NEWS.md

heatwaveR 0.5.0.9003 (2023-08-31)

• Added links to heatwave3 package on home page and gridded detection vignette.

heatwaveR 0.5.0.9003 (2023-07-31)

• Addressed CodeCov and created stable version for CRAN

heatwaveR 0.5.0.9003 (2023-07-25)

• Changed behaviour of category() to address edge case in polar MCS
• Corrected bug in category() that did not change the 'V Ice' category in the climatology output
• Also a bug that didn't return all of a users columns that are not part of the normal category() output
• And a bug that allowed users to unintentionally assign 'V Ice' category to MHWs

heatwaveR 0.5.0.9002 (2023-05-02)

• Addressed extreme edge case in category() when no Moderate I MCS are detected, just higher categories

heatwaveR 0.5.0.9001 (2023-04-17)

• Improvements to main pipeline to ensure lat column is passed forward for correct category seasons

heatwaveR 0.5.0.9000 (2023-03-30)

• Bug hunting in the build-up to v1.0.0
• Addressed issue of y column not passing through correctly from detect_event() to category() when called internally
• Changed documentation for category() to more accurately match the output of climatology = TRUE
• Looked into behaviour of protoEvents in detect_event()
• Added lat_col argument to category() to detect if time series are in N or S hemisphere

heatwaveR 0.5.0 (2023-03-20)

• Major update in preparation of removing all dependencies and releasing v1.0.0
• Also necessary due to cryptic CRAN error

heatwaveR 0.4.6.9004 (2023-03-13)

• Removed all dependencies from event_line() and block_average() except plyr
• Added line_colours argument to event_line(), allowing users to choose colours of line geoms

heatwaveR 0.4.6.9004 (2023-03-11)

• Removed all dependencies from category() and exceedance() except for plyr

heatwaveR 0.4.6.9004 (2023-03-07)

• Starting to remove as many dependencies as possible
• Started by removing all but **plyr** dependency from proto_event() and detect_event()

heatwaveR 0.4.6.9003 (2023-01-16)

• Updated SST data to end of 2022
• Changed behaviour of lolli_plot() and event_line() to now use tidyeval
• Note that this is a backwards compatibility breaking change that was required due to changes in ggplot2 v3.0.0

heatwaveR 0.4.6.9002 (2023-01-09)

• Updated citations page for all references to heatwaveR from 2022
• Added package names to all functions used in the downloading OISST vignette
• Added the MCSice argument to category(), which allows users to directly classify a MCS with a threshold below -1.7°C as a category 'V Ice' event sensu Schlegel et al. (2021; Marine cold-spells)

heatwaveR 0.4.6.9001 (2022-06-23)

• Added two new vignettes
  • Alternatives to downloading NOAA OISST data
  • Trend and break point analyses for MHW metrics

heatwaveR 0.4.6.9000 (2022-01-17)

• Updated SST time series to 2021-12-31

heatwaveR 0.4.6 (2021-10-26)

• Updated SST time series to 2020-12-31

heatwaveR 0.4.6 (2021-10-25)

• Explicitly loading Rcpp due to a change in the behaviour of the package causing ERRORs on CRAN checks

heatwaveR 0.4.5.9002 (2021-09-21)

• Updated the MCS colour palette throughout the package
  • The new colour palette is very similar, but with improved contrast
• Made a minor but important change to category() so that categories are based on temperature greater (lesser) than the thresholds and not greater (lesser) than or equal to

heatwaveR 0.4.5.9001 (2021-08-25)

• Updated the visualisation vignette to now include the code necessary to get geom_flame() to work with plotly now that it is no longer directly supported

heatwaveR 0.4.5.9001 (2021-03-17)

• Improved error trapping for ts2clm(), detect_event(), and exceedance()

heatwaveR 0.4.5.9000 (2021-02-10)

• Added more citations of the package

heatwaveR 0.4.5.9000 (2021-01-31)

• Added a categories argument to detect_event()
  • This allows one to determine the categories of events directly, rather than as a second step using the category() function

heatwaveR 0.4.5 (2021-01-23)

