R-scripts and data files applied in "Ninety years of coastal monitoring reveals baseline and extreme ocean temperatures are increasing off the Finnish coast" published in Communications Earth & Environment (2022-09-19; DOI: https://doi.org/10.1038/s43247-022-00545-z) Short description of data files: 1. 20220513_Storfjarden_interpol.txt (Input for 20220516_Creating different Reference Periods.R; 20220517_Long term trend-stripes-ranking.R; 20220517_Quantifying extreme events.R; 20220518_KS-test of RP31-60 and RP91-20.R; 20220519_RS-D and analyses.R; 20220520_Changing the perspective.R) 2. 20220516_Reference Period 1 - 1931-1960.txt (Input for 20220518_KS-test of RP31-60 and RP91-20.R) 3. 20220516_Reference Period 2WMO - 1961-1990.txt 4. 20220516_Reference Period 3_Sat - 1982-2011.txt (Input for 20220519_RS-D and analyses.R) 5. 20220516_Reference Period 4 - 1991-2020.txt (Input for 20220518_KS-test of RP31-60 and RP91-20.R) 6. 20220516_Reference Period all - 1931 - 2020.txt (Input for 20220517_Long term trend-stripes-ranking.R, 20220518_MHW.R, 20220517_Quantifying extreme events.R) 7. 20220518_DailyYSI.txt (Input for 20220518_MHW.R) 8. 20220518_MHW-metrics_Storfjarden_2016-20211209_RP31'20.txt (Output from 20220518_MHW.R) 9. DMI_BAL_SST_L4_REP_OBSERVATIONS_010_016_1634224072972.nc (Input for Input for 20220519_RS-D and analyses.R) Data File Details =================== Details for: 20220513_Storfjarden_interpol.txt --------------------------------------- Description: a space-delimited file containing daily temperature data from the study site starting 1926-08-23 until 2021-01-11 with designated gaps (see Materials & Methods in Article) Format: .txt Size: 3579 KB Dimensions: 67130 rows x 6 columns Variables: - Date: format YYYY-MM-DD - MeanTemp: Temperature [degree Celsius] - value: categorizes the Temperature ("MeanTemp") as measured = real or linearly filled = filled - gaps: indicates distance [days] to last "real" measured observation - over_thresh: "True" for gaps > 31 days; "False" for gaps <= 31 days (see identified gaps larger 31 days in Materials & Methods in Article) - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" Details for: 20220516_Reference Period 1 - 1931-1960.txt --------------------------------------- Description: a space-delimited file containing climatological means and thresholds based on Reference Period 1931-1960 Format: .txt Size: 105 KB Dimensions: 732 rows x 11 columns Variables: - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" - doy: Day of the Year; 1 to 366 - RefP1_Temp: climatological mean baseline Temperature [degree Celsius] - sd: Standard deviation [degree Celsius] - RefP1_n: Amount of datapoints available to estimate mean and thresholds for that day (max 30 for 30 years) - se: Standard error - RefP1_Q10: 10th percentile as threshold for negative extremes [degree Celsius] - RefP1_Q90: 90th percentile as threshold for positive extremes [degree Celsius] - smooth_Reftemp: 31 day (centered around respective doy) smoothed climatological mean Temperature [degree Celsius] - smooth_RefQ90: 31 day (centered around respective doy) smoothed 90th percentile threshold Temperature [degree Celsius] - smooth_RefQ10: 31 day (centered around respective doy) smoothed 10th percentile threshold Temperature [degree Celsius] Details for: 20220516_Reference Period 2WMO - 1961-1990.txt --------------------------------------- Description: a space-delimited file containing climatological means and thresholds based on Reference Period 1961-1990 Format: .txt Size: 104 KB Dimensions: 732 rows x 11 columns Variables: - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" - doy: Day of the Year; 1 to 366 - RefP2WMO_Temp: climatological mean baseline Temperature [degree Celsius] - sd: Standard deviation [degree Celsius] - RefP2WMO_n: Amount of datapoints available to estimate mean and thresholds for that day (max 30 for 30 years) - se: Standard error - RefP2WMO_Q10: 10th percentile as threshold for negative extremes [degree Celsius] - RefP2WMO_Q90: 90th percentile as threshold for positive extremes [degree Celsius] - smooth_Reftemp: 31 day (centered around respective doy) smoothed climatological mean Temperature [degree Celsius] - smooth_RefQ90: 31 day (centered around respective doy) smoothed 90th percentile threshold Temperature [degree Celsius] - smooth_RefQ10: 31 day (centered around respective doy) smoothed 10th percentile threshold Temperature [degree Celsius] Details for: 20220516_Reference Period 3_Sat - 1982-2011.txt --------------------------------------- Description: a space-delimited file containing climatological means and thresholds based on Reference Period 1982-2011 Format: .txt Size: 111 KB Dimensions: 732 rows x 11 columns Variables: - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" - doy: Day of the Year; 1 to 366 - RefP3_Temp: climatological mean baseline Temperature [degree Celsius] - sd: Standard deviation [degree Celsius] - RefP3_n: Amount of datapoints available to estimate mean and thresholds for that day (max 30 for 30 years) - se: Standard error - RefP3_Q10: 10th percentile as threshold for negative extremes [degree Celsius] - RefP3_Q90: 90th percentile as threshold for positive extremes [degree Celsius] - smooth_Reftemp: 31 day (centered around respective doy) smoothed climatological mean Temperature [degree Celsius] - smooth_RefQ90: 31 day (centered around respective doy) smoothed 90th percentile threshold Temperature [degree Celsius] - smooth_RefQ10: 31 day (centered around respective doy) smoothed 10th percentile threshold Temperature [degree Celsius] Details for: 20220516_Reference Period 4 - 1991-2020.txt --------------------------------------- Description: a space-delimited file containing climatological means and thresholds based on Reference Period 1991-2020 Format: .txt Size: 114 KB Dimensions: 732 rows x 11 columns Variables: - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" - doy: Day of the Year; 1 to 366 - RefP4_Temp: climatological mean baseline Temperature [degree Celsius] - sd: Standard deviation [degree Celsius] - RefP4_n: Amount of datapoints available to estimate mean and thresholds for that day (max 30 for 30 years) - se: Standard error - RefP4_Q10: 10th percentile as threshold for negative extremes [degree Celsius] - RefP4_Q90: 90th percentile as threshold for positive extremes [degree Celsius] - smooth_Reftemp: 31 day (centered around respective doy) smoothed climatological mean Temperature [degree Celsius] - smooth_RefQ90: 31 day (centered around respective doy) smoothed 90th percentile threshold Temperature [degree Celsius] - smooth_RefQ10: 31 day (centered around respective doy) smoothed 10th percentile threshold Temperature [degree Celsius] Details for: 20220516_Reference Period all - 1931-2020.txt --------------------------------------- Description: a space-delimited file containing climatological means and thresholds based on Reference Period 1931-2020 Format: .txt Size: 126 KB Dimensions: 732 rows x 13 columns Variables: - factored_depth: factorized Depth; for 0-2m = "surface", for <29m = "bottom" - doy: Day of the Year; 1 to 366 - RefP_all_Temp: climatological mean baseline Temperature [degree Celsius] - sd: Standard deviation [degree Celsius] - RefP_all_n: Amount of datapoints available to estimate mean and thresholds for that day (max 30 for 30 years) - se: Standard error - RefP_all_Q10: 10th percentile as threshold for negative extremes [degree Celsius] - RefP_all_Q90: 90th percentile as threshold for positive extremes [degree Celsius] - smooth_Reftemp: 