## TreatmentDeep tillage -0.8246471 0.2298114 63 -3.588365
## TreatmentShallow tillage -0.8167271 0.2298114 63 -3.553902
## Depth15 -- 20 0.7394740 0.2298114 63 3.217744
## TreatmentDeep tillage:Depth15 -- 20 -0.8437114 0.3250023 63 -2.596016
## TreatmentShallow tillage:Depth15 -- 20 -0.8354279 0.3250023 63 -2.570529
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.0007
## TreatmentShallow tillage 0.0007
## Depth15 -- 20 0.0020
## TreatmentDeep tillage:Depth15 -- 20 0.0117
## TreatmentShallow tillage:Depth15 -- 20 0.0125
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.671
## TreatmentShallow tillage -0.671 0.500
## Depth15 -- 20 -0.671 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.475 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.475 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.28813618 -0.49865679 -0.08929228 0.33124468 2.57232568
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "VS..kPa."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 681.448 698.9652 -332.724
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 10.5627 32.63209
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 184.54500 10.79956 63 17.088202
## TreatmentDeep tillage 69.48917 13.32199 63 5.216123
## TreatmentShallow tillage 35.31417 13.32199 63 2.650817
## Depth15 -- 20 5.69583 13.32199 63 0.427551
## TreatmentDeep tillage:Depth15 -- 20 -15.94833 18.84015 63 -0.846508
## TreatmentShallow tillage:Depth15 -- 20 -5.69583 18.84015 63 -0.302324
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.0000
## TreatmentShallow tillage 0.0101
## Depth15 -- 20 0.6704
## TreatmentDeep tillage:Depth15 -- 20 0.4005
## TreatmentShallow tillage:Depth15 -- 20 0.7634
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.617
## TreatmentShallow tillage -0.617 0.500
## Depth15 -- 20 -0.617 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.436 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.436 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.84562898 -0.63157868 0.07206476 0.76004888 1.48865434
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "CM...."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 116.8527 124.3353 -53.42636
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.866263 0.9934974
##
## Fixed effects: list(f)
## Value Std.Error DF t-value p-value
## (Intercept) 0.500000 0.5194766 30 0.962507 0.3435
## TreatmentDeep tillage 5.583333 0.4055936 30 13.765832 0.0000
## TreatmentShallow tillage 4.083333 0.4055936 30 10.067549 0.0000
## Correlation:
## (Intr) TrtmDt
## TreatmentDeep tillage -0.39
## TreatmentShallow tillage -0.39 0.50
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.6254153 -0.6231376 -0.1326676 0.3748725 3.2481952
##
## Number of Observations: 36
## Number of Groups: 4
## [1] "#############################################"
## [1] "SM...."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 255.1291 272.6463 -119.5646
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.1339641 1.317607
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 2.878200 0.3862131 63 7.452364
## TreatmentDeep tillage 0.238302 0.5379107 63 0.443015
## TreatmentShallow tillage 0.386106 0.5379107 63 0.717788
## Depth15 -- 20 0.767345 0.5379107 63 1.426528
## TreatmentDeep tillage:Depth15 -- 20 4.635556 0.7607206 63 6.093638
## TreatmentShallow tillage:Depth15 -- 20 3.204241 0.7607206 63 4.212113
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.6593
## TreatmentShallow tillage 0.4755
## Depth15 -- 20 0.1587
## TreatmentDeep tillage:Depth15 -- 20 0.0000
## TreatmentShallow tillage:Depth15 -- 20 0.0001
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.696
## TreatmentShallow tillage -0.696 0.500
## Depth15 -- 20 -0.696 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.492 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.492 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.3283014 -0.4749579 -0.1177505 0.2796501 2.7874175
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "BD..g.cm.2."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## -70.17455 -52.65731 43.08727
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 3.973082e-07 0.1125085
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 1.5285661 0.03247841 63 47.06406
