Detect heatwaves and cold-spells. — detect

Applies the Hobday et al. (2016) marine heat wave definition to an input time series of a given value (usually, but not necessarily limited to, temperature) along with a daily date vector and pre-calculated seasonal and threshold climatologies, which may either be created with ts2clm or some other means.

Usage

detect_event(
  data,
  x = t,
  y = temp,
  seasClim = seas,
  threshClim = thresh,
  threshClim2 = NA,
  minDuration = 5,
  minDuration2 = minDuration,
  joinAcrossGaps = TRUE,
  maxGap = 2,
  maxGap2 = maxGap,
  coldSpells = FALSE,
  protoEvents = FALSE,
  categories = FALSE,
  roundRes = 4,
  returnDF = TRUE,
  ...
)

Arguments

data: A data frame with at least four columns. In the default setting (i.e. omitting the arguments x, y, seas, and thresh; see immediately below), the data set is expected to have the headers t, temp, seas, and thresh. The t column is a vector of dates of class Date, temp is the measured variable (by default it is assumed to be temperature), seas is the seasonal cycle daily climatology (366 days), and thresh is the seasonal cycle daily threshold above which events may be detected. Data of the appropriate format are created by the function ts2clm, but your own data can be supplied if they meet the criteria specified by ts2clm. If the column names of data match those outlined here, the following four arguments may be ignored. Note that it is also possible to provide hourly data in the x column as class POSIXct.
x: This column is expected to contain a vector of dates as per the specification of ts2clm. If a column headed t is present in the dataframe, this argument may be omitted; otherwise, specify the name of the column with dates here. Note that it is also possible to provide hourly data as class POSIXct.
y: This is a column containing the measurement variable. If the column name differs from the default (i.e. temp), specify the name here.
seasClim: The dafault for this argument assumes that the seasonal climatology column is called seas as this matches the output of ts2clm. If the column name for the seasonal climatology is different, provide that here.
threshClim: The threshold climatology column should be called thresh. If it is not, provide the name of the threshold column here.
threshClim2: If one wishes to provide a second climatology threshold filter for the more rigorous detection of events, a vector or column containing logical values (i.e. TRUE FALSE) should be provided here. By default this argument is ignored. It's primary purpose is to allow for the inclusion of tMin and tMax thresholds.
minDuration: The minimum duration for acceptance of detected events. The default is 5 days.
minDuration2: The minimum duration for acceptance of events after filtering by threshClim and threshClim. By default minDuration2 = minDuration and is ignored if threshClim2 has not been specified.
joinAcrossGaps: Boolean switch indicating whether to join events which occur before/after a short gap as specified by maxGap. The default is TRUE.
maxGap: The maximum length of gap allowed for the joining of MHWs. The default is 2 time steps.
maxGap2: The maximum gap length after applying both thresholds. By default maxGap2 = maxGap and is ignored if threshClim2 has not been specified.
coldSpells: Boolean specifying if the code should detect cold events instead of warm events. The default is FALSE. Please note that the climatological thresholds for cold-spells are considered to be the inverse of those for MHWs. For example, the default setting for the detection of MHWs is pctile = 90, as seen in ts2clm. Should one want to use detect_event for MCSs, this threshold would best be generated in ts2clm by setting pctile = 10 (see example below). Any value may be used, but this is the setting used for the calculation of MCSs in Schlegel et al. (2017a).
protoEvents: The default, protoEvents = FALSE, will return the full output comprised of a list of two data frames, one with the climatology and the other with the event metrics. See Value below. If protoEvents = TRUE, the output will contain the original time series together with columns indicating if the threshold criterion (threshCriterion) and duration criterion (durationCriterion) have been exceeded, a column showing if a heatwave is present (i.e. both threshCriterion and durationCriterion TRUE), and a sequential number uniquely identifying the detected event(s); heatwave metrics will not be reported in the event dataframe. Note also that if protoEvents = TRUE it will ignore whatever the user provides to the categories argument and anything else passed to ....
categories: Rather than using category as a separate step to determine the categories of the detected MHWs, one may choose to set this argument to TRUE. One may pass the same arguments used in the category function to this function to affect the output. Note that the default behaviour of category is to return the event data only. To return the same list structure that detect_event outputs by default, add the argument climatology = TRUE.
roundRes: This argument allows the user to choose how many decimal places the MHW metric outputs will be rounded to. Default is 4. To prevent rounding set roundRes = FALSE. This argument may only be given numeric values or FALSE.
returnDF: The default (TRUE) tells the function to return the results as type data.frame. FALSE will return the results as a data.table.
...: Other arguments that will be passed internally to category when categories = TRUE. See the documentation for category for the list of possible arguments.