31 day (centered around respective doy) smoothed climatological mean Temperature [degree Celsius] - smooth_RefQ90: 31 day (centered around respective doy) smoothed 90th percentile threshold Temperature [degree Celsius] - smooth_RefQ10: 31 day (centered around respective doy) smoothed 10th percentile threshold Temperature [degree Celsius] - 10% and 90%: Unnecessary columns as identical to RefP_all_Q10 and RefP_all_Q90 Details for: 20220518_DailyYSI.txt --------------------------------------- Description: a space-delimited file containing daily averaged Temperatures from YSI placed at the seafloor of the study site starting 2016-08-02 until 2020-12-09 Format: .txt Size: 48 KB Dimensions: 1335 rows x 3 columns Variables: - Date: format YYYY-MM-DD - doy: Day of the Year; 1 to 366 - MeanTemp: Daily averaged Temperature [degree Celsius] from YSI placed at the seafloor of study site Details for: 20220518_MHW-metrics_Storfjarden_2016-20211209_RP31'20.txt --------------------------------------- Description: a space-delimited file containing several resulting MHW metrics (see https://cran.r-project.org/web/packages/heatwaveR/heatwaveR.pdf) Format: .txt Size: 3 KB Dimensions: 16 rows x 22 columns Variables: - event_no: Indicating the ID and order of the events - index_start: Start index of event - index_peak: Peak index of event - index_end: End index of event - duration: Duration of event [days] - date_start: Start date of event [date; format = YYYY-MM-DD ] - date_end: End date of event [date; format = YYYY-MM-DD] - date_peak: Date of event peak [date; format = YYYY-MM-DD] - intensity_mean: Mean intensity [degree Celsius] - intensity_max: Maximum (peak) intensity [degree Celsius] - intensity_var: Intensity variability (standard deviation) [degree Celsius] - intensity_cumulative: Cumulative intensity [degree Celsius x days] - intensity_mean_relThresh Mean intensity [degree Celsius] relative to threshold - intensity_max_relThresh Maximum (peak) intensity [degree Celsius] relative to threshold - intensity_var_relThresh Intensity variability (standard deviation) [degree Celsius] relative to threshold - intensity_cumulative_rel Cumulative intensity [degree Celsius x days] relative to threshold - intensity_mean_abs Mean intensity [degree Celsius] relative to 0 degree Celsius - intensity_max_abs Maximum (peak) intensity [degree Celsius] relative to 0 degree Celsius - intensity_var_abs Intensity variability (standard deviation) [degree Celsius] relative to 0 degree Celsius - intensity_cumulative_abs Cumulative intensity [degree Celsius x days] relative to 0 degree Celsius - rate_onset: Onset rate of event [degree Celsius / day] - rate_decline: Decline rate of event [degree Celsius / day] Details for: DMI_BAL_SST_L4_REP_OBSERVATIONS_010_016_1634224072972.nc --------------------------------------- Description (retrieved from https://resources.marine.copernicus.eu/product-detail/SST_BAL_SST_L4_REP_OBSERVATIONS_010_016/INFORMATION) : For the Baltic Sea- The DMI Sea Surface Temperature reprocessed analysis aims at providing daily gap-free maps of sea surface temperature, referred as L4 product, at 0.02deg. x 0.02deg. horizontal resolution, using satellite data from infra-red radiometers. The product uses SST satellite products from the ESA CCI and Copernicus C3S projects, including the sensors: NOAA AVHRRs 7, 9, 11, 12, 14, 15, 16, 17, 18 , 19, Metop, ATSR1, ATSR2, AATSR and SLSTR. Product identifier: SST_BAL_SST_L4_REP_OBSERVATIONS_010_016; Location: https://resources.marine.copernicus.eu/product-detail/SST_BAL_SST_L4_REP_OBSERVATIONS_ 010_016/INFORMATION, accessed 2021-10-14) Format: .nc Size: 2963 KB Dimensions: - 4 variables (excluding dimension variables): - short analysis_error[lon,lat,time] - byte sea_ice_fraction[lon,lat,time] - short