NEWS.md

In cmu-delphi/epiprocess: Tools for basic signal processing in epidemiology

epiprocess

Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicate PR's.

epiprocess 0.10

Breaking changes

• Moved example datasets from being hosted in the package to being reexported from the epidatasets package. The datasets can no longer be loaded with data() but can be accessed with epiprocess:: or, after loading the package, just the name of the dataset (#520). Those with names starting with jhu have been renamed to a more uniform scheme and now have names starting with covid. The data set previously named jhu_confirmed_cumulative_num has been removed from the package, but a renamed version is has been removed from the package, but a renamed version is still available in epidatasets.

Bug fixes

• Removed .window_size = 1 default from epi_slide_{mean,sum,opt}; this argument is now mandatory, and should nearly always be greater than 1 except for testing purposes.

Improvements

• epi_slide and epix_slide now provide some hints if you forget a ~ when using a formula to specify the slide computation, and other bits of forgotten syntax.
• Improved validation of .window_size arguments.
• Rewrote a lot of the package documentation to be more consistent and informative. Simplified and streamlined the vignettes.

Cleanup

• Removed vignette dependency on covidcast.

epiprocess 0.9

Breaking changes

• epi_slide interface has major breaking changes.
• All variables are now dot-prefixed to be more consistent with tidyverse style for functions that allow tidyeval.
• The before/after arguments have been replaced with the .window_size and .align arguments.
• names_sep has been removed. If you return data frames from your computations:
  • without a name, they will be unpacked into separate columns without name prefixes
  • with a name, it will become a packed data.frame-class column (see tidyr::pack).
• as_list_col has been removed. You can now directly return a list from your slide computations instead. If you were using as_list_col=TRUE, you will need to wrap your output in a list.
• Ungrouped slides are no longer allowed in epi_slide. If you used this for geographic aggregation up to national, consider using sum_groups_epi_df.
• Added sum_groups_epi_df to allow aggregation across key columns prior to sliding.
• epix_slide interface has major changes.
• All variables are now dot-prefixed to be more consistent with tidyverse style for functions that allow tidyeval.
• names_sep has been removed. If you return data frames from your computations:
  • without a name, they will be unpacked into separate columns without name prefixes
  • with a name, it will become a packed data.frame-class column (see tidyr::pack).
• as_list_col has been removed. You can now directly return a list from your slide computations instead. If you were using as_list_col=TRUE, you will need to wrap your output in a list.
• as_epi_df() now checks that every group has unique time values and errors if this is not the case. The same check is performed at the beginning of epi_slide(). This check is currently not enforced in dplyr operations (like for joins, mutates, or select), but we plan to add it in the future.
• as_epi_df() or as_epi_archive() no longer accept additional_metadata. Use the new other_keys arg to specify additional key columns, such as age group columns or other demographic breakdowns. Miscellaneous metadata are no longer handled by epiprocess, but you can use R's built-in attr<- instead for a similar feature.

Improvements

• Added complete.epi_df, which fills in missing values in an epi_df with NAs. Uses tidyr::complete underneath and preserves epi_df metadata.
• Inclusion of the function revision_summary to provide basic revision information for epi_archives out of the box. (#492)

Bug fixes

• Fix epi_slide_opt (and related functions) to correctly handle before=Inf. Also allow multiple columns specified as a list of strings.
• Disallow after=Inf in slide functions, since it doesn't seem like a likely use case and complicates code.

epiprocess 0.8

Breaking changes

• epi_df's are now more strict about what types they allow in the time column. Namely, we are explicit about only supporting Date at the daily and weekly cadence and generic integer types (for yearly cadence).
• epi_slide before and after arguments are now require the user to specific time units in certain cases. The time_step argument has been removed.
• epix_slide before argument now defaults to Inf, and requires the user to specify units in some cases. The time_step argument has been removed.
• detect_outlr_stl(seasonal_period = NULL) is no longer accepted. Use detect_outlr_stl(seasonal_period = <value>, seasonal_as_residual = TRUE) instead. See ?detect_outlr_stl for more details.

