Package 'targeted'

Description

AIPW for the mean (and linear projections of the EIF) with missing observations

Usage

aipw(
  response.model,
  propensity.model,
  formula = ~1,
  data,
  response_model = deprecated,
  propensity_model = deprecated,
  ...
)

Arguments

Examples

m <- lava::lvm(y ~ x+z, r ~ x) |>
     lava::distribution(~ r, value = lava::binomial.lvm()) |>
     transform(y0~r+y, value = \(x) { x[x[,1]==0,2] <- NA; x[,2] })
d <- lava::sim(m,1e3,seed=1)

aipw(y0 ~ x, data=d)

Description

Assumption lean inference via cross-fitting (Double ML). See <doi:10.1111/rssb.12504

Usage

alean(
  response_model,
  exposure_model,
  data,
  link = "identity",
  g_model,
  nfolds = 1,
  silent = FALSE,
  mc.cores,
  ...
)

Arguments

Details

Let $Y$ be the response variable, $A$ the exposure and $W$ covariates. The target parameter is:

$\Psi(P) = \frac{E(Cov[A, g\{E(Y|A,W)\}\mid W])} {E\{Var(A\mid W)\}}$

The response_model is the model for $E(Y|A,W)$, and exposure_model is the model for $E(A|W)$. link specifies $g$.

Value

alean.targeted object

Author(s)

Klaus Kähler Holst

Examples

sim1 <- function(n, family=gaussian(), ...) {
   m <- lava::lvm() |>
     lava::distribution(~y, value=lava::binomial.lvm()) |>
     lava::regression('a', value=function(l) l) |>
     lava::regression('y', value=function(a,l) a + l)
     if (family$family=="binomial")
        lava::distribution(m, ~a) <- lava::binomial.lvm()
   lava::sim(m, n)
}

library(splines)
f <- binomial()
d <- sim1(1e4, family=f)
e <- alean(
 response_model=learner_glm(y ~ a + bs(l, df=3), family=binomial),
 exposure_model=learner_glm(a ~ bs(l, df=3), family=f),
 data=d,
 link = "logit", mc.cores=1, nfolds=1
)
e

e <- alean(response_model=learner_glm(y ~ a + l, family=binomial),
           exposure_model=learner_glm(a ~ l),
           data=d,
           link = "logit", mc.cores=1, nfolds=1)
e

Description

Augmented Inverse Probability Weighting estimator for the Average (Causal) Treatment Effect. All nuisance models are here parametric (glm). For a more general approach see the cate implementation. In this implementation the standard errors are correct even when the nuisance models are mis-specified (the influence curve is calculated including the term coming from the parametric nuisance models). The estimate is consistent if either the propensity model or the outcome model / Q-model is correctly specified.

Usage

ate(
  formula,
  data = parent.frame(),
  weights,
  offset,
  family = stats::gaussian(identity),
  nuisance = NULL,
  propensity = nuisance,
  all,
  labels = NULL,
  adjust.nuisance = TRUE,
  adjust.propensity = TRUE,
  ...
)

Arguments

Details

The formula may either be specified as: response ~ treatment | nuisance-formula | propensity-formula

For example: ate(y~a | x+z+a | x*z, data=...)

Alternatively, as a list: ate(list(y~a, ~x+z, ~x*z), data=...)

Or using the nuisance (and propensity argument): ate(y~a, nuisance=~x+z, ...)

Value

An object of class 'ate.targeted' is returned. See targeted-class for more details about this class and its generic functions.

Author(s)

Klaus K. Holst

See Also

cate

Examples

m <- lava::lvm(y ~ a+x, a~x) |>
     lava::distribution(~y, value = lava::binomial.lvm()) |>
     lava::ordinal(K=4, ~a) |>
     transform(~a, value = factor)
d <- lava::sim(m, 1e3, seed=1)
# (a <- ate(y~a|a*x|x, data=d))
(a <- ate(y~a, nuisance=~a*x, propensity=~x, data = d))

# Comparison with randomized experiment
m0 <- lava::cancel(m, a~x)
lm(y~a-1, lava::sim(m0,2e4))

# Choosing a different contrast for the association measures
summary(a, contrast=c(2,4))

Description

Calibration for multiclassication methods

Usage

calibration(
  pr,
  cl,
  weights = NULL,
  threshold = 10,
  method = "bin",
  breaks = nclass.Sturges,
  df = 3,
  ...
)

Arguments

Details

...

Value

An object of class 'calibration' is returned. See calibration-class for more details about this class and its generic functions.

Author(s)

Klaus K. Holst

Examples

sim1 <- function(n, beta=c(-3, rep(.5,10)), rho=.5) {
 p <- length(beta)-1
 xx <- lava::rmvn0(n,sigma=diag(nrow=p)*(1-rho)+rho)
 y <- rbinom(n, 1, lava::expit(cbind(1,xx)%*%beta))
 d <- data.frame(y=y, xx)
 names(d) <- c("y",paste0("x",1:p))
 return(d)
}

set.seed(1)
beta <- c(-2,rep(1,10))
d <- sim1(1e4, beta=beta)
a1 <- naivebayes(y ~ ., data=d)
a2 <- glm(y ~ ., data=d, family=binomial)
## a3 <- randomForest(factor(y) ~ ., data=d, family=binomial)

d0 <- sim1(1e4, beta=beta)
p1 <- predict(a1, newdata=d0)
p2 <- predict(a2, newdata=d0, type="response")
## p3 <- predict(a3, newdata=d0, type="prob")