## TreatmentDeep tillage -0.2368510 0.04593141 63 -5.15662
## TreatmentShallow tillage -0.1605383 0.04593141 63 -3.49517
## Depth15 -- 20 0.0511512 0.04593141 63 1.11364
## TreatmentDeep tillage:Depth15 -- 20 -0.0178484 0.06495683 63 -0.27477
## TreatmentShallow tillage:Depth15 -- 20 -0.0756794 0.06495683 63 -1.16507
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.0000
## TreatmentShallow tillage 0.0009
## Depth15 -- 20 0.2697
## TreatmentDeep tillage:Depth15 -- 20 0.7844
## TreatmentShallow tillage:Depth15 -- 20 0.2484
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.707
## TreatmentShallow tillage -0.707 0.500
## Depth15 -- 20 -0.707 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.500 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.500 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.2323815 -0.6588525 -0.1249656 0.5886175 2.9914301
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "Total.porosity..clculated."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 409.066 426.5833 -196.533
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.0002380539 4.245605
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 42.31826 1.225601 63 34.52859
## TreatmentDeep tillage 8.93777 1.733261 63 5.15662
## TreatmentShallow tillage 6.05805 1.733261 63 3.49517
## Depth15 -- 20 -1.93023 1.733261 63 -1.11364
## TreatmentDeep tillage:Depth15 -- 20 0.67352 2.451201 63 0.27477
## TreatmentShallow tillage:Depth15 -- 20 2.85583 2.451201 63 1.16507
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.0000
## TreatmentShallow tillage 0.0009
## Depth15 -- 20 0.2697
## TreatmentDeep tillage:Depth15 -- 20 0.7844
## TreatmentShallow tillage:Depth15 -- 20 0.2484
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.707
## TreatmentShallow tillage -0.707 0.500
## Depth15 -- 20 -0.707 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.500 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.500 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.9914301 -0.5886175 0.1249656 0.6588525 2.2323815
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "CaCO3...."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 321.5559 339.0731 -152.7779
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.9858441 2.109969
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 26.564270 0.7835620 63 33.90194
## TreatmentDeep tillage 1.039062 0.8613911 63 1.20626
## TreatmentShallow tillage 0.491859 0.8613911 63 0.57101
## Depth15 -- 20 -0.567979 0.8613911 63 -0.65937
## TreatmentDeep tillage:Depth15 -- 20 0.271861 1.2181910 63 0.22317
## TreatmentShallow tillage:Depth15 -- 20 0.068304 1.2181910 63 0.05607
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.2322
## TreatmentShallow tillage 0.5700
## Depth15 -- 20 0.5121
## TreatmentDeep tillage:Depth15 -- 20 0.8241
## TreatmentShallow tillage:Depth15 -- 20 0.9555
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.550
## TreatmentShallow tillage -0.550 0.500
## Depth15 -- 20 -0.550 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.389 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.389 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.48796431 -0.44236567 -0.06589552 0.59687593 3.41969223
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "TOC..g.kg."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 468.2615 485.7787 -226.1307
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.0002834363 6.648121
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 22.961903 1.919147 63 11.964638
## TreatmentDeep tillage -0.211858 2.714084 63 -0.078059
## TreatmentShallow tillage -5.427593 2.714084 63 -1.999788
## Depth15 -- 20 2.501102 2.714084 63 0.921527
## TreatmentDeep tillage:Depth15 -- 20 -2.780835 3.838295 63 -0.724497
## TreatmentShallow tillage:Depth15 -- 20 1.815336 3.838295 63 0.472954
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.9380
## TreatmentShallow tillage 0.0498
## Depth15 -- 20 0.3603
## TreatmentDeep tillage:Depth15 -- 20 0.4714
## TreatmentShallow tillage:Depth15 -- 20 0.6379
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.707
## TreatmentShallow tillage -0.707 0.500
## Depth15 -- 20 -0.707 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.500 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.500 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.4377439 -0.6213261 -0.2051760 0.3996879 2.6823258
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "SOC.tratification.ratio"
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 323.9971 331.4796 -156.9985
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 4.994289 24.81667