Value

The function will return a list of two data.frames, climatology and event, which are, surprisingly, the climatology and event results, respectively. The climatology contains the full time series of daily temperatures, as well as the the seasonal climatology, the threshold and various aspects of the events that were detected. The software was designed for detecting extreme thermal events, and the units specified below reflect that intended purpose. However, various other kinds of extreme events may be detected according to the specifications, and if that is the case, the appropriate units need to be determined by the user.

The climatology results will contain the same column produced by ts2clm as well as the following:

threshCriterion: Boolean indicating if temp exceeds thresh.
durationCriterion: Boolean indicating whether periods of consecutive threshCriterion are >= min_duration.
event: Boolean indicating if all criteria that define an extreme event are met.
event_no: A sequential number indicating the ID and order of occurrence of the events.
intensity: The difference between temp (or whichever column is provided for y) and seas. Only added if categories = TRUE and climatology = TRUE.
category: The category classification per day. Only added if categories = TRUE and climatology = TRUE.

The event results are summarised using a range of event metrics:

event_no: A sequential number indicating the ID and order of the events.
index_start: Start index of event.
index_end: End index of event.
duration: Duration of event [days].
date_start: Start date of event [date].
date_end: End date of event [date].
date_peak: Date of event peak [date].
intensity_mean: Mean intensity [deg. C].
intensity_max: Maximum (peak) intensity [deg. C].
intensity_var: Intensity variability (standard deviation) [deg. C].
intensity_cumulative: Cumulative intensity [deg. C x days].
rate_onset: Onset rate of event [deg. C / day].
rate_decline: Decline rate of event [deg. C / day].
event_name: The name of the event. Generated from the name value provided and the year of the date_peak of the event. If no name value is provided the default "Event" is used. As proposed in Hobday et al. (2018), Moderate events are not given a name so as to prevent multiple repeat names within the same year. If two or more events ranked greater than Moderate are reported within the same year, they will be differentiated with the addition of a trailing letter (e.g. Event 2001a, Event 2001b). Only added if categories = TRUE.
category: The maximum category threshold reached/exceeded by the event. Only added if categories = TRUE.
p_moderate: The proportion of the total duration (days) spent at or above the first threshold, but below any further thresholds. Only added if categories = TRUE.
p_strong: The proportion of the total duration (days) spent at or above the second threshold, but below any further thresholds. Only added if categories = TRUE.
p_severe: The proportion of the total duration (days) spent at or above the third threshold, but below the fourth threshold. Only added if categories = TRUE.
p_extreme: The proportion of the total duration (days) spent at or above the fourth and final threshold. Only added if categories = TRUE.
season: The season(s) during which the event occurred. If the event occurred across two seasons this will be displayed as e.g. "Winter/Spring". Across three seasons as e.g. "Winter-Summer". Events lasting across four or more seasons are listed as "Year-round". December (June) is used here as the start of Austral (Boreal) summer. If "start", "peak", or "end" was given to the season argument then only the one season during that chosen period will be given. Only added if categories = TRUE.

intensity_max_relThresh, intensity_mean_relThresh, intensity_var_relThresh, and intensity_cumulative_relThresh are as above except relative to the threshold (e.g., 90th percentile) rather than the seasonal climatology.

intensity_max_abs, intensity_mean_abs, intensity_var_abs, and intensity_cumulative_abs are as above except as absolute magnitudes rather than relative to the seasonal climatology or threshold.

Note that rate_onset and rate_decline will return NA when the event begins/ends on the first/last day of the time series. This may be particularly evident when the function is applied to large gridded data sets. Although the other metrics do not contain any errors and provide sensible values, please take this into account in its interpretation.

