comparisons: Comparisons Between Predictions Made With Different Regressor...
In marginaleffects: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests
comparisons R Documentation
Comparisons Between Predictions Made With Different Regressor Values
Description
Predict the outcome variable at different regressor values (e.g., college
graduates vs. others), and compare those predictions by computing a difference,
ratio, or some other function. comparisons() can return many quantities of
interest, such as contrasts, differences, risk ratios, changes in log odds, lift,
slopes, elasticities, etc.
-
comparisons(): unit-level (conditional) estimates.
-
avg_comparisons(): average (marginal) estimates.
variables identifies the focal regressors whose "effect" we are interested in. comparison determines how predictions with different regressor values are compared (difference, ratio, odds, etc.). The newdata argument and the datagrid() function control where statistics are evaluated in the predictor space: "at observed values", "at the mean", "at representative values", etc.
See the comparisons vignette and package website for worked examples and case studies:
Usage
comparisons(
model,
newdata = NULL,
variables = NULL,
comparison = "difference",
type = NULL,
vcov = TRUE,
by = FALSE,
conf_level = 0.95,
transform = NULL,
cross = FALSE,
wts = FALSE,
hypothesis = NULL,
equivalence = NULL,
p_adjust = NULL,
df = Inf,
eps = NULL,
numderiv = "fdforward",
...
)
avg_comparisons(
model,
newdata = NULL,
variables = NULL,
type = NULL,
vcov = TRUE,
by = TRUE,
conf_level = 0.95,
comparison = "difference",
transform = NULL,
cross = FALSE,
wts = FALSE,
hypothesis = NULL,
equivalence = NULL,
p_adjust = NULL,
df = Inf,
eps = NULL,
numderiv = "fdforward",
...
)
Arguments
model
Model object
newdata
Grid of predictor values at which we evaluate the comparisons.
Warning: Avoid modifying your dataset between fitting the model and calling a marginaleffects function. This can sometimes lead to unexpected results.
-
NULL (default): Unit-level contrasts for each observed value in the dataset (empirical distribution). The dataset is retrieved using insight::get_data(), which tries to extract data from the environment. This may produce unexpected results if the original data frame has been altered since fitting the model.
data frame: Unit-level contrasts for each row of the newdata data frame.
string:
"mean": Contrasts at the Mean. Contrasts when each predictor is held at its mean or mode.
"median": Contrasts at the Median. Contrasts when each predictor is held at its median or mode.
"balanced": Contrasts evaluated on a balanced grid with every combination of categories and numeric variables held at their means.
"tukey": Contrasts at Tukey's 5 numbers.
"grid": Contrasts on a grid of representative numbers (Tukey's 5 numbers and unique values of categorical predictors).
-
datagrid() call to specify a custom grid of regressors. For example:
-
newdata = datagrid(cyl = c(4, 6)): cyl variable equal to 4 and 6 and other regressors fixed at their means or modes.
-
newdata = datagrid(mpg = fivenum): mpg variable held at Tukey's five numbers (using the fivenum function), and other regressors fixed at their means or modes.
See the Examples section and the datagrid documentation.
-
subset() call with a single argument to select a subset of the dataset used to fit the model, ex: newdata = subset(treatment == 1)
-
dplyr::filter() call with a single argument to select a subset of the dataset used to fit the model, ex: newdata = filter(treatment == 1)
variables
Focal variables
-
NULL: compute comparisons for all the variables in the model object (can be slow).
Character vector: subset of variables (usually faster).
Named list: names identify the subset of variables of interest, and values define the type of contrast to compute. Acceptable values depend on the variable type:
Factor or character variables:
"reference": Each factor level is compared to the factor reference (base) level
"all": All combinations of observed levels
"sequential": Each factor level is compared to the previous factor level
"pairwise": Each factor level is compared to all other levels
"minmax": The highest and lowest levels of a factor.
"revpairwise", "revreference", "revsequential": inverse of the corresponding hypotheses.
Vector of length 2 with the two values to compare.
Data frame with the same number of rows as newdata, with two columns of "lo" and "hi" values to compare.
Function that accepts a vector and returns a data frame with two columns of "lo" and "hi" values to compare. See examples below.
Logical variables:
NULL: contrast between TRUE and FALSE
Data frame with the same number of rows as newdata, with two columns of "lo" and "hi" values to compare.
Function that accepts a vector and returns a data frame with two columns of "lo" and "hi" values to compare. See examples below.
Numeric variables:
Numeric of length 1: Forward contrast for a gap of x, computed between the observed value and the observed value plus x. Users can set a global option to get a "center" or "backward" contrast instead: options(marginaleffects_contrast_direction="center")
Numeric vector of length 2: Contrast between the largest and the smallest elements of the x vector.
Data frame with the same number of rows as newdata, with two columns of "lo" and "hi" values to compare.
Function that accepts a vector and returns a data frame with two columns of "lo" and "hi" values to compare. See examples below.
"iqr": Contrast across the interquartile range of the regressor.
"sd": Contrast across one standard deviation around the regressor mean.
"2sd": Contrast across two standard deviations around the regressor mean.
"minmax": Contrast between the maximum and the minimum values of the regressor.
Examples:
-
variables = list(gear = "pairwise", hp = 10)
-
variables = list(gear = "sequential", hp = c(100, 120))
-
variables = list(hp = \(x) data.frame(low = x - 5, high = x + 10))
See the Examples section below for more.
comparison
How should pairs of predictions be compared? Difference, ratio, odds ratio, or user-defined functions.
string: shortcuts to common contrast functions.
