Update README with preliminary 2022 data

README.md

@@ -4,7 +4,7 @@ _Sean Rohan and Lewis Barnett_
 
 This repository contains an R package that is used to calculate the *cold pool index*, mean sea surface temperature, and mean bottom temperature using temperature data collected during bottom trawl surveys of the eastern Bering Sea conducted by NOAA/AFSC/RACE's Groundfish Assessment Program. The cold pool index is defined as the area of the NOAA/AFSC/RACE eastern Bering Sea bottom trawl survey footprint with bottom temperatures less than or equal to 2° Celsius, in square kilometers. This package includes temperature products (mean temperatures, cold pool area, interpolated temperature raster) that are updated on an annual basis following the eastern Bering Sea shelf bottom trawl survey. Temperature trends are described below in the section titled [Cold pool area and temperature trends](https://github.com/afsc-gap-products/coldpool#cold-pool-area-and-temperature-trends). 
 
-The most recent version of this package was developed and tested using R 4.1.1.
+The most recent version of this package was developed and tested using R 4.1.3.
 
 # Installation
 
@@ -49,17 +49,17 @@ cold_pool_index
 
 <dl>
 <dt><b>cold_pool_index</b></dt>
-<dd><p>Data frame containing the total area of EBS waters with bottom temperatures less than or equal to 2, 1, 0, and -1 °C, mean bottom temperatures, and mean surface temperature during the EBS survey for 1982-2021 (excluding 2020 due to cancelled survey).</p></dd>
+<dd><p>Data frame containing the total area of EBS waters with bottom temperatures less than or equal to 2, 1, 0, and -1 °C, mean bottom temperatures, and mean surface temperature during the EBS survey for 1982-2022 (excluding 2020 due to cancelled survey).</p></dd>
 <dt><b>nbs_mean_bottom_temperature</b></dt>
-<dd><p>Data frame of mean bottom temperature in the NBS during years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021).</p></dd>
+<dd><p>Data frame of mean bottom temperature in the NBS during years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021, 2022 [preliminary]).</p></dd>
 <dt><b>ebs_bottom_temperature</b></dt>
-<dd><p>Interpolated rasters of bottom temperature for the EBS survey area from 1982-2021 (excluding 2020 due to cancelled survey).</p></dd>
+<dd><p>Interpolated rasters of bottom temperature for the EBS survey area from 1982-2022 (excluding 2020 due to cancelled survey).</p></dd>
 <dt><b>ebs_surface_temperature</b></dt> 
-<dd><p>Interpolated rasters of sea surface temperature for the EBS survey area from 1982-2021 (excluding 2020 due to cancelled survey).</p></dd>
+<dd><p>Interpolated rasters of sea surface temperature for the EBS survey area from 1982-2022 (excluding 2020 due to cancelled survey).</p></dd>
 <dt><b>nbs_ebs_bottom_temperature</b></dt> 
-<dd><p>Interpolated rasters of bottom temperature for the full EBS and NBS survey area for years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021).</p></dd>
+<dd><p>Interpolated rasters of bottom temperature for the full EBS and NBS survey area for years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021, 2022 [preliminary]).</p></dd>
 <dt><b>nbs_ebs_surface_temperature</b></dt> 
-<dd><p>Interpolated rasters of sea surface temperature for the full EBS and NBS survey area for years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021).</p></dd>
+<dd><p>Interpolated rasters of sea surface temperature for the full EBS and NBS survey area for years with a full EBS+NBS standardized survey (2010, 2017, 2019, 2021, 2022 [preliminary]).</p></dd>
 <dt><b>cpa_pre2021</b></dt>
 <dd><p>Data frame of cold pool area and mean temperatures calculated using the interpolation method used prior to 2021.</p></dd>
 </dl>
@@ -72,7 +72,7 @@ The temperature data products in this package are an annual snapshot of temperat
 