c2 <- calibration(p2, d0$y, method="isotonic")
c1 <- calibration(p1, d0$y, breaks=100)
if (interactive()) {
  plot(c1)
  plot(c2,col="red",add=TRUE)
  abline(a=0,b=1)
  with(c1$xy[[1]], points(pred,freq,type="b", col="red"))
}

set.seed(1)
beta <- c(-2,rep(1,10))
dd <- lava::csplit(sim1(1e4, beta=beta), k=3)
mod <- naivebayes(y ~ ., data=dd[[1]])
p1 <- predict(mod, newdata=dd[[2]])
cal <- calibration(p1, dd[[2]]$y)
p2 <- predict(mod, newdata=dd[[3]])
pp <- predict(c1, p2)
cc <- calibration(pp, dd[[3]]$y)
if (interactive()) {#'
  plot(cal)
  plot(cc, add=TRUE, col="blue")
}

Description

The functions calibration returns an object of the class calibration.

An object of class 'calibration' is a list with at least the following components:

stepfun

estimated step-functions (see stepfun) for each class

classes

the unique classes

model

model/method type (string)

xy

list of data.frame's with predictions (pr) and estimated probabilities of success (only for 'bin' method)

Value

objects of the S3 class 'calibration'

S3 generics

The following S3 generic functions are available for an object of class calibration:

predict

Apply calibration to new data.

plot

Plot the calibration curves (reliability plot).

print

Basic print method.

See Also

calibration, calibrate

Examples

## See example(calibration) for examples

Description

Conditional Average Treatment Effect estimation with cross-fitting.

Usage

cate(
  response.model,
  treatment.model,
  cate.model = ~1,
  calibration.model = NULL,
  data,
  contrast,
  nfolds = 1,
  rep = 1,
  silent = FALSE,
  stratify = FALSE,
  mc.cores = NULL,
  var.type = "IC",
  second.order = TRUE,
  response_model = deprecated,
  cate_model = deprecated,
  propensity_model = deprecated,
  propensity.model = deprecated,
  treatment = deprecated,
  ...
)

Arguments

Details

We have observed data $(Y,A,W)$ where $Y$ is the response variable, $A$ the binary treatment, and $W$ covariates. We further let $V$ be a subset of the covariates. Define the conditional potential mean outcome

$\psi_{a}(P)(V) = E_{P}[E_{P}(Y\mid A=a, W)|V]$

and let $m(V; \beta)$ denote a parametric working model, then the target parameter is the mean-squared error

$\beta(P) = \operatorname{argmin}_{\beta} E_{P}[\{\Psi_{1}(P)(V)-\Psi_{0}(P)(V)\} - m(V; \beta)]^{2}$

Value

cate.targeted object

Author(s)

Klaus Kähler Holst, Andreas Nordland

References

Mark J. van der Laan (2006) Statistical Inference for Variable Importance, The International Journal of Biostatistics.

Bannick, Shao & Liu et al. (2025) A General Form of Covariate Adjustment in Clinical Trials under Covariate-Adaptive Randomization, Biometrika.

Examples

sim1 <- function(n=1000, ...) {
  w1 <- rnorm(n)
  w2 <- rnorm(n)
  a <- rbinom(n, 1, plogis(-1 + w1))
  y <- cos(w1) + w2*a + 0.2*w2^2 + a + rnorm(n)
  data.frame(y, a, w1, w2)
}

d <- sim1(5000)
## ATE
cate(cate.model=~1,
     response.model=y~a*(w1+w2),
     treatment.model=a~w1+w2,
     data=d)
## CATE
cate(cate.model=~1+w2,
     response.model=y~a*(w1+w2),
     treatment.model=a~w1+w2,
     data=d)

## Not run:  ## superlearner example
mod1 <- list(
   glm = learner_glm(y~w1+w2),
   gam = learner_gam(y~s(w1) + s(w2))
)
s1 <- learner_sl(mod1, nfolds=5)
cate(cate.model=~1,
     response.model=s1,
     treatment.model=learner_glm(a~w1+w2, family=binomial),
     data=d,
     stratify=TRUE)

## End(Not run)

Description

Conditional average treatment effect estimation via Double Machine Learning

Usage

cate_link(
  treatment,
  link = "identity",
  response_model,
  propensity_model,
  importance_model,
  contrast = c(1, 0),
  data,
  nfolds = 5,
  type = "dml1",
  ...
)

Arguments

Value

cate.targeted object

Author(s)

Klaus Kähler Holst & Andreas Nordland

Examples

# Example 1:
sim1 <- function(n=1e4,
                 seed=NULL,
                 return_model=FALSE, ...){
suppressPackageStartupMessages(require("lava"))
if (!is.null(seed)) set.seed(seed)
m <- lava::lvm()
distribution(m, ~x) <- gaussian.lvm()
distribution(m, ~v) <- gaussian.lvm(mean = 10)
distribution(m, ~a) <- binomial.lvm("logit")
regression(m, "a") <- function(v, x){.1*v + x}
distribution(m, "y") <- gaussian.lvm()
regression(m, "y") <- function(a, v, x){v+x+a*x+a*v*v}
if (return_model) return(m)
lava::sim(m, n = n)
}

if (require("SuperLearner",quietly=TRUE)) {
  d <- sim1(n = 1e3, seed = 1)
  e <- cate_link(data=d,
           type = "dml2",
           treatment = a ~ v,
           response_model = y~ a*(x + v + I(v^2)),
           importance_model = SL(D_ ~ v + I(v^2)),
           nfolds = 10)
  summary(e) # the true parameters are c(1,1)
}

Description

Construct a learner

Arguments

Value

learner object.