Supported shortcuts strings: difference, differenceavg, differenceavgwts, dydx, eyex, eydx, dyex, dydxavg, eyexavg, eydxavg, dyexavg, dydxavgwts, eyexavgwts, eydxavgwts, dyexavgwts, ratio, ratioavg, ratioavgwts, lnratio, lnratioavg, lnratioavgwts, lnor, lnoravg, lnoravgwts, lift, liftavg, liftavgwts, expdydx, expdydxavg, expdydxavgwts
See the Comparisons section below for definitions of each transformation.
function: accept two equal-length numeric vectors of adjusted predictions (hi and lo) and returns a vector of contrasts of the same length, or a unique numeric value.
See the Transformations section below for examples of valid functions.
type
string indicates the type (scale) of the predictions used to
compute contrasts or slopes. This can differ based on the model
type, but will typically be a string such as: "response", "link", "probs",
or "zero". When an unsupported string is entered, the model-specific list of
acceptable values is returned in an error message. When type is NULL, the
first entry in the error message is used by default.
vcov
Type of uncertainty estimates to report (e.g., for robust standard errors). Acceptable values:
FALSE: Do not compute standard errors. This can speed up computation considerably.
TRUE: Unit-level standard errors using the default vcov(model) variance-covariance matrix.
String which indicates the kind of uncertainty estimates to return.
Heteroskedasticity-consistent: "HC", "HC0", "HC1", "HC2", "HC3", "HC4", "HC4m", "HC5". See ?sandwich::vcovHC
Heteroskedasticity and autocorrelation consistent: "HAC"
Mixed-Models degrees of freedom: "satterthwaite", "kenward-roger"
Other: "NeweyWest", "KernHAC", "OPG". See the sandwich package documentation.
One-sided formula which indicates the name of cluster variables (e.g., ~unit_id). This formula is passed to the cluster argument of the sandwich::vcovCL function.
Square covariance matrix
Function which returns a covariance matrix (e.g., stats::vcov(model))
by
Aggregate unit-level estimates (aka, marginalize, average over). Valid inputs:
-
FALSE: return the original unit-level estimates.
-
TRUE: aggregate estimates for each term.
Character vector of column names in newdata or in the data frame produced by calling the function without the by argument.
Data frame with a by column of group labels, and merging columns shared by newdata or the data frame produced by calling the same function without the by argument.
See examples below.
For more complex aggregations, you can use the FUN argument of the hypotheses() function. See that function's documentation and the Hypothesis Test vignettes on the marginaleffects website.
conf_level
numeric value between 0 and 1. Confidence level to use to build a confidence interval.
transform
string or function. Transformation applied to unit-level estimates and confidence intervals just before the function returns results. Functions must accept a vector and return a vector of the same length. Support string shortcuts: "exp", "ln"
cross
-
FALSE: Contrasts represent the change in adjusted predictions when one predictor changes and all other variables are held constant.
-
TRUE: Contrasts represent the changes in adjusted predictions when all the predictors specified in the variables argument are manipulated simultaneously (a "cross-contrast").
wts
logical, string or numeric: weights to use when computing average predictions, contrasts or slopes. These weights only affect the averaging in avg_*() or with the by argument, and not unit-level estimates. See ?weighted.mean
string: column name of the weights variable in newdata. When supplying a column name to wts, it is recommended to supply the original data (including the weights variable) explicitly to newdata.
numeric: vector of length equal to the number of rows in the original data or in newdata (if supplied).
FALSE: Equal weights.
TRUE: Extract weights from the fitted object with insight::find_weights() and use them when taking weighted averages of estimates. Warning: newdata=datagrid() returns a single average weight, which is equivalent to using wts=FALSE
hypothesis
specify a hypothesis test or custom contrast using a numeric value, vector, or matrix; a string equation; string; a formula, or a function.
Numeric:
Single value: the null hypothesis used in the computation of Z and p (before applying transform).
Vector: Weights to compute a linear combination of (custom contrast between) estimates. Length equal to the number of rows generated by the same function call, but without the hypothesis argument.
Matrix: Each column is a vector of weights, as describe above, used to compute a distinct linear combination of (contrast between) estimates. The column names of the matrix are used as labels in the output.
String equation to specify linear or non-linear hypothesis tests. If the term column uniquely identifies rows, terms can be used in the formula. Otherwise, use b1, b2, etc. to identify the position of each parameter. The b* wildcard can be used to test hypotheses on all estimates. If a named vector is used, the names are used as labels in the output. Examples:
-
hp = drat
-
hp + drat = 12
-
b1 + b2 + b3 = 0
-
b* / b1 = 1
String:
"pairwise": pairwise differences between estimates in each row.
"reference": differences between the estimates in each row and the estimate in the first row.
"sequential": difference between an estimate and the estimate in the next row.
"meandev": difference between an estimate and the mean of all estimates.
"meanotherdev": difference between an estimate and the mean of all other estimates, excluding the current one.
"revpairwise", "revreference", "revsequential": inverse of the corresponding hypotheses, as described above.
Formula:
-
comparison ~ pairs | group
Left-hand side determines the type of comparison to conduct: difference or ratio. If the left-hand side is empty, difference is chosen.
Right-hand side determines the pairs of estimates to compare: reference, sequential, or meandev
Optional: Users can supply grouping variables after a vertical bar to conduct comparisons withing subsets.
Examples:
-
~ reference
-
ratio ~ pairwise
-
difference ~ pairwise | groupid
Function:
Accepts an argument x: object produced by a marginaleffects function or a data frame with column rowid and estimate
Returns a data frame with columns term and estimate (mandatory) and rowid (optional).
The function can also accept optional input arguments: newdata, by, draws.
This function approach will not work for Bayesian models or with bootstrapping. In those cases, it is easy to use posterior_draws() to extract and manipulate the draws directly.
