mimar implements a compact chained-imputation workflow
in R for missing-data analysis, artificial amputation, native and
learner-backed single and multiple imputation, diagnostic evaluation,
and post-imputation pooling.
The package is built around a complete missing-data workflow: describe the missingness, create benchmark amputations when needed, impute with native or learner-backed update rules, inspect diagnostics, evaluate recovered cells when truth is available, and pool post-fit quantities. The goal is a concise grammar for the whole workflow, not a replacement for every specialist feature in larger imputation systems.
The package owns the imputation loop. Every imputer, whether implemented natively or backed by a learner package, is called the same way:
impute(data, imputer = "pmm", m = 5, maxit = 5, seed = 1)
impute(data, imputer = "rf", m = 5, seed = 1)
impute(data, imputer = "xgboost", m = 5, seed = 1)There is no dependency on funcml. Learner-backed
imputers call their original packages directly, and those backend
packages are hard dependencies so users can run any registered imputer
without manually resolving learner installations.
Install the released version from CRAN:
install.packages("mimar")The CRAN package page is https://CRAN.R-project.org/package=mimar.
You can install the development version from GitHub:
install.packages("remotes")
remotes::install_github("ielbadisy/mimar")Then load the package:
library(mimar)For normal use, impute() is the only function you need.
The input data can contain NA, and the completed outputs
returned by complete() do not. Set
verbose = TRUE when you want a concise progress log for the
chained imputation workflow.
i <- impute(a, imputer = "knn", m = 5, maxit = 5, seed = 1)
complete(i, 1)
complete(i, "all")describe()
ampute()
imputer_registry()
imputer()
impute()
complete()
evaluate()
pool()
plot()library(mimar)
set.seed(1)
dat <- data.frame(
age = rnorm(120, 50, 10),
bmi = rnorm(120, 25, 4),
sex = factor(sample(c("F", "M"), 120, TRUE)),
group = factor(sample(c("A", "B", "C"), 120, TRUE)),
smoker = sample(c(TRUE, FALSE), 120, TRUE)
)
a <- ampute(
dat,
prop = 0.25,
mechanism = "MAR",
target = c("bmi", "group"),
by = c("age", "sex"),
seed = 1
)
i <- impute(a, imputer = "knn", m = 5, maxit = 5, seed = 1, ncore = 2)
complete(i, 1)## age bmi sex group smoker
## <num> <num> <fctr> <fctr> <lgcl>
## 1: 43.73546 22.97617 M C FALSE
## 2: 51.83643 30.37216 F A FALSE
## 3: 41.64371 24.14168 F B TRUE
## 4: 65.95281 24.28177 F C TRUE
## 5: 53.29508 24.59924 F A FALSE
## ---
## 116: 46.07192 13.44432 M C TRUE
## 117: 46.80007 27.24328 F C TRUE
## 118: 47.20887 24.76111 F A FALSE
## 119: 54.94188 29.38711 M C FALSE
## 120: 48.22670 24.97862 M B FALSEsummary(i)## mimar imputation summary
## rows columns n_imputations imputer maxit ncore stochastic
## <int> <int> <int> <char> <num> <int> <lgcl>
## 1: 120 5 5 knn 5 2 TRUE
## total_missing_before total_imputed remaining_missing variables_imputed
## <int> <int> <int> <int>
## 1: 53 53 0 2
##
## Variables:
## variable type method n_missing_before prop_missing_before n_imputed
## <char> <char> <char> <int> <num> <int>
## 1: age numeric none 0 0.0000000 0
## 2: bmi numeric knn 26 0.2166667 26
## 3: sex factor none 0 0.0000000 0
## 4: group factor knn 27 0.2250000 27
## 5: smoker logical none 0 0.0000000 0
## prop_imputed remaining_missing between_imputation_sd
## <num> <int> <num>
## 1: 0 0 0.000000
## 2: 1 0 0.341076
## 3: 0 0 0.000000
## 4: 1 0 0.000000
## 5: 0 0 0.000000evaluate(i)## mimar imputation evaluation
## n_imputations imputer total_missing evaluated_cells
## <int> <char> <int> <int>
## 1: 5 knn 53 53plot(i, type = "density")
Inspect available imputers with:
