Summary: “Introduction to stratamatch” covers the
basic functionality of stratamatch: stratifying a data set,
assessing the quality of the match, and matching the data within strata.
This vignette features more advanced functionality of
stratamatch.
This vignette contains:
We’ll start with some sample data:
library(stratamatch)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
set.seed(123)
mydata <- make_sample_data(n = 5000)An important consideration for pilot designs like the
stratamatch approach is the selection of the pilot set.
Ideally, the individuals in the pilot set should be similarto the
individuals in the treatment group, so a prognostic model built on this
pilot set will not beextrapolating heavily when estimating prognostic
scores on the analysis set. To more closely ensure that the selected
pilot set is a representative sample of controls, one easy step is to
specify a list of categorical or binary covariates and sample the pilot
set proportionally based on these covariates.
This can be done in one step using auto_stratify, for
example:
a.strat1 <- auto_stratify(mydata, "treat",
prognosis = outcome ~ X1 + X2,
group_by_covariates = c("C1", "B2"), size = 500)
#> Constructing a pilot set by subsampling 10% of controls.
#> Subsampling while balancing on:
#> C1, B2
#> Fitting prognostic model via logistic regression: outcome ~ X1 + X2Another method is to use the split_pilot_set function,
which allows the user to split the pilot set (and examine the balance)
before passing the result to auto_stratify to fit the
prognostic score.
mysplit <- split_pilot_set(mydata, "treat", group_by_covariates = c("C1", "B2"))
#> Constructing a pilot set by subsampling 10% of controls.
#> Subsampling while balancing on:
#> C1, B2The result, mysplit, is a list containing a
pilot_set and an analysis_set, in this case
partitioned while balancing on B1 and C2. At this point, we might pass
the result to auto_stratify as follows:
a.strat2 <- auto_stratify(mysplit$analysis_set, "treat",
prognosis = outcome ~ X1 + X2,
pilot_sample = mysplit$pilot_set, size = 500)
#> Using user-specified set for prognostic score modeling.
#> Fitting prognostic model via logistic regression: outcome ~ X1 + X2In this case, the pilot set splitting method is the same for
a.strat1 and a.strat2, so each should be
qualitatively similar.
By default, auto_stratify uses a logistic regression
(for binary outcomes) or a linear regression (for continuous outcomes)
to fit the prognostic model. auto_stratify is built to
accomodate other prognostic score estimation approaches: rather than
letting auto_stratify do the model fitting, the user can
specify a pre-fit model or a vector of prognostic scores.
A word of caution is advisable: Logistic regression is generally the
norm when fitting propensity scores (Stuart
(2010)), and most studies discussing the prognostic score have
likewise focused on linear or logistic regression (Ben B. Hansen (2008), Leacy and Stuart (2014), Aikens et al. (2020)), or less commonly the
lasso (Antonelli et al. (2018)). The
nuances of modeling and checking the fit of the prognostic score are
still understudied. In particular, prognostic models generally are fit
on only control observations, meaning that they must necessarily
extrapolate to the treatment group. Users should, as always, consider
diagnostics for their specific model, for their stratified data set (see
“Intro to statamatch”), and for their matched dataset (see, as an
introduction Stuart (2010)). Additionally,
in order to maintain the integrity of the pilot set and prevent
over-fitting, users interested in trying many modeling or matching
schemes are encouraged to define a single pilot/analysis set split
(e.g. with split_pilot_set, above) and use the same pilot
set throughout their design process.
To an extent, any prognostic score stratification – even on a poor quality model – will increase the speed of matching for large datasets. In addition, if the strata are sufficiently large, the subsequent within-strata matching step may compensate for a poor-quality prognostic model. To one view, the diagnostic check that matters most is the quality of the final matching result, whereas specific prognostic modeling concerns are perhaps secondary. Nonetheless, simulation and theory results suggest that incorporating a prognostic score into a study design (in combination, generally, with a propensity score) can have favorable statistical properties, such as decreasing variance, increasing power in gamma sensitivity analyses, and decreasing dependence on the propensity score (Stuart (2010), Aikens, Greaves, and Baiocchi (2020), Antonelli et al. (2018), Ben B. Hansen (2008)). To that end, prognostic models which produce high-quality prognostic score estimates are expected to ultimately produce higher quality designs by improving the prognostic balance of the matched set.