See the Examples section below and the vignette: https://marginaleffects.com/vignettes/hypothesis.html
equivalence
Numeric vector of length 2: bounds used for the two-one-sided test (TOST) of equivalence, and for the non-inferiority and non-superiority tests. See Details section below.
p_adjust
Adjust p-values for multiple comparisons: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", or "fdr". See stats::p.adjust
df
Degrees of freedom used to compute p values and confidence intervals. A single numeric value between 1 and Inf. When df is Inf, the normal distribution is used. When df is finite, the t distribution is used. See insight::get_df for a convenient function to extract degrees of freedom. Ex: slopes(model, df = insight::get_df(model))
eps
NULL or numeric value which determines the step size to use when
calculating numerical derivatives: (f(x+eps)-f(x))/eps. When eps is
NULL, the step size is 0.0001 multiplied by the difference between
the maximum and minimum values of the variable with respect to which we
are taking the derivative. Changing eps may be necessary to avoid
numerical problems in certain models.
numderiv
string or list of strings indicating the method to use to for the numeric differentiation used in to compute delta method standard errors.
"fdforward": finite difference method with forward differences
"fdcenter": finite difference method with central differences (default)
"richardson": Richardson extrapolation method
Extra arguments can be specified by passing a list to the numDeriv argument, with the name of the method first and named arguments following, ex: numderiv=list("fdcenter", eps = 1e-5). When an unknown argument is used, marginaleffects prints the list of valid arguments for each method.
...
Additional arguments are passed to the predict() method
supplied by the modeling package.These arguments are particularly useful
for mixed-effects or bayesian models (see the online vignettes on the
marginaleffects website). Available arguments can vary from model to
model, depending on the range of supported arguments by each modeling
package. See the "Model-Specific Arguments" section of the
?slopes documentation for a non-exhaustive list of available
arguments.
Value
A data.frame with one row per observation (per term/group) and several columns:
-
rowid: row number of the newdata data frame
-
type: prediction type, as defined by the type argument
-
group: (optional) value of the grouped outcome (e.g., categorical outcome models)
-
term: the variable whose marginal effect is computed
-
dydx: slope of the outcome with respect to the term, for a given combination of predictor values
-
std.error: standard errors computed by via the delta method.
-
p.value: p value associated to the estimate column. The null is determined by the hypothesis argument (0 by default), and p values are computed before applying the transform argument.
-
s.value: Shannon information transforms of p values. How many consecutive "heads" tosses would provide the same amount of evidence (or "surprise") against the null hypothesis that the coin is fair? The purpose of S is to calibrate the analyst's intuition about the strength of evidence encoded in p against a well-known physical phenomenon. See Greenland (2019) and Cole et al. (2020).
-
conf.low: lower bound of the confidence interval (or equal-tailed interval for bayesian models)
-
conf.high: upper bound of the confidence interval (or equal-tailed interval for bayesian models)
See ?print.marginaleffects for printing options.
Functions
-
avg_comparisons(): Average comparisons
Standard errors using the delta method
Standard errors for all quantities estimated by marginaleffects can be obtained via the delta method. This requires differentiating a function with respect to the coefficients in the model using a finite difference approach. In some models, the delta method standard errors can be sensitive to various aspects of the numeric differentiation strategy, including the step size. By default, the step size is set to 1e-8, or to 1e-4 times the smallest absolute model coefficient, whichever is largest.
marginaleffects can delegate numeric differentiation to the numDeriv package, which allows more flexibility. To do this, users can pass arguments to the numDeriv::jacobian function through a global option. For example:
-
options(marginaleffects_numDeriv = list(method = "simple", method.args = list(eps = 1e-6)))
-
options(marginaleffects_numDeriv = list(method = "Richardson", method.args = list(eps = 1e-5)))
-
options(marginaleffects_numDeriv = NULL)
See the "Standard Errors and Confidence Intervals" vignette on the marginaleffects website for more details on the computation of standard errors:
https://marginaleffects.com/vignettes/uncertainty.html
Note that the inferences() function can be used to compute uncertainty estimates using a bootstrap or simulation-based inference. See the vignette:
https://marginaleffects.com/vignettes/bootstrap.html
Model-Specific Arguments
Some model types allow model-specific arguments to modify the nature of
marginal effects, predictions, marginal means, and contrasts. Please report
other package-specific predict() arguments on Github so we can add them to
the table below.
https://github.com/vincentarelbundock/marginaleffects/issues
Package Class Argument Documentation
brms brmsfit ndraws brms::posterior_predict
re_formula brms::posterior_predict
lme4 merMod re.form lme4::predict.merMod
allow.new.levels lme4::predict.merMod
glmmTMB glmmTMB re.form glmmTMB::predict.glmmTMB
allow.new.levels glmmTMB::predict.glmmTMB
zitype glmmTMB::predict.glmmTMB
mgcv bam exclude mgcv::predict.bam
gam exclude mgcv::predict.gam
robustlmm rlmerMod re.form robustlmm::predict.rlmerMod
allow.new.levels robustlmm::predict.rlmerMod
MCMCglmm MCMCglmm ndraws
sampleSelection selection part sampleSelection::predict.selection
comparison argument functions
The following transformations can be applied by supplying one of the shortcut strings to the
comparison argument.
hi is a vector of adjusted predictions for the "high" side of the
contrast. lo is a vector of adjusted predictions for the "low" side of the
contrast. y is a vector of adjusted predictions for the original data. x
is the predictor in the original data. eps is the step size to use to
compute derivatives and elasticities.
