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Changelog

Source: NEWS.md

ohvbd (development version)

ohvbd 1.0.0

First CRAN release

Major API change

  • extract_ functions are now glean_.
    • This means that if tidyverse is loaded after ohvbd, there are no direct namespace collisions.

Full list of function name changes:

New functions & arguments:

  • ohvbd now interfaces with GBIF for occurrence data.
    • New *_gbif functions (e.g. fetch_gbif()) allow for retrieving and extracting data from GBIF.
    • A GBIF account and the rgbif package are required to retrieve data from GBIF.
    • The account details must also be set up as shown in the rgbif documentation.
  • New tee() command allows one to extract data from the middle of a pipeline and save it to an environment.
    • This is definitely not only useful for ohvbd workflows, and can be used in any base R pipeline (|>). It has not been tested in magrittr pipelines but should work as-is.
  • New filter_db() command allows for filtering out of only one database’s results from hub searches.
  • check_db_status() now returns (invisibly) whether all databases are up or not.
  • New fetch_citation() and fetch_citation_* commands provide an interface to attempt to retrieve citations from a vectorbyte dataset.
    • This will (by default) possibly redownload parts or all of the data if the columns are not currently present.
  • New force_db() function enables one to force ohvbd to consider a particular object as having a particular provenance.
  • New simplify argument to search_hub() makes hub searches return an ohvbd.ids object if only one database was searched for. This behaviour is on by default.
    • To match this, filter_db() will now transparently return ohvbd.ids objects if it gets them.
  • New taxonomy argument to search_hub() allows for filtering searches by GBIF backbone IDs.
  • New match_species() function allows for quick and flexible matching of species names to their GBIF backbone IDs.
  • New match_country() function allows for matching of country names to WKT polygons via naturalearth.
  • New ohvbd_db(), has_db(), and is_from() functions allow for quick testing of object provenance (according to ohvbd).
  • New get_default_ohvbd_cache() function allows for custom functions that interface with cached ohvbd data files.
  • New list_ohvbd_cache() and clean_ohvbd_cache() functions enable better interactive cache management.
  • search_x_smart() functions can now take "tags" as a search field, enabling support for tagged datasets.

Other:

  • Entire code base is now continuously formatted using Air v0.7.1.
  • Examples are no longer wrapped in \dontrun{} so they should be runnable from an installed version of the package.
  • A good chunk of the functional logic of ohvbd is now covered with unit tests (using the vcr package).
  • fetch_vd() no longer tries to retrieve ids with no pages of data.
  • Functions that interface with vectorbyte databases no longer recommend using set_ohvbd_compat() as unexpected SSL errors should break pipelines by default.
    • These errors are no longer expected to occur when interfacing with vectorbyte.
  • Running fetch() on an ohvbd.hub.search or glean() on an ohvbd.ids object now provides a hint that you may have forgotten something.
    • Occasionally users would use forget a fetch() command and run search_hub() |> glean() which didn’t previously give an interpretable error.
  • Vignettes now use vcr to massively reduce their build time. This should only matter to developers of ohvbd, or users who download from github and build the vignettes themselves.
  • ohvbd.ids() now warns you and fixes the problem if you provide ids with duplicate values.
  • glean_vt() and glean_vd() now force the inclusion of the dataset ID when filtering columns (using the cols argument).
    • This is intended to encourage you to preserve at least one means of retrieving citation data later.
  • WKT parsing and formatting is now significantly more robust.
  • Cached AREAData now includes the cache timestamp as an attribute rather than a separate variable in the cache file.
  • glean_ad() now correctly returns a matrix even when there is only 1 row or column.
  • gadm spatial files are now cached as GeoPackage rather than shapefiles, leading to a >50% speedup in loading! (Thanks to @josiah.rs on bluesky for the suggestion!)
  • fetch_vd_counts() is now significantly faster, more robust, and temporarily caches data.
    • You will see particular improvements if you are trying to retrieve more than about 10 ids in one go or if you are repeatedly running the same download code in the same day.
    • This speedup also applies to fetch_vd() under the hood, particularly if you are running it multiple times in a day.
  • Explicit term checking (such as in fetch_ad() for metrics and search_vt_smart() for operators and fields) is now fuzzy, allowing for a small amount of deviation from the actual term name.
  • assoc_ad() now tries to guess LatLong column names if none (or the wrong ones) are provided.
  • Errors in internal functions now make it more clear which user-facing functions they originate from.
  • Multiple functions now default to NULL rather than NA for default missing values (except date arguments to AD-related functions, where NA is more reasonable in the grand scheme).
  • fetch_ad() now caches and tries to read from cache by default.
    • Generally speaking unless exceedingly up-to-date data is required, this will be the best for most people.
    • If you do require guaranteed new data, it’s worth setting refresh_cache = TRUE or use_cache = FALSE (depending on if you want to replace your existing cache or not).
  • All downloaders that can potentially cache data also attach the download time if not loading from cache.

