Create bootstrap replicate weights for a general survey design, using the Rao-Wu-Yue-Beaumont bootstrap method

Creates bootstrap replicate weights for a multistage stratified sample design using the method of Beaumont and Émond (2022), which is a generalization of the Rao-Wu-Yue bootstrap.

The design may have different sampling methods used at different stages. Each stage of sampling may potentially use unequal probabilities (with or without replacement) and may potentially use Poisson sampling.

Usage

make_rwyb_bootstrap_weights(
  num_replicates = 100,
  samp_unit_ids,
  strata_ids,
  samp_unit_sel_probs,
  samp_method_by_stage = rep("PPSWOR", times = ncol(samp_unit_ids)),
  allow_final_stage_singletons = TRUE,
  output = "weights"
)

Arguments

num_replicates

Positive integer giving the number of bootstrap replicates to create

samp_unit_ids

Matrix or data frame of sampling unit IDs for each stage of sampling

strata_ids

Matrix or data frame of strata IDs for each sampling unit at each stage of sampling

samp_unit_sel_probs

Matrix or data frame of selection probabilities for each sampling unit at each stage of sampling.

samp_method_by_stage

A vector with length equal to the number of stages of sampling, corresponding to the number of columns in samp_unit_ids. This describes the method of sampling used at each stage. Each element should be one of the following:

"SRSWOR" - Simple random sampling, without replacement
"SRSWR" - Simple random sampling, with replacement
"PPSWOR" - Unequal probabilities of selection, without replacement
"PPSWR" - Unequal probabilities of selection, with replacement
"Poisson" - Poisson sampling: each sampling unit is selected into the sample at most once, with potentially different probabilities of inclusion for each sampling unit.

allow_final_stage_singletons

Logical value indicating whether to allow non-certainty singleton strata at the final sampling stage (rather than throw an error message).
If TRUE, the sampling unit in a non-certainty singleton stratum will have its final-stage adjustment factor calculated as if it was selected with certainty at the final stage (i.e., its adjustment factor will be 1), and then its final bootstrap weight will be calculated by combining this adjustment factor with its final-stage selection probability.

output

Either "weights" (the default) or "factors". Specifying output = "factors" returns a matrix of replicate adjustment factors which can later be multiplied by the full-sample weights to produce a matrix of replicate weights. Specifying output = "weights" returns the matrix of replicate weights, where the full-sample weights are inferred using samp_unit_sel_probs.

Value

A matrix of with the same number of rows as samp_unit_ids and the number of columns equal to the value of the argument num_replicates. Specifying output = "factors" returns a matrix of replicate adjustment factors which can later be multiplied by the full-sample weights to produce a matrix of replicate weights. Specifying output = "weights" returns the matrix of replicate weights, where the full-sample weights are inferred using samp_unit_sel_probs.

Details

Beaumont and Émond (2022) describe a general algorithm for forming bootstrap replicate weights for multistage stratified samples, based on the method of Rao-Wu-Yue, with extensions to sampling without replacement and use of unequal probabilities of selection (i.e., sampling with probability proportional to size) as well as Poisson sampling. These methods are guaranteed to produce nonnegative replicate weights and provide design-unbiased and design-consistent variance estimates for totals, for designs where sampling uses one or more of the following methods:

"SRSWOR" - Simple random sampling, without replacement
"SRSWR" - Simple random sampling, with replacement
"PPSWR" - Unequal probabilities of selection, with replacement
"Poisson" - Poisson sampling: each sampling unit is selected into the sample at most once, with potentially different probabilities of inclusion for each sampling unit.

For designs where at least one stage's strata have sampling without replacement with unequal probabilities of selection ("PPSWOR"), the bootstrap method of Beaumont and Émond (2022) is guaranteed to produce nonnegative weights, but is not design-unbiased, since the method only approximates the joint selection probabilities which would be needed for unbiased estimation.

Unless any stages use simple random sampling without replacement, the resulting bootstrap replicate weights are guaranteed to all be strictly positive, which may be useful for calibration or analyses of domains with small sample sizes. If any stages use simple random sampling without replacement, it is possible for some replicate weights to be zero.

If there is survey nonresponse, it may be useful to represent the response/nonresponse as an additional stage of sampling, where sampling is conducted with Poisson sampling where each unit's "selection probability" at that stage is its response propensity (which typically has to be estimated).

The formulas and algorithms for the replication factors are described by Beaumont and Émond (2022). Below, we list the relevant equations and sections of the paper for each sampling method.

