Reproduce State of CA Current Report figures

[bbest]

Hi @evsatt,

Is the latest version of the report here?

• Weber et al (2021) State of the California Current 2019–2020: Back to the Future With Marine Heatwaves? Front. Mar. Sci.

And specific to the figures:

• How would you prioritize production of these figures online?
• What interactivity would you like to see with them?
• Can all the data sources be identified in the database?
• Are there any existing code or instructions available for creating these?

Will use this issue as parent to individual issues per figure.

[bbest]

CalCOFI uniquely collected

FIGURE 1. Surveys map

Figure 1 | Hydrological and biological surveys used to assess the state of the California Current ecosystem.

Figure 9. Larval time series

FIGURE 9 | Time series of abundances of fishes, zooplankton, and other invertebrates as measured by biological surveys in the CCS. Bars at left indicate the latitudinal sampling range of the surveys with colors corresponding to graphed data. Numbers to the right of each series indicate the value of the final measurement (black dot) and long-term mean (horizontal bar) in parentheses. Vertical bars are at 5-year intervals with the right-most bar at January 1, 2020. Dotted lines
indicate ± 1 SE or blue shading indicates confidence limits as indicated.

Figure 10. Larval NMDS plot

FIGURE 10 | Non-metric multidimensional scaling of ichthyoplankton species by year for winter cruises at the Newport Hydrographic Line (A) and on CalCOFI lines 80 and 90 (B). Symbol colors indicate positive/negative PDO, and species colors indicate their preferred distributions. Arrows denote actual species positions where they have been moved to improve clarity.

Figure 11. Anchovy egg density map

FIGURE 11 | Densities of anchovy eggs (black bars) captured in the Continuous Underway Fish Egg Sampler during winter CalCOFI cruises, 2017–2020. Green lines indicate the ship’s positions during sampling. Data were overlaid on satellite-derived sea surface temperatures (AVHRR 1.4-km resolution).

Figure 12. Diets of fish, seabirds and mammals time series plots

FIGURE 12 | Diet compositions of Albacore, seabirds, and sea lions in the CCS. Bars at left indicate the latitudinal sampling range of the surveys with colors corresponding to graphed data.

Figure 13. Bird and mammal condition and abundance time series plots

FIGURE 13 | Time series of abundance or condition of seabirds and marine mammals as measured by biological surveys in the CCS. Bars at left indicate the latitudinal sampling range of the surveys with colors corresponding to graphed data. Numbers to the right of each series indicate the value of the final measurement (black dot) and long-term mean (horizontal bar) in parentheses. Vertical bars are at 5-year intervals with the right-most bar at January 1, 2020. Dotted lines
indicate ± 1 SE.

Figure 14. Indicators

FIGURE 14 | Status of selected indicators at the basin scale and in each region for the period 2014–2020. Arrows indicate conditions based on ranking years over the long-term means reported for each indicator in previous sections of this article. Arrows pointing upward indicate the value was ranked in the greatest 1/3 of years sampled, sideways arrows the middle 1/3, and downward arrows the least 1/3. We note that sampling periods and effort varied by indicator as described in the text.

Other / non-CalCOFI data

Figure 2. Basin-scale indicators time series plot

FIGURE 2 | Basin-scale indicators that are particularly relevant to the regional climate of the California Current: (A) Monthly values of the Oceanic Niño Index (ONI), (B) Monthly values of the Pacific Decadal Oscillation (PDO), (C) Monthly values of the North Pacific Gyre Oscillation (NPGO), and (D) Area of high atmospheric pressure of the North Pacific High averaged over January and February each year, as indicated by the areal extent of the 1020 hPa isobar located in the eastern North Pacific.

Figure 3. Surface wind and temperature anomaly maps

FIGURE 3 | Surface wind velocity and sea surface temperature anomalies in the North Pacific Ocean for fall (September–November) 2019 (A), winter (December–February) 2020 (B), spring (March–May) 2020 (C), and summer (June–August) 2020 (D). Arrows denote magnitude and direction of wind anomaly (scale arrow at top). Contours denote temperature anomaly. Shading interval is 0.25◦C and contour intervals at ±1◦C are shown in red and blue, respectively. Climatology period is 1980–2010 for both data sets.

Figure 4. SST anomalies over time (summarized from map)

FIGURE 4 | Sea-surface temperature anomalies in the CCS for the period January 2014 to September 2020 in panel (A) the coastal region 0–100 km from the coast, and (B) the transition zone, 100–300 km from the coast. Data are from the optimally interpolated global blended AVHRR temperatures data set version 2.0 (Reynolds et al., 2007) and anomalies are relative to 1982–2010 monthly means. Black contour lines mark anomalies at 1◦-C intervals.

[bbest]

Start with CalCOFI dashboard mockup

[bbest]

Map as snapshot of time series summary; play as movie

https://shiny.marinebon.app/seascapes/

[bbest]

Supplementary Figures

Figure S1. Marine heatwave duration

Supplementary Figure 1. Duration of individual large marine heatwaves vs maximum area of each heatwave, from January 1982 to October 2020. Background color indicates the number of heatwaves (out of 208), whereas outliers are marked with numbers indicating the year the heatwave was initiated. Methods for tracking and classifying heatwaves are described in Thompson et al. 2019 and https://www.integratedecosystemassessment.noaa.gov/regions/california-current/cc-projects- blobtracker.

Figure S2.