Shortcut Function
difference \(hi, lo) hi - lo
differenceavg \(hi, lo) mean(hi - lo)
dydx \(hi, lo, eps) (hi - lo)/eps
eyex \(hi, lo, eps, y, x) (hi - lo)/eps * (x/y)
eydx \(hi, lo, eps, y, x) ((hi - lo)/eps)/y
dyex \(hi, lo, eps, x) ((hi - lo)/eps) * x
dydxavg \(hi, lo, eps) mean((hi - lo)/eps)
eyexavg \(hi, lo, eps, y, x) mean((hi - lo)/eps * (x/y))
eydxavg \(hi, lo, eps, y, x) mean(((hi - lo)/eps)/y)
dyexavg \(hi, lo, eps, x) mean(((hi - lo)/eps) * x)
ratio \(hi, lo) hi/lo
ratioavg \(hi, lo) mean(hi)/mean(lo)
lnratio \(hi, lo) log(hi/lo)
lnratioavg \(hi, lo) log(mean(hi)/mean(lo))
lnor \(hi, lo) log((hi/(1 - hi))/(lo/(1 - lo)))
lnoravg \(hi, lo) log((mean(hi)/(1 - mean(hi)))/(mean(lo)/(1 - mean(lo))))
lift \(hi, lo) (hi - lo)/lo
liftavg \(hi, lo) (mean(hi - lo))/mean(lo)
expdydx \(hi, lo, eps) ((exp(hi) - exp(lo))/exp(eps))/eps
expdydxavg \(hi, lo, eps) mean(((exp(hi) - exp(lo))/exp(eps))/eps)
Bayesian posterior summaries
By default, credible intervals in bayesian models are built as equal-tailed
intervals. This can be changed to a highest density interval by setting a global
option:
options("marginaleffects_posterior_interval" = "eti")
options("marginaleffects_posterior_interval" = "hdi")
By default, the center of the posterior distribution in bayesian models is
identified by the median. Users can use a different summary function by setting a
global option:
options("marginaleffects_posterior_center" = "mean")
options("marginaleffects_posterior_center" = "median")
When estimates are averaged using the by argument, the tidy() function, or
the summary() function, the posterior distribution is marginalized twice over.
First, we take the average across units but within each iteration of the
MCMC chain, according to what the user requested in by argument or
tidy()/summary() functions. Then, we identify the center of the resulting
posterior using the function supplied to the
"marginaleffects_posterior_center" option (the median by default).
Equivalence, Inferiority, Superiority
\theta is an estimate, \sigma_\theta its estimated standard error, and [a, b] are the bounds of the interval supplied to the equivalence argument.
Non-inferiority:
-
H_0: \theta \leq a
-
H_1: \theta > a
-
t=(\theta - a)/\sigma_\theta
p: Upper-tail probability
Non-superiority:
-
H_0: \theta \geq b
-
H_1: \theta < b
-
t=(\theta - b)/\sigma_\theta
p: Lower-tail probability
Equivalence: Two One-Sided Tests (TOST)
p: Maximum of the non-inferiority and non-superiority p values.
Thanks to Russell V. Lenth for the excellent emmeans package and documentation which inspired this feature.
Prediction types
The type argument determines the scale of the predictions used to compute quantities of interest with functions from the marginaleffects package. Admissible values for type depend on the model object. When users specify an incorrect value for type, marginaleffects will raise an informative error with a list of valid type values for the specific model object. The first entry in the list in that error message is the default type.
The invlink(link) is a special type defined by marginaleffects. It is available for some (but not all) models, and only for the predictions() function. With this link type, we first compute predictions on the link scale, then we use the inverse link function to backtransform the predictions to the response scale. This is useful for models with non-linear link functions as it can ensure that confidence intervals stay within desirable bounds, ex: 0 to 1 for a logit model. Note that an average of estimates with type="invlink(link)" will not always be equivalent to the average of estimates with type="response". This type is default when calling predictions(). It is available—but not default—when calling avg_predictions() or predictions() with the by argument.
Some of the most common type values are:
response, link, E, Ep, average, class, conditional, count, cum.prob, cumhaz, cumprob, density, detection, disp, ev, expected, expvalue, fitted, hazard, invlink(link), latent, latent_N, linear, linear.predictor, linpred, location, lp, mean, numeric, p, ppd, pr, precision, prediction, prob, probability, probs, quantile, risk, rmst, scale, survival, unconditional, utility, variance, xb, zero, zlink, zprob
Order of operations
Behind the scenes, the arguments of marginaleffects functions are evaluated in this order:
-
newdata
-
variables
-
comparison and slopes
-
by
-
vcov
-
hypothesis
-
transform
Parallel computation
The slopes() and comparisons() functions can use parallelism to
speed up computation. Operations are parallelized for the computation of
standard errors, at the model coefficient level. There is always
considerable overhead when using parallel computation, mainly involved
in passing the whole dataset to the different processes. Thus, parallel
computation is most likely to be useful when the model includes many parameters
and the dataset is relatively small.
Warning: In many cases, parallel processing will not be useful at all.
To activate parallel computation, users must load the future.apply package,
call plan() function, and set a global option. For example:
library(future.apply)
plan("multicore", workers = 4)
options(marginaleffects_parallel = TRUE)
slopes(model)
To disable parallelism in marginaleffects altogether, you can set a global option:
options(marginaleffects_parallel = FALSE)
Global options
The behavior of marginaleffects functions can be modified by setting global options.
Disable some safety checks:
options(marginaleffects_safe = FALSE)
Omit some columns from the printed output:
options(marginaleffects_print_omit = c("p.value", "s.value"))`
References
Greenland S. 2019. "Valid P-Values Behave Exactly as They Should: Some Misleading Criticisms of P-Values and Their Resolution With S-Values." The American Statistician. 73(S1): 106–114.