"SRSWR" - Equation 19 of Beaumont and Émond (2022)
"PPSWR" - Equation 19 of Beaumont and Émond (2022)
"SRSWOR" - Equation 20 of Beaumont and Émond (2022)
"PPSWOR" - Equations 24 and 21 of Beaumont and Émond (2022)
"Poisson" - See section 3.1 of Beaumont and Émond (2022)

For stratified sampling, the replicate factors are generated independently in each stratum. For cluster sampling at a given stage, the replicate factors are generated at the cluster level and then the cluster's replicate factors are applied to all units in the cluster.

For multistage sampling, replicate factors are generated using the method described in Section 7 ("Bootstrap for Multistage Sampling").

References

Beaumont, J.-F.; Émond, N. (2022). "A Bootstrap Variance Estimation Method for Multistage Sampling and Two-Phase Sampling When Poisson Sampling Is Used at the Second Phase." Stats, 5: 339–357. https://doi.org/10.3390/stats5020019

Rao, J.N.K.; Wu, C.F.J.; Yue, K. (1992). "Some recent work on resampling methods for complex surveys." Surv. Methodol., 18: 209–217.

Examples

if (FALSE) { # \dontrun{
 library(survey)

 # Example 1: A multistage sample with two stages of SRSWOR

     ## Load an example dataset from a multistage sample, with two stages of SRSWOR
     data("mu284", package = 'survey')
     multistage_srswor_design <- svydesign(data = mu284,
                                           ids = ~ id1 + id2,
                                           fpc = ~ n1 + n2)

     ## Create bootstrap replicate weights
     set.seed(2022)
     bootstrap_replicate_weights <- make_rwyb_bootstrap_weights(
       num_replicates = 5000,
       samp_unit_ids = multistage_srswor_design$cluster,
       strata_ids = multistage_srswor_design$strata,
       samp_unit_sel_probs = multistage_srswor_design$fpc$sampsize /
                             multistage_srswor_design$fpc$popsize,
       samp_method_by_stage = c("SRSWOR", "SRSWOR")
     )

     ## Create a replicate design object with the survey package
     bootstrap_rep_design <- svrepdesign(
       data = multistage_srswor_design$variables,
       repweights = bootstrap_replicate_weights,
       weights = weights(multistage_srswor_design, type = "sampling"),
       type = "bootstrap"
     )

     ## Compare std. error estimates from bootstrap versus linearization
     data.frame(
       'Statistic' = c('total', 'mean', 'median'),
       'SE (bootstrap)' = c(SE(svytotal(x = ~ y1, design = bootstrap_rep_design)),
                            SE(svymean(x = ~ y1, design = bootstrap_rep_design)),
                            SE(svyquantile(x = ~ y1, quantile = 0.5,
                                           design = bootstrap_rep_design))),
       'SE (linearization)' = c(SE(svytotal(x = ~ y1, design = multistage_srswor_design)),
                                SE(svymean(x = ~ y1, design = multistage_srswor_design)),
                                SE(svyquantile(x = ~ y1, quantile = 0.5,
                                               design = multistage_srswor_design))),
       check.names = FALSE
     )

 # Example 2: A single-stage sample selected with unequal probabilities, without replacement

     ## Load an example dataset of U.S. counties states with 2004 Presidential vote counts
     data("election", package = 'survey')
     pps_wor_design <- svydesign(data = election_pps,
                                 pps = "overton",
                                 fpc = ~ p, # Inclusion probabilities
                                 ids = ~ 1)

     ## Create bootstrap replicate weights
     set.seed(2022)
     bootstrap_replicate_weights <- make_rwyb_bootstrap_weights(
       num_replicates = 5000,
       samp_unit_ids = pps_wor_design$cluster,
       strata_ids = pps_wor_design$strata,
       samp_unit_sel_probs = pps_wor_design$prob,
       samp_method_by_stage = c("PPSWOR")
     )

     ## Create a replicate design object with the survey package
     bootstrap_rep_design <- svrepdesign(
       data = pps_wor_design$variables,
       repweights = bootstrap_replicate_weights,
       weights = weights(pps_wor_design, type = "sampling"),
       type = "bootstrap"
     )

     ## Compare std. error estimates from bootstrap versus linearization
     data.frame(
       'Statistic' = c('total', 'mean'),
       'SE (bootstrap)' = c(SE(svytotal(x = ~ Bush, design = bootstrap_rep_design)),
                            SE(svymean(x = ~ I(Bush/votes),
                                       design = bootstrap_rep_design))),
       'SE (Overton\'s PPS approximation)' = c(SE(svytotal(x = ~ Bush,
                                                           design = pps_wor_design)),
                                               SE(svymean(x = ~ I(Bush/votes),
                                                          design = pps_wor_design))),
       check.names = FALSE
     )
} # }