mice.impute.pmm: Imputation by predictive mean matching

View source: R/mice.impute.pmm.R

mice.impute.pmmR Documentation

Imputation by predictive mean matching


Imputation by predictive mean matching


  wy = NULL,
  donors = 5L,
  matchtype = 1L,
  exclude = -99999999,
  ridge = 1e-05,
  use.matcher = FALSE,



Vector to be imputed


Logical vector of length length(y) indicating the the subset y[ry] of elements in y to which the imputation model is fitted. The ry generally distinguishes the observed (TRUE) and missing values (FALSE) in y.


Numeric design matrix with length(y) rows with predictors for y. Matrix x may have no missing values.


Logical vector of length length(y). A TRUE value indicates locations in y for which imputations are created.


The size of the donor pool among which a draw is made. The default is donors = 5L. Setting donors = 1L always selects the closest match, but is not recommended. Values between 3L and 10L provide the best results in most cases (Morris et al, 2015).


Type of matching distance. The default choice (matchtype = 1L) calculates the distance between the predicted value of yobs and the drawn values of ymis (called type-1 matching). Other choices are matchtype = 0L (distance between predicted values) and matchtype = 2L (distance between drawn values).


Value or vector of values to exclude from the imputation donor pool in y


The ridge penalty used in .norm.draw() to prevent problems with multicollinearity. The default is ridge = 1e-05, which means that 0.01 percent of the diagonal is added to the cross-product. Larger ridges may result in more biased estimates. For highly noisy data (e.g. many junk variables), set ridge = 1e-06 or even lower to reduce bias. For highly collinear data, set ridge = 1e-04 or higher.


Logical. Set use.matcher = TRUE to specify the C function matcher(), the now deprecated matching function that was default in versions 2.22 (June 2014) to 3.11.7 (Oct 2020). Since version 3.12.0 mice() uses the much faster matchindex C function. Use the deprecated matcher function only for exact reproduction.


Other named arguments.


Imputation of y by predictive mean matching, based on van Buuren (2012, p. 73). The procedure is as follows:

  1. Calculate the cross-product matrix S=X_{obs}'X_{obs}.

  2. Calculate V = (S+{diag}(S)\kappa)^{-1}, with some small ridge parameter \kappa.

  3. Calculate regression weights \hat\beta = VX_{obs}'y_{obs}.

  4. Draw q independent N(0,1) variates in vector \dot z_1.

  5. Calculate V^{1/2} by Cholesky decomposition.

  6. Calculate \dot\beta = \hat\beta + \dot\sigma\dot z_1 V^{1/2}.

  7. Calculate \dot\eta(i,j)=|X_{{obs},[i]|}\hat\beta-X_{{mis},[j]}\dot\beta with i=1,\dots,n_1 and j=1,\dots,n_0.

  8. Construct n_0 sets Z_j, each containing d candidate donors, from Y_obs such that \sum_d\dot\eta(i,j) is minimum for all j=1,\dots,n_0. Break ties randomly.

  9. Draw one donor i_j from Z_j randomly for j=1,\dots,n_0.

  10. Calculate imputations \dot y_j = y_{i_j} for j=1,\dots,n_0.

The name predictive mean matching was proposed by Little (1988).


Vector with imputed data, same type as y, and of length sum(wy)


Gerko Vink, Stef van Buuren, Karin Groothuis-Oudshoorn


Little, R.J.A. (1988), Missing data adjustments in large surveys (with discussion), Journal of Business Economics and Statistics, 6, 287–301.

Morris TP, White IR, Royston P (2015). Tuning multiple imputation by predictive mean matching and local residual draws. BMC Med Res Methodol. ;14:75.

Van Buuren, S. (2018). Flexible Imputation of Missing Data. Second Edition. Chapman & Hall/CRC. Boca Raton, FL.

Van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1-67. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v045.i03")}

See Also

Other univariate imputation functions: mice.impute.cart(), mice.impute.lasso.logreg(), mice.impute.lasso.norm(), mice.impute.lasso.select.logreg(), mice.impute.lasso.select.norm(), mice.impute.lda(), mice.impute.logreg.boot(), mice.impute.logreg(), mice.impute.mean(), mice.impute.midastouch(), mice.impute.mnar.logreg(), mice.impute.mpmm(), mice.impute.norm.boot(), mice.impute.norm.nob(), mice.impute.norm.predict(), mice.impute.norm(), mice.impute.polr(), mice.impute.polyreg(), mice.impute.quadratic(), mice.impute.rf(), mice.impute.ri()


# We normally call mice.impute.pmm() from within mice()
# But we may call it directly as follows (not recommended)

xname <- c("age", "hgt", "wgt")
r <- stats::complete.cases(boys[, xname])
x <- boys[r, xname]
y <- boys[r, "tv"]
ry <- !is.na(y)

# percentage of missing data in tv
sum(!ry) / length(ry)

# Impute missing tv data
yimp <- mice.impute.pmm(y, ry, x)
hist(yimp, xlab = "Imputed missing tv")

# Impute all tv data
yimp <- mice.impute.pmm(y, ry, x, wy = rep(TRUE, length(y)))
hist(yimp, xlab = "Imputed missing and observed tv")
plot(jitter(y), jitter(yimp),
  main = "Predictive mean matching on age, height and weight",
  xlab = "Observed tv (n = 224)",
  ylab = "Imputed tv (n = 224)"
abline(0, 1)
cor(y, yimp, use = "pair")

# Use blots to exclude different values per column
# Create blots object
blots <- make.blots(boys)
# Exclude ml 1 through 5 from tv donor pool
blots$tv$exclude <- c(1:5)
# Exclude 100 random observed heights from tv donor pool
blots$hgt$exclude <- sample(unique(boys$hgt), 100)
imp <- mice(boys, method = "pmm", print = FALSE, blots = blots, seed=123)
blots$hgt$exclude %in% unlist(c(imp$imp$hgt)) # MUST be all FALSE
blots$tv$exclude %in% unlist(c(imp$imp$tv)) # MUST be all FALSE

mice documentation built on June 7, 2023, 5:38 p.m.