Cole, Stephen R, Jessie K Edwards, and Sander Greenland. 2020. "Surprise!" American Journal of Epidemiology 190 (2): 191–93. https://doi.org/10.1093/aje/kwaa136
Examples
library(marginaleffects)
# Linear model
tmp <- mtcars
tmp$am <- as.logical(tmp$am)
mod <- lm(mpg ~ am + factor(cyl), tmp)
avg_comparisons(mod, variables = list(cyl = "reference"))
avg_comparisons(mod, variables = list(cyl = "sequential"))
avg_comparisons(mod, variables = list(cyl = "pairwise"))
# GLM with different scale types
mod <- glm(am ~ factor(gear), data = mtcars)
avg_comparisons(mod, type = "response")
avg_comparisons(mod, type = "link")
# Contrasts at the mean
comparisons(mod, newdata = "mean")
# Contrasts between marginal means
comparisons(mod, newdata = "marginalmeans")
# Contrasts at user-specified values
comparisons(mod, newdata = datagrid(am = 0, gear = tmp$gear))
comparisons(mod, newdata = datagrid(am = unique, gear = max))
m <- lm(mpg ~ hp + drat + factor(cyl) + factor(am), data = mtcars)
comparisons(m, variables = "hp", newdata = datagrid(FUN_factor = unique, FUN_numeric = median))
# Numeric contrasts
mod <- lm(mpg ~ hp, data = mtcars)
avg_comparisons(mod, variables = list(hp = 1))
avg_comparisons(mod, variables = list(hp = 5))
avg_comparisons(mod, variables = list(hp = c(90, 100)))
avg_comparisons(mod, variables = list(hp = "iqr"))
avg_comparisons(mod, variables = list(hp = "sd"))
avg_comparisons(mod, variables = list(hp = "minmax"))
# using a function to specify a custom difference in one regressor
dat <- mtcars
dat$new_hp <- 49 * (dat$hp - min(dat$hp)) / (max(dat$hp) - min(dat$hp)) + 1
modlog <- lm(mpg ~ log(new_hp) + factor(cyl), data = dat)
fdiff <- \(x) data.frame(x, x + 10)
avg_comparisons(modlog, variables = list(new_hp = fdiff))
# Adjusted Risk Ratio: see the contrasts vignette
mod <- glm(vs ~ mpg, data = mtcars, family = binomial)
avg_comparisons(mod, comparison = "lnratioavg", transform = exp)
# Adjusted Risk Ratio: Manual specification of the `comparison`
avg_comparisons(
mod,
comparison = function(hi, lo) log(mean(hi) / mean(lo)),
transform = exp)
# cross contrasts
mod <- lm(mpg ~ factor(cyl) * factor(gear) + hp, data = mtcars)
avg_comparisons(mod, variables = c("cyl", "gear"), cross = TRUE)
# variable-specific contrasts
avg_comparisons(mod, variables = list(gear = "sequential", hp = 10))
# hypothesis test: is the `hp` marginal effect at the mean equal to the `drat` marginal effect
mod <- lm(mpg ~ wt + drat, data = mtcars)
comparisons(
mod,
newdata = "mean",
hypothesis = "wt = drat")
# same hypothesis test using row indices
comparisons(
mod,
newdata = "mean",
hypothesis = "b1 - b2 = 0")
# same hypothesis test using numeric vector of weights
comparisons(
mod,
newdata = "mean",
hypothesis = c(1, -1))
# two custom contrasts using a matrix of weights
lc <- matrix(c(
1, -1,
2, 3),
ncol = 2)
comparisons(
mod,
newdata = "mean",
hypothesis = lc)
# Effect of a 1 group-wise standard deviation change
# First we calculate the SD in each group of `cyl`
# Second, we use that SD as the treatment size in the `variables` argument
library(dplyr)
mod <- lm(mpg ~ hp + factor(cyl), mtcars)
tmp <- mtcars %>%
group_by(cyl) %>%
mutate(hp_sd = sd(hp))
avg_comparisons(mod,
variables = list(hp = function(x) data.frame(x, x + tmp$hp_sd)),
by = "cyl")
# `by` argument
mod <- lm(mpg ~ hp * am * vs, data = mtcars)
comparisons(mod, by = TRUE)
mod <- lm(mpg ~ hp * am * vs, data = mtcars)
avg_comparisons(mod, variables = "hp", by = c("vs", "am"))
library(nnet)
mod <- multinom(factor(gear) ~ mpg + am * vs, data = mtcars, trace = FALSE)
by <- data.frame(
group = c("3", "4", "5"),
by = c("3,4", "3,4", "5"))
comparisons(mod, type = "probs", by = by)
marginaleffects documentation built on Oct. 5, 2024, 5:06 p.m.
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| comparisons | R Documentation |
Comparisons Between Predictions Made With Different Regressor Values
Description
Predict the outcome variable at different regressor values (e.g., college
graduates vs. others), and compare those predictions by computing a difference,
ratio, or some other function. comparisons() can return many quantities of
interest, such as contrasts, differences, risk ratios, changes in log odds, lift,
slopes, elasticities, etc.
-
comparisons(): unit-level (conditional) estimates. -
avg_comparisons(): average (marginal) estimates.
variables identifies the focal regressors whose "effect" we are interested in. comparison determines how predictions with different regressor values are compared (difference, ratio, odds, etc.). The newdata argument and the datagrid() function control where statistics are evaluated in the predictor space: "at observed values", "at the mean", "at representative values", etc.