Description

The functions cv returns an object of the type cross_validated.

An object of class 'cross_validated' is a list with at least the following components:

cv

An array with the model score(s) evaluated for each fold, repetition, and model estimates (see estimate.default)

names

Names (character vector) of the models

rep

number of repetitions of the CV

folds

Number of folds of the CV

Value

objects of the S3 class 'cross_validated'

S3 generics

The following S3 generic functions are available for an object of class cross_validated:

coef

Extract average model scores from the cross-validation procedure.

print

Basic print method.

summary

Summary of the cross-validation procedure.

'

See Also

cv

Examples

# See example(cv) for examples

Description

Conditional Relative Risk estimation via Double Machine Learning

Usage

crr(
  treatment,
  response_model,
  propensity_model,
  importance_model,
  contrast = c(1, 0),
  data,
  nfolds = 5,
  type = "dml1",
  ...
)

Arguments

Value

cate.targeted object

Author(s)

Klaus Kähler Holst & Andreas Nordland

Examples

sim1 <- function(n=1e4,
                 seed=NULL,
                 return_model=FALSE, ...){
suppressPackageStartupMessages(require("lava"))
if (!is.null(seed)) set.seed(seed)
m <- lava::lvm()
distribution(m, ~x) <- gaussian.lvm()
distribution(m, ~v) <- gaussian.lvm(mean = 10)
distribution(m, ~a) <- binomial.lvm("logit")
regression(m, "a") <- function(v, x){.1*v + x}
distribution(m, "y") <- gaussian.lvm()
regression(m, "y") <- function(a, v, x){v+x+a*x+a*v*v}
if (return_model) return(m)
lava::sim(m, n = n)
}

d <- sim1(n = 2e3, seed = 1)
if (require("SuperLearner",quietly=TRUE)) {
  e <- crr(data=d,
   type = "dml2",
   treatment = a ~ v,
   response_model = learner_glm(y~ a*(x + v + I(v^2))),
   importance_model = learner_glm(D_ ~ v + I(v^2)),
   propensity_model = learner_glm(a ~ x + v + I(v^2), family=binomial),
           nfolds = 2)
  summary(e) # the true parameters are c(1,1)
}

Description

Predict the cumulative hazard/survival function for a survival model

Usage

cumhaz(
  object,
  newdata,
  times = NULL,
  individual.time = FALSE,
  extend = FALSE,
  ...
)

Arguments

Value

List with elements:

• time: numeric vector

• chf: cumulative hazard function. If individual.time = FALSE, matrix with dimension (nrow(newdata), length(times)). If individual.time = TRUE, vector of length length(times).

• surv: survival function, exp(-chf).

• dchf: t(diff(rbind(0, t(chf))))

Author(s)

Klaus K. Holst, Andreas Nordland

Description

Generic cross-validation function

Usage

## Default S3 method:
cv(
  object,
  data,
  response = NULL,
  nfolds = 5,
  rep = 1,
  weights = NULL,
  model.score = scoring,
  seed = NULL,
  shared = NULL,
  args.pred = NULL,
  args.future = list(),
  mc.cores,
  silent = FALSE,
  ...
)

Arguments

Details

object should be list of objects of class learner. Alternatively, each element of models should be a list with a fitting function and a prediction function.

The response argument can optionally be a named list where the name is then used as the name of the response argument in models. Similarly, if data is a named list with a single data.frame/matrix then this name will be used as the name of the data/design matrix argument in models.

Value

An object of class 'cross_validated' is returned. See cross_validated-class for more details about this class and its generic functions.

Author(s)

Klaus K. Holst

See Also

cv.learner_sl

Examples

m <- list(learner_glm(Sepal.Length~1),
          learner_glm(Sepal.Length~Species),
          learner_glm(Sepal.Length~Species + Petal.Length))
x <- cv(m, rep=10, data=iris)
x

Cross-validation for learner_sl

Description

Cross-validation estimation of the generalization error of the super learner and each of the separate models in the ensemble. Both the chosen model scoring metrics as well as the model weights of the stacked ensemble.

Usage

## S3 method for class 'learner_sl'
cv(object, data, nfolds = 5, rep = 1, model.score = scoring, ...)

Arguments

Examples

sim1 <- function(n = 5e2) {
   x1 <- rnorm(n, sd = 2)
   x2 <- rnorm(n)
   y <- x1 + cos(x1) + rnorm(n, sd = 0.5**.5)
   data.frame(y, x1, x2)
}
sl <- learner_sl(list(
                   "mean" = learner_glm(y ~ 1),
                   "glm" = learner_glm(y ~ x1),
                   "glm2" = learner_glm(y ~ x1 + x2)
                  ))
cv(sl, data = sim1(), rep = 2)

Description

Cast warning for deprecated function argument names

Usage

deprecate_arg_warn(old, new, fun, vers)

Arguments

Description

Deprecated argument names

Arguments

Description

Extract design matrix from data.frame and formula

Usage

design(
  formula,
  data,
  ...,
  intercept = FALSE,
  response = TRUE,
  rm_envir = FALSE,
  specials = NULL,
  specials.call = NULL,
  levels = NULL,
  design.matrix = TRUE
)

Arguments

Value

An object of class 'design'

Author(s)

Klaus Kähler Holst

Description

Let $Y$ denote the clinical outcome, $A$ the binary treatment variable, $X$ baseline covariates, $T$ the failure time, and $epsilon=1,2$ the cause of failure. The following are our two target parameters