##
## Fixed effects: list(f)
## Value Std.Error DF t-value p-value
## (Intercept) 92.50687 7.586699 30 12.193296 0.0000
## TreatmentDeep tillage 8.89277 10.131365 30 0.877747 0.3871
## TreatmentShallow tillage -10.58191 10.131365 30 -1.044471 0.3046
## Correlation:
## (Intr) TrtmDt
## TreatmentDeep tillage -0.668
## TreatmentShallow tillage -0.668 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.5169047 -0.6893916 -0.1666192 0.5708039 2.4222068
##
## Number of Observations: 36
## Number of Groups: 4
## [1] "#############################################"
## [1] "FC...."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 343.9277 361.4449 -163.9638
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.2890523 2.579981
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 20.921933 0.7586696 63 27.577135
## TreatmentDeep tillage 0.527964 1.0532727 63 0.501260
## TreatmentShallow tillage -0.669531 1.0532727 63 -0.635667
## Depth15 -- 20 0.059034 1.0532727 63 0.056048
## TreatmentDeep tillage:Depth15 -- 20 4.990373 1.4895525 63 3.350250
## TreatmentShallow tillage:Depth15 -- 20 5.302252 1.4895525 63 3.559627
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.6179
## TreatmentShallow tillage 0.5273
## Depth15 -- 20 0.9555
## TreatmentDeep tillage:Depth15 -- 20 0.0014
## TreatmentShallow tillage:Depth15 -- 20 0.0007
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.694
## TreatmentShallow tillage -0.694 0.500
## Depth15 -- 20 -0.694 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.491 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.491 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.9413890 -0.5768363 0.2127127 0.6516217 2.2130066
##
## Number of Observations: 72
## Number of Groups: 4
## [1] "#############################################"
## [1] "BRA"
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 1749.903 1764.872 -866.9513
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 1917.968 14727394
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 27601769 4909131 46 5.622536
## TreatmentDeep tillage 79641886 6942560 46 11.471544
## TreatmentShallow tillage 34868962 6942560 46 5.022493
## Depth15 -- 20 -20631569 6942560 46 -2.971752
## TreatmentDeep tillage:Depth15 -- 20 -73168977 9818263 46 -7.452334
## TreatmentShallow tillage:Depth15 -- 20 -33004061 9818263 46 -3.361497
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.0000
## TreatmentShallow tillage 0.0000
## Depth15 -- 20 0.0047
## TreatmentDeep tillage:Depth15 -- 20 0.0000
## TreatmentShallow tillage:Depth15 -- 20 0.0016
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.707
## TreatmentShallow tillage -0.707 0.500
## Depth15 -- 20 -0.707 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.500 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.500 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.13683357 -0.40945870 -0.05567042 0.25889227 3.69758298
##
## Number of Observations: 54
## Number of Groups: 3
## [1] "#############################################"
## [1] "AWC...."
## [1] "#############################################"
## Linear mixed-effects model fit by REML
## Data: tmp
## AIC BIC logLik
## 278.1948 293.1644 -131.0974
##
## Random effects:
## Formula: ~1 | Block
## (Intercept) Residual
## StdDev: 0.0001249048 3.23792
##
## Fixed effects: list(f)
## Value Std.Error DF t-value
## (Intercept) 11.305650 1.079306 46 10.474921
## TreatmentDeep tillage 1.014722 1.526370 46 0.664794
## TreatmentShallow tillage -0.304959 1.526370 46 -0.199794
## Depth15 -- 20 -1.469440 1.526370 46 -0.962702
## TreatmentDeep tillage:Depth15 -- 20 5.783623 2.158613 46 2.679324
## TreatmentShallow tillage:Depth15 -- 20 6.272876 2.158613 46 2.905975
## p-value
## (Intercept) 0.0000
## TreatmentDeep tillage 0.5095
## TreatmentShallow tillage 0.8425
## Depth15 -- 20 0.3407
## TreatmentDeep tillage:Depth15 -- 20 0.0102
## TreatmentShallow tillage:Depth15 -- 20 0.0056
## Correlation:
## (Intr) TrtmDt TrtmSt D15--2 TDt:-2
## TreatmentDeep tillage -0.707
## TreatmentShallow tillage -0.707 0.500
## Depth15 -- 20 -0.707 0.500 0.500
## TreatmentDeep tillage:Depth15 -- 20 0.500 -0.707 -0.354 -0.707
## TreatmentShallow tillage:Depth15 -- 20 0.500 -0.354 -0.707 -0.707 0.500
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.5436478 -0.5259908 0.0234113 0.7045633 1.9428862
##
## Number of Observations: 54
## Number of Groups: 3