See the comparisons vignette and package website for worked examples and case studies:
Usage
comparisons(
model,
newdata = NULL,
variables = NULL,
comparison = "difference",
type = NULL,
vcov = TRUE,
by = FALSE,
conf_level = 0.95,
transform = NULL,
cross = FALSE,
wts = FALSE,
hypothesis = NULL,
equivalence = NULL,
p_adjust = NULL,
df = Inf,
eps = NULL,
numderiv = "fdforward",
...
)
avg_comparisons(
model,
newdata = NULL,
variables = NULL,
type = NULL,
vcov = TRUE,
by = TRUE,
conf_level = 0.95,
comparison = "difference",
transform = NULL,
cross = FALSE,
wts = FALSE,
hypothesis = NULL,
equivalence = NULL,
p_adjust = NULL,
df = Inf,
eps = NULL,
numderiv = "fdforward",
...
)
Arguments
model |
Model object |
newdata |
Grid of predictor values at which we evaluate the comparisons.
|
variables |
Focal variables
|
comparison |
How should pairs of predictions be compared? Difference, ratio, odds ratio, or user-defined functions.
|
type |
string indicates the type (scale) of the predictions used to
compute contrasts or slopes. This can differ based on the model
type, but will typically be a string such as: "response", "link", "probs",
or "zero". When an unsupported string is entered, the model-specific list of
acceptable values is returned in an error message. When |
vcov |
Type of uncertainty estimates to report (e.g., for robust standard errors). Acceptable values:
|
by |
Aggregate unit-level estimates (aka, marginalize, average over). Valid inputs:
|
conf_level |
numeric value between 0 and 1. Confidence level to use to build a confidence interval. |
transform |
string or function. Transformation applied to unit-level estimates and confidence intervals just before the function returns results. Functions must accept a vector and return a vector of the same length. Support string shortcuts: "exp", "ln" |
cross |
|
wts |
logical, string or numeric: weights to use when computing average predictions, contrasts or slopes. These weights only affect the averaging in
|
hypothesis |
specify a hypothesis test or custom contrast using a numeric value, vector, or matrix; a string equation; string; a formula, or a function.
|
equivalence |
Numeric vector of length 2: bounds used for the two-one-sided test (TOST) of equivalence, and for the non-inferiority and non-superiority tests. See Details section below. |
p_adjust |
Adjust p-values for multiple comparisons: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", or "fdr". See stats::p.adjust |
df |
Degrees of freedom used to compute p values and confidence intervals. A single numeric value between 1 and |
eps |
NULL or numeric value which determines the step size to use when
calculating numerical derivatives: (f(x+eps)-f(x))/eps. When |
numderiv |
string or list of strings indicating the method to use to for the numeric differentiation used in to compute delta method standard errors.
|
... |
Additional arguments are passed to the |
Value
A data.frame with one row per observation (per term/group) and several columns:
-
rowid: row number of thenewdatadata frame -
type: prediction type, as defined by thetypeargument -
group: (optional) value of the grouped outcome (e.g., categorical outcome models) -
term: the variable whose marginal effect is computed -
dydx: slope of the outcome with respect to the term, for a given combination of predictor values -
std.error: standard errors computed by via the delta method. -
p.value: p value associated to theestimatecolumn. The null is determined by thehypothesisargument (0 by default), and p values are computed before applying thetransformargument. -
s.value: Shannon information transforms of p values. How many consecutive "heads" tosses would provide the same amount of evidence (or "surprise") against the null hypothesis that the coin is fair? The purpose of S is to calibrate the analyst's intuition about the strength of evidence encoded in p against a well-known physical phenomenon. See Greenland (2019) and Cole et al. (2020). -
conf.low: lower bound of the confidence interval (or equal-tailed interval for bayesian models) -
conf.high: upper bound of the confidence interval (or equal-tailed interval for bayesian models)
See ?print.marginaleffects for printing options.
Functions
-
avg_comparisons(): Average comparisons
Standard errors using the delta method
Standard errors for all quantities estimated by marginaleffects can be obtained via the delta method. This requires differentiating a function with respect to the coefficients in the model using a finite difference approach. In some models, the delta method standard errors can be sensitive to various aspects of the numeric differentiation strategy, including the step size. By default, the step size is set to 1e-8, or to 1e-4 times the smallest absolute model coefficient, whichever is largest.
marginaleffects can delegate numeric differentiation to the numDeriv package, which allows more flexibility. To do this, users can pass arguments to the numDeriv::jacobian function through a global option. For example:
-
options(marginaleffects_numDeriv = list(method = "simple", method.args = list(eps = 1e-6))) -
options(marginaleffects_numDeriv = list(method = "Richardson", method.args = list(eps = 1e-5))) -
options(marginaleffects_numDeriv = NULL)
See the "Standard Errors and Confidence Intervals" vignette on the marginaleffects website for more details on the computation of standard errors:
https://marginaleffects.com/vignettes/uncertainty.html
Note that the inferences() function can be used to compute uncertainty estimates using a bootstrap or simulation-based inference. See the vignette:
https://marginaleffects.com/vignettes/bootstrap.html
Model-Specific Arguments
Some model types allow model-specific arguments to modify the nature of
marginal effects, predictions, marginal means, and contrasts. Please report
other package-specific predict() arguments on Github so we can add them to
the table below.
https://github.com/vincentarelbundock/marginaleffects/issues
| Package | Class | Argument | Documentation |
brms | brmsfit | ndraws | brms::posterior_predict |
re_formula | brms::posterior_predict | ||
lme4 | merMod | re.form | lme4::predict.merMod |
allow.new.levels | lme4::predict.merMod | ||
glmmTMB | glmmTMB | re.form | glmmTMB::predict.glmmTMB |
allow.new.levels | glmmTMB::predict.glmmTMB | ||
zitype | glmmTMB::predict.glmmTMB | ||
mgcv | bam | exclude | mgcv::predict.bam |
gam | exclude | mgcv::predict.gam | |
robustlmm | rlmerMod | re.form | robustlmm::predict.rlmerMod |
allow.new.levels | robustlmm::predict.rlmerMod | ||
MCMCglmm | MCMCglmm | ndraws | |
sampleSelection | selection | part | sampleSelection::predict.selection |
comparison argument functions
The following transformations can be applied by supplying one of the shortcut strings to the
comparison argument.