imputer_registry()## imputer implementation package supports_numeric supports_binary
## <char> <char> <char> <lgcl> <lgcl>
## 1: mean mimar internal TRUE TRUE
## 2: median mimar internal TRUE TRUE
## 3: mode mimar internal TRUE TRUE
## 4: naive mimar internal TRUE TRUE
## 5: norm mimar internal TRUE TRUE
## 6: pmm mimar internal TRUE TRUE
## 7: spmm mimar internal TRUE TRUE
## 8: logreg mimar internal TRUE TRUE
## 9: polyreg mimar internal TRUE TRUE
## 10: rf wrapped ranger TRUE TRUE
## 11: ranger wrapped ranger TRUE TRUE
## 12: rpart wrapped rpart TRUE TRUE
## 13: nbayes wrapped naivebayes TRUE TRUE
## 14: svm wrapped e1071 TRUE TRUE
## 15: bart wrapped BART TRUE TRUE
## 16: glmnet wrapped glmnet TRUE TRUE
## 17: gbm wrapped gbm TRUE TRUE
## 18: xgboost wrapped xgboost TRUE TRUE
## 19: knn mimar internal TRUE TRUE
## 20: hotdeck mimar internal TRUE TRUE
## 21: famd wrapped missMDA TRUE TRUE
## 22: superlearner mimar internal TRUE TRUE
## 23: sl mimar internal TRUE TRUE
## 24: densemlp wrapped densemlp TRUE TRUE
## 25: missknn wrapped missknn TRUE TRUE
## imputer implementation package supports_numeric supports_binary
## <char> <char> <char> <lgcl> <lgcl>
## supports_multiclass stochastic
## <lgcl> <lgcl>
## 1: TRUE FALSE
## 2: TRUE FALSE
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## 21: TRUE TRUE
## 22: TRUE TRUE
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## 24: TRUE TRUE
## 25: TRUE TRUE
## supports_multiclass stochastic
## <lgcl> <lgcl>
## description
## <char>
## 1: Mean imputation for numeric targets
## 2: Median imputation for numeric targets
## 3: Mode imputation for categorical targets
## 4: Median/mode chained baseline
## 5: Bayesian normal-style linear regression draw
## 6: Predictive mean matching
## 7: Single-step predictive mean matching
## 8: Binary logistic regression draw
## 9: One-vs-rest multinomial logistic regression draw
## 10: MissForest-style random forest imputer
## 11: Random forest imputer through ranger
## 12: Tree imputer through rpart
## 13: Naive Bayes imputer
## 14: Support vector machine imputer
## 15: BART imputer
## 16: Penalized regression imputer through glmnet
## 17: Gradient boosting imputer through gbm
## 18: Gradient boosted tree imputer through xgboost
## 19: Nearest-neighbor donor imputer
## 20: Hot-deck donor imputer
## 21: FAMD-assisted donor imputer
## 22: Cross-validated Super Learner-style ensemble imputer
## 23: Short alias for superlearner
## 24: Dense multilayer perceptron imputer through densemlp
## 25: Whole-table masked k-nearest-neighbor imputer through missknn (single-shot strategy)
## description
## <char>
## available status
## <lgcl> <char>
## 1: TRUE available
## 2: TRUE available
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## available status
## <lgcl> <char>describe("imputers")## mimar available imputers
## imputer implementation package supports_numeric supports_binary
## <char> <char> <char> <lgcl> <lgcl>
## 1: mean mimar internal TRUE TRUE
## 2: median mimar internal TRUE TRUE
## 3: mode mimar internal TRUE TRUE
## 4: naive mimar internal TRUE TRUE
## 5: norm mimar internal TRUE TRUE
## 6: pmm mimar internal TRUE TRUE
## 7: spmm mimar internal TRUE TRUE
## 8: logreg mimar internal TRUE TRUE
## 9: polyreg mimar internal TRUE TRUE
## 10: rf wrapped ranger TRUE TRUE
## 11: ranger wrapped ranger TRUE TRUE
## 12: rpart