surveytidy 0.6.0

New features

survey_collection support

Collection-aware methods for all standard dplyr/tidyr verbs are now dispatched per-survey when called on a survey_collection. The result is a new survey_collection whose @id, @if_missing_var, and @groups properties are preserved.

• Data-masking verbs: filter(), filter_out(), mutate(), arrange()
• Tidyselect verbs: select(), relocate(), rename(), rename_with(), drop_na(), distinct(), rowwise()
• Grouping verbs: group_by(), ungroup(), group_vars(), is_rowwise()
• Slicing verbs: slice(), slice_head(), slice_tail(), slice_min(), slice_max(), slice_sample()
• Collapsing verbs: pull() (returns a vector via vctrs::vec_c()), glimpse() (default mode binds members; .by_survey = TRUE per-member)

The .if_missing_var argument on each verb ("error" (default) or "skip") lets you override the collection’s stored missing-variable behaviour for a single call. Skipped surveys are reported via the typed message class surveytidy_message_collection_skipped_surveys.

The 6 join verbs (left_join(), right_join(), inner_join(), full_join(), semi_join(), anti_join()) error with surveytidy_error_collection_verb_unsupported when called on a survey_collection. Apply joins inside a per-survey pipeline before constructing the collection.

surveycore re-exports

library(surveytidy) is now sufficient to use the collection construction and setter API. The following surveycore symbols are re-exported:

• as_survey_collection()
• set_collection_id()
• set_collection_if_missing_var()
• add_survey()
• remove_survey()

Bug fixes

• replace_when() and replace_values() no longer retain stale value labels for values absent from the recoded result. Previously, collapsing or replacing values left label entries (e.g. "High" = 4) attached to a vector that contained no such values. User-supplied .value_labels are always preserved.

New error / warning / message classes

• surveytidy_error_collection_verb_emptied
• surveytidy_error_collection_verb_failed
• surveytidy_error_collection_by_unsupported
• surveytidy_error_collection_select_group_removed
• surveytidy_error_collection_rename_group_partial
• surveytidy_error_collection_slice_zero
• surveytidy_error_collection_pull_incompatible_types
• surveytidy_error_collection_glimpse_id_collision
• surveytidy_error_collection_verb_unsupported
• surveytidy_warning_collection_rowwise_mixed
• surveytidy_message_collection_skipped_surveys

Dependency changes

• Adds vctrs (>= 0.6.0) to Imports (used by pull.survey_collection and glimpse.survey_collection).
• Bumps surveycore minimum-version pin to (>= 0.8.2).

surveytidy 0.5.0

New features

Survey-aware join functions

Eight join and binding functions are now available for combining survey design objects with plain data frames. All join functions protect design variable columns (weights, strata, PSU, etc.) from being overwritten by y and append a typed sentinel to @variables$domain for traceability by Phase 1 estimation functions.

• left_join() — appends lookup columns from y without removing any rows. Errors if duplicate keys in y would expand rows.

• inner_join() — two modes: domain-aware (.domain_aware = TRUE, default) marks unmatched rows out-of-domain without removing them; physical mode (.domain_aware = FALSE) removes rows and issues a warning. Physical mode is not supported for survey_twophase designs.

• semi_join() — marks rows matching y as in-domain; unmatched rows are marked out-of-domain. No rows are physically removed.

• anti_join() — inverse of semi_join(); marks rows that do NOT match y as in-domain.

• right_join() and full_join() — always error when called on a survey object. Both would add rows with NA design variable values, which would invalidate variance estimation.

• bind_cols() — appends columns from ... to a survey object. Validates that all inputs have the same row count. Passes through to dplyr::bind_cols() for non-survey inputs.

• bind_rows() — always errors when called with a survey object. Combining two survey designs has undefined variance structure. Passes through to dplyr::bind_rows() for non-survey inputs.

Row statistic helpers

Two helper functions are now available for computing row-wise statistics inside mutate(). Both propagate metadata automatically and accept .label and .description to document the new variable in a single step.