Details

This function assumes that the input time series consists of continuous daily values with few missing values. Time ranges which start and end part-way through the calendar year are supported. The accompanying function ts2clm aids in the preparation of a time series that is suitable for use with detect_event, although this may also be accomplished 'by hand' as long as the criteria are met as discussed in the documentation to ts2clm.
The calculation of onset and decline rates assumes that the events started a half-day before the start day and ended a half-day after the end-day. This is consistent with the duration definition as implemented, which assumes duration = end day - start day + 1. An event that is already present at the beginning of a time series, or an event that is still present at the end of a time series, will report the rate of onset or the rate of decline as NA, as it is impossible to know what the temperature half a day before or after the start or end of the event is.
For the purposes of event detection, any missing temperature values not interpolated over (through optional maxPadLength in ts2clm) will be set equal to the seasonal climatology. This means they will trigger the end/start of any adjacent temperature values which satisfy the event definition criteria.
If the code is used to detect cold events (coldSpells = TRUE), then it works just as for heat waves except that events are detected as deviations below the (100 - pctile)th percentile (e.g., the 10th instead of 90th) for at least 5 days. Intensities are reported as negative values and represent the temperature anomaly below climatology.

The original Python algorithm was written by Eric Oliver, Institute for Marine and Antarctic Studies, University of Tasmania, Feb 2015, and is documented by Hobday et al. (2016). The marine cold spell option was implemented in version 0.13 (21 Nov 2015) of the Python module as a result of our preparation of Schlegel et al. (2017), wherein the cold events receive a brief overview.

References

Hobday, A.J. et al. (2016). A hierarchical approach to defining marine heatwaves, Progress in Oceanography, 141, pp. 227-238, doi:10.1016/j.pocean.2015.12.014

Schlegel, R. W., Oliver, C. J., Wernberg, T. W., Smit, A. J. (2017). Nearshore and offshore co-occurrences of marine heatwaves and cold-spells. Progress in Oceanography, 151, pp. 189-205, doi:10.1016/j.pocean.2017.01.004

Author

Albertus J. Smit, Robert W. Schlegel, Eric C. J. Oliver

Examples

data.table::setDTthreads(threads = 1)
res_clim <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"))
out <- detect_event(res_clim)
# show a portion of the climatology:
out$climatology[1:10, ]
#>    doy          t  temp    seas  thresh threshCriterion durationCriterion event
#> 1    1 1982-01-01 20.94 21.6080 22.9605           FALSE             FALSE FALSE
#> 2    2 1982-01-02 21.25 21.6348 22.9987           FALSE             FALSE FALSE
#> 3    3 1982-01-03 21.38 21.6621 23.0376           FALSE             FALSE FALSE
#> 4    4 1982-01-04 21.16 21.6895 23.0771           FALSE             FALSE FALSE
#> 5    5 1982-01-05 21.26 21.7169 23.1130           FALSE             FALSE FALSE
#> 6    6 1982-01-06 21.61 21.7436 23.1460           FALSE             FALSE FALSE
#> 7    7 1982-01-07 21.74 21.7699 23.1775           FALSE             FALSE FALSE
#> 8    8 1982-01-08 21.50 21.7958 23.2080           FALSE             FALSE FALSE
#> 9    9 1982-01-09 21.40 21.8217 23.2366           FALSE             FALSE FALSE
#> 10  10 1982-01-10 21.36 21.8478 23.2649           FALSE             FALSE FALSE
#>    event_no
#> 1        NA
#> 2        NA
#> 3        NA
#> 4        NA
#> 5        NA
#> 6        NA
#> 7        NA
#> 8        NA
#> 9        NA
#> 10       NA
# show some of the heat waves:
out$event[1:5, 1:10]
#>   event_no index_start index_peak index_end duration date_start  date_peak
#> 1        1         885        887       889        5 1984-06-03 1984-06-05
#> 2        2         899        901       904        6 1984-06-17 1984-06-19
#> 3        3         908        922       926       19 1984-06-26 1984-07-10
#> 4        4        1023       1027      1029        7 1984-10-19 1984-10-23
#> 5        5        1033       1034      1037        5 1984-10-29 1984-10-30
#>     date_end intensity_mean intensity_max
#> 1 1984-06-07         1.7042        1.9218
#> 2 1984-06-22         1.9851        2.1063
#> 3 1984-07-14         1.9094        2.2165
#> 4 1984-10-25         1.4626        1.8304
#> 5 1984-11-02         1.3034        1.4887