• Created a new vignette that shows how to save gridded MHW results to a NetCDF file

heatwaveR 0.4.5 (2021-01-07)

• Pushed new major version to CRAN

heatwaveR 0.4.4.9006 (2021-01-06)

• Some minor tweaks to satisfy CRAN

heatwaveR 0.4.4.9005 (2020-12-30)

• Pushing to GitHub actions now triggers codecov correctly

heatwaveR 0.4.4.9005 (2020-12-22)

• exceedance now outputs a one row all NA data.frame when there are no events in exceedance of the threshold
• The previous version would return an error if no exceedances were detected, making it generally unusable in gridded data
• All plotly dependencies were removed due to the orphaning of the package
  • The code to allow geom_flame to work with plotly may be found here: https://github.com/robwschlegel/MHWapp/blob/master/shiny/functions.R

heatwaveR 0.4.4.9004 (2020-12-16)

• Moved away from Travis CI to GitHub actions

heatwaveR 0.4.4.9004 (2020-11-18)

• Fixed bug in proto_event that caused joinAcrossGaps argument to flag the first n days of a time series as part of an event

heatwaveR 0.4.4.9003 (2020-11-13)

• Minor fixes for passing build

heatwaveR 0.4.4.9002 (2020-11-06)

• Remove the last offending trace of zoo from make_whole.
• Fix miscellaneous typos and formatting inconsistencies.

heatwaveR 0.4.4.9001 (2020-10-31)

• Added MCScorrect argument to catgegory function that allows the user to bound the bottom threshold for MCS categories to -1.8C

heatwaveR 0.4.4.9000 (2020-07-30)

• dplyr v1.0.0 no longer handles empty data.frames the same

  • It now forces them to logical type, so empty data.frames no longer unnest with normal results
  • This was fixed by having detect_event and category return single row NA data.frames instead

• Thinking about phasing out data.table

heatwaveR 0.4.4 (2020-06-27)

• Released v0.4.4 to CRAN

heatwaveR 0.4.3.9001 (2020-06-26)

• Re-wrote OISST and gridded detection vignettes after finding an ERDDAP server that hosts the NOAA OISST v2.1 data.
• Updated the packaged time series to now use v2.1 data from 1982 to 2019

heatwaveR 0.4.3.9000 (2020-06-25)

• Minor bug fix in gridded detection vignette

heatwaveR 0.4.3.9000 (2020-06-15)

• category() now works with MCS generated by detect_event()
• codecov pushed back up to 100%

heatwaveR 0.4.3 (2020-06-12)

• Release pushed to CRAN in light of changes to data.table and dplyr
• Waiting until NOAA OISST data area available on an ERDDAP server before updating them

heatwaveR 0.4.2.9005 (2020-06-06)

• Updated the gridded data vignette to work with OISST v2.1

heatwaveR 0.4.2.9005 (2020-06-03)

• Ensured that newly released dplyr v1.0.0 did not introduce any bugs
• Updated vignettes to now work with v2.1 of the OISST data

heatwaveR 0.4.2.9004 (2020-05-15)

• Fixed bug in detect_event() caused by data.table

  • data.table no longer allows rounding of NA values

heatwaveR 0.4.2.9003 (2020-05-08)

• Fixed bug in event_line() caused by data.table

heatwaveR 0.4.2.9002 (2020-05-05)

• Cleaned up the CITATION file

heatwaveR 0.4.2.9002 (2020-03-23)

• Improvement to legend appearance for event_line()
• Improvement to plotting in category vignette

heatwaveR 0.4.2.9001 (2020-02-24)

• Minor spelling error fixes
• Minor tweak to make_whole_fast()

heatwaveR 0.4.2.9001 (2020-02-13)

• Added a new citation that used the heatwaveR package

heatwaveR 0.4.2.9001 (2020-02-05)

• Minor internal tweak to exceedance function

heatwaveR 0.4.2.9001 (2020-01-13)

• Added one small test to get codecov back up to 100%

heatwaveR 0.4.2.9001 (2020-01-08)

