eHDPrep 2.0.0

Date variable support

• Date and date-time variables are now supported throughout. A new "date" datatype is accepted by import_var_classes() and produced by assume_var_classes() for Date and POSIXct/POSIXt columns.
• New function coerce_dates() converts variables classed as "date" to Date, parsing common formats ("2020-01-15", "15/01/2020", and the /- and --separated variants of each) and reporting values which could not be interpreted, in the same manner as coerce_numeric_vars(). Date-time columns are converted to dates with a message noting the loss of the time of day. It is applied automatically by apply_quality_ctrl(), after missingness strings have been standardised so that they are not reported as unparseable.
• Beyond this coercion, date variables are left unmodified by apply_quality_ctrl(), as they are already ordered and machine interpretable. They are included in completeness assessment, may be used in internal consistency rules (e.g. requiring a date of birth to precede a date of death), and are converted to days since 1970-01-01 by encode_as_num_mat().
• impute_missing_values() now imputes dates and date-times with their median (or mean) rather than falling back to the mode. Medians and means are meaningful for dates as they are ordered, even though is.numeric() is FALSE for them. The original class, and the time zone of a date-time, are preserved.

Bug fixes for date and categorical handling

• assume_var_classes() no longer fails on date-time variables. class() returns two values for a POSIXct column ("POSIXct" and "POSIXt"), which caused the error Result must be length 1, not 2 and prevented the function from being used at all on such datasets.
• apply_quality_ctrl() no longer fails when a dataset contains no character or factor variables. encode_cats() was called unconditionally and errored with “cols must select at least one column” when it selected none, unlike the other encoding steps which are skipped when they have nothing to do.

Single-variable consistency rules

• identify_inconsistency() and validate_consistency_tbl() now support rules which constrain one variable against fixed values, in addition to rules which compare two variables. Such a rule leaves the second column of the consistency table NA and gives the boundary in the fourth column:
  • a comparison against a value, where the third column holds the logical test and the fourth the value, e.g. "age", NA, ">=", "70", NA requires every value of age to be at least 70;
  • permitted values, where the third column is NA and the fourth holds either a colon-separated numeric range or a single category, e.g. "tumoursize", NA, NA, "0:100", NA. This makes range and plausibility checks possible, which previously could not be expressed as every rule required two variables. Missing values are not reported by these rules as they cannot be assessed against a boundary. Single-variable and two-variable rules can be mixed in one table, and existing consistency tables are unaffected.

Missing value imputation

• New function impute_missing_values() fills missing (NA) values using either simple summary statistics or k-nearest-neighbours (kNN).
  • method = "auto" (default) imputes numeric variables with their median and non-numeric variables with their mode (most frequent value). "median", "mean", "mode" and "constant" are also available. Variables to impute can be selected with tidyselect syntax; all are imputed by default.
  • method = "knn" estimates each missing value from the k most similar rows using Gower distance, so mixed numeric and categorical data are handled together and relationships between variables are better preserved. Variables such as row identifiers can be excluded from the distance calculation with ignore. This method uses the ‘VIM’ package, which is a suggested (not mandatory) dependency and is only required when the method is used.
  • The number of values imputed per variable is reported as a message, so imputation can be reviewed with review_quality_ctrl().
• apply_quality_ctrl() gains impute (default FALSE) and impute_method. Imputation is applied after missing values are standardised but before any encoding, so it operates on the raw variable values. All variables except the identifier and free-text variables are imputed.

Improved variable class detection

• assume_var_classes() gains a factor_threshold argument (default 5). Character and factor variables with exactly two unique non-missing values are now labelled "binary", and character variables with more than two but no more than factor_threshold unique non-missing values are labelled "factor". Factor detection can be disabled with factor_threshold = 0 or NULL.
• import_var_classes() now accepts the "binary" and "logical" datatypes.
• apply_quality_ctrl() automatically treats character and factor variables with exactly two unique non-missing values as binary.
• encode_bin_cat_vec() (and therefore encode_binary_cats()) now normalises mixed boolean encodings before matching. A variable recording the same two categories inconsistently (e.g. "False", "no", "N" alongside "True", "yes", "Y") is collapsed to canonical "false"/"true" so that the default pair matches. Numeric "0"/"1" are deliberately excluded as they are ambiguous; handle these with strings_to_NA() beforehand.
• New function coerce_numeric_vars() converts variables classed as numeric to numeric, reporting how many values (and which) could not be parsed and were therefore set to NA. It is applied automatically by apply_quality_ctrl().