$E(Y|T>t, A=1)- E(Y|T>t, A=0)$

$P(T<t,\epsilon=1|A=1)- P(T<t,\epsilon=1|A=0)$

Usage

estimate_truncatedscore(
  data,
  mod.y,
  mod.r,
  mod.a,
  mod.event,
  time,
  cause = NULL,
  cens.code = 0,
  naive = FALSE,
  control = list(),
  ...
)

Arguments

Value

lava::estimate.default object

Author(s)

Klaus Kähler Holst

Examples

data(truncatedscore)
mod1 <- learner_glm(y ~ a * (x1 + x2))
mod2 <- learner_glm(r ~ a * (x1 + x2), family = binomial)
a <- estimate_truncatedscore(
  data = truncatedscore,
  mod.y = mod1,
  mod.r = mod2,
  mod.a = a ~ 1,
  mod.event = mets::Event(time, status) ~ x1+x2,
  time = 2
)
s <- summary(a, noninf.t = -0.1)
print(s)
parameter(s)

# the above is equivalent to
# a <- estimate_truncatedscore(
#   data = truncatedscore,
#   mod.y = y ~ a * (x1 + x2),
#   mod.r = r ~ a * (x1 + x2),
#   mod.a = a ~ 1,
#   mod.event = mets::Event(time, status) ~ x1+x2,
#   time = 2
# )

Description

Similar to expand.grid function, this function creates all combinations of the input arguments but returns the result as a list.

Usage

expand.list(..., INPUT = NULL, envir = NULL)

Arguments

Value

list

Author(s)

Klaus Kähler Holst

Examples

expand.list(x = 2:4, z = c("a", "b"))

Description

Fit survival nuisance models

Usage

fit_survival_models(
  data,
  response,
  censoring,
  response_call = "phreg",
  response_args = list(),
  censoring_call = "phreg",
  censoring_args = list()
)

Arguments

Value

List with elements T_model and C_model

Author(s)

Andreas Nordland, Klaus K. Holst

Description

Computes an approximation of $\int_start^stop S(t) dt$, where $S(t)$ is a survival function, for a selection of start and stop time points.

Usage

int_surv(times, surv, start = 0, stop = max(times), extend = FALSE)

Arguments

Value

Numeric vector, value of the integral.

Author(s)

Andreas Nordland

Description

Interface for statistical and machine learning models to be used for nuisance model estimation in targeted learning.

The following list provides an overview of constructors for many commonly used models.

Regression and classification: learner_glm, learner_gam, learner_grf, learner_hal, learner_glmnet_cv, learner_svm, learner_xgboost, learner_mars
Regression: learner_isoreg
Classification: learner_naivebayes
Ensemble (super learner): learner_sl

Public fields

Active bindings

Methods

Public methods

• learner$new()

• learner$estimate()

• learner$predict()

• learner$update()

• learner$print()

• learner$summary()

• learner$response()

• learner$design()

• learner$opt()

• learner$clone()

learner$new()

Create a new prediction model object

Usage

learner$new(
  formula = NULL,
  estimate,
  predict = stats::predict,
  predict.args = NULL,
  estimate.args = NULL,
  info = NULL,
  specials = c(),
  formula.keep.specials = FALSE,
  predict.filter = function(data, ...) function(pred, newdata, ...) pred,
  intercept = FALSE
)

Arguments

learner$estimate()

Estimation method

Usage

learner$estimate(data, ..., store = TRUE)

Arguments

learner$predict()

Prediction method

Usage

learner$predict(newdata, ..., object = NULL)

Arguments

learner$update()

Update formula

Usage

learner$update(formula)

Arguments

learner$print()

Print method

Usage

learner$print()

learner$summary()

Summary method to provide more extensive information than learner$print().

Usage

learner$summary()

Returns

summarized_learner object, which is a list with the following elements:

info

description of the learner

formula

formula specifying outcome and design matrix

estimate

function for fitting the model

estimate.args

arguments to estimate function

predict

function for making predictions from fitted model

predict.args

arguments to predict function

specials

provided special terms

intercept

include intercept in design matrix

Examples

lr <- learner_glm(y ~ x, family = "nb")
lr$summary()

lr_sum <- lr$summary() # store returned summary in new object
names(lr_sum)
print(lr_sum)

learner$response()

Extract response from data

Usage

learner$response(data, eval = TRUE, ...)

Arguments

learner$design()

Generate design object (design matrix and response) from data

Usage

learner$design(data, ...)

Arguments

learner$opt()

Get options

Usage

learner$opt(arg)

Arguments

learner$clone()

The objects of this class are cloneable with this method.

Usage

learner$clone(deep = FALSE)

Arguments

Author(s)

Klaus Kähler Holst, Benedikt Sommer

Examples

data(iris)
rf <- function(formula, ...) {
  learner$new(formula,
    info = "grf::probability_forest",
    estimate = function(x, y, ...) {
      grf::probability_forest(X = x, Y = y, ...)
    },
    predict = function(object, newdata) {
      predict(object, newdata)$predictions
    },
    estimate.args = list(...)
  )
}

args <- expand.list(
  num.trees = c(100, 200), mtry = 1:3,
  formula = c(Species ~ ., Species ~ Sepal.Length + Sepal.Width)
)
models <- lapply(args, function(par) do.call(rf, par))

x <- models[[1]]$clone()
x$estimate(iris)
predict(x, newdata = head(iris))


