Construct BayesX Model Terms in A Formula
Description
Function sx
is a model term constructor function for terms used within the formula
argument of function bayesx
. The function does not evaluate matrices etc., the
behavior is similar to function s
from package mgcv
. It
purely exists to build a basic setup for the model term which can be processed by function
bayesx.construct
.
Usage
1 
Arguments
x 
the covariate the model term is a function of. 
z 
a second covariate. 
bs 
a 
by 
a 
... 
special controlling arguments or objects used for the model term, see also
the examples and function 
Details
The following term types may be specified using argument bs
:

"rw1"
,"rw2"
: Zero degree Psplines: Defines a zero degree Pspline with first or second order difference penalty. A zero degree Pspline typically estimates for every distinct covariate value in the dataset a separate parameter. Usually there is no reason to prefer zero degree Psplines over higher order Psplines. An exception are ordinal covariates or continuous covariates with only a small number of different values. For ordinal covariates higher order Psplines are not meaningful while zero degree Psplines might be an alternative to modeling nonlinear relationships via a dummy approach with completely unrestricted regression parameters. 
"season"
: Seasonal effect of a time scale. 
"ps"
,"psplinerw1"
,"psplinerw2"
: Pspline with first or second order difference penalty. 
"te"
,"pspline2dimrw1"
: Defines a twodimensional Pspline based on the tensor product of onedimensional Psplines with a twodimensional first order random walk penalty for the parameters of the spline. 
"kr"
,"kriging"
: Kriging with stationary Gaussian random fields. 
"gk"
,"geokriging"
: Geokriging with stationary Gaussian random fields: Estimation is based on the centroids of a map object provided in boundary format (see functionread.bnd
andshp2bnd
) as an additional argument namedmap
within functionsx
, or supplied within argumentxt
when using functions
, e.g.,xt = list(map = MapBnd)
. 
"gs"
,"geospline"
: Geosplines based on twodimensional Psplines with a twodimensional first order random walk penalty for the parameters of the spline. Estimation is based on the coordinates of the centroids of the regions of a map object provided in boundary format (see functionread.bnd
andshp2bnd
) as an additional argument namedmap
(see above). 
"mrf"
,"spatial"
: Markov random fields: Defines a Markov random field prior for a spatial covariate, where geographical information is provided by a map object in boundary or graph file format (see functionread.bnd
,read.gra
andshp2bnd
), as an additional argument namedmap
(see above). 
"bl"
,"baseline"
: Nonlinear baseline effect in hazard regression or multistate models: Defines a Pspline with second order random walk penalty for the parameters of the spline for the logbaseline effect log(λ(time)). 
"factor"
: Special BayesX specifier for factors, especially meaningful ifmethod = "STEP"
, since the factor term is then treated as a full term, which is either included or removed from the model. 
"ridge"
,"lasso"
,"nigmix"
: Shrinkage of fixed effects: defines a shrinkageprior for the corresponding parameters γ_j, j = 1, …, q, q ≥q 1 of the linear effects x_1, …, x_q. There are three priors possible: ridge, lasso and Normal Mixture of inverse Gamma prior. 
"re"
: Gaussian i.i.d. Random effects of a unit or cluster identification covariate.
Value
A list
of class "xx.smooth.spec"
, where "xx"
is a basis/type identifying code
given by the bs
argument of f
.
Note
Some care has to be taken with the identifiability of varying coefficients terms. The standard in
BayesX is to center nonlinear main effects terms around zero whereas varying coefficient terms are
not centered. This makes sense since main effects nonlinear terms are not identifiable and varying
coefficients terms are usually identifiable. However, there are situations where a varying
coefficients term is not identifiable. Then the term must be centered. Since centering is not
automatically accomplished it has to be enforced by the user by adding option
center = TRUE
in function f
. To give an example, the varying coefficient terms in
η = … + g_1(z_1)z + g_2(z_2)z + γ_0 + γ_1 z + … are not
identified, whereas in η = … + g_1(z_1)z + γ_0 + …, the varying
coefficient term is identifiable. In the first case, centering is necessary, in the second case,
it is not.
Author(s)
Nikolaus Umlauf, Thomas Kneib, Stefan Lang, Achim Zeileis.