This section contains a few examples to introduce users who may be
new to the modeling space. By no means does it begin to cover all of the
modeling possibilities, or even all of the nuances of any one model.
This is not a tutorial on predictive modeling. Users looking to become
more familiar with modeling in R more broadly may be interested in the
caret
package (Kuhn (2021)), which implements
support for a wide variety of predictive models.
It’s important to select a model which is appropriate to the nature of the outcome of interest. In this tutorial, our sample data has a binary outcome, so we use models appropriate to that outcome. Users with continuous outcomes should use regression models appropriate to continuous outcomes. Other types of outcomes – such as categorical – have not yet been characterized in the prognostic score literature.
The lasso is a sparsifying linear model – it is a mathematical cousin to linear regression, but it functions well when a substaintial number of the measured covariates are actually uninformative to the outcome. This may be a particularly useful and intuitive approach when there are many measured covariates which may be redundant or uninformative.
The code below uses the glmnet package (Friedman, Hastie, and Tibshirani (2010)) to fit
a cross-validated lasso on the pilot set based on all the measured
covariates. In this example, since the outcome is binary, we will run a
logistic lasso. This is done by specifying the
family = "binomial" argument to cv.glmnet
(although other modeling steps are simular for continuous outcomes.)
The code below does some preprocessing to convert the pilot set data
to the right format before passing it to cv.glmnet.
glmnet expects the input data to be a model matrix rather
than a data frame, and it expects outcomes (y_pilot) to be
separated from the covariate data (x_pilot).
library(glmnet)
#> Loading required package: Matrix
#> Loaded glmnet 4.1-3
# fit model on pilot set
x_pilot <- model.matrix(outcome ~ X1 + X2 + B1 + B2 + C1,
data = mysplit$pilot_set)
y_pilot <- mysplit$pilot_set %>%
dplyr::select(outcome) %>%
as.matrix()
cvlasso <- cv.glmnet(x_pilot, y_pilot, family = "binomial")At this point, we can run diagnostics on cvlasso. The Introduction to
glmnet vignette contains an accessible starting point. In this
simulated data, we happen to know that the only variable that actually
affects the outcome is X1. The sparsifying model often does
a great job of picking out X1 as the most important
variable. We can see this by printing the coefficients:
coef(cvlasso)
#> 8 x 1 sparse Matrix of class "dgCMatrix"
#> s1
#> (Intercept) 0.02870109
#> (Intercept) .
#> X1 -0.64374310
#> X2 .
#> B1 .
#> B2 .
#> C1b .
#> C1c .When we are satisfied with our prognostic model, we can estimate the
scores on the analysis set with predict and pass the result
to auto_stratify.
# estimate scores on analysis set
x_analysis <- model.matrix(outcome ~ X1 + X2 + B1 + B2 + C1,
data = mysplit$analysis_set)
lasso_scores <- predict(cvlasso, newx = x_analysis, s = "lambda.min", type = "response")
# pass the scores to auto_stratify
a.strat_lasso <- auto_stratify(data = mysplit$analysis_set,
treat = "treat",
outcome = "outcome",
prognosis = lasso_scores,
pilot_sample = mysplit$pilot_set,
size = 500)An elastic net is a fairly straightforward extension of the code
above – we can use the same form of the pilot set data that we used
above. An additional task is to select the alpha “mixing”
parameter determining the amount of L2-regularization (1 for lasso, 0
for ridge regression). Here, I set alpha = 0.2. The
tutorial for glmnet also contains some advice for selecting
the alpha parameter via cross-validation. As above, we specify a
logistic elastic net with family = "binomial", since in
this case our outcome is binary.
cvenet <- cv.glmnet(x_pilot, y_pilot, family = "binomial", alpha = 0.2)
enet_scores <- predict(cvenet, newx = x_analysis, s = "lambda.min", type = "response")
# pass the scores to auto_stratify
a.strat_enet <- auto_stratify(data = mysplit$analysis_set,
treat = "treat",
outcome = "outcome",
prognosis = enet_scores,
pilot_sample = mysplit$pilot_set,
size = 500)Random forests are a popular option for both classification and
regression modeling, particularly because of their strengths in modeling
nonlinear relationships in the data. Below is an example which fits a
random forest for our binary outcome using randomForest. A
note for users with binary outcomes: randomForest will run
regression by default if the outcome column is numeric. To circumvent
this (e.g. for 0/1 coded data), the outcome can be cast as a factor.
library(randomForest)
#> randomForest 4.7-1
#> Type rfNews() to see new features/changes/bug fixes.