• Beginning to phase out dplyr and tibble dependencies
• Replacing some dplyr functions with plyr as they appear to be slightly faster and also don't have the same multicore issues that more recent dplyr developments have created
• Added roundRes argument to detect_event() to allow users to decide the rounding precision of the returned results

heatwaveR 0.4.2 (2019-12-10)

• Minor change to ts2clm() that does not alter any functionality

heatwaveR 0.4.2 (2019-11-29)

• Publishing new stable version to CRAN due to removal of tidyverse from the list of suggested packages and the important bug fixes to category()

heatwaveR 0.4.2 (2019-11-26)

• Fixed bug in category() that incorrectly returned the difference between seas and thresh as the daily intensity value, rather than the actual temperature anomaly above seas

  • Also fixed the labelling of days below thresh as Moderate, they are now NA

• category() now adds lower case letters to the ends of event names if there were multiple large events within the same year

  • This may cause backwards compatibility issues in very rare cases, but is a necessary change

• Added roundVal argument to category() to allow users to decide the rounding precision of the returned results

heatwaveR 0.4.1.9004 (2019-11-23)

• Tripled the resolution of the logo in anticipation of creating hex stickers

heatwaveR 0.4.1.9004 (2019-11-19)

• Removed tidyverse from the list of suggested packages

heatwaveR 0.4.1.9003 (2019-11-03)

• The potentially backward compatibility breaking design change to have empty data.frames returned as one row of NA values was not as rare of a problem as first thought
• While still respecting the need to not use 1:n vector creation, detect_event() and category() now produce empty data.frames and not one row NA dataframe
• This should ensure continued backwards compatibility

heatwaveR 0.4.1.9002 (2019-11-03)

• A bug was discovered where the ts2clm() function does not first check that the time series being fed to it is in correct chronological order

  • This was fixed by ordering the data being fed to the function before beginning of the further calculations

heatwaveR 0.4.1.9001 (2019-10-30)

• An update to data.table sometime in August, 2019 reduced the packages tolerance for code with 1:n in it

  • As this is a potential memory weakness, when this creates an empty vector in multicore calculations it causes the entire run to fall over
  • Therefore, all use of 1:n has been replaced with seq_len(n)
  • This changed the list outputs when no MHWs are detected to be one row of NA values, rather than an empty list
  • This may cause backward compatibility issues, but is extremely unlikely

heatwaveR 0.4.1.9000 (2019-10-26)

• An update to the ggplot2 package some time back in August, 2019 changed slightly how Geoms work internally

  • This allowed geom_lolli() to fall over in very rare circumstances so this issue has been addressed

heatwaveR 0.4.1 (2019-09-09)

• Updated the OISST Preparation vignette to match the improvements to the rerddap package

• Also updated the vignette to be more clear to contact NOAA about data retrieval issues

• Added season argument to category(), which allows the user to specify which season of the MHWs they are interested in:

  • 'range' - The beginning and ending season of the MHW
  • 'start' - The season during the start of the MHW
  • 'peak' - The season during the peak of the MHW
  • 'end' - The season during the end of the MHW

heatwaveR 0.4.0.9000 (2019-07-22)

• Updated NOAA OISST data downloading tutorial to account for minor changes to NOAA ERDDAP servers

heatwaveR 0.4.0 (2019-07-10)

• Introduced the Algiers time series for examples on using multiple thresholds for atmospheric data
• Fixed a bug in event_line()

heatwaveR 0.4.0 (2019-07-09)

• Changed the data.table and ggplot2 dependencies to imports
• heatwaveR is now dependency free

heatwaveR 0.3.6.9004 (2019-05-29)

• Added the ability to choose the number of digits rounded to for the output of ts2clm()

heatwaveR 0.3.6.9003 (2019-02-11)

• Updated the end date for three time series packaged with heatwaveR to 2018-12-31

heatwaveR 0.3.6.9002 (2019-02-11)

• Added n and n_gap arguments to geom_flame() to allow proper screening of heatspikes
• These additions also propagate through to geom2trace.GeomFlame

heatwaveR 0.3.6.9001 (2019-01-28)

