The primary entry point for heatwave3. Runs
ts2clm3 followed by detect_event3 in a
single call, with optional inline category computation.
Usage
detect3(
file_in,
name,
climatologyPeriod,
var_name = NULL,
lon_range = NULL,
lat_range = NULL,
time_range = NULL,
depth = NULL,
depth_range = NULL,
maxPadLength = FALSE,
windowHalfWidth = 5L,
pctile = 90,
smoothPercentile = TRUE,
smoothPercentileWidth = 31L,
detrend = FALSE,
minDuration = 5L,
minDuration2 = minDuration,
joinAcrossGaps = TRUE,
maxGap = 2L,
maxGap2 = maxGap,
threshClim2 = NULL,
threshClim2_var_name = NULL,
coldSpells = FALSE,
category = FALSE,
hemisphere = "south",
roundClm = 4L,
roundRes = 4L,
daily = c("none", "also", "only"),
slim = FALSE,
protoEvent = FALSE,
n_threads = NULL,
compression = 1L,
skip_bad_files = FALSE,
quiet = FALSE
)Arguments
- file_in
Path to input NetCDF file (or directory/vector of daily files).
- name
Output base name (a path stem) shared by both stages. Produces
paste0(name, "_clim.nc")andpaste0(name, "_events.nc")(plus the per-day products; seedailyandprotoEvent). The directory must exist.- climatologyPeriod
Character vector of length 2 with start and end dates of the baseline period, for example
c("1991-01-01", "2020-12-31").- var_name
Name of the SST variable. If
NULL, auto-detected.- lon_range
Optional
c(min, max)longitude range.- lat_range
Optional
c(min, max)latitude range.- time_range
Optional
c("start", "end")date range.- depth
Optional depth/level index for 4D data.
- depth_range
Optional numeric vector of length 2:
c(min_depth, max_depth). Runs the climatology and event detection natively across this contiguous band of depth levels instead of a single squeezed level – seets2clm3'sdepth_rangefor details. Mutually exclusive withdepth. Compatible withdaily/protoEvent: the per-day product gains adepthdimension the same way the climatology and event files do.- maxPadLength
Max consecutive NAs to interpolate. Default
FALSE.- windowHalfWidth
Half-width of climatology window. Default
5.- pctile
Percentile for threshold. Default
90(heatwaves); use10for cold-spells.- smoothPercentile
Apply rolling mean smoothing? Default
TRUE.- smoothPercentileWidth
Smoothing window width. Default
31.- detrend
Logical. Remove a linear trend before climatology calculation? Default
FALSE.- minDuration
Minimum event duration in days. Default
5.- minDuration2
Secondary minimum duration. See
detect_event3.- joinAcrossGaps
Join events across short gaps? Default
TRUE.- maxGap
Maximum gap length to join. Default
2.- maxGap2
Secondary maximum gap length. See
detect_event3.- threshClim2
Optional gridded NetCDF logical criterion for secondary event detection. See
detect_event3.- threshClim2_var_name
Name of the
threshClim2variable. IfNULL, it is auto-detected.- coldSpells
Detect cold-spells? Default
FALSE.- category
Logical. Compute Hobday et al. (2018) severity categories inline? Default
FALSE.- hemisphere
Character.
"south"(default) or"north".- roundClm
Decimal places for climatology rounding. Default
4.- roundRes
Decimal places for event metric rounding. Default
4.- daily
Per-day output control:
"none"(default),"also", or"only". Seedetect_event3.- slim
Logical. Per-day file with only
intensityandcategory; seedetect_event3. DefaultFALSE.- protoEvent
Logical. Write the per-day proto-event series (
paste0(name, "_protoevents.nc")) instead of the event table. Seedetect_event3. DefaultFALSE.- n_threads
Number of threads for parallel computation. Default
NULL: the session default, half the available cores unless changed withsetHW3threadsor theR_HEATWAVE3_NUM_THREADSenvironment variable.- compression
Integer from 0 to 9. zlib compression level of the NetCDF output: 1 (the default) compresses fastest, 9 gives the smallest files (a few percent smaller), and 0 writes uncompressed files, which are several times larger but much quicker to write. Gridded outputs are compressed on
n_threadsthreads when heatwave3 was built with HDF5.- skip_bad_files
Logical. For multi-file inputs, skip unreadable files or files with mismatched grids instead of failing. Default
FALSE.- quiet
Logical. Suppress all console output: the progress messages and the post-computation summaries? Warnings, such as skipped files, are still shown. Default
FALSE.
