From a1905e0ffa5f6ccc6f6adfbb7e842be673fee050 Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Thu, 21 Nov 2024 17:03:26 -0500 Subject: [PATCH] Updated rmds built with new plot functions Plot functions adjusted for missing data required a catalog rebuild. Added catalog_files folder to gitignore --- .gitignore | 3 +- chapters/New Indicator.rmd | 6 ++-- chapters/SAV.rmd | 8 ++++++ chapters/abc_acl.rmd | 4 +++ chapters/aggregate_biomass.rmd | 24 ++++++++++++++++ chapters/aquaculture.rmd | 3 +- chapters/bottom_temp_insitu.rmd | 16 +++++++++++ chapters/bottom_temp_model_anom.rmd | 18 ++++++------ chapters/bottom_temp_model_gridded.rmd | 3 +- chapters/cetacean_dist.rmd | 3 +- chapters/ches_bay_sst.rmd | 4 +-- chapters/ches_bay_wq.rmd | 17 ++++++++---- chapters/cold_pool.rmd | 19 ++++++------- chapters/comdat.rmd | 16 +++++------ chapters/commercial_div.rmd | 3 +- chapters/condition.rmd | 3 +- chapters/engagement.rmd | 14 +++------- chapters/exp_n.rmd | 8 +++--- chapters/forage_index.rmd | 8 +++--- chapters/gom_salmon.rmd | 9 ++++-- chapters/grayseal.rmd | 9 ++---- chapters/gsi.rmd | 8 +++--- chapters/habs.rmd | 9 ++---- chapters/harborporpoise.rmd | 6 ++-- chapters/heatwave.rmd | 8 +++--- chapters/hms_stock_status.rmd | 18 ++++-------- chapters/long_term_sst.rmd | 6 ++++ chapters/mab_inshore_survey.rmd | 8 ++++++ chapters/mass_inshore_survey.rmd | 8 ++++++ chapters/narw.rmd | 9 ++---- chapters/ocean_acidification.rmd | 3 +- chapters/ppr.rmd | 3 +- chapters/productivity_anomaly.rmd | 9 ++---- chapters/recdat.rmd | 21 +++++++------- chapters/seabird_ne.rmd | 12 ++++---- chapters/seasonal_oisst_anom.rmd | 24 ++++++++++++++++ chapters/spawn_timing.rmd | 38 ++++++++++++-------------- chapters/species_dist.rmd | 11 ++++---- chapters/species_groupings.rmd | 6 ++-- chapters/stock_status.rmd | 10 +++---- chapters/thermal_habitat_area.rmd | 5 ++-- chapters/thermal_habitat_gridded.rmd | 6 ++-- chapters/trans_dates.rmd | 8 +++--- chapters/wind_revenue.rmd | 3 +- chapters/zoo_abundance_anom.rmd | 14 ++++------ chapters/zoo_diversity.rmd | 16 +++++++++++ 46 files changed, 267 insertions(+), 200 deletions(-) diff --git a/.gitignore b/.gitignore index ba6d3be3..21c65e53 100644 --- a/.gitignore +++ b/.gitignore @@ -6,4 +6,5 @@ # local files/folders _book _bookdown_files -docs \ No newline at end of file +docs +catalog_files \ No newline at end of file diff --git a/chapters/New Indicator.rmd b/chapters/New Indicator.rmd index 29caa2af..468d0206 100644 --- a/chapters/New Indicator.rmd +++ b/chapters/New Indicator.rmd @@ -69,11 +69,9 @@ The relative dominance of large and small copepods in Northeast US ecosystems ha **Variable definitions** -Naming key * *Calanus finmarchicus* (calfin_100m3) = “calfin” , -* Large copepods (calfin_100m3, mlucens_100m3, calminor_100m3, euc_100m3, calspp_100m3) = “lgcopeALL”, +Naming key * *Calanus finmarchicus* (calfin_100m3) = “calfin” , * Large copepods (calfin_100m3, mlucens_100m3, calminor_100m3, euc_100m3, calspp_100m3) = “lgcopeALL”, * Small copepods (all) (ctyp_100m3, pseudo_100m3, tlong_100m3, cham_100m3, para_100m3, acarspp_100m3, clauso, acarlong_100m3, fur_100m3, ost_100m3, temspp_100m3, tort_100m3, paraspp_100m3) = “smallcopeALL” and -* Small copepods (SOE) (ctyp_100m3, pseudo_100m3, tlong_100m3, cham_100m3) = “smallcopeSOE”. -Variables **TO BE ADDED ONCE DATA IN ECODATA, NOT ALL DATASETS COULD BE READ INTO FORM** +* Small copepods (SOE) (ctyp_100m3, pseudo_100m3, tlong_100m3, cham_100m3) = “smallcopeSOE”. Variables **TO