• row_means() — computes the row mean across selected columns. Accepts na.rm to control NA handling. Issues a warning if any selected column is a design variable.

• row_sums() — computes the row sum across selected columns. Accepts na.rm to control NA handling. Issues a warning if any selected column is a design variable.

Bug fixes

• mutate() — transformation metadata is now correctly written back to the design object. Previously, [[<- assignment on S7 properties silently failed; the fix uses S7::prop<-() to sync all six metadata properties correctly (#25).

surveytidy 0.4.0

New features

Survey-aware transformation functions

Five vector-level transformation functions are now available for converting, collapsing, and reversing variables inside mutate(). All five propagate value labels automatically and accept .label and .description arguments to attach metadata in a single step.

• make_factor() — converts labelled, numeric, character, or factor vectors to an R factor. Levels are ordered by the numeric value of each value label. Accepts ordered, drop_levels, force, and na.rm to control level creation.

• make_dicho() — collapses a multi-level factor to two levels by stripping the first word of each label and merging labels that reduce to the same stem. Accepts .exclude to keep specific levels as NA, and flip_levels to reverse the resulting order.

• make_binary() — converts a dichotomous variable to a 0/1 integer. Thin wrapper around make_dicho(); accepts flip_values to control which level maps to 1.

• make_rev() — reverses a numeric scale using min + max - x and remaps value labels to match. Issues a warning when all values are NA.

• make_flip() — reverses the semantic valence of a variable by reversing the label strings while keeping the underlying values unchanged. Requires a label argument to document the new meaning.

surveytidy 0.3.0

New features

Survey-aware recoding functions

Six vector-level recoding functions are now available. Each shadows its dplyr equivalent and adds optional arguments for attaching variable labels, value labels, and transformation notes directly inside mutate(). Without any of those arguments, output is identical to dplyr.

• case_when() — a survey-aware dplyr::case_when(). Evaluates a sequence of condition ~ value formulas and uses the first match for each element. Use this to create an entirely new vector from conditions. Accepts .label to set a variable label, .value_labels to attach a named vector of value labels, .factor = TRUE to return an ordered factor (levels follow formula order), and .description to record a plain-language note about the transformation.

• if_else() — a survey-aware dplyr::if_else(). Applies a single binary condition element-wise (true/false/missing). Stricter than base ifelse(): true, false, and missing are cast to a common type. Accepts .label, .value_labels, and .description.

• na_if() — a survey-aware dplyr::na_if(). Converts specific values to NA. Unlike dplyr’s scalar-only y, this version accepts a vector y and replaces all matching values in a single call. When the input carries value labels, they are inherited automatically; .update_labels = TRUE (the default) removes label entries for the NA’d values, while .update_labels = FALSE retains them (useful for documenting what was set to missing). Also accepts .description.

• recode_values() — a survey-aware dplyr::recode_values(). Replaces values found in from with the corresponding value from to; values not in from are kept unchanged or trigger an error (.unmatched = "error"). Intended for full remapping of every value in a vector. Set .use_labels = TRUE to build the from/to map automatically from the input’s existing value labels (codes become from; label strings become to). Also accepts .label, .value_labels, .factor, and .description.

• replace_values() — a survey-aware dplyr::replace_values(). Replaces values found in from with the corresponding value from to; all other values are left unchanged. Use this for partial in-place replacement of specific values in an existing vector. Automatically inherits both the variable label and value labels from the input; supply .label or .value_labels to override. Also accepts .description.

• replace_when() — a survey-aware dplyr::replace_when(). Like case_when() but for partial in-place updates: evaluates condition ~ value formulas and replaces only matching elements, leaving all others at their original value. Automatically inherits labels from the input; supply .label or .value_labels to override. Also accepts .description.