# Reduce Ex. timing
a <- targeted::cv(models, data = iris)
cbind(coef(a), attr(args, "table"))


# defining learner via function with arguments y (response)
# and x (design matrix)
f1 <- learner$new(
  estimate = function(y, x) lm.fit(x = x, y = y),
  predict = function(object, newdata) newdata %*% object$coefficients
)
# defining the learner via arguments formula and data
f2 <- learner$new(
  estimate = function(formula, data, ...) glm(formula, data, ...)
)
# generic learner defined from function (predict method derived per default
# from stats::predict
f3 <- learner$new(
  estimate = function(dt, ...) {
    lm(y ~ x, data = dt)
  }
)

## ------------------------------------------------
## Method `learner$summary()`
## ------------------------------------------------

lr <- learner_glm(y ~ x, family = "nb")
lr$summary()

lr_sum <- lr$summary() # store returned summary in new object
names(lr_sum)
print(lr_sum)

Description

Construct learners from a grid of parameters

Usage

learner_expand_grid(fun, args, names = TRUE, params = FALSE)

Arguments

Value

list

Examples

lrs <- learner_expand_grid(
  learner_xgboost,
  list(formula = Sepal.Length ~ ., eta = c(0.2, 0.5, 0.3))
)
lrs # use info of constructed learner as names

lrs <- learner_expand_grid(
  learner_xgboost,
  list(formula = Sepal.Length ~ ., eta = c(0.2, 0.5, 0.3)),
  names = "xgboost"
)
names(lrs) # use xgboost instead of info field for names

lrs <- learner_expand_grid(
  learner_xgboost,
  list(formula = Sepal.Length ~ ., eta = c(0.2, 0.5, 0.3)),
  names = "xgboost",
  params = TRUE
)
names(lrs) # also add parameters to names

lrs <- learner_expand_grid(
  learner_xgboost,
  list(formula = Sepal.Length ~ ., eta = c(0.2, 0.5, 0.3)),
  names = FALSE
)
names(lrs) # unnamed list since names = FALSE

Description

Constructs learner class object for fitting generalized additive models with mgcv::gam.

Usage

learner_gam(
  formula,
  info = "mgcv::gam",
  family = gaussian(),
  select = FALSE,
  gamma = 1,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
y <- x1 + cos(x1) + rnorm(n, sd = 0.5**.5)
d0 <- data.frame(y, x1, x2)

lr <- learner_gam(y ~ s(x1) + x2)
lr$estimate(d0)
if (interactive()) {
  plot(lr$fit)
}

Description

Constructs a learner class object for fitting generalized linear models with stats::glm and MASS::glm.nb. Negative binomial regression is supported with family = "nb" (or alternatively family = "negbin").

Usage

learner_glm(
  formula,
  info = "glm",
  family = gaussian(),
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n <- 5e2
x <- rnorm(n)
w <- 50 + rexp(n, rate = 1 / 5)
y <- rpois(n, exp(2 + 0.5 * x + log(w)) * rgamma(n, 1 / 2, 1 / 2))
d0 <- data.frame(y, x, w)

lr <- learner_glm(y ~ x) # linear Gaussian model
lr$estimate(d0)
coef(lr$fit)

# negative binomial regression model with offset (using MASS::glm.nb)
lr <- learner_glm(y ~ x + offset(log(w)), family = "nb")
lr$estimate(d0)
coef(lr$fit)
lr$predict(data.frame(x = 1, w = c(1, 5))) # response scale
lr$predict(data.frame(x = 1, w = c(1, 5)), type = "link") # link scale

Description

Constructs a learner class object for fitting entire lasso or elastic-net regularization paths for various linear and non-linear regression models with glmnet::cv.glmnet. Predictions are returned for the value of lambda that gives minimum cvm. That is, glmnet::predict.cv.glmnet is called with s = "lambda.min".

Usage

learner_glmnet_cv(
  formula,
  info = "glmnet::cv.glmnet",
  family = gaussian(),
  lambda = NULL,
  alpha = 1,
  nfolds = 10,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

# continuous outcome
n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
lp <- x1 + x2*x1 + cos(x1)
y <- rnorm(n, lp, sd = 2)
d0 <- data.frame(y, x1, x2)

lr <- learner_glmnet_cv(y ~ x1 + x2)
lr$estimate(d0, nfolds = 3)
lr$predict(data.frame(x1 = c(0, 1), x2 = 1))

# count outcome with different exposure time
w <- 50 + rexp(n, rate = 1 / 5)
y <- rpois(n, exp(0.5 * x1 - 1 * x2 + log(w)) * rgamma(n, 1 / 2, 1 / 2))
d0 <- data.frame(y, x1, x2, w)

lr <- learner_glmnet_cv(y ~ x1 + x2 + offset(log(w)), family = "poisson")
lr$estimate(d0, nfolds = 3)
lr$predict(data.frame(x1 = 1, x2 = 1, w = c(1, 5)))

Description

Constructs a learner class object for fitting generalized random forest models with grf::regression_forest or grf::probability_forest. As shown in the examples, the constructed learner returns predicted class probabilities of class 2 in case of binary classification. A ⁠n times p⁠ matrix, with n being the number of observations and p the number of classes, is returned for multi-class classification.