 ## Data collection
 
-Temperature data have been collected annually during AFSC's standardized summer bottom trawl surveys of the eastern Bering Sea continental shelf (EBS shelf) and northern Bering Sea (BS). The EBS shelf survey has been conducted annually since 1982 (except for 2020) and the NBS survey was conducted in 2010, 2017, 2019, and 2021. In the eastern Bering Sea, surveys are conducted from late May or early June through late July to early August and the northern Bering Sea survey is conducted immediately after the EBS shelf survey (July-August). The EBS shelf survey samples 376 index stations and the NBS survey samples 143 index stations per year, although the survey footprint and number of stations has changed over time (e.g. EBS NW strata added in 1987). The EBS shelf survey progresses from the nearshore waters inside Bristol Bay to the outer continental shelf in the NW portion of southeastern Bering Sea (Figure 1). The NBS survey starts offshore where the EBS shelf survey ends, then progresses northward towards the Bering Strait and Norton Sound, before heading south towards Nunivak Island.
+Temperature data have been collected annually during AFSC's standardized summer bottom trawl surveys of the eastern Bering Sea continental shelf (EBS shelf) and northern Bering Sea (BS). The EBS shelf survey has been conducted annually since 1982 (except for 2020) and the NBS survey was conducted in 2010, 2017, 2019, 2021, and 2022. In the eastern Bering Sea, surveys are conducted from late May or early June through late July to early August and the northern Bering Sea survey is conducted immediately after the EBS shelf survey (July-August). The EBS shelf survey samples 376 index stations and the NBS survey samples 143 index stations per year, although the survey footprint and number of stations has changed over time (e.g. EBS NW strata added in 1987). The EBS shelf survey progresses from the nearshore waters inside Bristol Bay to the outer continental shelf in the NW portion of southeastern Bering Sea (Figure 1). The NBS survey starts offshore where the EBS shelf survey ends, then progresses northward towards the Bering Strait and Norton Sound, before heading south towards Nunivak Island.
 
 ![Map of eastern Bering Sea and northern Bering Sea survey areas showing the EBS standard, EBS NW, and NBS survey strata.](./plots/ebs_nbs_survey_area.png)
  <font size="2"><i>Figure 1. Map of eastern Bering Sea (EBS) shelf and northern Bering Sea (NBS) shelf survey areas and station grid, including EBS standard (sampled since 1982) and northwest (sampled since 1987) subareas. Thick black lines denote survey boundaries and fill color denotes the average day of year when stations are sampled by the survey.</i></font>
@@ -89,22 +89,16 @@ Temperature data products in the coldpool package are updated on an annual basis
 
 
 # Cold pool area and temperature trends
-*Updated: November 2021*
+*Updated: September 2022*
 
 Cold pool area and temperature trends are reported in the annual [Ecosystem Status Reports](https://www.fisheries.noaa.gov/alaska/ecosystems/ecosystem-status-reports-gulf-alaska-bering-sea-and-aleutian-islands) for the eastern Bering Sea and ecosystem and socioeconomic profiles for EBS stocks. Temperature products are also used as covariates in some [stock assessment](https://www.fisheries.noaa.gov/alaska/population-assessments/north-pacific-groundfish-stock-assessments-and-fishery-evaluation) models or their inputs (e.g. abundance indices).
 
-![Cold pool area from 1982-2021, based on interpolated survey bottom temperatures](./plots/2021_coldpool_with_area.png)
- <font size="2"><i>Figure 2. Cold pool extent in the eastern Bering Sea from 2002–2021, showing areas with bottom temperatures ≤ 2°C, ≤ 1°C, ≤ 0°C, and ≤ -1°C (upper panels), and proportion of the southeastern Bering Sea survey area with bottom temperatures ≤ 2°C, ≤ 1°C, ≤ 0°C, and ≤ -1°C (lower panel). Solid black lines in the interior of the surface represent the 50m and 100m isobaths.</i></font>
+![Cold pool area from 1982-2022, based on interpolated survey bottom temperatures](./plots/2022_coldpool_with_area.png)
+ <font size="2"><i>Figure 2. Cold pool extent in the eastern Bering Sea from 2002–2022, showing areas with bottom temperatures ≤ 2°C, ≤ 1°C, ≤ 0°C, and ≤ -1°C (upper panels), and proportion of the southeastern Bering Sea survey area with bottom temperatures ≤ 2°C, ≤ 1°C, ≤ 0°C, and ≤ -1°C (lower panel). Solid black lines in the interior of the surface represent the 50m and 100m isobaths.</i></font>
 
