rms.trans: rms Special Transformation Functions

Description

This is a series of functions (asis, pol, lsp, rcs, catg, scored, strat, matrx, and %ia%) that set up special attributes (such as knots and nonlinear term indicators) that are carried through to fits (using for example lrm,cph, ols, psm). anova.rms, summary.rms, Predict, survplot, fastbw, validate, specs, which.influence, nomogram and latex.rms use these attributes to automate certain analyses (e.g., automatic tests of linearity for each predictor are done by anova.rms). Many of the functions are called implicitly. Some S functions such as ns derive data-dependent transformations that are not "remembered" when predicted values are later computed, so the predictions will be incorrect. The functions listed here solve that problem.

asis is the identity transformation, pol is an ordinary (non-orthogonal) polynomial, rcs is a linear tail-restricted cubic spline function (natural spline, for which the rcspline.eval function generates the design matrix and the presence of system option rcspc causes rcspline.eval to be invoked with pc=TRUE), catg is for a categorical variable, scored is for an ordered categorical variable, strat is for a stratification factor in a Cox model, matrx is for a matrix predictor, and %ia% represents restricted interactions in which products involving nonlinear effects on both variables are not included in the model. asis, catg, scored, matrx are seldom invoked explicitly by the user (only to specify label or name, usually).

In the list below, functions asis through strat can have arguments x, parms, label, name except that parms does not apply to asis, matrx, strat.

Usage

asis(x, parms, label, name)
matrx(x, label, name)
pol(x, parms, label, name)
lsp(x, parms, label, name)
rcs(x, parms, label, name)
catg(x, parms, label, name)
scored(x, parms, label, name)
strat(x, label, name)
x1 %ia% x2

Arguments

a predictor variable (or a function of one). If you specify e.g. pol(pmin(age,10),3), a cubic polynomial will be fitted in pmin(age,10) (pmin is the S vector element--by--element function). The predictor will be lab

parms

parameters of transformation (e.g. number or location of knots). For pol the argument is the order of the polynomial, e.g. 2 for quadratic (the usual default). For lsp it is a vector of knot locations (lsp

label

label of predictor for plotting (default = "label" attribute or variable name)

name

Name to use for predictor in model. Default is name of argument to function

two continuous variables for which to form a non-doubly-nonlinear interaction

...

a variety of things

synopsis

asis(...) matrx(...) pol(...) lsp(...) rcs(...) catg(...) scored(...) strat(...) %ia%(x1, x2)

concept

logistic regression model
transformation

Examples

Run this code

options(knots=4, poly.degree=2)
country <- factor(country.codes)
blood.pressure <- cbind(sbp=systolic.bp, dbp=diastolic.bp)
fit <- lrm(Y ~ sqrt(x1)*rcs(x2) + rcs(x3,c(5,10,15)) + 
       lsp(x4,c(10,20)) + country + blood.pressure + poly(age,2))
# sqrt(x1) is an implicit asis variable, but limits of x1, not sqrt(x1)
#       are used for later plotting and effect estimation
# x2 fitted with restricted cubic spline with 4 default knots
# x3 fitted with r.c.s. with 3 specified knots
# x4 fitted with linear spline with 2 specified knots
# country is an implied catg variable
# blood.pressure is an implied matrx variable
# since poly is not an rms function (pol is), it creates a
#       matrx type variable with no automatic linearity testing
#       or plotting
f1 <- lrm(y ~ rcs(x1) + rcs(x2) + rcs(x1) %ia% rcs(x2))
# %ia% restricts interactions. Here it removes terms nonlinear in
# both x1 and x2
f2 <- lrm(y ~ rcs(x1) + rcs(x2) + x1 %ia% rcs(x2))
# interaction linear in x1
f3 <- lrm(y ~ rcs(x1) + rcs(x2) + x1 %ia% x2)
# simple product interaction (doubly linear)
# Use x1 %ia% x2 instead of x1:x2 because x1 %ia% x2 triggers
# anova to pool x1*x2 term into x1 terms to test total effect
# of x1

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