Improvements

• epi_slide computations are now 2-4 times faster after changing how reference time values, made accessible within sliding functions, are calculated (#397).
• Add new epi_slide_mean function to allow much (~30x) faster rolling average computations in some cases (#400).
• Add new epi_slide_sum function to allow much faster rolling sum computations in some cases (#433).
• Add new epi_slide_opt function to allow much faster rolling computations in some cases, using data.table and slider optimized rolling functions (#433).
• Add tidyselect interface for epi_slide_opt and derivatives (#452).
• regenerated the jhu_csse_daily_subset dataset with the latest versions of the data from the API
• changed approach to versioning, see DEVELOPMENT.md for details
• select on grouped epi_dfs now only drops epi_dfness if it makes sense; PR #390
• Minor documentation updates; PR #393
• Improved epi_archive print method. Compactified metadata and shows a snippet of the underlying DT (#341).
• Added autoplot method for epi_df objects, which creates a ggplot2 plot of the epi_df (#382).
• Refactored internals to use cli for warnings/errors and checkmate for argument checking (#413).
• Fix logic to auto-assign epi_df time_type to week (#416) and year (#441).
• Clarified "Get started" example of getting Ebola line list data into epi_df format.
• Improved documentation web site landing page's introduction.
• Fixed documentation referring to old epi_slide() interface (#466, thanks @XuedaShen!).
• as_epi_df and as_epi_archive now support arguments to specify column names e.g. as_epi_df(some_tibble, geo_value=state). In addition, there is a list of default conversions, see time_column_names for a list of columns that will automatically be recognized and converted to time_value column (there are similar functions for geo and version).
• Fixed bug where epix_slide_ref_time_values_default() on datetimes would output a huge number of ref_time_values spaced apart by mere seconds.
• In epi_slide() and epix_slide():
• Multiple "data-masking" tidy evaluation expressions can be passed in via ..., rather than just one.
• Additional tidy evaluation features from dplyr::mutate are supported: !! name_var := value, unnamed expressions evaluating to data frames, and = NULL; see ?epi_slide for more details.

Cleanup

• Resolved some linting messages in package checks (#468).
• Added optional decay_to_tibble attribute controlling as_tibble() behavior of epi_dfs to let {epipredict} work more easily with other libraries (#471).
• Removed some external package dependencies.

epiprocess 0.7.0

Breaking changes:

• Switched epi_df's other_keys default from NULL to character(0); PR #390
• Refactored epi_archive to use S3 instead of R6 for its object model. The functionality stay the same, but it will break the member function interface. For migration, you can usually just convert epi_archive$merge(...) to epi_archive <- epi_archive %>% epix_merge(...) (and the same for fill_through_version and truncate_after_version) and epi_archive$slide(...) to epi_archive %>% epix_slide(...) (and the same for as_of, group_by, slide, etc.) (#340). In some limited situations, such as if you have a helper function that calls epi_archive$merge etc. on one of its arguments, then you may need to more carefully refactor them.

epiprocess 0.7.0

Improvements

• Updated vignettes for compatibility with epidatr 1.0.0 in PR #377.

Breaking changes

• Changes to epi_slide and epix_slide:
• If f is a function, it is now required to take at least three arguments. f must take an epi_df with the same column names as the archive's DT, minus the version column; followed by a one-row tibble containing the values of the grouping variables for the associated group; followed by a reference time value, usually as a Date object. Optionally, it can take any number of additional arguments after that, and forward values for those arguments through epi[x]_slide's ... args.
  • To make your existing slide computations work, add a third argument to your f function to accept this new input: e.g., change f = function(x, g, <any other arguments>) { <body> } to f = function(x, g, rt, <any other arguments>) { <body> }.

New features

• epi_slide and epix_slide also make the window data, group key and reference time value available to slide computations specified as formulas or tidy evaluation expressions, in additional or completely new ways.
• If f is a formula, it can now access the reference time value via .z or .ref_time_value.
• If f is missing, the tidy evaluation expression in ... can now refer to the window data as an epi_df or tibble with .x, the group key with .group_key, and the reference time value with .ref_time_value. The usual .data and .env pronouns also work, butpick() and cur_data() are not; work off of .x instead.
• epix_slide has been made more like dplyr::group_modify. It will no longer perform element/row recycling for size stability, accepts slide computation outputs containing any number of rows, and no longer supports all_rows.
• To keep the old behavior, manually perform row recycling within f computations, and/or left_join a data frame representing the desired output structure with the current epix_slide() result to obtain the desired repetitions and completions expected with all_rows = TRUE.
• epix_slide will only output grouped or ungrouped tibbles. Previously, it would sometimes output epi_dfs, but not consistently, and not always with the metadata desired. Future versions will revisit this design, and consider more closely whether/when/how to output an epi_df.
• To keep the old behavior, convert the output of epix_slide() to epi_df when desired and set the metadata appropriately.