-The cold pool extent has increased since 2018, yet the 2021 extent (58,975 km2) was the fourth lowest on record and remains one to two standard deviations below the grand mean of the time series (Figure 2). Estimates from 2018 and 2019 were the lowest on record, followed by 2003, which was only slightly lower than the 2021 estimate. In general, the extent of isotherms at all thresholds ≤ 1°C were similar, if slightly greater than prior record lows (Figure 2). As is typical when the extent is small, the cold pool in 2021 was restricted to the northern edge of the eastern Bering Sea shelf (Figure 2). 
+![Mean bottom temperature in the eastern Bering Sea during 2022, based on interpolated survey bottom temperatures](./plots/2022_nbs_ebs_temperature_map_grid.png)
+ <font size="2"><i>Figure 3. Contour map of bottom temperatures from the past four eastern and northern Bering Sea shelf bottom trawl surveys (2018-2022). Solid black contour lines denote stratum boundaries.</i></font>
 
-![Mean bottom temperature in the eastern Bering Sea during 2021, based on interpolated survey bottom temperatures](./plots/2021_nbs_ebs_temperature_map.png)
- <font size="2"><i>Figure 3. Contour map of bottom temperatures from the 2021 eastern and northern Bering Sea shelf bottom trawl survey. Solid black lines in the interior of the surface represent stratum boundaries.</i></font>
-
-The coldest waters at the seafloor were restricted to the far northeast corner of the eastern Bering Sea shelf survey area in 2021, where temperatures were greater than -1°C, with an extremely small extent of waters ≤ 1°C (14,925 km2) and ≤ 0°C (4,800 km2). However, cooler bottom temperatures were observed in the northern Bering Sea, including a substantial area of waters ≤ -1°C located west-southwest of St. Lawrence Island, while extremely warm bottom temperatures were observed from Norton Sound to Nunivak Island (Figure 3).
-
-![Mean bottom and sea surface temperatures in the eastern Bering Sea from 1982-2021, based on interpolated survey temperatures](./plots/2021_average_temperature.png)
- <font size="2"><i>Figure 4. Average summer surface (green triangles) and bottom (blue circles) temperatures (°C) of the eastern Bering Sea (EBS) shelf and northern Bering Sea (NBS) shelf based on data collected during standardized summer bottom trawl surveys from 1982–2021. Dashed lines represent the time series mean for the EBS (1982–2021, except 2020) and NBS (2010, 2017, 2019, 2021).</i></font>
-
-Mean surface and bottom temperatures in 2021 were cooler than the prior sampled year (2019), yet remained within one standard deviation above the grand mean of the time series (Figure 4). In 2021, mean bottom temperature was 3.3°C, the fifth highest on record after 2019, 2018, and 2017, and 0.9°C above the grand mean of the time series (2.5°C). The 2021 mean surface temperature was 7.2°C, which was 2.0°C lower than in 2019 yet 0.5°C higher than the grand mean of the time series (6.7°C).
+![Mean bottom and sea surface temperatures in the eastern Bering Sea from 1982-2022, based on interpolated survey temperatures](./plots/2022_average_temperature.png)
+ <font size="2"><i>Figure 4. Average summer surface (green triangles) and bottom (blue circles) temperatures (°C) of the eastern Bering Sea (EBS) shelf and northern Bering Sea (NBS) shelf based on data collected during standardized summer bottom trawl surveys from 1982–2022. Dashed lines represent the time series mean for the EBS (1982–2022, except 2020) and NBS (2010, 2017, 2019, 2021, 2022).</i></font>