ohvbd 0.6.1

  • New search_hub() function enables searching across multiple databases at once via vbdhub.
    • This includes new functionality for specifying searches using spatial extent polygons and generally more intelligent search behaviour.
  • New function generate_vt_template() which quickly generates a VecTraits template for later upload.

ohvbd 0.6.0

  • Internally ohvbd now only uses base R pipes (|>).
  • The magrittr pipe (%>%) is no longer used internally, nor is it exported for use.
  • httr2 v1.1.1 deprecated the pool argument of req_perform_parallel() which broke fetch() commands across ohvbd.
    • These have now been rewritten using the new max_active argument, which does simplify everything a bit.
    • This change does bump the required version of httr2 to be v1.1.1.

ohvbd 0.5.2

  • fetch_ad() now searches for and retrieves the most up-to-date GID2 files from AREAdata.
  • New timeout parameter of fetch_ad() to control timeouts of AD downloads. Defaults to 4 minutes.
  • assoc_ad() now correctly extracts data (this functionality regressed in 0.5.0 as a consequence of the new dynamic method dispatch approach to data retrieval).
  • assoc_ad() also gives now consistent output even when a 1-dimensional output is returned from extract_ad()
  • All fetch_ functions now have a default connections argument of 2, leading to faster retrieval across the board.
  • check_src argument has been removed from all functions. It no longer serves much of a purpose due to the sanity checking changes implemented in 0.5.0.

ohvbd 0.5.1

  • fetch_vd() now correctly returns all data from datasets over 50 rows.
  • fetch_vd() also now tells you how much data you are retrieving and a coarse estimate of how long this will take.
  • New function fetch_vd_counts() allows for quick checking of dataset sizes. This is very important as some datasets in VecDyn are over 40,000 rows long!
  • All fetch_ functions (and thus also fetch()) now use parallel data retrieval, even when only 1 connection is used. This seems to lead to a 20% gain in download speed for no cost.

ohvbd 0.5.0

Major API change

  • get_ functions have been split into two new types of function, based upon exact usage.
    • find_ functions retrieve metadata such as column definitions and ids.
    • fetch_ functions retrieve actual datasets.
  • New set of S3 classes (ohvbd.ids, ohvbd.responses, ohvbd.data.frame, ohvbd.ad.matrix) to allow for nicer checks of data integrity.
    • This has the side effect of no longer falsely triggering the data continuity checks of fetch_ functions when indexing the output of find_x_ids() functions.
  • New convenience functions fetch() and extract() leverage dynamic method dispatch along with the above classes to infer the correct underlying fetch_ and extract_ functions to use.
    • As such you can now write code such as find_vt_ids() |> fetch() |> extract() without having to remember the correct extractor to use.
    • You can still use the specific extractor functions as before should you desire.
  • All major functions interfacing with AD, VD, and VT output one of these classes.
  • Cached data from AD now contains an attribute to signify that it is cached.
  • New classes are subclassed from other base R classes, and so mostly behave in the same way (i.e. you can subset an ohvbd.data.frame in the same way as just subsetting a normal df).
  • New function ohvbd.ids() allows users to create objects of the same S3 class as output by the find_ and search_ functions.
  • New is_cached() function enables a simple check to see if an object has been loaded from the cache by ohvbd.

Full list of function name changes:

ohvbd 0.4.4

  • New function check_ohvbd_config() allows easy printing of the current status of ohvbd’s options.
  • New clean_ad_cache() function enables users to clean their cached AREAdata files easily.
  • Build timings now appear in all vignettes.
  • Cli outputs are now suppressed when running vignettes in non-interactive mode (e.g. while knitting).
  • Default cache path is now in the user directory (obtained from tools::R_user_dir()).
  • use-areadata vignette now has part of its content complete.
  • Generally this update is setting the stage for another major API overhaul in 0.5.0.

ohvbd 0.4.3

  • Large changes to all vb get_ and search_ function error handling
  • All of these functions now check automatically for SSL issues, and recommend set_ohvbd_compat() if these are detected.
  • All get_ calls requesting more than 10 ids run a pre-flight ssl check before attempting the whole thing.
  • get_vd() and get_vt() now also return a list of ids that were missing and any curl errors that were found in the process of trying to get data.

ohvbd 0.4.2

  • set_ohvbd_compat() now asks for user confirmation in interactive mode. This makes running on linux a little annoying, but is worth it due to the seriousness of disabling SSL identity verification.
  • This is not asked if the R session is running in batch mode, under knittr, or under testthat.
  • retrieving-data vignette now only enables compatibility mode if running under linux. Generally it is best to keep package usage of set_ohvbd_compat() to an absolute minimum.
  • Copyright holder now listed in DESCRIPTION

ohvbd 0.4.1

  • New parallel downloading options for get_x() and get_extract_x() functions.
  • These are to be used with caution, as they put significantly more load on the server than a sequential run would.
  • New argument check_src allows for toggling of id-sanity checking for most functions.
  • retrieving-data vignette now contains instructions for the use of search_x_smart().