Improvements

• epi_slide and epix_slide now support as_list_col = TRUE when the slide computations output atomic vectors, and output a list column in "chopped" format (see tidyr::chop).
• epi_slide now works properly with slide computations that output just a Date vector, rather than converting slide_value to a numeric column.
• Fix ?archive_cases_dv_subset information regarding modifications of upstream data by @brookslogan in (#299).
• Update to use updated epidatr (fetch_tbl -> fetch) by @brookslogan in (#319).

epiprocess 0.6.0

Breaking changes

• Changes to both epi_slide and epix_slide:
• The n, align, and before arguments have been replaced by new before and after arguments. To migrate to the new version, replace these arguments in every epi_slide and epix_slide call. If you were only using the n argument, then this means replacing n = <n value> with before = <n value> - 1.
  • epi_slide's time windows now extend before time steps before and after time steps after the corresponding ref_time_values. See ?epi_slide for details on matching old alignments.
  • epix_slide's time windows now extend before time steps before the corresponding ref_time_values all the way through the latest data available at the corresponding ref_time_values.
• Slide functions now keep any grouping of x in their results, like mutate and group_modify.
  • To obtain the old behavior, dplyr::ungroup the slide results immediately.
• Additional epi_slide changes:
• When using as_list_col = TRUE together with ref_time_values and all_rows=TRUE, the marker for excluded computations is now a NULL entry in the list column, rather than a NA; if you are using tidyr::unnest() afterward and want to keep these missing data markers, you will need to replace the NULL entries with NAs. Skipped computations are now more uniformly detectable using vctrs methods.
• Additionalepix_slide changes:
• epix_slide's group_by argument has been replaced by dplyr::group_by and dplyr::ungroup S3 methods. The group_by method uses "data masking" (also referred to as "tidy evaluation") rather than "tidy selection".
  • Old syntax:
  • x %>% epix_slide(<other args>, group_by=c(col1, col2))
  • x %>% epix_slide(<other args>, group_by=all_of(colname_vector))
  • New syntax:
  • x %>% group_by(col1, col2) %>% epix_slide(<other args>)
  • x %>% group_by(across(all_of(colname_vector))) %>% epix_slide(<other args>)
• epix_slide no longer defaults to grouping by non-time_value, non-version key columns, instead considering all data to be in one big group.
  • To obtain the old behavior, precede each epix_slide call lacking a group_by argument with an appropriate group_by call.
• epix_slide now guesses ref_time_values to be a regularly spaced sequence covering all the DT$version values and the version_end, rather than the distinct DT$time_values. To obtain the old behavior, pass in ref_time_values = unique(<ungrouped archive>$DT$time_value).
• epi_archive's clobberable_versions_start's default is now NA, so there will be no warnings by default about potential nonreproducibility. To obtain the old behavior, pass in clobberable_versions_start = max_version_with_row_in(x).

Potentially-breaking changes

• Fixed [ on grouped epi_dfs to maintain the grouping if possible when dropping the epi_df class (e.g., when removing the time_value column).
• Fixed epi_df operations to be more consistent about decaying into non-epi_dfs when the result of the operation doesn't make sense as an epi_df (e.g., when removing the time_value column).
• Changed bind_rows on grouped epi_dfs to not drop the epi_df class. Like with ungrouped epi_dfs, the metadata of the result is still simply taken from the first result, and may be inappropriate (#242).
• epi_slide and epix_slide now raise an error rather than silently filtering out ref_time_values that don't meet their expectations.

New features

• epix_slide, <epi_archive>$slide have a new parameter all_versions. With all_versions=TRUE, epix_slide will pass a filtered epi_archive to each computation rather than an epi_df snapshot. This enables, e.g., performing pseudoprospective forecasts with a revision-aware forecaster using nested epix_slide operations.

Improvements

• Added dplyr::group_by and dplyr::ungroup S3 methods for epi_archive objects, plus corresponding $group_by and $ungroup R6 methods. The group_by implementation supports the .add and .drop arguments, and ungroup supports partial ungrouping with ....
• as_epi_archive, epi_archive$new now perform checks for the key uniqueness requirement (part of #154).

