NAG Library Function Document
nag_anova_random (g04bbc)
1 Purpose
nag_anova_random (g04bbc) computes the analysis of variance and treatment means and standard errors for a randomized block or completely randomized design.
2 Specification
#include <nag.h> |
#include <nagg04.h> |
void |
nag_anova_random (Integer n,
const double y[],
Nag_Blocks blocks,
Integer iblock,
Integer nt,
const Integer it[],
double *gmean,
double bmean[],
double tmean[],
double table[],
double c[],
Integer tdc,
Integer irep[],
double r[],
double ef[],
double tol,
Integer irdf,
NagError *fail) |
|
3 Description
In a completely randomized design the experimental material is divided into a number of units, or plots, to which a treatment can be applied. In a randomized block design the units are grouped into blocks so that the variation within blocks is less than the variation between blocks. If every treatment is applied to one plot in each block it is a complete block design. If there are fewer plots per block than treatments then the design will be an incomplete block design and may be balanced or partially balanced.
For a completely randomized design, with
treatments and
plots per treatment, the linear model is
where
is the
th observation for the
th treatment,
is the overall mean,
is the effect of the
th treatment and
is the random error term. For a randomized block design, with
treatments and
blocks of
plots, the linear model is
where
is the effect of the
th block and the
notation indicates that the
th treatment is applied to the
th plot in the
th block.
The completely randomized design gives rise to a one-way analysis of variance. The treatments do not have to be equally replicated, i.e., do not have to occur the same number of times. First the overall mean, , is computed and subtracted from the observations to give . The estimated treatment effects, are then computed as the treatment means of the mean adjusted observations, , and the treatment sum of squares can be computed from the sum of squares of the treatment totals of the divided by the number of observations per treatment total, . The final residuals are computed as , and, from the residuals, the residual sum of squares is calculated.
For the randomized block design the mean is computed and subtracted from the observations to give . The estimated block effects, ignoring treatment effects, , are then computed using the block means of the and the unadjusted sum of squares computed as the sum of squared block totals for the divided by number of plots per block, . The block adjusted observations are then computed as . In the case of the complete block design, with the same replication for each treatment within each block, the blocks and treatments are orthogonal, and so the treatment effects are estimated as the treatment means of the block adjusted observations, . The treatment sum of squares is computed as the sum of squared treatment totals of the divided by the number of replicates to the treatments, . Finally the residuals, and hence the residual sum of squares, are given by .
For a design without the same replication for each treatment within each block the treatments and the blocks will not be orthogonal, so the treatments adjusted for blocks need to be computed. The adjusted treatment effects are found as the solution to the equations
where
is the vector of the treatment totals for block adjusted observations,
,
is a diagonal matrix with
equal to the number of times the
th treatment is replicated, and
is the
by
incidence matrix, with
equal to the number of times treatment
occurs in block
. The solution to the equations can be written as
where
is a generalized inverse of
. The solution is found from the eigenvalue decomposition of
. The residuals are first calculated by subtracting the estimated treatment effects from the block adjusted observations to give
. However, since only the unadjusted block effects have been removed and blocks and treatments are not orthogonal, the block means of the
have to be subtracted to give the correct residuals,
and residual sum of squares.
The mean squares are computed as the sum of squares divided by the degrees of freedom. The degrees of freedom for the unadjusted blocks is
, for the completely randomized and the complete block designs the degrees of freedom for the treatments is
. In the general case the degrees of freedom for treatments is the rank of the matrix
. The
-statistic given by the ratio of the treatment mean square to the residual mean square tests the hypothesis
The standard errors for the difference in treatment effects, or treatment means, for the completely randomized or the complete block designs, are given by
where
is the residual mean square and
in the complete block design. In the general case the variances of the treatment effects are given by
from which the appropriate standard errors of the difference between treatment effects or the difference between adjusted means can be calculated.