Supplementary Figure 2. Sea level pressure and wind speed cubed anomalies in the North Pacific Ocean for fall (September-November) 2019, winter (December-February) 2020, spring (March- May) 2020, and summer (June-August) 2020. Labeled contours are for sea level pressure at 25 m3s3 and shaded contours are wind speed cubed at 1hPa intervals. Climatology period is 1980- 2010 for both data sets. Wind NCEP/NCAR Reanalysis data from http://www.esrl.noaa.gov and U.S. Navy Fleet Numerical Meteorology and Oceanography Center (FNMOC) pressure data from https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdlasFnPres6.

Figure S3.

Supplementary Figure 3. Time series plots of local physical and biological anomalies (monthly climatology for the same period removed) from 1996–present at NH-25 (Latitude: 44.6517 N Longitude: 124.65 W; top panel) NH-5 (Latitude: 44.6517 N Longitude: 124.1770 W; lower five panels) along the Newport Hydrographic Line. Temperature are from 150 m and 50 at NH-25 and NH-5 respectively, Oxygen data are from near bottom (50 m; blue line indicates 1.4 ml/L with values <1.4ml/L considered hypoxic), NO2 + NO3 are from the surface, and copepod biomass anomalies are integrated over the upper 60 m. All data except oxygen data were smoothed with a 3-month running mean to remove high frequency variability.

Figure S4.

Supplementary Figure 4. Recent hydrographic observations at station TH02 (mid-shelf) along the Trinidad Head Line in context of seasonal climatology. Panels from top to bottom show A) temperature at 15 m, B) temperature at 65 m, C) salinity at 15 m, D) salinity at 65 m, E) mean (uncalibrated) chlorophyll concentration from 2-30 m, F) dissolved oxygen concentration at 65 m. Grey points indicate individual cruise observations. Thin black line indicates climatology derived from GAM of environmental parameter on day-of-year; light grey ribbon about this mean indicates range of mean residual around this climatology (based on GAM of absolute residuals on day of year). Dark grey line indicates observations during 2019. Black line indicates observations during 2020. Break between March and June 2020 indicates missed sampling due to COVID-19 restrictions.

Figure S5.

Supplementary Figure 5. Hovmoller diagrams of temperature (°C) and salinity (PSU) anomalies at 10 m from CUGN gliders on CalCOFI lines 66.7, 80.0, and 90.0. The climatology period is 2007-2020.

Figure S6.

Supplementary Figure 6. Anomalies of hydrographic properties at the σ=26.4 isopycnal (open diamonds) averaged for each cruise over the standard CalCOFI stations. Shown are anomalies of A: isopycnal depth, B: spiciness, C: oxygen, D: concentrations of nitrate and E: N*. The solid blue line connects annual averages. The climatology period is 1984-2013.

Figure S7.

Supplementary Figure 7. Cruise averages of mixed layer properties for the 66 standard CalCOFI stations, 1984 to the summer of 2020. A: the log10 of chlorophyll-a, B: the cube root of nitrate, and C: nitracline depth. Whiskers indicate the 95% confidence intervals for the means. Red solid lines represent annual averages, grey horizontal lines the climatological mean, which is zero in the case of anomalies. Anomalies are based on the period 1984-2013.

Figure S8.

Supplementary Figure 8. a) Integrated primary production from the Vertical Generalized Production Model of Behrenfeld and Falkowski (1997a, 1997b) with data from VIIRS sensor for the week of 1-6 December 2019. b) Bar graph of net primary production at 30% surface irradiance (~ 18-25 m), integrated primary production from VGPM model andrate of respiration of the microbal community with the rate of respiration of procaryotes. c) spatial distribution of net primary production at 30% light. d) spatial distribution of the rate of respiration of the microbal community at 30 % of surface irradiance.* http://sites.science.oregonstate.edu/ocean.productivity/vgpm.model.php

Figure S9.

Supplementary Figure 9. Abundance anomalies (mean 2007-2019) for the main grazing groups (Copepoda, Euphausiacea, Appendicularia, Thaliacea; Line 100 and Line 103, Station 30). Data were converted to logarithms previous estimation of the anomalies, removing the seasonal means.

Figure S10.

Supplementary Figure 10. Zooplankton volume off north Baja California (Lines 100-117). Small volume a) is the displacement volume after removing large organism (>5 ml) and Total volume b) includes the complete zooplankton sample. The anomalies were estimated removing the seasonal means (2007-2019). The lower panel c) shows the composition of the main large organisms removed. The colors indicated the geometric means of red crabs, salps, pyrosomes, heteropods, the pteropod Corolla spectabilis, medusae, and ctenophores.

Figure S11.

Supplementary Figure 11. Sampling area in orange (a) and size range (b) for albacore tuna. Mean lengths (black diamond) and boxplots of length distributions for market squid (dark grey) and forage fishes (light grey) are depicted in panel (c). Fish prey size were quantified as standard lengths (SL), while market squid size was quantified as mantle length (ML). Annual variability from the time series mean proportional abundance of prey (“mean”, and "sd") are given as a heat map of z-scores in units of standard deviations (“sd”) in panel (d). Non CPS, groundfish, or market squid prey were included in an "other" group.

Figure S2.

Supplementary Figure 12. Whale sightings during CalCOFI cruises in 2019–2020. CalCOFI stations are represented by black dots and the ship’s trackline is represented as a solid black line between stations.

[evsatt]

Hey @bbest Here is a mockup of the things that I am thinking are important in the app:
https://docs.google.com/presentation/d/1X_09_XEpOzmv8XVyZZclnxparnBfZ_go/edit#slide=id.gf42739c32a_0_57
Please feel free to edit and provide feedback

I think we captured the main ways to visualize the data including:
-Space
-time
-depth
-Space, time
-Depth, space
-Depth, space, and time

[evsatt]

Another thought for the video component (not including the current/particles) but more broadly as a concept: https://faculty.washington.edu/pmacc/LO/p5_PS_speed_top.html