rms: nomogram – R documentation

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nomogram

Draw a Nomogram Representing a Regression Fit

Description

Draws a partial nomogram that can be used to manually obtain predicted values from a regression model that was fitted with rms. The nomogram does not have lines representing sums, but it has a reference line for reading scoring points (default range 0–100). Once the reader manually totals the points, the predicted values can be read at the bottom. Non-monotonic transformations of continuous variables are handled (scales wrap around), as are transformations which have flat sections (tick marks are labeled with ranges). If interactions are in the model, one variable is picked as the “axis variable”, and separate axes are constructed for each level of the interacting factors (preference is given automatically to using any discrete factors to construct separate axes) and levels of factors which are indirectly related to interacting factors (see DETAILS). Thus the nomogram is designed so that only one axis is actually read for each variable, since the variable combinations are disjoint. For categorical interacting factors, the default is to construct axes for all levels. The user may specify coordinates of each predictor to label on its axis, or use default values. If a factor interacts with other factors, settings for one or more of the interacting factors may be specified separately (this is mandatory for continuous variables). Optional confidence intervals will be drawn for individual scores as well as for the linear predictor. If more than one confidence level is chosen, multiple levels may be displayed using different colors or gray scales. Functions of the linear predictors may be added to the nomogram.

The datadist object that was in effect when the model was fit is used to specify the limits of the axis for continuous predictors when the user does not specify tick mark locations in the nomogram call.

print.nomogram prints axis information stored in an object returned by nomogram. This is useful in producing tables of point assignments by levels of predictors. It also prints how many linear predictor units there are per point and the number of points per unit change in the linear predictor.

legend.nomabbrev draws legends describing abbreviations used for labeling tick marks for levels of categorical predictors.

Usage

nomogram(fit, ..., adj.to, lp=TRUE, lp.at=NULL,
         fun=NULL, fun.at=NULL, fun.lp.at=NULL, funlabel="Predicted Value",
         interact=NULL, kint=NULL,  conf.int=FALSE, 
         conf.lp=c("representative", "all", "none"),
         est.all=TRUE, posterior.summary=c('mean', 'median', 'mode'),
         abbrev=FALSE, minlength=4, maxscale=100, nint=10, 
         vnames=c("labels","names"),
         varname.label=TRUE, varname.label.sep="=",
         omit=NULL, verbose=FALSE)

## S3 method for class 'nomogram'
print(x, dec=0, ...)

## S3 method for class 'nomogram'
plot(x, lplabel="Linear Predictor", fun.side,
 col.conf=c(1, 0.3),
 conf.space=c(.08,.2), label.every=1, force.label=FALSE, 
 xfrac=.35, cex.axis=.85, cex.var=1, col.grid=NULL,
 varname.label=TRUE, varname.label.sep="=", ia.space=.7, 
 tck=NA, tcl=-0.25, lmgp=.4, naxes,
 points.label='Points', total.points.label='Total Points',
 total.sep.page=FALSE, total.fun, cap.labels=FALSE, ...)

legend.nomabbrev(object, which, x, y, ncol=3, ...)