Shared label arguments

All six functions support a common set of label arguments that propagate into @metadata when used inside mutate():

• .label — a character string stored in @metadata@variable_labels as the human-readable variable label for the new column.
• .value_labels — a named vector stored in @metadata@value_labels, where names are label strings and values are the corresponding data values.
• .description — a plain-language string stored in @metadata@transformations describing how the variable was derived.

case_when() and recode_values() also accept .factor = TRUE, which returns an ordered factor instead of a character vector (levels follow formula or to order respectively). .factor and .label cannot be combined.

mutate() enhancements

mutate() now coordinates label propagation automatically: it pre-attaches label attributes from @metadata before the inner dplyr call so recode functions can see existing labels, reads the label output back from recoded columns, and writes it into @metadata — all without extra user steps. The weight-column warning has also been split into two distinct classes: surveytidy_warning_mutate_weight_col for the weight column and surveytidy_warning_mutate_structural_var for strata, PSU, FPC, and replicate weights.

surveytidy 0.2.1

Website & branding

• Added package hex logo.
• Updated pkgdown site colours to a teal theme.
• README now displays the hex logo.
• LICENSE.md updated to credit third-party hex sticker icon (Freepik / Flaticon, CC BY 3.0).
• DESCRIPTION author entry updated with current email, ORCID, and copyright-holder (cph) role.

Infrastructure

• Added a hotfix-sync check to the CI strategy and merge-main skill to detect commits on main that have not been merged back to develop.
• Archived planning documents for the survey-result and dedup-rename-rowwise phases.

surveytidy 0.2.0

New verbs

• filter_out() — the complement of filter(). Marks rows matching the condition as out-of-domain while leaving all other rows in-domain. Like filter(), no rows are removed. Chains with filter() via AND-accumulation on the domain column. filter_out(d, group == "control") is often clearer than filter(d, group != "control") for exclusion use-cases.

• distinct() — removes duplicate rows while always retaining all columns (design variables are never dropped). With no column arguments, deduplicates on non-design columns only (survey-safe default). Always issues surveycore_warning_physical_subset.

• rename_with() — function-based column renaming. Applies .fn to columns selected by .cols and propagates renames to @variables, @metadata, @groups, and visible_vars. Validates .fn output and errors with surveytidy_error_rename_fn_bad_output for non-character, wrong-length, or duplicate output.

• rowwise() — enables row-by-row computation in mutate() (e.g., max(c_across(...))). Rowwise state is stored in @variables$rowwise — never in @groups, keeping those clean for estimation functions. group_by() and ungroup() exit rowwise mode, mirroring dplyr behaviour.

New predicates

• is_rowwise() — returns TRUE when the survey object is in rowwise mode.
• is_grouped() — returns TRUE when @groups is non-empty.
• group_vars() — returns the current grouping column names from @groups.

Verb support for survey_result objects

• filter(), arrange(), mutate(), slice(), slice_head(), slice_tail(), slice_min(), slice_max(), slice_sample(), and drop_na() are now registered for survey_result objects (the S3 base class for surveycore analysis outputs: survey_means, survey_freqs, survey_totals, survey_quantiles, survey_corr, survey_ratios). Previously, applying dplyr verbs to these objects could silently strip the class and .meta attribute. Now both are preserved, and mutate() keeps meta$group coherent when .keep drops grouping columns.

• select(), rename(), and rename_with() are now registered for survey_result objects with active .meta updates. select() prunes stale meta$group entries when grouping columns are dropped and handles inline renames (select(r, grp = group)). rename() and rename_with() propagate column renames to all .meta key references ($group, $x, $numerator$name, $denominator$name). rename_with() errors with surveytidy_error_rename_fn_bad_output if .fn returns non-character, wrong-length, NA, or duplicate names.

Bug fixes

• drop_na() now performs domain-aware filtering instead of physically removing rows. Previously, drop_na() removed rows with NA values, changing which units contributed to variance estimation and producing incorrect standard errors. It now marks incomplete rows as out-of-domain — equivalent to the corresponding filter(!is.na(col1), ...) chain — giving correct variance estimates for downstream analyses.