wrapped rpart TRUE TRUE
## 13: nbayes wrapped naivebayes TRUE TRUE
## 14: svm wrapped e1071 TRUE TRUE
## 15: bart wrapped BART TRUE TRUE
## 16: glmnet wrapped glmnet TRUE TRUE
## 17: gbm wrapped gbm TRUE TRUE
## 18: xgboost wrapped xgboost TRUE TRUE
## 19: knn mimar internal TRUE TRUE
## 20: hotdeck mimar internal TRUE TRUE
## 21: famd wrapped missMDA TRUE TRUE
## 22: superlearner mimar internal TRUE TRUE
## 23: sl mimar internal TRUE TRUE
## 24: densemlp wrapped densemlp TRUE TRUE
## 25: missknn wrapped missknn TRUE TRUE
## imputer implementation package supports_numeric supports_binary
## <char> <char> <char> <lgcl> <lgcl>
## supports_multiclass stochastic
## <lgcl> <lgcl>
## 1: TRUE FALSE
## 2: TRUE FALSE
## 3: TRUE FALSE
## 4: TRUE FALSE
## 5: TRUE TRUE
## 6: TRUE TRUE
## 7: TRUE TRUE
## 8: TRUE TRUE
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## 10: TRUE TRUE
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## 23: TRUE TRUE
## 24: TRUE TRUE
## 25: TRUE TRUE
## supports_multiclass stochastic
## <lgcl> <lgcl>
## description
## <char>
## 1: Mean imputation for numeric targets
## 2: Median imputation for numeric targets
## 3: Mode imputation for categorical targets
## 4: Median/mode chained baseline
## 5: Bayesian normal-style linear regression draw
## 6: Predictive mean matching
## 7: Single-step predictive mean matching
## 8: Binary logistic regression draw
## 9: One-vs-rest multinomial logistic regression draw
## 10: MissForest-style random forest imputer
## 11: Random forest imputer through ranger
## 12: Tree imputer through rpart
## 13: Naive Bayes imputer
## 14: Support vector machine imputer
## 15: BART imputer
## 16: Penalized regression imputer through glmnet
## 17: Gradient boosting imputer through gbm
## 18: Gradient boosted tree imputer through xgboost
## 19: Nearest-neighbor donor imputer
## 20: Hot-deck donor imputer
## 21: FAMD-assisted donor imputer
## 22: Cross-validated Super Learner-style ensemble imputer
## 23: Short alias for superlearner
## 24: Dense multilayer perceptron imputer through densemlp
## 25: Whole-table masked k-nearest-neighbor imputer through missknn (single-shot strategy)
## description
## <char>
## available status
## <lgcl> <char>
## 1: TRUE available
## 2: TRUE available
## 3: TRUE available
## 4: TRUE available
## 5: TRUE available
## 6: TRUE available
## 7: TRUE available
## 8: TRUE available
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## available status
## <lgcl> <char>Core native imputers:
mean, median, modenaive: median/mode chained baselinenorm: linear normal drawpmm, spmm: predictive mean matchinglogreg: binary logistic regression drawpolyreg: one-vs-rest multinomial drawknn: nearest-neighbor donor imputationhotdeck: stochastic donor imputationLearner-backed imputers:
rf: MissForest-style chained random forest imputer
through rangerranger: random forest through rangerrpart: tree imputer through rpartnbayes: naive Bayes through
naivebayessvm: support vector machine through
e1071bart: Bayesian additive regression trees through
BARTglmnet: penalized regression through
glmnetgbm: gradient boosting through gbmxgboost: gradient boosted trees through
xgboostfamd: FAMD-assisted donor imputation through
missMDAsuperlearner, sl: cross-validated Super
Learner-style ensemble imputerImputer names are strict: use the names shown by
imputer_registry(). Learner-backed imputers are applied as
requested to numeric, binary, and multiclass targets; mimar
does not silently swap them for another imputer inside benchmark
runs.