# Or if one wants to calculate MCSs
res_clim <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"),
                   pctile = 10)
out <- detect_event(res_clim, coldSpells = TRUE)
# show a portion of the climatology:
out$climatology[1:10, ]
#>    doy          t  temp    seas  thresh threshCriterion durationCriterion event
#> 1    1 1982-01-01 20.94 21.6080 20.5471           FALSE             FALSE FALSE
#> 2    2 1982-01-02 21.25 21.6348 20.5713           FALSE             FALSE FALSE
#> 3    3 1982-01-03 21.38 21.6621 20.5961           FALSE             FALSE FALSE
#> 4    4 1982-01-04 21.16 21.6895 20.6218           FALSE             FALSE FALSE
#> 5    5 1982-01-05 21.26 21.7169 20.6499           FALSE             FALSE FALSE
#> 6    6 1982-01-06 21.61 21.7436 20.6776           FALSE             FALSE FALSE
#> 7    7 1982-01-07 21.74 21.7699 20.7053           FALSE             FALSE FALSE
#> 8    8 1982-01-08 21.50 21.7958 20.7362           FALSE             FALSE FALSE
#> 9    9 1982-01-09 21.40 21.8217 20.7655           FALSE             FALSE FALSE
#> 10  10 1982-01-10 21.36 21.8478 20.7927           FALSE             FALSE FALSE
#>    event_no
#> 1        NA
#> 2        NA
#> 3        NA
#> 4        NA
#> 5        NA
#> 6        NA
#> 7        NA
#> 8        NA
#> 9        NA
#> 10       NA
# show some of the cold-spells:
out$event[1:5, 1:10]
#>   event_no index_start index_peak index_end duration date_start  date_peak
#> 1        1          83         83        87        5 1982-03-24 1982-03-24
#> 2        2         194        199       207       14 1982-07-13 1982-07-18
#> 3        3         270        272       277        8 1982-09-27 1982-09-29
#> 4        4         296        303       306       11 1982-10-23 1982-10-30
#> 5        5         672        681       685       14 1983-11-03 1983-11-12
#>     date_end intensity_mean intensity_max
#> 1 1982-03-28        -1.4543       -1.5877
#> 2 1982-07-26        -1.8033       -2.7304
#> 3 1982-10-04        -1.2378       -1.3891
#> 4 1982-11-02        -1.0167       -1.2813
#> 5 1983-11-16        -1.1806       -1.4954

# It is also possible to calculate the categories of events directly
# See the \code{\link{category}} documentation for more functionality
res_clim <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"))
out_event <- detect_event(res_clim, categories = TRUE)
out_list <- detect_event(res_clim, categories = TRUE, climatology = TRUE)

# It is also possible to give two separate sets of threshold criteria

# To use a second static threshold we first use the exceedance function
thresh_19 <- exceedance(sst_Med, threshold = 19, minDuration = 10, maxGap = 0)$threshold
# Then we use that output when detecting our events
events_19 <- detect_event(ts2clm(sst_Med, climatologyPeriod = c("1982-01-01", "2011-12-31")),
                         threshClim2 = thresh_19$exceedance, minDuration2 = 10, maxGap2 = 0)

# If we want to use two different percentile thresholds we use detect_event
thresh_95 <- detect_event(ts2clm(sst_Med, pctile = 95,
                                 climatologyPeriod = c("1982-01-01", "2011-12-31")),
                          minDuration = 2, maxGap = 0)$climatology
# Then we use that output when detecting our events
events_95 <- detect_event(ts2clm(sst_Med, climatologyPeriod = c("1982-01-01", "2011-12-31")),
                          threshClim2 = thresh_95$event, minDuration2 = 2, maxGap2 = 0)