BE ADDED ONCE DATA IN ECODATA, NOT ALL DATASETS COULD BE READ INTO FORM** No Data diff --git a/chapters/SAV.rmd b/chapters/SAV.rmd index f099d007..5f0b6008 100644 --- a/chapters/SAV.rmd +++ b/chapters/SAV.rmd @@ -21,6 +21,14 @@ Underwater grass beds are critical to the Chesapeake Bay ecosystem. They provide ## Key Results and Visualizations SAV increased in the Mesohaline and Polyhaline zones, where SAV continued to recover from recent declines in some areas. The Mesohaline zone showed a 28% increase from 2021 (2,768 hectares, 6,840 acres). The Polyhaline zone showed a 17% increase from 2021 (1,145 hectares, 2,828 acres). The Tidal Fresh zone stayed essentially the same with a small decrease (29 hectares, 73 acres) while the Oligohaline zone showed a 15% decrease (501 hectares, 1,239 acres). The increases in the Mesohaline and Polyhaline zone largely reflect recovery following the SAV crash in 2019. Those losses in 2019 were largely due to declines in widgeongrass which has expanded over the past decade due to increases in water quality but is sensitive to wet springs like the one experienced in 2019. The expansion in polyhaline zone is also attributable to a La Nina climate cycle which has resulted in cooler summers, benefiting eelgrass. The primary losses in the Oligohaline were concentrated in a small area, the Gunpowder River, the Middle River, and the adjacent mainstem. These declines may have been influenced by phytoplankton blooms observed in those segments in the spring and summer of 2022. +### MAB + +```{r plot_SAVMAB} +# Plot indicator +ggplotObject <- ecodata::plot_SAV(report='MidAtlantic',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: The data covers the tidal Chesapeake Bay region. diff --git a/chapters/abc_acl.rmd b/chapters/abc_acl.rmd index 50ab1510..b3a7ea55 100644 --- a/chapters/abc_acl.rmd +++ b/chapters/abc_acl.rmd @@ -27,12 +27,14 @@ Catch divided by ABC/ACL for MAFMC managed fisheries. Red line indicates the med ```{r plot_abc_aclMidAtlanticStacked} # Plot indicator ggplotObject <- ecodata::plot_abc_acl(report= 'MidAtlantic', plottype= 'Stacked') +ggplotObject <- ecodata::plot_abc_acl(report= 'MidAtlantic', plottype= 'Stacked') ggplotObject ``` ```{r plot_abc_aclMidAtlanticCatch} # Plot indicator ggplotObject <- ecodata::plot_abc_acl(report= 'MidAtlantic', plottype= 'Catch') +ggplotObject <- ecodata::plot_abc_acl(report= 'MidAtlantic', plottype= 'Catch') ggplotObject ``` @@ -41,12 +43,14 @@ ggplotObject ```{r plot_abc_aclNewEnglandStacked} # Plot indicator ggplotObject <- ecodata::plot_abc_acl(report= 'NewEngland', plottype= 'Stacked') +ggplotObject <- ecodata::plot_abc_acl(report= 'NewEngland', plottype= 'Stacked') ggplotObject ``` ```{r plot_abc_aclNewEnglandCatch} # Plot indicator ggplotObject <- ecodata::plot_abc_acl(report= 'NewEngland', plottype= 'Catch') +ggplotObject <- ecodata::plot_abc_acl(report= 'NewEngland', plottype= 'Catch') ggplotObject ``` diff --git a/chapters/aggregate_biomass.rmd b/chapters/aggregate_biomass.rmd index 2a16eb9d..5ade429a 100644 --- a/chapters/aggregate_biomass.rmd +++ b/chapters/aggregate_biomass.rmd @@ -21,6 +21,30 @@ The NEFSC has been conducting bi-annual bottom trawl surveys along the Northeast ## Key Results and Visualizations Aggregate biomass levels have been relatively stable over time. +### MAB + +```{r plot_aggregate_biomassMAB} +# Plot indicator +ggplotObject <- ecodata::plot_aggregate_biomass(report='MidAtlantic',n=10) +ggplotObject +``` + +### GB + +```{r