Value
Invisibly returns a named character vector of the NetCDF files
written (clim plus a subset of events, daily,
protoevents). Use hw3_export to read or export any of
them.
Examples
# \donttest{
sst_file <- system.file("extdata/sst_test.nc", package = "heatwave3")
detect3(sst_file, name = file.path(tempdir(), "demo"),
climatologyPeriod = c("1982-01-01", "2011-12-31"))
#> Reading SST data from /Users/rschlegel/Library/R/arm64/4.6/library/heatwave3/extdata/sst_test.nc...
#> Grid: 2 lon x 3 lat x 14276 time = 6 pixels
#> Computing climatology with 1 thread(s)...
#>
1/6 pixels (16%)
2/6 pixels (33%)
3/6 pixels (50%)
4/6 pixels (66%)
5/6 pixels (83%)
6/6 pixels (100%)
#> Writing climatology to /var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_clim.nc...
#> Done.
#>
#> ------------------------------------------------------------------
#> Climatology written to: /var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_clim.nc
#> Rows (long format): 2,196 grid: 2 lon x 3 lat
#>
#> Head:
#> lon lat doy seas thresh
#> 1 26.525 -34.125 1 294.4175 295.9932
#> 2 26.525 -34.125 2 294.4615 296.0291
#> 3 26.525 -34.125 3 294.5055 296.0700
#> 4 26.525 -34.125 4 294.5491 296.1114
#> 5 26.525 -34.125 5 294.5922 296.1533
#>
#> Tail:
#> lon lat doy seas thresh
#> 2192 26.575 -34.025 362 293.5284 295.1877
#> 2193 26.575 -34.025 363 293.5648 295.2171
#> 2194 26.575 -34.025 364 293.6041 295.2490
#> 2195 26.575 -34.025 365 293.6456 295.2806
#> 2196 26.575 -34.025 366 293.6883 295.3129
#>
#> Summary:
#> ocean pixels (valid climatology): 6
#> seas: 291.1 to 295.6
#> thresh: 292.4 to 297.6
#>
#> Examine with hw3_export("/var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_clim.nc", n = 20)
#> or export with hw3_export("/var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_clim.nc", file_out = "out.csv") (.csv/.rds/.parquet)
#> ------------------------------------------------------------------
#> Reading climatology from /var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_clim.nc...
#> Reading SST data from /Users/rschlegel/Library/R/arm64/4.6/library/heatwave3/extdata/sst_test.nc...
#> Grid: 2 lon x 3 lat x 14276 time = 6 pixels
#> Detecting events with 1 thread(s)...
#>
1/6 pixels (16%)
2/6 pixels (33%)
3/6 pixels (50%)
4/6 pixels (66%)
5/6 pixels (83%)
6/6 pixels (100%)
#> Found 609 events across 6 pixels
#> Writing events to /var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_events.nc...
#> Done.