Cleanup

• Added a NEWS.md file to track changes to the package.
• Implemented ?dplyr::dplyr_extending for epi_dfs (#223).
• Fixed various small documentation issues (#217).

epiprocess 0.5.0

Potentially-breaking changes

• epix_slide, <epi_archive>$slide now feed f an epi_df rather than converting to a tibble/tbl_df first, allowing use of epi_df methods and metadata, and often yielding epi_dfs out of the slide as a result. To obtain the old behavior, convert to a tibble within f.

Improvements

• Fixed epix_merge, <epi_archive>$merge always raising error on sync="truncate".

Cleanup

• Added Remotes: entry for genlasso, which was removed from CRAN.
• Added as_epi_archive tests.
• Added missing epix_merge test for sync="truncate".

epiprocess 0.4.0

Potentially-breaking changes

• Fixed [.epi_df to not reorder columns, which was incompatible with downstream packages.
• Changed [.epi_df decay-to-tibble logic to more coherent with epi_dfs current tolerance of nonunique keys: stopped decaying to a tibble in some cases where a unique key wouldn't have been preserved, since we don't enforce a unique key elsewhere.
• Fixed [.epi_df to adjust "other_keys" metadata when corresponding columns are selected out.
• Fixed [.epi_df to raise an error if resulting column names would be nonunique.
• Fixed [.epi_df to drop metadata if decaying to a tibble (due to removal of essential columns).

Improvements

• Added check that epi_df additional_metadata is list.
• Fixed some incorrect as_epi_df examples.

Cleanup

• Applied rename of upstream package in examples: delphi.epidata -> epidatr.
• Rounded out [.epi_df tests.

epiprocess 0.3.0

Breaking changes

• as_epi_archive, epi_archive$new:
• Compactification (see below) by default may change results if working directly with the epi_archive's DT field; to disable, pass in compactify=FALSE.
• epi_archive's wrappers and R6 methods have been updated to follow these rules regarding reference semantics:
• epix_<method> will not mutate input epi_archives, but may alias them or alias their fields (which should not be a worry if a user sticks to these epix_* functions and "regular" R functions with copy-on-write-like behavior, avoiding mutating functions [.data.table).
• x$<method> may mutate x; if it mutates x, it will return x invisibly (where this makes sense), and, for each of its fields, may either mutate the object to which it refers or reseat the reference (but not both); if x$<method> does not mutate x, its result may contain aliases to x or its fields.
• epix_merge, <epi_archive>$merge:
• Removed ..., locf, and nan parameters.
• Changed the default behavior, which now corresponds to using by=key(x$DT) (but demanding that is the same set of column names as key(y$DT)), all=TRUE, locf=TRUE, nan=NaN (but with the post-filling step fixed to only apply to gaps, and no longer fill over NAs originating from x$DT and y$DT).
• x and y are no longer allowed to share names of non-by columns.
• epix_merge no longer mutates its x argument (but $merge continues to do so).
• Removed (undocumented) capability of passing a data.table as y.
• epix_slide:
• Removed inappropriate/misleading n=7 default argument (due to reporting latency, n=7 will not yield 7 days of data in a typical daily-reporting surveillance data source, as one might have assumed).

New features

• as_epi_archive, epi_archive$new:
• New compactify parameter allows removal of rows that are redundant for the purposes of epi_archive's methods, which use the last version of each observation carried forward.
• New clobberable_versions_start field allows marking a range of versions that could be "clobbered" (rewritten without assigning new version tags); previously, this was hard-coded as max(<epi_archive>$DT$version).
• New versions_end field allows marking a range of versions beyond max(<epi_archive>$DT$version) that were observed, but contained no changes.
• epix_merge, $merge:
• New sync parameter controls what to do if x and y aren't equally up to date (i.e., if x$versions_end and y$versions_end are different).
• New function epix_fill_through_version, method <epi_archive>$fill_through_version: non-mutating & mutating way to ensure that an archive contains versions at least through some fill_versions_end, extrapolating according to how if necessary.
• Example archive data object is now constructed on demand from its underlying data, so it will be based on the user's version of epi_archive rather than an outdated R6 implementation from whenever the data object was generated.

epiprocess 0.2.0

Breaking changes

• Removed default n=7 argument to epix_slide.

Improvements

• Ignore NAs when printing time_value range for an epi_archive.
• Fixed misleading column naming in epix_slide example.
• Trimmed down epi_slide examples.
• Synced out-of-date docs.