plot_aggregate_biomassNEGB} +# Plot indicator +ggplotObject <- ecodata::plot_aggregate_biomass(report='NewEngland',EPU='GB',n=10) +ggplotObject +``` + +### GOM + +```{r plot_aggregate_biomassNEGOM} +# Plot indicator +ggplotObject <- ecodata::plot_aggregate_biomass(report='NewEngland',EPU='GOM',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: By EPU diff --git a/chapters/aquaculture.rmd b/chapters/aquaculture.rmd index ff7a2731..82c78e02 100644 --- a/chapters/aquaculture.rmd +++ b/chapters/aquaculture.rmd @@ -55,8 +55,7 @@ Aquaculture production contributes to overall seafood production in the Northeas **Variable definitions** -Pieces: number of oysters produced (all regions) -Shellfish lease Acres: area used for shellfish production (New England states only), acres +Pieces: number of oysters produced (all regions) Shellfish lease Acres: area used for shellfish production (New England states only), acres Production/Acre: Pieces divided by Shellfish lease acres (New England states only) ```{r vars_aquaculture} diff --git a/chapters/bottom_temp_insitu.rmd b/chapters/bottom_temp_insitu.rmd index b4ffab42..508f6aa3 100644 --- a/chapters/bottom_temp_insitu.rmd +++ b/chapters/bottom_temp_insitu.rmd @@ -21,6 +21,22 @@ The bottom temperature index incorporates near-bottom temperature measurements c ## Key Results and Visualizations _No response_ +### MAB + +```{r plot_bottom_temp_insituMAB} +# Plot indicator +ggplotObject <- ecodata::plot_bottom_temp_insitu(report='MidAtlantic',n=10) +ggplotObject +``` + +### NE + +```{r plot_bottom_temp_insituNE} +# Plot indicator +ggplotObject <- ecodata::plot_bottom_temp_insitu(report='NewEngland',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: by EPU diff --git a/chapters/bottom_temp_model_anom.rmd b/chapters/bottom_temp_model_anom.rmd index e0d111ba..8ccbbd9f 100644 --- a/chapters/bottom_temp_model_anom.rmd +++ b/chapters/bottom_temp_model_anom.rmd @@ -29,13 +29,13 @@ Time series plots for seasonal bottom temperature anomaly for each EPU shows a l ```{r plot_bottom_temp_model_anomMidAtlanticseasonalMAB} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'MidAtlantic', varName= 'seasonal' ,EPU= 'MAB') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'MidAtlantic', varName= 'seasonal' ,EPU= 'MAB',n=10) ggplotObject ``` ```{r plot_bottom_temp_model_anomMidAtlanticannualMAB} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'MidAtlantic', varName= 'annual' ,EPU= 'MAB') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'MidAtlantic', varName= 'annual' ,EPU= 'MAB',n=10) ggplotObject ``` @@ -43,25 +43,25 @@ ggplotObject ```{r plot_bottom_temp_model_anomNewEnglandseasonalGB} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'seasonal' ,EPU= 'GB') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'seasonal' ,EPU= 'GB',n=10) ggplotObject ``` ```{r plot_bottom_temp_model_anomNewEnglandseasonalGOM} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'seasonal' ,EPU= 'GOM') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'seasonal' ,EPU= 'GOM',n=10) ggplotObject ``` ```{r plot_bottom_temp_model_anomNewEnglandannualGB} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'annual' ,EPU= 'GB') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'annual' ,EPU= 'GB',n=10) ggplotObject ``` ```{r plot_bottom_temp_model_anomNewEnglandannualGOM} # Plot indicator -ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'annual' ,EPU= 'GOM') +ggplotObject <- ecodata::plot_bottom_temp_model_anom(report= 'NewEngland', varName= 