hi is a vector of adjusted predictions for the "high" side of the
contrast. lo is a vector of adjusted predictions for the "low" side of the
contrast. y is a vector of adjusted predictions for the original data. x
is the predictor in the original data. eps is the step size to use to
compute derivatives and elasticities.
| Shortcut | Function |
| difference | \(hi, lo) hi - lo |
| differenceavg | \(hi, lo) mean(hi - lo) |
| dydx | \(hi, lo, eps) (hi - lo)/eps |
| eyex | \(hi, lo, eps, y, x) (hi - lo)/eps * (x/y) |
| eydx | \(hi, lo, eps, y, x) ((hi - lo)/eps)/y |
| dyex | \(hi, lo, eps, x) ((hi - lo)/eps) * x |
| dydxavg | \(hi, lo, eps) mean((hi - lo)/eps) |
| eyexavg | \(hi, lo, eps, y, x) mean((hi - lo)/eps * (x/y)) |
| eydxavg | \(hi, lo, eps, y, x) mean(((hi - lo)/eps)/y) |
| dyexavg | \(hi, lo, eps, x) mean(((hi - lo)/eps) * x) |
| ratio | \(hi, lo) hi/lo |
| ratioavg | \(hi, lo) mean(hi)/mean(lo) |
| lnratio | \(hi, lo) log(hi/lo) |
| lnratioavg | \(hi, lo) log(mean(hi)/mean(lo)) |
| lnor | \(hi, lo) log((hi/(1 - hi))/(lo/(1 - lo))) |
| lnoravg | \(hi, lo) log((mean(hi)/(1 - mean(hi)))/(mean(lo)/(1 - mean(lo)))) |
| lift | \(hi, lo) (hi - lo)/lo |
| liftavg | \(hi, lo) (mean(hi - lo))/mean(lo) |
| expdydx | \(hi, lo, eps) ((exp(hi) - exp(lo))/exp(eps))/eps |
| expdydxavg | \(hi, lo, eps) mean(((exp(hi) - exp(lo))/exp(eps))/eps) |
Bayesian posterior summaries
By default, credible intervals in bayesian models are built as equal-tailed intervals. This can be changed to a highest density interval by setting a global option:
options("marginaleffects_posterior_interval" = "eti")
options("marginaleffects_posterior_interval" = "hdi")
By default, the center of the posterior distribution in bayesian models is identified by the median. Users can use a different summary function by setting a global option:
options("marginaleffects_posterior_center" = "mean")
options("marginaleffects_posterior_center" = "median")
When estimates are averaged using the by argument, the tidy() function, or
the summary() function, the posterior distribution is marginalized twice over.
First, we take the average across units but within each iteration of the
MCMC chain, according to what the user requested in by argument or
tidy()/summary() functions. Then, we identify the center of the resulting
posterior using the function supplied to the
"marginaleffects_posterior_center" option (the median by default).
Equivalence, Inferiority, Superiority
\theta is an estimate, \sigma_\theta its estimated standard error, and [a, b] are the bounds of the interval supplied to the equivalence argument.
Non-inferiority:
-
H_0:\theta \leq a -
H_1:\theta > a -
t=(\theta - a)/\sigma_\theta p: Upper-tail probability
Non-superiority:
-
H_0:\theta \geq b -
H_1:\theta < b -
t=(\theta - b)/\sigma_\theta p: Lower-tail probability
Equivalence: Two One-Sided Tests (TOST)
p: Maximum of the non-inferiority and non-superiority p values.
Thanks to Russell V. Lenth for the excellent emmeans package and documentation which inspired this feature.
Prediction types
The type argument determines the scale of the predictions used to compute quantities of interest with functions from the marginaleffects package. Admissible values for type depend on the model object. When users specify an incorrect value for type, marginaleffects will raise an informative error with a list of valid type values for the specific model object. The first entry in the list in that error message is the default type.
The invlink(link) is a special type defined by marginaleffects. It is available for some (but not all) models, and only for the predictions() function. With this link type, we first compute predictions on the link scale, then we use the inverse link function to backtransform the predictions to the response scale. This is useful for models with non-linear link functions as it can ensure that confidence intervals stay within desirable bounds, ex: 0 to 1 for a logit model. Note that an average of estimates with type="invlink(link)" will not always be equivalent to the average of estimates with type="response". This type is default when calling predictions(). It is available—but not default—when calling avg_predictions() or predictions() with the by argument.
Some of the most common type values are:
response, link, E, Ep, average, class, conditional, count, cum.prob, cumhaz, cumprob, density, detection, disp, ev, expected, expvalue, fitted, hazard, invlink(link), latent, latent_N, linear, linear.predictor, linpred, location, lp, mean, numeric, p, ppd, pr, precision, prediction, prob, probability, probs, quantile, risk, rmst, scale, survival, unconditional, utility, variance, xb, zero, zlink, zprob
Order of operations
Behind the scenes, the arguments of marginaleffects functions are evaluated in this order:
-
newdata -
variables -
comparisonandslopes -
by -
vcov -
hypothesis -
transform
Parallel computation
The slopes() and comparisons() functions can use parallelism to
speed up computation. Operations are parallelized for the computation of
standard errors, at the model coefficient level. There is always
considerable overhead when using parallel computation, mainly involved
in passing the whole dataset to the different processes. Thus, parallel
computation is most likely to be useful when the model includes many parameters
and the dataset is relatively small.