Arguments

`fit`	a regression model fit that was created with `rms`, and (usually) with `options(datadist = "object.name")` in effect.
`...`	settings of variables to use in constructing axes. If `datadist` was in effect, the default is to use `pretty(total range, nint)` for continuous variables, and the class levels for discrete ones. For `legend.nomabbrev`, `...` specifies optional parameters to pass to `legend`. Common ones are `bty = "n"` to suppress drawing the box. You may want to specify a non-proportionally spaced font (e.g., courier) number if abbreviations are more than one letter long. This will make the abbreviation definitions line up (e.g., specify `font = 2`, the default for courier). Ignored for `print` and `plot`.
`adj.to`	If you didn't define `datadist` for all predictors, you will have to define adjustment settings for the undefined ones, e.g. `adj.to= list(age = 50, sex = "female")`.
`lp`	Set to `FALSE` to suppress creation of an axis for scoring X beta.
`lp.at`	If `lp=TRUE`, `lp.at` may specify a vector of settings of X beta. Default is to use `pretty(range of linear predictors, nint)`.
`fun`	an optional function to transform the linear predictors, and to plot on another axis. If more than one transformation is plotted, put them in a list, e.g. `list(function(x) x/2, function(x) 2*x)`. Any function values equal to `NA` will be ignored.
`fun.at`	function values to label on axis. Default `fun` evaluated at `lp.at`. If more than one `fun` was specified, using a vector for `fun.at` will cause all functions to be evaluated at the same argument values. To use different values, specify a list of vectors for `fun.at`, with elements corresponding to the different functions (lists of vectors also applies to `fun.lp.at` and `fun.side`).
`fun.lp.at`	If you want to evaluate one of the functions at a different set of linear predictor values than may have been used in constructing the linear predictor axis, specify a vector or list of vectors of linear predictor values at which to evaluate the function. This is especially useful for discrete functions. The presence of this attribute also does away with the need for `nomogram` to compute numerical approximations of the inverse of the function. It also allows the user-supplied function to return `factor` objects, which is useful when e.g. a single tick mark position actually represents a range. If the `fun.lp.at` parameter is present, the `fun.at` vector for that function is ignored.
`funlabel`	label for `fun` axis. If more than one function was given but funlabel is of length one, it will be duplicated as needed. If `fun` is a list of functions for which you specified names (see the final example below), these names will be used as labels.
`interact`	When a continuous variable interacts with a discrete one, axes are constructed so that the continuous variable moves within the axis, and separate axes represent levels of interacting factors. For interactions between two continuous variables, all but the axis variable must have discrete levels defined in `interact`. For discrete interacting factors, you may specify levels to use in constructing the multiple axes. For continuous interacting factors, you must do this. Examples: `interact = list(age = seq(10,70,by=10), treat = c("A","B","D"))`.
`kint`	for models such as the ordinal models with multiple intercepts, specifies which one to use in evaluating the linear predictor. Default is to use `fit$interceptRef` if it exists, or 1.
`conf.int`	confidence levels to display for each scoring. Default is `FALSE` to display no confidence limits. Setting `conf.int` to `TRUE` is the same as setting it to `c(0.7, 0.9)`, with the line segment between the 0.7 and 0.9 levels shaded using gray scale.
`conf.lp`	default is `"representative"` to group all linear predictors evaluated into deciles, and to show, for the linear predictor confidence intervals, only the mean linear predictor within the deciles along with the median standard error within the deciles. Set `conf.lp = "none"` to suppress confidence limits for the linear predictors, and to `"all"` to show all confidence limits.
`est.all`	To plot axes for only the subset of variables named in `...`, set `est.all = FALSE`. Note: This option only works when zero has a special meaning for the variables that are omitted from the graph.
`posterior.summary`	when operating on a Bayesian model such as a result of `blrm` specifies whether to use posterior mean (default) vs. posterior mode/median of parameter values in constructing the nomogram
`abbrev`	Set to `TRUE` to use the `abbreviate` function to abbreviate levels of categorical factors, both for labeling tick marks and for axis titles. If you only want to abbreviate certain predictor variables, set `abbrev` to a vector of character strings containing their names.
`minlength`	applies if `abbrev = TRUE`. Is the minimum abbreviation length passed to the `abbreviate` function. If you set `minlength = 1`, the letters of the alphabet are used to label tick marks for categorical predictors, and all letters are drawn no matter how close together they are. For labeling axes (interaction settings), `minlength = 1` causes `minlength = 4` to be used.
`maxscale`	default maximum point score is 100
`nint`	number of intervals to label for axes representing continuous variables. See `pretty`.
`vnames`	By default, variable labels are used to label axes. Set `vnames = "names"` to instead use variable names.
`omit`	vector of character strings containing names of variables for which to suppress drawing axes. Default is to show all variables.
`verbose`	set to `TRUE` to get printed output detailing how tick marks are chosen and labeled for function axes. This is useful in seeing how certain linear predictor values cannot be solved for using inverse linear interpolation on the (requested linear predictor values, function values at these lp values). When this happens you will see `NA`s in the verbose output, and the corresponding tick marks will not appear in the nomogram.
`x`	an object created by `nomogram`, or the x coordinate for a legend
`dec`	number of digits to the right of the decimal point, for rounding point scores in `print.nomogram`. Default is to round to the nearest whole number of points.
`lplabel`	label for linear predictor axis. Default is `"Linear Predictor"`.
`fun.side`	a vector or list of vectors of `side` parameters for the `axis` function for labeling function values. Values may be 1 to position a tick mark label below the axis (the default), or 3 for above the axis. If for example an axis has 5 tick mark labels and the second and third will run into each other, specify `fun.side=c(1,1,3,1,1)` (assuming only one function is specified as `fun`).
`col.conf`	colors corresponding to `conf.int`.
`conf.space`	a 2-element vector with the vertical range within which to draw confidence bars, in units of 1=spacing between main bars. Four heights are used within this range (8 for the linear predictor if more than 16 unique values were evaluated), cycling them among separate confidence intervals to reduce overlapping.
`label.every`	Specify `label.every = i` to label on every `i`th tick mark.
`force.label`	set to `TRUE` to force every tick mark intended to be labeled to have a label plotted (whether the labels run into each other or not)
`xfrac`	fraction of horizontal plot to set aside for axis titles
`cex.axis`	character size for tick mark labels
`cex.var`	character size for axis titles (variable names)
`col.grid`	If left unspecified, no vertical reference lines are drawn. Specify a vector of length one (to use the same color for both minor and major reference lines) or two (corresponding to the color for the major and minor divisions, respectively) containing colors, to cause vertical reference lines to the top points scale to be drawn. For R, a good choice is `col.grid = gray(c(0.8, 0.95))`.
`varname.label`	In constructing axis titles for interactions, the default is to add `(interacting.varname = level)` on the right. Specify `varname.label = FALSE` to instead use `"(level)"`.
`varname.label.sep`	If `varname.label = TRUE`, you can change the separator to something other than `=` by specifying this parameter.
`ia.space`	When multiple axes are draw for levels of interacting factors, the default is to group combinations related to a main effect. This is done by spacing the axes for the second to last of these within a group only 0.7 (by default) of the way down as compared with normal space of 1 unit.
`tck`	see `tck` under `par`
`tcl`	length of tick marks in nomogram
`lmgp`	spacing between numeric axis labels and axis (see `par` for `mgp`)
`naxes`	maximum number of axes to allow on one plot. If the nomogram requires more than one “page”, the “Points” axis will be repeated at the top of each page when necessary.
`points.label`	a character string giving the axis label for the points scale
`total.points.label`	a character string giving the axis label for the total points scale
`total.sep.page`	set to `TRUE` to force the total points and later axes to be placed on a separate page
`total.fun`	a user-provided function that will be executed before the total points axis is drawn. Default is not to execute a function. This is useful e.g. when `total.sep.page = TRUE` and you wish to use `locator` to find the coordinates for positioning an abbreviation legend before it's too late and a new page is started (i.e., `total.fun = function() print(locator(1))`).
`cap.labels`	logical: should the factor labels have their first letter capitalized?
`object`	the result returned from `nomogram`
`which`	a character string giving the name of a variable for which to draw a legend with abbreviations of factor levels
`y`	y-coordinate to pass to the `legend` function. This is the upper left corner of the legend box. You can omit `y` if `x` is a list with named elements `x` and `y`. To use the mouse to locate the legend, specify `locator(1)` for `x`. For `print`, `x` is the result of `nomogram`.
`ncol`	the number of columns to form in drawing the legend.