See Also
bayesx
, bayesx.term.options
, s
,
bayesx.construct
.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148  ## funktion sx() returns a list
## which is then processed by function
## bayesx.construct to build the
## BayesX model term structure
sx(x)
bayesx.construct(sx(x))
bayesx.construct(sx(x, bs = "rw1"))
bayesx.construct(sx(x, bs = "factor"))
bayesx.construct(sx(x, bs = "offset"))
bayesx.construct(sx(x, z, bs = "te"))
## varying coefficients
bayesx.construct(sx(x1, by = x2))
bayesx.construct(sx(x1, by = x2, center = TRUE))
## using a map for markov random fields
data("FantasyBnd")
plot(FantasyBnd)
bayesx.construct(sx(id, bs = "mrf", map = FantasyBnd))
## random effects
bayesx.construct(sx(id, bs = "re"))
## examples using optional controlling
## parameters and objects
bayesx.construct(sx(x, bs = "ps", knots = 20))
bayesx.construct(sx(x, bs = "ps", nrknots = 20))
bayesx.construct(sx(x, bs = "ps", knots = 20, nocenter = TRUE))
## use of bs with original
## BayesX syntax
bayesx.construct(sx(x, bs = "psplinerw1"))
bayesx.construct(sx(x, bs = "psplinerw2"))
bayesx.construct(sx(x, z, bs = "pspline2dimrw2"))
bayesx.construct(sx(id, bs = "spatial", map = FantasyBnd))
bayesx.construct(sx(x, z, bs = "kriging"))
bayesx.construct(sx(id, bs = "geospline", map = FantasyBnd, nrknots = 5))
bayesx.construct(sx(x, bs = "catspecific"))
## Not run:
## generate some data
set.seed(111)
n < 200
## regressor
dat < data.frame(x = runif(n, 3, 3))
## response
dat$y < with(dat, 1.5 + sin(x) + rnorm(n, sd = 0.6))
## estimate models with
## bayesx REML and MCMC
b1 < bayesx(y ~ sx(x), method = "REML", data = dat)
## increase inner knots
## decrease degree of the Pspline
b2 < bayesx(y ~ sx(x, knots = 30, degree = 2), method = "REML", data = dat)
## compare reported output
summary(c(b1, b2))
## plot the effect for both models
plot(c(b1, b2), residuals = TRUE)
## more examples
set.seed(111)
n < 500
## regressors
dat < data.frame(x = runif(n, 3, 3), z = runif(n, 3, 3),
w = runif(n, 0, 6), fac = factor(rep(1:10, n/10)))
## response
dat$y < with(dat, 1.5 + sin(x) + cos(z) * sin(w) +
c(2.67, 5, 6, 3, 4, 2, 6, 7, 9, 7.5)[fac] + rnorm(n, sd = 0.6))
## estimate model
b < bayesx(y ~ sx(x) + sx(z, w, bs = "te") + fac,
data = dat, method = "MCMC")
summary(b)
plot(b)
## now a mrf example
## note: the regional identification
## covariate and the map regionnames
## should be coded as integer
set.seed(333)
## simulate some geographical data
data("MunichBnd")
N < length(MunichBnd); n < N*5
names(MunichBnd) < 1:N
## regressors
dat < data.frame(x1 = runif(n, 3, 3),
id = as.factor(rep(names(MunichBnd), length.out = n)))
dat$sp < with(dat, sort(runif(N, 2, 2), decreasing = TRUE)[id])
## response
dat$y < with(dat, 1.5 + sin(x1) + sp + rnorm(n, sd = 1.2))
## estimate models with
## bayesx MCMC and REML
b < bayesx(y ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd),
method = "REML", data = dat)
## summary statistics
summary(b)
## plot the effects
op < par(no.readonly = TRUE)
par(mfrow = c(1,2))
plot(b, term = "sx(id)", map = MunichBnd,
main = "bayesx() estimate")
plotmap(MunichBnd, x = dat$sp, id = dat$id,
main = "Truth")
par(op)
## model with random effects
set.seed(333)
N < 30
n < N*10
## regressors
dat < data.frame(id = sort(rep(1:N, n/N)), x1 = runif(n, 3, 3))
dat$re < with(dat, rnorm(N, sd = 0.6)[id])
## response
dat$y < with(dat, 1.5 + sin(x1) + re + rnorm(n, sd = 0.6))
## estimate model
b < bayesx(y ~ sx(x1, bs = "psplinerw1") + sx(id, bs = "re"), data = dat)
summary(b)
plot(b)
## extract estimated random effects
## and compare with true effects
plot(fitted(b, term = "sx(id)")$Mean ~ unique(dat$re))
## End(Not run)