#>
#> Attaching package: 'randomForest'
#> The following object is masked from 'package:dplyr':
#>
#> combine
forest <- randomForest(as.factor(outcome) ~ X1 + X2 + B1 + B2, data = mysplit$pilot_set)Random forests can be somewhat more opaque than linear models in
terms of understanding how predictions are made. A good starting point
is running importance(forest) to check on which features
are weighted heavily in the model.
Below, we extract a “prognostic score” from the random forest.
Another note for users with binary outcomes: The predict
method for random forest classifiers outputs 0/1 predictions by default.
These will be useless for stratification. Instead, we need to specify
type = "prob" in the call to predict and extract the
probabilities for the “positive” outcome class.
forest_scores <- predict(forest,
newdata = mysplit$analysis_set,
type = "prob")[,1]
a.strat_forest <- auto_stratify(data = mysplit$analysis_set,
treat = "treat",
outcome = "outcome",
prognosis = forest_scores,
pilot_sample = mysplit$pilot_set,
size = 500)“Intro to Stratamatch” covers only the default functionality of
stratamatch, which is a fixed 1:k propensity score match
within strata. This tutorial covers some alternative options. Note that
the examples that follow all require the R package optmatch
(Ben B. Hansen and Klopfer (2006)) to be
installed.
Users can opt to use Mahalanobis distance rather then propensity
score for the within-strata matching step by specifying the “method” to
strata_match. We set k = 2, so that precisely
2 control observations are matched to each treated observation.
mahalmatch <- strata_match(a.strat2, model = treat ~ X1 + X2 + B1 + B2,
method = "mahal", k = 2)
#> Using Mahalanobis distance: treat ~ X1 + X2 + B1 + B2
summary(mahalmatch)
#> Structure of matched sets:
#> 1:2 0:1
#> 1146 1176
#> Effective Sample Size: 1528
#> (equivalent number of matched pairs).Full matching may be a particularly useful approach when the ratio of
treated to control individuals varies within strata, but the researcher
still would prefer to use as much of the data as possible. To do full
matching, set k = "full". This can be used in combination
with mahalanobis distance matching, as shown below:
fullmahalmatch <- strata_match(a.strat2, model = treat ~ X1 + X2 + B1 + B2,
method = "mahal", k = "full")
#> Using Mahalanobis distance: treat ~ X1 + X2 + B1 + B2
summary(fullmahalmatch)
#> Structure of matched sets:
#> 5+:1 4:1 3:1 2:1 1:1 1:2 1:3 1:4 1:5+
#> 8 6 14 42 453 132 84 70 206
#> Effective Sample Size: 1331.8
#> (equivalent number of matched pairs).stratamatch doesn’t natively support all possible
matching schemes. Luckily, it can be fairly straightforward to stratify
a data set with auto_stratify and match the results with
other software. As an example, the code below uses the
optmatch package (Ben B. Hansen and
Klopfer (2006)) to match within-strata using Mahalanobis distance
with a propensity score caliper.
library(optmatch)
#> Loading required package: survival
# mahalanobis distance matrix for within-strata matching
mahaldist <- match_on(treat ~ X1 + X2 + B1 + B2,
within = exactMatch(treat ~ stratum,
data = a.strat2$analysis_set),
data = a.strat2$analysis_set)
# add propensity score caliper
propdist <- match_on(glm(treat ~ X1 + X2 + B1 + B2,
family = "binomial",
data = a.strat2$analysis_set))
mahalcaliper <- mahaldist + caliper(propdist, width = 1)
mahalcaliper_match <- pairmatch(mahalcaliper, data = a.strat2$analysis_set)
#> Warning in fullmatch.BlockedInfinitySparseMatrix(x = x, min.controls = controls, : At least one subproblem matching failed.
#> (Restrictions impossible to meet?)
#> Enter ?matchfailed for more info.
summary(mahalcaliper_match)
#> Matches made in 8 of 10 subgroups, accounting for 3691 of 4614 total observations.
#>
#>
#> Structure of matched sets:
#> 1:0 1:1 0:1
#> 192 954 2514
#> Effective Sample Size: 954
#> (equivalent number of matched pairs).