Cleanup

• Removed dependency of some epi_archive tests on an example archive. object, and made them more understandable by reading without running.
• Fixed epi_df tests relying on an S3 method for epi_df implemented externally to epiprocess.
• Added tests for epi_archive methods and wrapper functions.
• Removed some dead code.
• Made .{Rbuild,git}ignore files more comprehensive.

epiprocess 0.1.2

New features

• New new_epi_df function is similar to as_epi_df, but (i) recalculates, overwrites, and/or drops most metadata of x if it has any, (ii) may still reorder the columns of x even if it's already an epi_df, and (iii) treats x as optional, constructing an empty epi_df by default.

Improvements

• Fixed geo_type guessing on alphabetical strings with more than 2 characters to yield "custom", not US "nation".
• Fixed time_type guessing to actually detect Date-class time_values regularly spaced 7 days apart as "week"-type as intended.
• Improved printing of epi_dfs, epi_archivess.
• Fixed as_of to not cut off any (forecast-like) data with time_value > max_version.
• Expanded epi_df docs to include conversion from tsibble/tbl_ts objects, usage of other_keys, and pre-processing objects not following the geo_value, time_value naming scheme.
• Expanded epi_slide examples to show how to use an f argument with named parameters.
• Updated examples to print relevant columns given a common 80-column terminal width.
• Added growth rate examples.
• Improved as_epi_archive and epi_archive$new/$initialize documentation, including constructing a toy archive.

Cleanup

• Added tests for epi_slide, epi_cor, and internal utility functions.
• Fixed currently-unused internal utility functions MiddleL, MiddleR to yield correct results on odd-length vectors.

epiprocess 0.1.1

New features

• New example data objects allow one to quickly experiment with epi_dfs and epi_archives without relying/waiting on an API to fetch data.

Improvements

• Improved epi_slide error messaging.
• Fixed description of the appropriate parameters for an f argument to epi_slide; previous description would give incorrect behavior if f had named parameters that did not receive values from epi_slide's ....
• Added some examples throughout the package.
• Using example data objects in vignettes also speeds up vignette compilation.

Cleanup

• Set up gh-actions CI.
• Added tests for epi_dfs.

epiprocess 0.1.0

Implemented core functionality, vignettes

• Classes:
• epi_df: specialized tbl_df for geotemporal epidemiological time series data, with optional metadata recording other key columns (e.g., demographic breakdowns) and as_of what time/version this data was current/published. Associated functions:
  • as_epi_df converts to an epi_df, guessing the geo_type, time_type, other_keys, and as_of if not specified.
  • as_epi_df.tbl_ts and as_tsibble.epi_df automatically set other_keys and key&index, respectively.
  • epi_slide applies a user-supplied computation to a sliding/rolling time window and user-specified groups, adding the results as new columns, and recycling/broadcasting results to keep the result size stable. Allows computation to be provided as a function, purrr-style formula, or tidyeval dots. Uses slider underneath for efficiency.
  • epi_cor calculates Pearson, Kendall, or Spearman correlations between two (optionally time-shifted) variables in an epi_df within user-specified groups.
  • Convenience function: is_epi_df.
• epi_archive: R6 class for version (patch) data for geotemporal epidemiological time series data sets. Comes with S3 methods and regular functions that wrap around this functionality for those unfamiliar with R6 methods. Associated functions:
  • as_epi_archive: prepares an epi_archive object from a data frame containing snapshots and/or patch data for every available version of the data set.
  • as_of: extracts a snapshot of the data set as of some requested version, in epi_df format.
  • epix_slide, <epi_archive>$slide: similar to epi_slide, but for epi_archives; for each requested ref_time_value and group, applies a time window and user-specified computation to a snapshot of the data as of ref_time_value.
  • epix_merge, <epi_archive>$merge: like merge for epi_archives, but allowing for the last version of each observation to be carried forward to fill in gaps in x or y.
  • Convenience function: is_epi_archive.
• Additional functions:
• growth_rate: estimates growth rate of a time series using one of a few built-in methods based on relative change, linear regression, smoothing splines, or trend filtering.
• detect_outlr: applies one or more outlier detection methods to a given signal variable, and optionally aggregates the outputs to create a consensus result.
• detect_outlr_rm: outlier detection function based on a rolling-median-based outlier detection function; one of the methods included in detect_outlr.
• detect_outlr_stl: outlier detection function based on a seasonal-trend decomposition using LOESS (STL); one of the methods included in detect_outlr.

cmu-delphi/epiprocess documentation built on Oct. 29, 2024, 5:37 p.m.