dlnm (version 1.1.0)

dlnm-internal: Internal functions for package dlnm

Description

Generate the basis functions for the space of predictor and lags. These functions are built for internal use only.

Usage

mkbasis(var, type="ns", df=1, degree=1, knots=NULL, bound=range(var),
	int=FALSE, cen=TRUE, cenvalue=mean(var))

mklagbasis(maxlag=0, type="ns", df=1, degree=1, knots=NULL,
	bound=c(0, maxlag), int=TRUE)

Arguments

var

a numeric vector of ordered observations.

type

type of basis.

df

dimension of the basis. They depend on knots or degree if provided.

degree

degree of polynomial. Used only for type equal to "bs" of "poly".

knots

knots location for the basis.

bound

boundary knots. Used only for type equal to "ns" of "bs".

int

logical. If TRUE, an intercept is included in the basis.

cen

logical. If TRUE, the basis functions are centered.

cenvalue

centering value.

maxlag

maximum lag.

Value

• basis
  matrix of basis functions
• Additional values are returned that correspond to the arguments above, and explicitly give type, df, ddegree, knots, bound, int, varcen, cenvalue and maxlag related to the corresponding basis.

Details

These two internal functions are called by crossbasis to build the basis matrices for the two dimensions of predictor and lags. Even if they are not expected to be directly run by the users, they are included in the namespace of the package and therefore made accessible, with the intention to keep the process more transparent and give the opportunity to change or improve them. mkbasis applies a set basis functions on the vector of the predictor specified in var. mklagbasis calls mkbasis to build the basis matrix for the space of lags. Basically, it creates a new vector 0:maxlag (a vector of integers from 0 to the maximum lag allowed) and then apply the related basis functions. The functions for the 2 spaces are defined by the arguments above. See crossbasis for additional information.

References

Armstrong, B. Models for the relationship between ambient temperature and daily mortality. Epidemiology. 2006, 17(6):624-31.

Examples

# natural cubic spline with a knot at 3
basis.var <- mkbasis(1:5, knots=3)
basis.var

# quadratic spline selected by df, automatic knots location
mkbasis(1:5, type="bs", df=4, degree=2)

# linear centered at 4
mkbasis(1:5, type="lin", cenvalue=4)

# polynomial with degree 3, with intercept
mklagbasis(maxlag=5, type="poly", degree=3)

# integer
mklagbasis(maxlag=5, type="integer")

# threshold-type: double and single threshold or piecewise
mkbasis(1:5, type="dthr", knots=c(2,3))
mkbasis(1:5, type="hthr", knots=3)
mkbasis(1:5, type="hthr", knots=c(2,3))

# the intercept: strata defined by 2 cut-off points
mklagbasis(maxlag=10, type="strata", knots=c(4,7))
mklagbasis(maxlag=10, type="strata", knots=c(4,7), int=FALSE)

# centering: polynomial
mkbasis(0:10, type="poly", degree=3)
mkbasis(0:10, type="poly", degree=3, cen=FALSE)

### See the vignette 'dlnmOverview' for a detailed explanation of this example