Usage

learner_grf(
  formula,
  num.trees = 2000,
  min.node.size = 5,
  alpha = 0.05,
  sample.fraction = 0.5,
  num.threads = 1,
  model = "grf::regression_forest",
  info = model,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
lp <- x2*x1 + cos(x1)
yb <- rbinom(n, 1, lava::expit(lp))
y <-  lp + rnorm(n, sd = 0.5**.5)
d <- data.frame(y, yb, x1, x2)

# regression
lr <- learner_grf(y ~ x1 + x2)
lr$estimate(d)
lr$predict(head(d))

# binary classification
lr <- learner_grf(as.factor(yb) ~ x1 + x2, model = "probability_forest")
lr$estimate(d)
lr$predict(head(d)) # predict class probabilities of class 2

# multi-class classification
lr <- learner_grf(Species ~ ., model = "probability_forest")
lr$estimate(iris)
lr$predict(head(iris))

Description

Constructs a learner class object for fitting a highly adaptive lasso model with hal9001::fit_hal.

Usage

learner_hal(
  formula,
  info = "hal9001::fit_hal",
  smoothness_orders = 0,
  reduce_basis = NULL,
  family = "gaussian",
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

## Not run: 
n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
y <- x1 + cos(x1) + rnorm(n, sd = 0.5**.5)
d <- data.frame(y, x1, x2)
lr <- learner_hal(y ~ x1 + x2, smoothness_orders = 0.5, reduce_basis = 1)
lr$estimate(d)
lr$predict(data.frame(x1 = 0, x2 = c(-1, 1)))

## End(Not run)

Description

Constructs a learner class object for isotonic regression with isoregw.

Usage

learner_isoreg(formula, info = "targeted::isoregw", learner.args = NULL, ...)

Arguments

Value

learner object.

Examples

x <- runif(5e3, -5, 5)
pr <- lava::expit(-1 + x)
y <- rbinom(length(pr), 1, pr)
d <- data.frame(y, x)

lr <- learner_isoreg(y ~ x)
lr$estimate(d)
pr_iso <- lr$predict(d)

if (interactive()) {
  plot(pr ~ x, cex=0.3)
  lines(sort(x), pr_iso[order(x)], col="red", type="s")
}

Description

Constructs a learner class object for fitting multivariate adaptive regression splines with earth::earth.

Usage

learner_mars(
  formula,
  info = "earth::earth",
  degree = 1,
  nprune = NULL,
  glm = NULL,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

# poisson regression
n <- 5e2
x <- rnorm(n)
w <- 50 + rexp(n, rate = 1 / 5)
y <- rpois(n, exp(2 + 0.5 * x + log(w)) * rgamma(n, 1 / 2, 1 / 2))
d0 <- data.frame(y, x, w)

lr <- learner_mars(y ~ x + offset(log(w)), degree = 2,
  glm = list(family = poisson())
)
lr$estimate(d0)
lr$predict(data.frame(x = 0, w = c(1, 2)))

Description

Constructs a learner class object for fitting a naive bayes classifier with naivebayes. As shown in the examples, the constructed learner returns predicted class probabilities of class 2 in case of binary classification. A ⁠n times p⁠ matrix, with n being the number of observations and p the number of classes, is returned for multi-class classification.

Usage

learner_naivebayes(
  formula,
  info = "Naive Bayes",
  laplace.smooth = 0,
  kernel = FALSE,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
y <- rbinom(n, 1, lava::expit(x2*x1 + cos(x1)))
d <- data.frame(y, x1, x2)

# binary classification
lr <- learner_naivebayes(y ~ x1 + x2)
lr$estimate(d)
lr$predict(head(d))

# multi-class classification
lr <- learner_naivebayes(Species ~ .)
lr$estimate(iris)
lr$predict(head(iris))

Description

Constructs a learner class object for fitting a superlearner.

Usage

learner_sl(
  learners,
  info = NULL,
  nfolds = 5L,
  meta.learner = metalearner_nnls,
  model.score = mse,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

See Also

cv.learner_sl

Examples

sim1 <- function(n = 5e2) {
   x1 <- rnorm(n, sd = 2)
   x2 <- rnorm(n)
   y <- x1 + cos(x1) + rnorm(n, sd = 0.5**.5)
   data.frame(y, x1, x2)
}
d <- sim1()

m <- list(
  "mean" = learner_glm(y ~ 1),
  "glm" = learner_glm(y ~ x1 + x2),
  "iso" = learner_isoreg(y ~ x1)
)

s <- learner_sl(m, nfolds = 10)
s$estimate(d)
pr <- s$predict(d)
if (interactive()) {
    plot(y ~ x1, data = d)
    points(d$x1, pr, col = 2, cex = 0.5)
    lines(cos(x1) + x1 ~ x1, data = d[order(d$x1), ],
          lwd = 4, col = lava::Col("darkblue", 0.3))
}
print(s)
# weights(s$fit)
# score(s$fit)

cvres <- cv(s, data = d, nfolds = 3, rep = 2)
cvres
# coef(cvres)
# score(cvres)

Description

This function creates a stratified learner from an existing learner wrapper function such as learner_glm or learner_xgboost. The stratification variable can be specified either using the stratify argument (which can be given as a string "a" or a formula , for example ~ I(a==0)), or it can be defined as a special term directly in the formula, y ~ ... + stratify(a). The formula will subsequently be passed to the learner_ wrapper without the stratify special term.

Usage

learner_stratify(
  formula,
  learner,
  stratify = NULL,
  info = NULL,
  learner.args = list(),
  ...
)

Arguments

Value

learner object

Examples

simdata <- function(n=1000) {
  a <- rbinom(n, 1, 0.5)
  x <- rnorm(n)
  y <- rbinom(n, 1, plogis(-1 + a + a * x))
  data.frame(y, a, x)
}
d <- simdata()

lr <- learner_stratify(
  y ~ x + stratify(a),
  learner_glm,
  family=binomial()
)
lr$estimate(d)
lr$predict(head(d))

Description

Constructs a learner class object for fitting Cox proportional hazards models.