The ncore argument runs independent completed datasets
in parallel. The parallel boundary is the outer imputation index: each
completed dataset gets a deterministic seed offset, so a fixed
seed, m, maxit, and imputer
remain reproducible.
i <- impute(a, imputer = "knn", m = 5, maxit = 5, seed = 1, ncore = 2)Use ncore = 1 for sequential execution, small examples,
and the most conservative behavior in constrained environments.
Learner-backed imputers expose their hyperparameters through
imputer() or directly through ... in
impute(). Donor-based imputers use the explicit
donors argument.
rf_spec <- imputer("rf", num.trees = 500)
xgb_spec <- imputer("xgboost", nrounds = 100, max_depth = 3)
i1 <- impute(a, imputer = rf_spec, m = 5, maxit = 5, seed = 1)
i2 <- impute(a, imputer = "xgboost", m = 5, maxit = 5, seed = 1,
nrounds = 100, max_depth = 3)
i3 <- impute(a, imputer = "knn", m = 5, maxit = 5, seed = 1, donors = 10)The same hyperparameter set is reused across all incomplete variables that a given imputer supports, which keeps the full chained-imputation pipeline reproducible and easy to tune.
superlearner combines candidate imputers by
cross-validating them on observed cells, assigning non-negative
loss-based weights, and using the weighted ensemble inside the
chained-imputation loop.
sl <- imputer(
"superlearner",
library = c("pmm", "knn", "rpart"),
folds = 5,
metalearner = "inverse_loss"
)
i_sl <- impute(a, imputer = sl, m = 5, maxit = 5, seed = 1)The short alias imputer = "sl" is equivalent to
imputer = "superlearner".
plot() methods return ggplot objects. For
mimar_imputation objects, the main diagnostic types
are:
plot(i) # imputed cell counts
plot(i, type = "missing") # observed/imputed cell map
plot(i, type = "trace", statistic = "mean") # convergence-screening trace
plot(i, type = "density", variable = "bmi") # line-only density overlays
plot(i, type = "boxplot", variable = "bmi") # observed vs imputation 1:m
plot(i, type = "strip", variable = "bmi") # individual values by imputation
Formula diagnostics are available for bivariate and categorical checks:
plot(i, type = "xy", formula = bmi ~ age | sex)
plot(i, type = "proportion", formula = group ~ sex)
For type = "xy", formulas use y ~ x or
y ~ x | group. For type = "proportion",
formulas use categorical_variable ~ strata. Density
diagnostics use line-only overlays so several imputations remain visible
rather than obscuring each other with filled areas.
Let X be an n x p data frame and let
R_ij = 1 when cell (i, j) is missing. For each
incomplete variable X_j:
O_j = {i : R_ij = 0} are the observed rowsM_j = {i : R_ij = 1} are the missing rowsAt each chained update, mimar fits an imputer-specific
model from the observed rows and then predicts the missing rows from the
current completed data. In compact form:
fit model on X_-j, O_j -> X_j, O_j
update X_j, M_j using the fitted modelMultiple imputation repeats the same chained procedure m
times with controlled seeds, bootstrap samples of observed rows, and
stochastic prediction where supported.
Learner-backed imputers are practical stochastic update rules inside this chained workflow. They can improve predictive recovery, but users should still inspect trace, distribution, categorical-proportion, and downstream sensitivity diagnostics rather than assuming every learner automatically supplies proper multiple-imputation uncertainty for every analysis.