'annual' ,EPU= 'GOM',n=10) ggplotObject ``` @@ -91,11 +91,9 @@ Bottom temperature is an important driver for benthic and demersal species growt **Variable definitions** -Season: 1 = winter (January – March), 2 = spring (April – June), 3 = summer (July – September), 4 = fall (October – December) -Subarea: EPU name +Season: 1 = winter (January – March), 2 = spring (April – June), 3 = summer (July – September), 4 = fall (October – December) Subarea: EPU name Source: ROMS (bias-corrected ROMS-NWA bottom temperature [@dupontavice_ocean_2022]), GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature), PSY (CMEM’s PSY global forecast bottom temperature) -bt_temp : mean bottom temperature for each year/season across entire EPU -ref_bt: bottom temperature climatology for season/EPU based on 1990-2020 +bt_temp : mean bottom temperature for each year/season across entire EPU ref_bt: bottom temperature climatology for season/EPU based on 1990-2020 ```{r vars_bottom_temp_model_anom} # Pull all var names diff --git a/chapters/bottom_temp_model_gridded.rmd b/chapters/bottom_temp_model_gridded.rmd index 354212d8..cf538853 100644 --- a/chapters/bottom_temp_model_gridded.rmd +++ b/chapters/bottom_temp_model_gridded.rmd @@ -55,8 +55,7 @@ Bottom temperature is a key environmental parameter in defining the habitat and **Variable definitions** -- Time: year - Lat: latitude - Lon: longitude - Variable: season -- Value: bottom temperature (degrees Celcius) +- Time: year - Lat: latitude - Lon: longitude - Variable: season - Value: bottom temperature (degrees Celcius) ```{r vars_bottom_temp_model_gridded} # Pull all var names diff --git a/chapters/cetacean_dist.rmd b/chapters/cetacean_dist.rmd index ed5b49f5..026e169c 100644 --- a/chapters/cetacean_dist.rmd +++ b/chapters/cetacean_dist.rmd @@ -57,8 +57,7 @@ Shifting species distributions alter both species interactions and fishery inter **Variable definitions** -1) Time=time period of centroid location. 2) species=cetacean species. 3) season. -4) wlat=latitude of centroid. 5) wlon=longitude of centroid. +1) Time=time period of centroid location. 2) species=cetacean species. 3) season. 4) wlat=latitude of centroid. 5) wlon=longitude of centroid. ```{r vars_cetacean_dist} # Pull all var names diff --git a/chapters/ches_bay_sst.rmd b/chapters/ches_bay_sst.rmd index 94887830..b44dabb0 100644 --- a/chapters/ches_bay_sst.rmd +++ b/chapters/ches_bay_sst.rmd @@ -61,9 +61,7 @@ In the fall season, there were warmer-than-average temperatures in the Western S **Variable definitions** -1) sst: sea surface temperature 2023, Celsius -2) sst_climatol: sea surface temperature climatology 2007-2022, Celsius -3) sst_anomaly: sea surface temperature anomaly 2023 minus 2007-2022, Celsius +1) sst: sea surface temperature 2023, Celsius 2) sst_climatol: sea surface temperature climatology 2007-2022, Celsius 3) sst_anomaly: sea surface temperature anomaly 2023 minus 2007-2022, Celsius ```{r vars_ches_bay_sst} # Pull all var names diff --git a/chapters/ches_bay_wq.rmd b/chapters/ches_bay_wq.rmd index 7e15d9a2..14bbc9e4 100644 --- a/chapters/ches_bay_wq.rmd +++ b/chapters/ches_bay_wq.rmd @@ -27,6 +27,14 @@ The multimetric indicator quantifies the fraction of segment-DU-criterion combin ## Key Results and Visualizations The indicator provides an integrated measure of Chesapeake Bay’s water quality condition (Figure 1). In 2019-2021, 28.1% of all tidal water segment-DU-criterion combinations are estimated to have met or exceeded applicable water