Details

A variable is considered to be discrete if it is categorical or ordered or if datadist stored values for it (meaning it had <11 unique values). A variable is said to be indirectly related to another variable if the two are related by some interaction. For example, if a model has variables a, b, c, d, and the interactions are a:c and c:d, variable d is indirectly related to variable a. The complete list of variables related to a is c, d. If an axis is made for variable a, several axes will actually be drawn, one for each combination of c and d specified in interact.

Note that with a caliper, it is easy to continually add point scores for individual predictors, and then to place the caliper on the upper “Points” axis (with extrapolation if needed). Then transfer these points to the “Total Points” axis. In this way, points can be added without writing them down.

Confidence limits for an individual predictor score are really confidence limits for the entire linear predictor, with other predictors set to adjustment values. If lp = TRUE, all confidence bars for all linear predictor values evaluated are drawn. The extent to which multiple confidence bars of differing widths appear at the same linear predictor value means that precision depended on how the linear predictor was arrived at (e.g., a certain value may be realized from a setting of a certain predictor that was associated with a large standard error on the regression coefficients for that predictor).

On occasion, you may want to reverse the regression coefficients of a model to make the “points” scales reverse direction. For parametric survival models, which are stated in terms of increasing regression effects meaning longer survival (the opposite of a Cox model), just do something like fit$coefficients <- -fit$coefficients before invoking nomogram, and if you add function axes, negate the function arguments. For the Cox model, you also need to negate fit$center. If you omit lp.at, also negate fit$linear.predictors.

Value

a list of class "nomogram" that contains information used in plotting the axes. If you specified abbrev = TRUE, a list called abbrev is also returned that gives the abbreviations used for tick mark labels, if any. This list is useful for making legends and is used by legend.nomabbrev (see the last example). The returned list also has components called total.points, lp, and the function axis names. These components have components x (at argument vector given to axis), y (pos for axis), and x.real, the x-coordinates appearing on tick mark labels. An often useful result is stored in the list of data for each axis variable, namely the exact number of points that correspond to each tick mark on that variable's axis.