ohvbd 0.4.0

Major API change

  • Major simplification of function names!
  • get_x_byid() -> get_x()
  • extract_x_data() -> extract_x()
  • assoc_x_y() -> assoc_x()
  • get_extract_x_byid_chunked() -> get_extract_x_chunked()
  • This breaks ALL PREVIOUS CODE!
  • Naming now follows a logical scheme of verb_target_modifier().
  • For example get_x_y() functions always retrieve data from database x with y specifying any special type of data.
  • Similarly extract_x() functions always extract data.
  • If a function does multiple things, it may get multiple verbs separated by underscores, e.g. get_extract_x_chunked()
  • Pipelines now internally attempt to confirm data integrity by checking that the correct functions are piped together.
  • This means it is no longer easy to accidentally do something like get_vd_current_ids() |> get_vt().

ohvbd 0.3.1

  • New function format_time_overlap_bar() allows for visually formatting a range of dates combined with another set of target dates to see where overlaps do or do not take place.
  • This is mostly used in the error handling of extract_ad() however it can also be used independently. It was designed to fill a more general role within UI design using the cli package, and should be usable (or hackable) by others needing the same tool.
  • extract_ad() now errors when all targetdate entries are outside of the range of the AREAdata dataset.
  • New assoc_ad() associates arbitrary data including lon/lat columns with AREAdata.
  • New get_vd_columns() provides quick reference about the currently present VecDyn columns. (This is currently not possible for VecTraits, but the feasibility is being investigated.)
  • New assoc_gadm() function associates gadm ids at all spatial scales with arbitrary data that include lon/lat columns.
  • Documentation now correctly displays favicons.
  • Logo now rotates through a variety of colourschemes according to the version number.

ohvbd 0.3.0

Major API change

  • *_basereq() calls are no longer required as the first argument for functions.
  • As such, data downloads no longer need to start with vb_basereq() |>.
  • Basereq can now be overridden by providing an alternative basereq to the basereq argument of these functions, which can be generated using vb_basereq().
  • This is usually only needed if using the argument unsafe = TRUE for vb_basereq().
  • It is also possible to set ohvbd to use compatability-mode ssl calls using set_ohvbd_compat().
  • This change breaks any code written prior to this version, and so major rewrites may be required.

ohvbd 0.2.5

  • extract_ad() now allows targetdate to be specified as a vector of full dates, e.g. c("2023-08-04", "2023-09-21").

ohvbd 0.2.4

  • VecTraits & VecDyn search functions no longer return stale responses if the search fails.

ohvbd 0.2.3

  • VecTraits functions now use the cli package to provide a nicer cli interface.
  • VecDyn functions now use the cli package to provide a nicer cli interface.

ohvbd 0.2.2

  • AREAdata functions now use the cli package to provide a nicer cli interface.
  • retrieving-data vignette now builds significantly quicker.

ohvbd 0.2.1

  • get_ad() now caches data from AREAdata to reduce extraneous data downloading and speed up re-execution and development.
  • This requires the new argument use_cache=TRUE and caches by default in the user directory.

ohvbd 0.2.0

  • Install instructions now include the correct command for building vignettes when installing from GitHub.
  • New check_db_status() allows for easy checking of the online status of various data providers.
  • ohvbd now interfaces with the AREAdata repository for historical climate data.
  • This includes functions to get and filter AREAdata datasets at different spatial scales.

ohvbd 0.1.4

  • Small framing change in retrieving-data vignette (courtesy of @willpearse).

ohvbd 0.1.3

  • New retrieving-data vignette to explain the basic process of downloading and extracting data from Vectraits and VecDyn.

ohvbd 0.1.2

ohvbd 0.1.1

  • get_vb_basereq() renamed to vb_basereq() for ease of writing.

ohvbd 0.1.0

  • Chunked retrieval now correctly uses the chunksize argument.
  • ohvbd now interfaces with the VecDyn database for vector population dynamic data.
  • This includes functions to get ids, get datasets, and to extract data from the responses.
  • These functions use the same api structure as for VecTraits data download, but with vd replacing vt in the function names (e.g. get_vd())

ohvbd 0.0.5

  • New search_vt() allows for keyword-based searching of VecTraits.
  • get_vt_current_ids() now handles 404 responses gracefully.

ohvbd 0.0.4

ohvbd 0.0.3

ohvbd 0.0.2

  • Add documentation for all current functions.

ohvbd 0.0.1

  • Initial commit.