• filter(): the .by unsupported-argument error was mis-classified as a surveycore_error_*; corrected to surveytidy_error_filter_by_unsupported.

Improvements

• rename() and rename_with() now update @groups when a grouped column is renamed, and correctly update twophase design variable references (@variables$phase1, @variables$phase2, @variables$subset). The domain column (..surveycore_domain..) is silently protected from renaming.

• filter() and filter_out() support if_any() and if_all() in conditions.

Documentation

• Roxygen documentation standardised across all verb files to mirror the dplyr/tidyr reference style, with @details subsections for surveytidy-specific behaviour and examples using nhanes_2017.

• Rd files consolidated from per-method (e.g., arrange.survey_base.Rd) to per-verb (e.g., arrange.Rd), fixing the “S3 methods shown with full name” R CMD check NOTE.

surveytidy 0.1.0

First release. Implements a complete set of dplyr and tidyr verbs for survey design objects created with the surveycore package.

New verbs

• filter() — domain-aware filtering. Marks rows in-domain rather than removing them, preserving correct variance estimation for subpopulation analyses. Chained filter() calls AND their conditions together.

• select() — column selection. Physically removes non-selected columns while always retaining design variables (weights, strata, PSU, FPC, replicate weights). Sets @variables$visible_vars so print() hides design columns the user did not explicitly request.

• relocate() — column reordering. Reorders visible_vars when a prior select() has been called; reorders @data directly otherwise.

• pull() — extract a column as a plain vector (terminal operation).

• glimpse() — concise column summary, respecting visible_vars.

• mutate() — add or modify columns. Re-attaches design variables dropped by .keep = "none" or .keep = "used". Issues surveytidy_warning_mutate_design_var when a mutation’s left-hand side names a design variable. Respects @groups set by group_by().

• rename() — rename columns. Automatically keeps @variables (design specification) and @metadata (variable labels, value labels, etc.) in sync with the new column names. Issues surveytidy_warning_rename_design_var when a design variable is renamed.

• arrange() — row sorting. The domain column moves correctly with the rows after sorting. Supports .by_group = TRUE using @groups.

• slice(), slice_head(), slice_tail(), slice_min(), slice_max(), slice_sample() — physical row selection with a surveycore_warning_physical_subset warning. slice_sample(weight_by = ) additionally issues surveytidy_warning_slice_sample_weight_by to flag that the weight_by column is independent of the survey design weights.

• group_by() — store grouping columns in @groups. Does not attach a grouped_df attribute to @data; grouping is kept on the survey object. Supports .add = TRUE for incremental grouping and computed expressions (e.g., group_by(d, above_median = y1 > median(y1))).

• ungroup() — remove all groups (no arguments) or remove specific columns from @groups (partial ungroup).

• drop_na() — domain-aware NA handling. Marks rows with NA in specified columns (or any column) as out-of-domain without removing them. Equivalent to filter(!is.na(col1), !is.na(col2), ...) and gives correct variance estimates for downstream analyses. Successive drop_na() calls AND their conditions together.

• subset() — physical row removal with surveycore_warning_physical_subset. Prefer filter() for subpopulation analyses.

Statistical design

The key design decision in surveytidy is that filter() never removes rows. Removing rows from a survey design changes which units contribute to variance estimation and produces incorrect standard errors for subpopulation statistics. filter() instead writes a logical domain column (..surveycore_domain..) to @data. Phase 1 estimation functions will read this column to restrict calculations to the domain while retaining all rows for variance estimation.

Infrastructure

• dplyr_reconstruct.survey_base() ensures complex dplyr pipelines (joins, across(), internal slice operations) return survey objects rather than plain tibbles. Errors with surveycore_error_design_var_removed if a pipeline drops a design variable.

• Invariant 6 added to test_invariants(): every column name listed in @variables$visible_vars must exist in @data.