• Added some additional options to event_line() to allow users to manipulate the output more without having to get into the source code.

heatwaveR 0.3.6.9000 (2019-01-23)

• Added S3 object geom2trace.GeomFlame that now allows geom_flame() to be converted to an interactive plotly object via plotly::ggplotly()

heatwaveR 0.3.6 (2019-01-16)

• Updated Zenodo badge to reflect the upload of v0.3.6

heatwaveR 0.3.6 (2019-01-16)

• Finished Alternative Thresholds (Complex Climatologies) vignette

• Bumped code coverage back up to 100%

• AN important potential backwards compatibility breaking change is that by default ts2clm() and exceedance() will no longer produce a var column

  • The argument var = TRUE may be given to produce this column

• Submitted v0.3.6 to CRAN

heatwaveR 0.3.5.9006 (2019-01-15)

• Began editing Alternative (Complex) Climatology vignette
• Changed the default argument for exceedance(maxPadLength) from 3 to FALSE to match the new default for ts2clm()
• Changed the default behaviour of event_line() to no longer require the user to provide start_date and end_date arguments

heatwaveR 0.3.5.9005 (2019-01-03)

• Corrected some typos in the gridded event detection vignette

heatwaveR 0.3.5.9004 (2019-01-02)

• First update of 2019
• Added 'protoEvents' argument to detect_events.R() for returning the proto events rather than a table for the event metrics

heatwaveR 0.3.5.9003 (2018-12-26)

• Boxing day update

heatwaveR 0.3.5.9003 (2018-12-21)

• Updated text for the OISST preparation vignette
• Updated text for the gridded event detection vignette

heatwaveR 0.3.5.9003 (2018-12-19)

• Updated text on the landing page to better reflect the updates that have been made over the past few months
• Fixed typo in event_line() output
• Updated text for the detection and visualisation vignette
• Updated text for the exceedance vignette
• Updated text for the categories vignette
• Updated text for the OISST preparation vignette

heatwaveR 0.3.5.9003 (2018-12-18)

• Changed time series checking behaviour of exceedance() so that it is the same as ts2clm()

heatwaveR 0.3.5.9002 (2018-12-12)

• Fixed bug in event_line() that caused it to graph events outside of the spread range
• Expanded testing back up to 100%

heatwaveR 0.3.5.9001 (2018-12-06)

• Fixed bug caused by R not liking dates older than 1970-01-01
• Changed maxPadLength behaviour in ts2clm() to match the Python default settings

heatwaveR 0.3.5.9000 (2018-12-05)

• Added 'duration_max' to block_average() output
• Resumed correct version numbering

heatwaveR 0.3.5 (2018-12-03)

• Increased functionality of block_average()

heatwaveR 0.3.5 (2018-11-01)

• Updated one figure in a vignette

heatwaveR 0.3.5 (2018-10-26)

• clim_calc() reinstated to allow for calculation of clims with missing data
• var calculations reinstated for documentation issues

heatwaveR 0.3.5 (2018-10-20)

• ts2clm() no longer calls clim_calc(), but clim_calc_cpp() only
• smooth_percentile() no longer provides option to create variance climatology (the need to no longer create var seemed to not be fully implemented in 0.3.4)

heatwaveR 0.3.4 (2018-10-19)

• ts2clm() no longer calculates variance column by default
• make_whole() has been deprecated in favour of make_whole_fast()

heatwaveR 0.3.4 (2018-10-17)

• All major functions now produce results only up to the fourth decimal place

heatwaveR 0.3.4 (2018-10-16)

• Clarified some information on the basic detection vignette
• Corrected a link that went to the wrong page

heatwaveR 0.3.4 (2018-10-03)

• Changed error handling in proto_event() to return no events than to stop message with an error.
• This change was picked up by detect_event() without any required changes
• category() required a bit of cajoling to also output a blank dataframe

heatwaveR 0.3.4 (2018-10-01)

• Minor tweak to make_whole_fast() to provide a cleaner internal output

heatwaveR 0.3.4 (2018-09-28)

• Removed several unnecessary columns from category climatology output

heatwaveR 0.3.4 (2018-09-27)