Usage

learner_surv_cox(formula, info = "mets::phreg", learner.args = NULL, ...)

Arguments

Value

learner object.

Author(s)

Klaus Kähler Holst

Examples

data(sTRACE, package="mets")
mod <- learner_surv_cox(Surv(time, status>0) ~ sex + strata(age))
mod$estimate(sTRACE)
mod$predict(head(sTRACE), times=5) # P(T>t|X)

Description

Constructs a learner class object for random survival forests

Usage

learner_surv_rf(
  formula,
  info = "survival forest (ranger)",
  num.threads = 1L,
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Author(s)

Klaus Kähler Holst

Examples

data(sTRACE, package="mets")
mod <- learner_surv_rf(Surv(time, status>0) ~ sex + age)
mod$estimate(sTRACE)
mod$predict(head(sTRACE), times=5) # P(T>t|X)

Description

Constructs a learner class object for fitting support vector machines with e1071::svm. As shown in the examples, the constructed learner returns predicted class probabilities of class 2 in case of binary classification. A ⁠n times p⁠ matrix, with n being the number of observations and p the number of classes, is returned for multi-class classification.

Usage

learner_svm(
  formula,
  info = "e1071::svm",
  cost = 1,
  epsilon = 0.1,
  kernel = "radial",
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n <- 5e2
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
lp <- x2*x1 + cos(x1)
yb <- rbinom(n, 1, lava::expit(lp))
y <-  lp + rnorm(n, sd = 0.5**.5)
d <- data.frame(y, yb, x1, x2)

# regression
lr <- learner_svm(y ~ x1 + x2)
lr$estimate(d)
lr$predict(head(d))

# binary classification
lr <- learner_svm(as.factor(yb) ~ x1 + x2)
# alternative to transforming response variable to factor
# lr <- learner_svm(yb ~ x1 + x2, type = "C-classification")
lr$estimate(d)
lr$predict(head(d)) # predict class probabilities of class 2
lr$predict(head(d), probability = FALSE) # predict labels

# multi-class classification
lr <- learner_svm(Species ~ .)
lr$estimate(iris)
lr$predict(head(iris))

Description

Constructs a learner class object for xgboost::xgboost.

Usage

learner_xgboost(
  formula,
  max_depth = 2L,
  learning_rate = 1,
  nrounds = 2L,
  subsample = 1,
  reg_lambda = 1,
  objective = "reg:squarederror",
  info = paste("xgboost", objective),
  learner.args = NULL,
  ...
)

Arguments

Value

learner object.

Examples

n  <- 1e3
x1 <- rnorm(n, sd = 2)
x2 <- rnorm(n)
lp <- x2*x1 + cos(x1)
yb <- rbinom(n, 1, lava::expit(lp))
y <-  lp + rnorm(n, sd = 0.5**.5)
d0 <- data.frame(y, yb, x1, x2)

# regression
lr <- learner_xgboost(y ~ x1 + x2, nrounds = 5)
lr$estimate(d0)
lr$predict(head(d0))

# binary classification
lr <- learner_xgboost(yb ~ x1 + x2, nrounds = 5,
 objective = "binary:logistic"
)
lr$estimate(d0)
lr$predict(head(d0))

# multi-class classification
d0 <- iris
d0$y <- as.numeric(d0$Species)- 1

lr <- learner_xgboost(y ~ ., objective = "multi:softprob", num_class = 3)
lr$estimate(d0)
lr$predict(head(d0))

Description

Naive Bayes Classifier

Usage

naivebayes(
  formula,
  data,
  weights = NULL,
  kernel = FALSE,
  laplace.smooth = 0,
  prior = NULL,
  ...
)

Arguments

Value

An object of class 'naivebayes' is returned. See naivebayes-class for more details about this class and its generic functions.

Author(s)

Klaus K. Holst

Examples

library(data.table)
data(iris)
m <- naivebayes(Species ~ Sepal.Width + Petal.Length, data = iris)
pr <- predict(m, newdata = iris)

# using weights to reduce the size of the dataset
n <- 5e2
x <- rnorm(n, sd = 2) > 0
y <- rbinom(n, 1, lava::expit(x))
# full data set
d1 <- data.frame(y, x = as.factor(x > 0))
m1 <- naivebayes(y ~ x, data = d1)
# reduced data set
d2 <- data.table(d1)[, .(.N), by = .(y, x)]
m2 <- naivebayes(y ~ x, data = d2, weights = d2$N)
all(predict(m1, d1) == predict(m2, d1))

Description

The functions naivebayes returns an object of the type naivebayes.

An object of class 'naivebayes' is a list with at least the following components:

prior

Matrix with prior probabilities, i.e. marginal class probabilities Pr(class)

pcond

list of matrices with conditional probabilities of the features given the classes (one list element per class), Pr(x|class)

classes

Names (character vector) of the classes

xvar

Names of predictors

xmodel

Conditional model for each predictor

design

Model design object

call

The function call which instantiated the object

Value

objects of the S3 class 'naivebayes'

S3 generics

The following S3 generic functions are available for an object of class naivebayes:

predict

Predict class probabilities for new features data.

print

Basic print method.

See Also

naivebayes()

Examples

## See example(naivebayes) for examples

Description

Find the non-dominated point of a set (minima of a point set).

