Description
modelFunctions: This class of special functions constructs model terms with specific properties.
Usage
con(obj) lin(obj) pow(obj, p=1, offset=0) pol(obj, t=1, init=NA) leg(obj,t=1,init=NA) spl(obj, k=0, init=NA) dev(obj, init=NA) ma(obj) at(obj,lvls) and(obj, times=1) mbf(obj) grp(obj) dsum(model, levels=NULL, outer=FALSE) C(obj, contr)
Arguments
obj |
An object in the data frame.mbf – A component name from the asreml() mbf list argument.grp – A component name from the asreml() group list argument. |
p |
The exponent in a power function term (pow). |
offset |
Constant added to obj; default 0. |
t |
pol – The maximum degree of a set of orthogonal polynomials formed from obj. If negative, the intercept polynomial is omitted.leg – The maximum degree of a set of Legendre polynomials formed from obj. If negative, the intercept polynomial is omitted. |
k |
The number of equally spaced knot points for a cubic smoothing spline. If zero or omitted, k is set to asreml.options()$knots (default 50). |
init |
Optional initial value for the default identity variance model (idv) when used in the random formula. |
lvls |
Vector of levels of the conditioning factor (obj) that define the conditioning covariates formed by at. If numeric, lvls indexes the levels vector of obj; that is, levels(obj)[lvls]. |
times |
Multiples (may be non-integer) of the design matrix for obj are added to the preceding design matrix. |
model |
A formula of the form ~A+B+...|Z, where A and B define variance matrices for simple or compound model terms, and Z is a simple conditioning factor whose levels identify and determine the number of sub-matrices in the direct sum. The “|” operator is applied associatively and operates with all terms on its left; that is, A+B|C implies (A+B)|C and is equivalent to A|C+B|C. |
levels |
A list of length the number of terms in the left hand side of model that are separated by “+”. The components of levels are vectors of factor levels of Z. If there is only one term in the left hand side of model (or if the context allows, see examples) then levels may be a vector. If NULL, the default is to use levels(Z). |
outer |
If TRUE, independent blocks of correlated observations are modelled with common variance and correlation parameters; the blocks can be of different sizes. |
contr |
An integer vector of contrast coefficients parallel to levels(obj). |
Functions
asr_con |
Sum to zero constraints. |
asr_lin: |
Create a variate from obj. |
asr_pow: |
Creates the model term (obj+offset)p. |
asr_pol: |
Orthogonal polynomials. |
asr_leg: |
Legendre polynomials. |
asr_spl: |
Cubic smoothing spline, random component. |
asr_dev: |
Spline deviations; create a factor from the variate obj. |
asr_ma: |
Construct a term with a moving-average order 1 design matrix from obj. |
asr_at: |
Form a conditioning covariable from obj for each level of obj specified in the lvls argument. |
asr_and: |
Multiply the design matrix for obj by times and add it to the preceding design matrix. |
asr_mbf: |
Create a model term from covariates not stored in data. |
asr_grp: |
Create a model term from covariates held in columns of data. |
asr_dsum: |
Direct sum structures for residual models. |
asr_C: |
Treatment contrasts. |
Examples
## Not run: ## separable autoregressive residual model at each level of Site residual = ~ dsum(~ ar1(Column):ar1(Row) | Site) ## different residual models at different levels of site residual = ~ dsum(~ ar1(Column):ar1(Row) + id(Column):ar1(Row) | Site, levels = list(c(1,3), c(2,4))) ## equivalent residual = ~ dsum(~ ar1(Column):ar1(Row) | Site, levels=c(1,3)) + dsum(~ id(Column):ar1(Row) | Site, levels=c(2,4)) ## "biological" Date within Plot residual = ~ dsum(~ ar1(Date) | Plot, outer=TRUE) ## "explicit" times residual = ~ dsum(~ exp(Date) | Plot, outer=TRUE) ## End(Not run)