• Fixed bug in ts2clm() that prevented calculation of clims with large contiguous missing periods of data (e.g. ice coverage).
• Added argument to category() that allows one to have the function also output the day-to-day (long) category values, rather than just the summary (wide) output.
• Added lon/lat values to documentation for built-in time series

heatwaveR 0.3.3 (2018-08-23)

• Added CITATION file so that package citation is now set to JOSS article

heatwaveR 0.3.3 (2018-07-31)

• Added Zenodo DOI badge
• JOSS review process complete
• Added JOSS DOI badge

heatwaveR 0.3.3 (2018-07-25)

• BUG FIX: corrected issue with clim_calc_cpp not being able to calculate clims from baselines not beginning and ending on the Julian year by making clim_spread plug the gaps beforehand with row-wise means.
• Rebuilt pkgdown site to reflect version increase
• v0.3.3 submitted to CRAN

heatwaveR 0.3.2 (2018-07-23)

• Edits suggested through JOSS review

heatwaveR 0.3.2 (2018-07-12)

• Remove unneeded copies of data from functions to improve memory-use efficiency.

heatwaveR 0.3.1 (2018-07-10)

• BUG FIX: corrected issue with make_whole_fast which did not create a whole, complete time series (i.e. missing dates were still present); the missing dates caused clim_calc_cpp to fail

heatwaveR 0.3.0 (2018-06-22)

• Re-submitted to CRAN in anticipation of ggplot2 changes
• proto_event now handles all event calculations 'in house'
• This allows detect_event to now be given a theoretically limitless number of thresholds

heatwaveR 0.2.7.9003 (2018-06-08)

• Logic catch for lolli_plot being asked to highlight more events than are present
• New vignette that looks at calculating more complex climatologies

heatwaveR 0.2.7.9002 (2018-06-07)

• Tweak to ts2clm

heatwaveR 0.2.7.9001 (2018-06-05)

• Tweaks to detect_event and exceedance

heatwaveR 0.2.7.9000 (2018-06-02)

• Unused Rcpp code removed from master branch
• Logo changed slightly
• Codecov back up to 100%
• Addressed one testthat issue that was causing the OSX CRAN build to fail
• Added CRAN link to pkgdown site
• Added Bug Report link to pkgdown site

heatwaveR 0.2.7 (2018-05-30)

• Accepted on CRAN

heatwaveR 0.2.7 (2018-05-28)

• Submitted to CRAN

heatwaveR 0.2.6.9002 (2018-05-25)

• Fixes to make_whole and testing
• Fixes to block_average
• No longer exporting make_whole and make_whole_fast
• No longer uses zoo for time series NA handling--made custom function to replace it
• Additional speed improvements
• Repair testthat tests

heatwaveR 0.2.6.9001 (2018-05-24)

• Moved all vignettes relating to the upcoming MHW_detection paper to that repo
• This helps to unclutter this repo as it should be primarily kept for package content

heatwaveR 0.2.6.9000 (2018-05-23)

• Added vignette that shows how tweaking arguments for detect changes the outputs between languages and how those outputs may differ
• Changed output of detect_event to better match Python version
• Corrections to testthat to match changes to detect_event output

heatwaveR 0.2.5.9003 (2018-05-22)

• Added C++ function, clim_calc_ccp() for faster climatology calculations; speed of climatology calculation comes down from 50.6 ms in R to 3.4 ms in C++ on my MacBook Pro (15-inch, 2017) 2.9 GHz Intel Core i7 16 GB RAM computer

heatwaveR 0.2.4.9003 (2018-05-21)

• Updated testthat for lolli_plot() and event_line()
• Updated testthat for ts2clm()
• Updated testthat for detect_event()

heatwaveR 0.2.4.9002 (2018-05-17)

• Take advantage of C++ speed enhancement in smooth_percentile() by using RcppRoll
• Update testthat accordingly

heatwaveR 0.2.3.9002 (2018-05-17)

• Basic R vs Python vignette finished

heatwaveR 0.2.3.9001 (2018-05-16)