Usage

nondom(x, ...)

Arguments

Details

A point x dominates y if it is never worse and at least in one case strictly better. Formally, let f_i denote the ith coordinate of the condition (objective) function, then for all i: f_i(x)<=f_i(y) and there exists j: f_j(x)<f_j(y).

Based on the algorithm of Kung et al. 1975.

Value

matrix

Author(s)

Klaus Kähler Holst

Examples

rbind(
  c(1.0, 0.5),
  c(0.0, 1.0),
  c(1.0, 0.0),
  c(0.5, 1.0),
  c(1.0, 1.0),
  c(0.8, 0.8)) |> nondom()

Description

Pooled Adjacent Violators Algorithm

Usage

pava(y, x = numeric(0), weights = numeric(0))

Arguments

Value

List with index (idx) of jump points and values (value) at each jump point.

Author(s)

Klaus K. Holst

Examples

x <- runif(5e3, -5, 5)
pr <- lava::expit(-1 + x)
y <- rbinom(length(pr), 1, pr)
pv <- pava(y, x)
plot(pr ~ x, cex=0.3)
with(pv, lines(sort(x)[index], value, col="red", type="s"))

Description

Kernel density estimator predictions

Usage

## S3 method for class 'density'
predict(object, xnew, ...)

Arguments

Author(s)

Klaus K. Holst

Description

Naive Bayes Classifier predictions

Usage

## S3 method for class 'naivebayes'
predict(object, newdata, expectation = NULL, threshold = c(0.001, 0.001), ...)

Arguments

Author(s)

Klaus K. Holst

Description

Obtains predictions for ensemble model or individual learners.

Usage

## S3 method for class 'superlearner'
predict(object, newdata, all.learners = FALSE, ...)

Arguments

Value

numeric (all.learners = FALSE) or matrix (all.learners = TRUE)

Description

Estimation of the Average Treatment Effect among Responders

Usage

RATE(
  response,
  post.treatment,
  treatment,
  data,
  M = 5,
  pr.treatment,
  treatment.level,
  SL.args.response = list(family = gaussian(), SL.library = c("SL.mean", "SL.glm")),
  SL.args.post.treatment = list(family = binomial(), SL.library = c("SL.mean", "SL.glm")),
  preprocess = NULL,
  efficient = TRUE,
  ...
)

Arguments

Value

estimate object

Author(s)

Andreas Nordland, Klaus K. Holst

Description

Estimation of the Average Treatment Effect among Responders for Survival Outcomes

Usage

RATE.surv(
  response,
  post.treatment,
  treatment,
  censoring,
  tau,
  data,
  M = 5,
  pr.treatment,
  call.response,
  args.response = list(),
  SL.args.post.treatment = list(family = binomial(), SL.library = c("SL.mean", "SL.glm")),
  call.censoring,
  args.censoring = list(),
  preprocess = NULL,
  ...
)

Arguments

Details

Estimation of

$\frac{P(T \leq \tau|A=1) - P(T \leq \tau|A=1)}{E[D|A=1]}$

under right censoring based on plug-in estimates of $P(T \leq \tau|A=a)$ and $E[D|A=1]$.

An efficient one-step estimator of $P(T \leq \tau|A=a)$ is constructed using the efficient influence function

$\frac{I\{A=a\}}{P(A = a)} \Big(\frac{\Delta}{S^c_{0}(\tilde T|X)} I\{\tilde T \leq \tau\} + \int_0^\tau \frac{S_0(u|X)-S_0(\tau|X)}{S_0(u|X)S^c_0(u|X)} d M^c_0(u|X)\Big)$

$+ \Big(1 - \frac{I\{A=a\}}{P(A = a)}\Big)F_0(\tau|A=a, W) - P(T \leq \tau|A=a).$

An efficient one-step estimator of $E[D|A=1]$ is constructed using the efficient influence function

$\frac{A}{P(A = 1)}\left(D-E[D|A=1, W]\right) + E[D|A=1, W] -E[D|A=1].$

Value

estimate object

Author(s)

Andreas Nordland, Klaus K. Holst

Description

For a user defined function $H(u|X)$, computes the integral $\int_0^\tau \frac{H(u)|X}{S^c}$ dM^c(u|X), where $S^c$ is the censoring time survival function and $M^c$ is the censoring is the right censoring martingale with the Doob-Meyer decomposition $M^c = N^c - L^c$, where $N^c$ is the counting process $N^c(s) = I\{\tilde T \leq s \Delta = 0\}$ and $L^c$ is the compensator $L^c(s) = \int_0^s I \{\tilde T \geq u\} d\Lambda^c(u|X)$.

Usage

rcai(
  T_model,
  C_model,
  data,
  time,
  event,
  tau,
  H_constructor,
  sample = 0,
  blocksize = 0,
  return_all = FALSE,
  ...
)

Arguments

Value

vector with integral from 0 to all jump-times

Author(s)

Andreas Nordland

Description

Risk regression with binary exposure and nuisance model for the odds-product.

Let $A$ be the binary exposure, $V$ the set of covariates, and $Y$ the binary response variable, and define $p_a(v) = P(Y=1 \mid A=a, V=v), a\in\{0,1\}$.

The target parameter is either the relative risk

$\mathrm{RR}(v) = \frac{p_1(v)}{p_0(v)}$

or the risk difference

$\mathrm{RD}(v) = p_1(v)-p_0(v)$

We assume a target parameter model given by either

$\log\{RR(v)\} = \alpha^t v$