SK.nest {ScottKnott} | R Documentation |
These are methods for objects of class vector
, matrix
or
data.frame
joined as default, aov
and aovlist
for
factorial, split-plot and split-split-plot experiments.
## Default S3 method: SK.nest(x, y=NULL, model, which, error, fl2, fl3=0, sig.level=.05, ...) ## S3 method for class 'aov': SK.nest(x, which, fl2, fl3=0, sig.level=.05, ...) ## S3 method for class 'aovlist': SK.nest(x, which, error, fl2, fl3=0, sig.level=.05, ...)
x |
A design matrix, data.frame or an aov object. |
y |
A vector of response variable. It is necessary to inform this
parameter only if x represent the design matrix without the response variable in it |
which |
The name of the treatment to be used in the comparison. The name must be inside quoting marks. |
model |
If x is a data.frame object, the model to be used in the
aov must be specified. |
fl2 |
A vector of length 1 giving the level of the second factor in nesting order tested. |
fl3 |
A vector of length 1 giving the level of the third factor in nesting order tested. |
error |
The error to be considered, only in case of split-plots experiments. |
sig.level |
Level of Significance used in the SK algorithm to create the groups of means. The default value is 0.05. |
... |
Potential further arguments (require by generic). |
The function SK.nest
returns an object of class
SK.nest
containing the groups of means plus other
necessary variables for summary and plot.
The generic functions summary
and plot
are used to obtain and
print a summary and a plot of the results.
The function SK.nest
returns a list of the class SK.nest
with the slots:
av |
A list storing the result of aov . |
groups |
A vector of length equal the number of treatments marking the groups generated. |
nms |
A vector of the labels of the treatments. |
ord |
A vector which keeps the position of the means of the treatments in decreasing order. |
means |
A vector which keeps the means of the treatments in decreasing order. |
sig.level |
A vector of length 1 giving the level of significance of the test. |
mnumber |
A vector of length 1 giving the number of treatments. |
r |
A vector of length 1 giving the number of replicates. |
which |
The name of the factor whose levels were tested. |
fl2 |
A vector of length 1 giving the level of the second factor in nesting order tested. |
fl3 |
A vector of length 1 giving the level of the third factor in nesting order tested. |
Enio Jelihovschi (eniojelihovs@gmail.com)
Jose Claudio Faria (joseclaudio.faria@gmail.com)
Sergio Oliveira (solive@uesc.br)
Ramalho MAP, Ferreira DF, Oliveira AC 2000. Experimentacao em Genetica e Melhoramento de Plantas. Editora UFLA.
Scott RJ, Knott M 1974. A cluster analysis method for grouping mans in the analysis of variance. Biometrics, 30, 507-512.
## ## Example: Split-split-plot Experiment (SSPE) ## A <- gl(3, 60, 180, 1:3) C <- rep(gl(3, 20, 60, 1:3), 3) D <- rep(gl(5, 4, 20, 1:5), 9) blo <- rep(gl(4, 1, 4, 1:4), 45) y <- c( 3029, 3857, 2448, 2448, 2438, 3086, 3771, 4657, 3543, 4314, 3888, 3945, 4318, 4514, 4497, 4215, 4610, 4590, 4499, 4545, 3448, 3600, 4267, 3895, 3533, 5048, 3467, 4095, 3770, 3840, 3699, 3801, 3975, 3840, 3725, 3952, 4010, 3880, 3785, 3903, 3706, 3815, 3795, 3900, 3870, 4003, 3987, 3938, 4040, 3879, 3777, 4218, 3888, 3964, 3800, 3715, 3815, 3793, 3905, 3918, 3074, 3852, 2483, 2453, 2553, 3121, 3786, 4672, 3558, 4429, 3913, 3860, 4233, 4538, 4612, 4240, 4635, 4615, 4524, 4570, 3473, 3625, 4292, 3920, 3558, 5193, 3492, 4210, 3780, 3850, 3709, 3723, 3895, 3940, 3735, 3962, 4190, 3890, 3795, 3813, 3716, 3825, 3825, 3985, 3862, 3898, 3982, 3993, 4105, 3874, 3772, 4213, 3896, 3982, 3808, 3833, 3893, 3871, 3923, 3936, 3256, 3804, 2745, 2475, 2565, 3163, 3798, 4684, 3770, 4341, 3815, 3972, 4355, 4541, 4411, 4229, 4624, 4504, 4713, 4509, 3462, 3614, 4281, 3909, 3547, 4962, 3481, 4109, 3874, 3654, 3713, 3828, 4092, 3867, 3752, 3979, 3837, 3707, 3872, 3730, 3833, 3942, 3722, 3912, 3882, 4015, 3989, 3890, 4052, 3891, 3765, 4197, 3899, 3905, 3911, 3726, 3876, 3804, 3916, 3819) dm <- data.frame(A, C, D, blo) # Design matrix (a data.frame object) dfm <- data.frame(A, C, D, blo, y) ## PARAMETERS ARE THE DESIGN MATRIX AND THE RESPONSE VARIABLE ## MAIN FACTOR ANALYSIS ## Main factor = A sk1 <- SK(dm, y, model='y ~ blo + D*C*A + Error(blo/A/C)', which='A', error='blo:A') summary(sk1) plot(sk1) # Main factor = C sk2 <- SK(dm, y, model='y ~ blo + D*C*A + Error(blo/A/C)', which='C', error='blo:A:C', sig.level=0.025) summary(sk2) plot(sk2, title='C', col=rainbow(3)) # Main factor = D sk3 <- SK(dm, y, model='y ~ blo + D*C*A + Error(blo/A/C)', which='D', error='Within', sig.level=0.1) summary(sk3) plot(sk3, title='D', col=heat.colors(3)) ## NESTED ANALYSIS ## Nested C/A=1 -> SK.nest sk4 <- SK.nest(dm, y, model='y ~ blo + D*C*A + Error(blo/A/C)', which='C:A', error='blo:A:C', fl2=1) summary(sk4) plot(sk4, title='C/A=1', col='darkgray')