Input: X, R, h, m, T
Initialize: X~(0) <- init(X)
For k = 1,...,m:
X~_k(0) <- X~(0)
For t = 1,...,T:
For each incomplete variable j:
B_j <- bootstrap sample of O_j
fit h on X~_k, B_j, -j and X_Bj,j
update missing rows M_j using the fitted model
restore observed rows O_j to their original values
Return: {X~_1(T), ..., X~_m(T)}When imputation is run on an ampute() object,
evaluate() uses the retained truth and scores only
artificially removed cells. Numeric recovery reports RMSE, MAE, bias,
and correlation. Categorical recovery reports accuracy and balanced
accuracy.
pool() combines post-fit quantities estimated separately
in each completed dataset. The statistical target is the quantity
itself, not a data frame. A quantity can be a scalar, coefficient
vector, covariance-aware parameter vector, matrix of survival
probabilities, or a scalar metric. Data frames are accepted only as a
tidy adapter for scalar model output.
For survival-probability matrices, pool_survmat()
applies the complementary log-log transform internally, pools on that
scale, and back-transforms the result.
For scalar quantities with complete-data variance estimates,
pool() applies Rubin-style pooling:
Q_bar = mean(Q_k)
U_bar = mean(U_k)
B = sample variance of Q_k
T = U_bar + (1 + 1/m) * Bresults <- data.frame(
term = rep(c("age", "bmi"), each = 3),
estimate = c(0.10, 0.11, 0.09, 0.30, 0.32, 0.29),
std.error = c(0.04, 0.05, 0.04, 0.08, 0.09, 0.08),
imputation = rep(1:3, times = 2)
)
pool(results)## mimar pooled results
## term estimate std.error statistic df p.value conf.low
## <char> <num> <num> <num> <num> <num> <num>
## 1: age 0.1000000 0.04509250 2.217664 465.125 0.027060256 0.01138975
## 2: bmi 0.3033333 0.08530989 3.555664 1094.452 0.000393134 0.13594390
## conf.high m within_variance between_variance total_variance
## <num> <int> <num> <num> <num>
## 1: 0.1886102 3 0.001900000 0.0001000000 0.002033333
## 2: 0.4707228 3 0.006966667 0.0002333333 0.007277778
## relative_increase_variance rule
## <num> <char>
## 1: 0.07017544 rubin
## 2: 0.04465710 rubinDirect quantity inputs are preferred when available:
pool(c(0.10, 0.11, 0.09), std.error = c(0.04, 0.05, 0.04), name = "age")## mimar pooled results
## term estimate std.error statistic df p.value conf.low conf.high
## <char> <num> <num> <num> <num> <num> <num> <num>
## 1: age 0.1 0.0450925 2.217664 465.125 0.02706026 0.01138975 0.1886102
## m within_variance between_variance total_variance
## <int> <num> <num> <num>
## 1: 3 0.0019 1e-04 0.002033333
## relative_increase_variance rule
## <num> <char>
## 1: 0.07017544 rubinbetas <- list(
c(age = 0.10, bmi = 0.30),
c(age = 0.11, bmi = 0.32),
c(age = 0.09, bmi = 0.29)
)
covariances <- list(
diag(c(0.04, 0.08)^2),
diag(c(0.05, 0.09)^2),
diag(c(0.04, 0.08)^2)
)
pool(betas, covariance = covariances)## mimar pooled results
## term estimate std.error statistic df p.value conf.low
## <char> <num> <num> <num> <num> <num> <num>
## 1: age 0.1000000 0.04509250 2.217664 465.125 0.027060256 0.01138975
## 2: bmi 0.3033333 0.08530989 3.555664 1094.452 0.000393134 0.13594390
## conf.high m within_variance between_variance total_variance
## <num> <int> <num> <num> <num>
## 1: 0.1886102 3 0.001900000 0.0001000000 0.002033333
## 2: 0.4707228 3 0.006966667 0.0002333333 0.007277778
## relative_increase_variance rule
## <num> <char>
## 1: 0.07017544 rubin
## 2: 0.04465710 rubinWhen no reliable complete-data variance is supplied, as is common for
some performance metrics, pool() reports robust summaries
by default: median, interquartile range, and range across
imputations.
Learner backends are hard dependencies. Installing mimar
installs the packages needed by the registered learner-backed imputers,
including ranger, rpart,
naivebayes, e1071, BART,
glmnet, gbm, xgboost, and
missMDA.