Author(s)

Frank Harrell
Department of Biostatistics
Vanderbilt University
fh@fharrell.com

References

Banks J: Nomograms. Encylopedia of Statistical Sciences, Vol 6. Editors: S Kotz and NL Johnson. New York: Wiley; 1985.

Lubsen J, Pool J, van der Does, E: A practical device for the application of a diagnostic or prognostic function. Meth. Inform. Med. 17:127–129; 1978.

Wikipedia: Nomogram, https://en.wikipedia.org/wiki/Nomogram.

Examples

n <- 1000    # define sample size
set.seed(17) # so can reproduce the results
d <- data.frame(age = rnorm(n, 50, 10),
                blood.pressure = rnorm(n, 120, 15),
                cholesterol = rnorm(n, 200, 25),
                sex = factor(sample(c('female','male'), n,TRUE)))

# Specify population model for log odds that Y=1
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
d <- upData(d,
  L = .4*(sex=='male') + .045*(age-50) +
       (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')),
  y = ifelse(runif(n) < plogis(L), 1, 0))

ddist <- datadist(d); options(datadist='ddist')


f <- lrm(y ~ lsp(age,50) + sex * rcs(cholesterol, 4) + blood.pressure,
         data=d)
nom <- nomogram(f, fun=function(x)1/(1+exp(-x)),  # or fun=plogis
    fun.at=c(.001,.01,.05,seq(.1,.9,by=.1),.95,.99,.999),
    funlabel="Risk of Death")
#Instead of fun.at, could have specified fun.lp.at=logit of
#sequence above - faster and slightly more accurate
plot(nom, xfrac=.45)
print(nom)
nom <- nomogram(f, age=seq(10,90,by=10))
plot(nom, xfrac=.45)
g <- lrm(y ~ sex + rcs(age, 3) * rcs(cholesterol, 3), data=d)
nom <- nomogram(g, interact=list(age=c(20,40,60)), 
                conf.int=c(.7,.9,.95))
plot(nom, col.conf=c(1,.5,.2), naxes=7)

w <- upData(d,
            cens = 15 * runif(n),
            h = .02 * exp(.04 * (age - 50) + .8 * (sex == 'Female')),
            d.time = -log(runif(n)) / h,
            death = ifelse(d.time <= cens, 1, 0),
            d.time = pmin(d.time, cens))


f <- psm(Surv(d.time,death) ~ sex * age, data=w, dist='lognormal')
med  <- Quantile(f)
surv <- Survival(f)  # This would also work if f was from cph
plot(nomogram(f, fun=function(x) med(lp=x), funlabel="Median Survival Time"))
nom <- nomogram(f, fun=list(function(x) surv(3, x),
                            function(x) surv(6, x)),
            funlabel=c("3-Month Survival Probability", 
                       "6-month Survival Probability"))
plot(nom, xfrac=.7)

## Not run: 
nom <- nomogram(fit.with.categorical.predictors, abbrev=TRUE, minlength=1)
nom$x1$points   # print points assigned to each level of x1 for its axis
#Add legend for abbreviations for category levels
abb <- attr(nom, 'info')$abbrev$treatment
legend(locator(1), abb$full, pch=paste(abb$abbrev,collapse=''), 
       ncol=2, bty='n')  # this only works for 1-letter abbreviations
#Or use the legend.nomabbrev function:
legend.nomabbrev(nom, 'treatment', locator(1), ncol=2, bty='n')

## End(Not run)


#Make a nomogram with axes predicting probabilities Y>=j for all j=1-3
#in an ordinal logistic model, where Y=0,1,2,3
w <- upData(w, Y = ifelse(y==0, 0, sample(1:3, length(y), TRUE)))
g <- lrm(Y ~ age+rcs(cholesterol,4) * sex, data=w)
fun2 <- function(x) plogis(x-g$coef[1]+g$coef[2])
fun3 <- function(x) plogis(x-g$coef[1]+g$coef[3])
f <- Newlabels(g, c(age='Age in Years'))  
#see Design.Misc, which also has Newlevels to change 
#labels for levels of categorical variables
g <- nomogram(f, fun=list('Prob Y>=1'=plogis, 'Prob Y>=2'=fun2, 
                     'Prob Y=3'=fun3), 
         fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99))
plot(g, lmgp=.2, cex.axis=.6)
options(datadist=NULL)

rms

Regression Modeling Strategies

v6.2-0

GPL (>= 2)

Authors

Frank E Harrell Jr <fh@fharrell.com>

Initial release

2021-03-17