#>
#> ------------------------------------------------------------------
#> Events written to: /var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_events.nc
#> Rows (long format): 609
#>
#> Head:
#> lon lat pixel_index event_no date_start date_peak date_end duration
#> 1 26.525 -34.125 0 1 1982-11-06 1982-11-14 1982-11-24 19
#> 2 26.525 -34.125 0 2 1983-04-19 1983-04-20 1983-04-23 5
#> 3 26.525 -34.125 0 3 1983-05-27 1983-05-30 1983-06-01 6
#> 4 26.525 -34.125 0 4 1983-06-24 1983-06-25 1983-06-30 7
#> 5 26.525 -34.125 0 5 1983-07-10 1983-07-12 1983-07-15 6
#> intensity_mean intensity_max intensity_var intensity_cumulative
#> 1 2.2099 3.1531 0.5616 41.9874
#> 2 3.4849 3.6150 0.1535 17.4243
#> 3 1.9696 2.0416 0.0668 11.8179
#> 4 1.9655 2.4626 0.3339 13.7587
#> 5 1.5890 1.8050 0.1784 9.5342
#> intensity_mean_relThresh intensity_max_relThresh intensity_var_relThresh
#> 1 0.6780 1.6275 0.5667
#> 2 1.6822 1.8107 0.1481
#> 3 0.2178 0.2885 0.0702
#> 4 0.5567 1.0416 0.3225
#> 5 0.2596 0.4747 0.1772
#> intensity_cumulative_relThresh intensity_mean_abs intensity_max_abs
#> 1 12.8813 295.2789 296.22
#> 2 8.4110 297.9640 298.10
#> 3 1.3069 295.6150 295.67
#> 4 3.8969 294.7100 295.27
#> 5 1.5575 294.0717 294.29
#> intensity_var_abs intensity_cumulative_abs rate_onset rate_decline
#> 1 0.5886 5610.30 0.2375 0.1539
#> 2 0.1573 1489.82 0.7084 0.3201
#> 3 0.0677 1773.69 0.0579 0.0985
#> 4 0.3945 2062.97 0.7383 0.2044
#> 5 0.1824 1764.43 0.2438 0.1360
#>
#> Tail:
#> lon lat pixel_index event_no date_start date_peak date_end
#> 605 26.575 -34.025 5 98 2019-07-07 2019-07-11 2019-07-14
#> 606 26.575 -34.025 5 99 2019-08-30 2019-09-02 2019-09-05
#> 607 26.575 -34.025 5 100 2019-10-21 2019-10-26 2019-11-01
#> 608 26.575 -34.025 5 101 2020-07-05 2020-07-06 2020-07-09
#> 609 26.575 -34.025 5 102 2020-08-24 2020-08-25 2020-08-30
#> duration intensity_mean intensity_max intensity_var intensity_cumulative
#> 605 8 1.9123 2.6167 0.3509 15.2983
#> 606 7 2.6135 3.2218 0.6238 18.2944
#> 607 12 2.7097 4.2806 0.9613 32.5162
#> 608 5 1.9184 2.4610 0.4567 9.5918
#> 609 7 1.7027 1.8887 0.1673 11.9191
#> intensity_mean_relThresh intensity_max_relThresh intensity_var_relThresh
#> 605 0.5331 1.2395 0.3545
#> 606 1.2196 1.8291 0.6356
#> 607 1.2481 2.8252 0.9574
#> 608 0.5193 1.0566 0.4505
#> 609 0.3486 0.5476 0.1719
#> intensity_cumulative_relThresh intensity_mean_abs intensity_max_abs
#> 605 4.2646 293.7725 294.47
#> 606 8.5369 293.8743 294.48
#> 607 14.9767 294.3308 295.87
#> 608 2.5966 293.8140 294.37
#> 609 2.4402 292.9757 293.17
#> intensity_var_abs intensity_cumulative_abs rate_onset rate_decline
#> 605 0.3438 2350.18 0.3962 0.3769
#> 606 0.6214 2057.12 0.4158 0.6025
#> 607 0.9940 3531.97 0.5238 0.4265
#> 608 0.4723 1469.07 0.6940 0.4588
#> 609 0.1695 2050.83 0.4821 0.1454
#>
#> Summary:
#> events: 609 pixels with events: 6
#> dates: 1982-11-06 to 2020-09-26
#> duration (days): 5 to 38
#> intensity_max: 1.314 to 4.911
#>
#> Examine with hw3_export("/var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_events.nc", n = 20)
#> or export with hw3_export("/var/folders/w8/8kw9l4sx1v57nx6l9s0rrklw0000gp/T//Rtmpe7lMQ4/demo_events.nc", file_out = "out.csv") (.csv/.rds/.parquet)
#> ------------------------------------------------------------------
# }