In the complete block design all the information on the treatment effects is given by the within block analysis. In other designs there may be a loss of information due to the non-orthogonality of treatments and blocks. The efficiency of the within block analysis in these cases is given by the (canonical) efficiency factors, these are the nonzero eigenvalues of the matrix
, divided by the number of replicates in the case of equal replication, or by the mean of the number of replicates in the unequally replicated case, see
John (1987). If more than one eigenvalue is zero then the design is said to be disconnected and some treatments can only be compared using a between block analysis.
4 References
Cochran W G and Cox G M (1957) Experimental Designs Wiley
Davis O L (1978) The Design and Analysis of Industrial Experiments Longman
John J A (1987) Cyclic Designs Chapman and Hall
John J A and Quenouille M H (1977) Experiments: Design and Analysis Griffin
Searle S R (1971) Linear Models Wiley
5 Arguments
- 1:
n – IntegerInput
On entry: the number of observations, .
Constraints:
- ;
- if , n must be a multiple of iblock.
- 2:
y[n] – const doubleInput
-
On entry: the observations in the order as described by
blocks and
nt.
- 3:
blocks – Nag_BlocksInput
On entry:
blocks indicates the block structure.
- There are no blocks, i.e., it is a completely randomized design.
- The data should be input by blocks, i.e., y must contain the observations for block 1 followed by the observations for block 2, etc.
- The data is input in parallel with respect to blocks, i.e., must contain the first observation for block 1, must contain the first observation for block must contain the first observation for block iblock, must contain the second observation for block 1, etc.
Constraint:
, or .
- 4:
iblock – IntegerInput
-
On entry:
iblock indicates the number of blocks,
.
Constraint:
if or then ; it is not referenced otherwise.
- 5:
nt – IntegerInput
On entry: the number of treatments, . If only blocks are required in the analysis then set .
Constraints:
- if , ;
- otherwise .
- 6:
it[n] – const IntegerInput
-
On entry:
indicates which of the
nt treatments plot
received, for
. If
,
it is not referenced.
Constraint:
, for .
- 7:
gmean – double *Output
-
On exit: the grand mean, .
- 8:
bmean[] – doubleOutput
-
On exit: if or , contains the mean for the th block, for . It is not referenced otherwise.
- 9:
tmean[nt] – doubleOutput
-
On exit: if , contains the (adjusted) mean for the th treatment, , for , where is the mean of the treatment adjusted observations, .
- 10:
table[] – doubleOutput
-
Note: the th element of the matrix is stored in .
On exit: the analysis of variance table. Column 1 contains the degrees of freedom, column 2 the sum of squares, and where appropriate, column 3 the mean squares, column 4 the -statistic and column 5 the significance level of the -statistic. Row 1 is for Blocks, row 2 for Treatments, row 3 for Residual and row 4 for Total. Mean squares are computed for all but the Total row; -statistics and significance are computed for Treatments and Blocks, if present. Any unfilled cells are set to zero.
- 11:
c[] – doubleOutput
-
On exit: if
, the upper triangular part of
c contains the variance-covariance matrix of the treatment effects, the strictly lower triangular part contains the standard errors of the difference between two treatment effects (means), i.e.,
contains the covariance of treatment
and
if
and the standard error of the difference between treatment
and
if
for
and
.
- 12:
tdc – IntegerInput
-
On entry: the stride separating matrix column elements in the array
c.
Constraint:
.
- 13:
irep[nt] – IntegerOutput
-
On exit: if , the treatment replications, , for .
- 14:
r[n] – doubleOutput
-
On exit: the residuals, , for .
- 15:
ef[nt] – doubleOutput
-
On exit: if , the canonical efficiency factors.
- 16:
tol – doubleInput
-
On entry: the tolerance value used to check for zero eigenvalues of the matrix . If a default value of is used.
Constraint:
.
- 17:
irdf – IntegerInput
-
On entry: an adjustment to the degrees of freedom for the residual and total.
- The degrees of freedom for the total is set to and the residual degrees of freedom adjusted accordingly.