Warning: In many cases, parallel processing will not be useful at all.
To activate parallel computation, users must load the future.apply package,
call plan() function, and set a global option. For example:
library(future.apply)
plan("multicore", workers = 4)
options(marginaleffects_parallel = TRUE)
slopes(model)
To disable parallelism in marginaleffects altogether, you can set a global option:
options(marginaleffects_parallel = FALSE)
Global options
The behavior of marginaleffects functions can be modified by setting global options.
Disable some safety checks:
options(marginaleffects_safe = FALSE)
Omit some columns from the printed output:
options(marginaleffects_print_omit = c("p.value", "s.value"))`
References
Greenland S. 2019. "Valid P-Values Behave Exactly as They Should: Some Misleading Criticisms of P-Values and Their Resolution With S-Values." The American Statistician. 73(S1): 106–114.
Cole, Stephen R, Jessie K Edwards, and Sander Greenland. 2020. "Surprise!" American Journal of Epidemiology 190 (2): 191–93. https://doi.org/10.1093/aje/kwaa136
Examples
library(marginaleffects)
# Linear model
tmp <- mtcars
tmp$am <- as.logical(tmp$am)
mod <- lm(mpg ~ am + factor(cyl), tmp)
avg_comparisons(mod, variables = list(cyl = "reference"))
avg_comparisons(mod, variables = list(cyl = "sequential"))
avg_comparisons(mod, variables = list(cyl = "pairwise"))
# GLM with different scale types
mod <- glm(am ~ factor(gear), data = mtcars)
avg_comparisons(mod, type = "response")
avg_comparisons(mod, type = "link")
# Contrasts at the mean
comparisons(mod, newdata = "mean")
# Contrasts between marginal means
comparisons(mod, newdata = "marginalmeans")
# Contrasts at user-specified values
comparisons(mod, newdata = datagrid(am = 0, gear = tmp$gear))
comparisons(mod, newdata = datagrid(am = unique, gear = max))
m <- lm(mpg ~ hp + drat + factor(cyl) + factor(am), data = mtcars)
comparisons(m, variables = "hp", newdata = datagrid(FUN_factor = unique, FUN_numeric = median))
# Numeric contrasts
mod <- lm(mpg ~ hp, data = mtcars)
avg_comparisons(mod, variables = list(hp = 1))
avg_comparisons(mod, variables = list(hp = 5))
avg_comparisons(mod, variables = list(hp = c(90, 100)))
avg_comparisons(mod, variables = list(hp = "iqr"))
avg_comparisons(mod, variables = list(hp = "sd"))
avg_comparisons(mod, variables = list(hp = "minmax"))
# using a function to specify a custom difference in one regressor
dat <- mtcars
dat$new_hp <- 49 * (dat$hp - min(dat$hp)) / (max(dat$hp) - min(dat$hp)) + 1
modlog <- lm(mpg ~ log(new_hp) + factor(cyl), data = dat)
fdiff <- \(x) data.frame(x, x + 10)
avg_comparisons(modlog, variables = list(new_hp = fdiff))
# Adjusted Risk Ratio: see the contrasts vignette
mod <- glm(vs ~ mpg, data = mtcars, family = binomial)
avg_comparisons(mod, comparison = "lnratioavg", transform = exp)
# Adjusted Risk Ratio: Manual specification of the `comparison`
avg_comparisons(
mod,
comparison = function(hi, lo) log(mean(hi) / mean(lo)),
transform = exp)
# cross contrasts
mod <- lm(mpg ~ factor(cyl) * factor(gear) + hp, data = mtcars)
avg_comparisons(mod, variables = c("cyl", "gear"), cross = TRUE)
# variable-specific contrasts
avg_comparisons(mod, variables = list(gear = "sequential", hp = 10))
# hypothesis test: is the `hp` marginal effect at the mean equal to the `drat` marginal effect
mod <- lm(mpg ~ wt + drat, data = mtcars)
comparisons(
mod,
newdata = "mean",
hypothesis = "wt = drat")
# same hypothesis test using row indices
comparisons(
mod,
newdata = "mean",
hypothesis = "b1 - b2 = 0")
# same hypothesis test using numeric vector of weights
comparisons(
mod,
newdata = "mean",
hypothesis = c(1, -1))
# two custom contrasts using a matrix of weights
lc <- matrix(c(
1, -1,
2, 3),
ncol = 2)
comparisons(
mod,
newdata = "mean",
hypothesis = lc)
# Effect of a 1 group-wise standard deviation change
# First we calculate the SD in each group of `cyl`
# Second, we use that SD as the treatment size in the `variables` argument
library(dplyr)
mod <- lm(mpg ~ hp + factor(cyl), mtcars)
tmp <- mtcars %>%
group_by(cyl) %>%
mutate(hp_sd = sd(hp))
avg_comparisons(mod,
variables = list(hp = function(x) data.frame(x, x + tmp$hp_sd)),
by = "cyl")
# `by` argument
mod <- lm(mpg ~ hp * am * vs, data = mtcars)
comparisons(mod, by = TRUE)
mod <- lm(mpg ~ hp * am * vs, data = mtcars)
avg_comparisons(mod, variables = "hp", by = c("vs", "am"))
library(nnet)
mod <- multinom(factor(gear) ~ mpg + am * vs, data = mtcars, trace = FALSE)
by <- data.frame(
group = c("3", "4", "5"),
by = c("3,4", "3,4", "5"))
comparisons(mod, type = "probs", by = by)
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