analysed_sst[lon,lat,time] - byte mask[lon,lat,time] - 3 dimensions: - time Size:13756 - lat Size:6 - lon Size:6 R-script Details (in recommended order of usage) =================== 1. Apply R-script 20220516_Creating different Reference Periods - Input: 20220513_Storfjarden_interpol.txt - short description of process: - get RefP1 01.01.1931-31.12.1960, RefP2WMO 01.01.1961-31.12.1990, RefP3 01.01.1982-30.12.2011, RefP4 01.01.1991-30.12.2020, RefP_all 01.01.1931-2019 - get climatological mean, 10th and 90th percentiles - get smoothed climatological mean and thresholds through moving average of 31 day range centered on desired doy by depth layer - merge everything - Output: 20220516_Reference Period 1 - 1931-1960.txt 20220516_Reference Period 2WMO - 1961-1990.txt 20220516_Reference Period 3_Sat - 1982-2011.txt 20220516_Reference Period 4 - 1991-2020.txt 20220516_Reference Period all - 1931 - 2020.txt 2. Figure 4 and 5 - Apply R-script 20220517_Quantifying extreme events - Input: 20220513_Storfjarden_interpol.txt; 20220516_Reference Period all - 1931 - 2020.txt - short description of process: - split timeseries to factored decades - assign "1" to every observation - evaluate each against observation climatological thresholds from RP31-20 - summarise counts by event category for decadal and monthly perspective - standardize by total number of observations - Output: Figure 4 and 5 3. Figure 2; long term trend; ranking - apply 20220517_long term trend-stripes-ranking - Input: 20220513_Storfjarden_interpol.txt, 20220516_Reference Period all - 1931 - 2020.txt - short description of process: - get yearly average of respective layer - assign "1" to every observation - evaluate each observation against climatological thresholds from RP31-20 - summarise counts by event category per year - standardize by total number of observations - order yearly averages by temperature for ranking (Supplementary Table 1) - linear regression (least squares) as Merkouriadi et al., 2014 - Output: Figure 2, Supplementary Table 1 4. Figure 3 and Supplementary Figure 1 - apply 20220518_KS-test of RP31-60 and RP91-20 - Input: 20220513_Storfjarden_interpol.txt, 20220516_Reference Period 1 - 1931-1960.txt, 20220516_Reference Period 4 - 1991-2020.txt - short description of process: - create dataframe consisting of day of the year, all temperatures of RP31-60, all temperatures of RP91-20 - apply KS-test - get p-value and Dmax for each day of the year - Output: Figure 3 and Supplementary Figure 1 5. Figure 6 and Supplementary Table 2 - apply 20220518_MHW - Input: 20220518_DailyYSI.txt, 20220516_Reference Period all - 1931 - 2020.txt - short desctription of process: - load climatological thresholds RP91-20 - apply heatwaveR by Schlegel et al. - get MHW metrics --> svg and pdf export doesnt display bottom ribbon correctly?! - Output: Figure 6 and MHW metrics (Supplementary Table 2; 20220518_MHW-metrics_Storfjarden_2016-20211209_RP31'20.txt) 6. Figure 7,8 and Supplementary Figure 2 - apply 20220519_RS-D and analyses - Input: DMI_BAL_SST_L4_REP_OBSERVATIONS_010_016_1634224072972.nc 20220513_Storfjarden_interpol.txt 20220516_Reference Period 3_Sat - 1982-2011.txt - short desctription of process: - read netCDF file from COP (copernicus) and get SST of closest pixel to Storfjärden - correlate in situ SST and COP SST 1982-2019 - create smoothed climatological mean and thresholds for COP - apply KS-test of in situ and COP RP82-11 - Output: Figure 7,8 and Supplementary Figure 2 7. Figure 9 - apply 20220520_Changing the perspective - Input: 20220513_Storfjarden_interpol.txt - short description of process: - Get yearly averages of 2019 and 2020, bottom layer - Get yearly averages per reference period - create pdfs per reference period - Output: Figure 9