- The total degrees of freedom for the total is set to , as usual.
Constraint:
.
- 18:
fail – NagError *Input/Output
-
The NAG error argument (see
Section 3.6 in the Essential Introduction).
6 Error Indicators and Warnings
- NE_2_INT_ARG_LT
-
On entry, while . These arguments must satisfy .
- NE_ALLOC_FAIL
-
Dynamic memory allocation failed.
- NE_ARRAY_CONSTANT
-
On entry, the elements of the array
y are constant.
- NE_BAD_PARAM
-
On entry, argument
blocks had an illegal value.
- NE_G04BB_CONV
-
The eigenvalue computation has failed to converge.
This is an unlikely error exit.
- NE_G04BB_DESIGN
-
The design is disconnected; the standard errors may not be valid. The design may be nested.
- NE_G04BB_RES_DF
-
The residual degrees of freedom or the residual sum of squares are zero, columns 3, 4 and 5 of the analysis of variance table will not be computed and the matrix of standard errors and covariances, C, will not be scaled by or the square of .
- NE_G04BB_STDERR
-
A computed standard error is zero due to rounding errors.
This is an unlikely error exit.
- NE_G04BB_TREAT
-
The treatments are totally confounded with blocks, so the treatment sum of squares and degrees of freedom are zero. The analysis of variance table is not computed, except for block and total sums of squares and degrees of freedom.
- NE_INT
-
On entry, .
Constraint: when .
On entry, .
Constraint: when .
- NE_INT_2
-
On entry,
,
.
Constraint: when
,
n must be a multiple of
iblock.
- NE_INT_ARG_LT
-
On entry, .
Constraint: .
On entry, .
Constraint: .
On entry, .
Constraint: .
- NE_INTARR
-
On entry, .
Constraint: , for .
- NE_IT_ARRAY
-
No value of for some .
- NE_REAL_ARG_LT
-
On entry,
tol must not be less than 0.0:
.
7 Accuracy
The algorithm used by nag_anova_random (g04bbc), described in
Section 3, achieves greater accuracy than the traditional algorithms based on the subtraction of sums of squares.
8 Parallelism and Performance
Not applicable.
To estimate missing values the Healy and Westmacott procedure or its derivatives may be used, see
John and Quenouille (1977). This is an iterative procedure in which estimates of the missing values are adjusted by subtracting the corresponding values of the residuals. The new estimates are then used in the analysis of variance. This process is repeated until convergence. A suitable initial value may be the grand mean
. When using this procedure
irdf should be set to the number of missing values plus one to obtain the correct degrees of freedom for the residual sum of squares.
For designs such as Latin squares one more of the blocking factors has to be removed in a preliminary analysis before the final analysis using extra calls to nag_anova_random (g04bbc). The residuals from the preliminary analysis are then input to nag_anova_random (g04bbc). In these cases
irdf should be set to the difference between
n and the residual degrees of freedom from preliminary analysis. Care should be taken when using this approach as there is no check on the orthogonality of the two analyses.
For analysis of covariance the residuals are obtained from an analysis of variance of both the response variable and the covariates. The residuals from the response variable are then regressed on the residuals from the covariates using, say,
nag_regress_confid_interval (g02cbc) or
nag_regsn_mult_linear (g02dac). The results from those functions can be used to test for the significance of the covariates. To test the significance of the treatment effects after fitting the covariate, the residual sum of squares from the regression should be compared with the residual sum of squares obtained from the equivalent regression but using the residuals from fitting blocks only.
10 Example
The data, given by
John and Quenouille (1977), is for a balanced incomplete block design with 10 blocks and 6 treatments and with 3 plots per block. The observations are the degree of pain experienced and the treatments are penicillin of different potency. The data is input and the analysis of variance table and treatment means are printed.
10.1 Program Text
Program Text (g04bbce.c)
10.2 Program Data
Program Data (g04bbce.d)
10.3 Program Results
Program Results (g04bbce.r)