Quality assessment

• assess_completeness() and assess_quality() gain a plot argument (default TRUE). Plots are now only displayed when a graphics device is active, and the completeness heatmap no longer draws over existing plots.

Bug fixes

• apply_quality_ctrl() no longer discards messages from the whole quality control pipeline. Piping into suppressMessages() forced the entire upstream chain inside the handler, which silently suppressed the reporting from coerce_numeric_vars() and impute_missing_values(). Suppression is now scoped to extract_freetext(), as intended.
• Imputation no longer changes the class of a variable:
  • integer variables are imputed with a rounded integer value, as the median or mean of a set of integers is frequently fractional (the rounding is reported);
  • factors gain the imputed value as an additional level rather than the value being silently dropped to NA;
  • a constant of an incompatible type (e.g. a character value for a numeric variable) is now an error instead of converting the entire variable.
• Variables containing no non-missing values are now reported as skipped by impute_missing_values() rather than being reported as imputed when no values had in fact changed.
• encode_ordinals(), encode_cats() and metavariable_info() were refactored to avoid notes from R CMD check about non-standard evaluation, and metavariable_info() now uses dplyr::pick().
• import_var_classes() now accepts the "ordinal_tstage" and "ordinal_nstage" datatypes. These are consumed by apply_quality_ctrl() and are the classes the documentation instructs users to assign to precoded cancer staging variables, but they were missing from the permitted datatypes and so the documented workflow (amend the output of assume_var_classes(), then import it) failed with “not a permitted datatype”.
• Resolved the tidyselect 1.2.0 deprecation warnings emitted by apply_quality_ctrl() and encode_cats() (use of .data in tidyselect expressions, and all_of() outside a selecting function).
• The bundled example_ontology was regenerated with a current version of ‘igraph’, so it no longer reports that it was created by an older version.

Testing

• Added tests/testthat.R, without which the test suite was silently skipped by R CMD check. The tests are now run when the package is checked.
• Added test coverage for impute_missing_values(), coerce_numeric_vars() and the imputation behaviour of apply_quality_ctrl().

eHDPrep 1.4.0

• encode_ordinals() now compares variable values to ord_levels as characters, so factor variables are checked against the supplied levels correctly rather than against their integer codes. The redundant second summary over the selected variables was also removed.
• Reduced the size of the vignette PDF.

eHDPrep 1.3.5

• Modified the apply_quality_ctrl function to accept data even without genomics variables

eHDPrep 1.3.4

• Fixed the cross-references issue in man/metavariable_agg.Rd and man/join_vars_to_ontol.Rd

eHDPrep 1.3.3

• Fixed typo in vignette
• Added CITATION file and added reference to citation in vignette

eHDPrep 1.3.2

General

• Added a NEWS.md file to track changes to the package.
• Added link to eHDPrep’s github repository in package documentation.
• Updated various documentation (functions and vignette).
• Now minimally requires and is compatible with dplyr 1.1.0 (#3, @DavisVaughan).

Quality Control

• completeness_heatmap() has been altered to avoid an issue of plotting over other plots. Now requires plot.new() call.

Semantic Enrichment

• Added function, metavariable_variable_descendants(), to more easily access relationships between meta-variables and their descendant variables.
• semantic_enrichment() now accepts a label attribute to label meta-variables with the parameter: label_attr.
• semantic_enrichment() now accepts an ontology as a data frame edge table, as a path to an edge table in CSV format, or as a tidygraph/igraph graph.
• Added function, edge_tbl_to_graph(), to convert edge tables, as data frames, to tidygraph graphs.
• Added data, example_edge_table, to demonstrate edge_tbl_to_graph().
• example_ontology is now generated from example_edge_table.
• metavariable_info() now can exclude meta-variables with an information content less than a threshold from output with the IC_threshold parameter. This will exclude non-specific meta-variables from consideration when output is passed to metavariable_agg() (e.g. ontology’s root node).

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