surveyCV (version 0.2.0)

cv.svydesign: CV for svydesign objects

Description

Wrapper function which takes a svydesign object and a vector of model formulas (as strings), and passes it into cv.svy. Returns survey CV estimates of the mean loss for each model (MSE for linear models, or binary cross-entropy for logistic models).

Usage

cv.svydesign(
  design_object,
  formulae,
  nfolds = 5,
  method = c("linear", "logistic"),
  na.rm = FALSE
)

Arguments

design_object

Name of a svydesign object created using the survey package. We do not yet support use of probs or pps.

formulae

Vector of formulas (as strings) for the GLMs to be compared in cross validation

nfolds

Number of folds to be used during cross validation, defaults to 5

method

String, must be either "linear" or "logistic", determines type of model fit during cross validation, defaults to linear

na.rm

Whether to drop cases with missing values when taking `svymean` of test losses

Value

Object of class svystat, which is a named vector of survey CV estimates of the mean loss (MSE for linear models, or binary cross-entropy for logistic models) for each model, with names ".Model_1", ".Model_2", etc. corresponding to the models provided in formulae; and with a var attribute giving the variances. See surveysummary for details.

Details

If you have already fitted a svyglm, you may prefer the convenience wrapper function cv.svyglm.

For models other than linear or logistic regression, you can use folds.svy or folds.svydesign to generate CV fold IDs that respect any stratification or clustering in the survey design. You can then carry out K-fold CV as usual, taking care to also use the survey design features and survey weights when fitting models in each training set and also when evaluating models against each test set.

See Also

surveysummary, svydesign

cv.svyglm for a wrapper to use with a svyglm object

Examples

# NOT RUN {
# Compare CV MSEs and their SEs under 3 linear models
# for a stratified sample and a one-stage cluster sample,
# using data from the `survey` package
library(survey)
data("api", package = "survey")
# stratified sample
dstrat <- svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat,
                    fpc = ~fpc)
cv.svydesign(formulae = c("api00~ell",
                          "api00~ell+meals",
                          "api00~ell+meals+mobility"),
             design_object = dstrat, nfolds = 5)
# one-stage cluster sample
dclus1 <- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
cv.svydesign(formulae = c("api00~ell",
                          "api00~ell+meals",
                          "api00~ell+meals+mobility"),
             design_object = dclus1, nfolds = 5)

# Compare CV MSEs and their SEs under 3 linear models
# for a stratified cluster sample with clusters nested within strata
data(NSFG_data)
library(splines)
NSFG.svydes <- svydesign(id = ~SECU, strata = ~strata, nest = TRUE,
                         weights = ~wgt, data = NSFG_data)
cv.svydesign(formulae = c("income ~ ns(age, df = 2)",
                          "income ~ ns(age, df = 3)",
                          "income ~ ns(age, df = 4)"),
             design_object = NSFG.svydes, nfolds = 4)

# Logistic regression example, using the same stratified cluster sample;
# instead of CV MSE, we calculate CV binary cross-entropy loss,
# where (as with MSE) lower values indicate better fitting models
# (NOTE: na.rm=TRUE is not usually ideal;
#  it's used below purely for convenience, to keep the example short,
#  but a thorough analysis would look for better ways to handle the missing data)
cv.svydesign(formulae = c("KnowPreg ~ ns(age, df = 1)",
                          "KnowPreg ~ ns(age, df = 2)",
                          "KnowPreg ~ ns(age, df = 3)"),
             design_object = NSFG.svydes, nfolds = 4,
             method = "logistic", na.rm = TRUE)
# }