• Minor fix to testthat
• codecov up to 100%
• Fix to geom_lolli() n argument
• Fix to lolli_plot() y-axis range
• Minor fix to make_whole()
• Skeleton of R vs Python vignette added

heatwaveR 0.2.3.9000 (2018-05-16)

• Major speed-up in the climatology creation function. clim_spread() now returns a matrix, not a data frame. This makes the loop in clim_calc() much faster. In testing with the sst_WA data, it leads to a 3.7 fold speed improvement (520 ms down to 140 ms).
• Speed-up of make_whole() (60 ms down to 40 ms)

heatwaveR 0.2.2.9000 (2018-05-15)

• Removed all instances of detect() in favour of the new pipeline
• Updated exceedance() to utilise the internal functions
• Updated object names in block_average()

heatwaveR 0.2.1.9001 (2018-05-15)

• Micro edits to documentation
• Testing for all exported and internal functions brought up to speed
• Ensuring that new ts2clm() and detect_event() pipeline returns the same results as the old make_whole() and detect() pipeline

heatwaveR 0.2.1.9000 (2018-05-14)

• Phasing in identical names as in the python version
• detect_event() now passing checks
• Must still test for MCSs
• The old detect() function was unpacked and simplified. Internal code is now in new functions, most of which will not be seen by the user. They are make_whole() proto_event(), clim_calc(), smooth_percentile(), clim_spread(), and ts2clm()
• ts2clm() used instead of detect_clim()
• Climatologies can now be calculated independently of the detect functionality
• exceedance() function testthat checks updated to account for change in variable naming

heatwaveR 0.2.0.9000 (2018-05-11)

• detect() has now been broken into detect_clim() and detect_event()
• These now also rely on internal functions
• The purpose of this is to create a family of functions that provide different options
• New vignette on making short climatologies.

heatwaveR 0.1.0.9000 (2018-05-10)

• One may now provide alternative baselines and climatologies to detect()

heatwaveR 0.0.7.9001 (2018-05-05)

• Testing for category()
• Testing for block_average()
• Testing for detect()
• Testing exceedance()
• Removed default threshold for exceedance()
• Tweaks to exceedance() error messages
• Testing for event_line()
• Testing for lolli_plot()
• Tweaks to lolli_plot() error messages

heatwaveR 0.0.7.9000 (2018-05-04)

• New category() function returns the category results for events
• Still requires testing and improved event naming scheme

heatwaveR 0.0.6.9000 (2018-05-03)

• Minor touch up to examples in geoms.R
• First draft of heatwaveR hex logo added to site
• Added category option to event_line()
• Simplifications and consistency checks to detect()
• Some writing on Baselines and climatology vignette

heatwaveR 0.0.5.9001 (2018-05-02)

• Fix to event_line() not plotting MCSs correctly
• Fix error with smooth_percentile and smooth_percentile_width descriptions that were interchanged in detect()
• Simplify initial lines of leap year calculations (remove redundant code)
• change from raster::quantile() to stats::quantile()

heatwaveR 0.0.5.9000 (2018-04-29)

• Add option to use a custom baseline to detect() as requested by Maxime Marin (), The University of Tasmania (IMAS) -- CSIRO (O&A), and which is present in the python version of the package

heatwaveR 0.0.4.9000 (2018-04-28)

• Remove restriction to require full years for start/end points of climatology calculations in detect()
• Documentation updated accordingly
• Vignette on OISST data processing added

heatwaveR 0.0.3.9000 (2018-04-26)

• Removed rlang dependency
• Touch-up to block_average()
• Tested make_whole()
• Basic testing for other functions

heatwaveR 0.0.2.9000 (2018-04-25)

• Established theme for changelog
• Synced ganalytics
• Fixed event_line() to acknowledge column names other than t and temp
• Fixed lolli_plot() to use underlying geom_lolli()
• Search bar now live
• Removed all but one use of plyr code

heatwaveR 0.0.1.9000 (2018-04-24)

• Added a NEWS.md file to track changes to the package.
• Cloned RmarineHeatWaves package to this repo
• First build of pkgdown site live