quality criteria thresholds. Overall, the indicator has a positive and statistically significant trend between 1985-1987 and 2019-2021, which shows that Chesapeake Bay is on a positive trajectory toward recovery. This pattern has been statistically linked to total nitrogen reduction, indicating responsiveness of attainment status to management actions implemented to reduce nutrients ([@zhang_chesapeake_2018]). +### MAB + +```{r plot_ches_bay_wqMAB} +# Plot indicator +ggplotObject <- ecodata::plot_ches_bay_wq(report='MidAtlantic',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: Chesapeake Bay @@ -53,13 +61,10 @@ Patterns of attainment of individual designated uses are variable (Figure 1). Th **Variable definitions** -Period: Assessment period Year 1: Starting year of the assessment period -Year 2: Ending year of the assessment period Total: The overall attainment indicator +Period: Assessment period Year 1: Starting year of the assessment period Year 2: Ending year of the assessment period Total: The overall attainment indicator MSN-DO: Estimated attainment of the dissolved oxygen criterion for the migratory spawning and nursery designated use -OW-DO: Estimated attainment of the dissolved oxygen criterion for the open water designated use -DW-DO: Estimated attainment of the dissolved oxygen criterion for the deep water designated use -DC-DO: Estimated attainment of the dissolved oxygen criterion for the deep channel designated use -OW-CHLA: Estimated attainment of the chlorophyll-a criterion +OW-DO: Estimated attainment of the dissolved oxygen criterion for the open water designated use DW-DO: Estimated attainment of the dissolved oxygen criterion for the deep water designated use +DC-DO: Estimated attainment of the dissolved oxygen criterion for the deep channel designated use OW-CHLA: Estimated attainment of the chlorophyll-a criterion SW-Clarity/SAV: Estimated attainment of the bay grasses / water clarity criterion for the shallow water designated use ```{r vars_ches_bay_wq} diff --git a/chapters/cold_pool.rmd b/chapters/cold_pool.rmd index 91bfa157..5d297f7f 100644 --- a/chapters/cold_pool.rmd +++ b/chapters/cold_pool.rmd @@ -27,19 +27,19 @@ Time series plots of the three cold pool indices. Cold pool index shows the mean ```{r plot_cold_poolMidAtlanticcold_pool} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'cold_pool') +ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'cold_pool',n=10) ggplotObject ``` ```{r plot_cold_poolMidAtlanticpersistence} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'persistence') +ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'persistence',n=10) ggplotObject ``` ```{r plot_cold_poolMidAtlanticextent} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'extent') +ggplotObject <- ecodata::plot_cold_pool(report= 'MidAtlantic', varName= 'extent',n=10) ggplotObject ``` @@ -47,19 +47,19 @@ ggplotObject ```{r plot_cold_poolNewEnglandcold_pool} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'cold_pool') +ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'cold_pool',n=10) ggplotObject ``` ```{r plot_cold_poolNewEnglandpersistence} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'persistence') +ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'persistence',n=10) ggplotObject ``` ```{r plot_cold_poolNewEnglandextent} # Plot indicator -ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'extent') +ggplotObject <- ecodata::plot_cold_pool(report= 'NewEngland', varName= 'extent',n=10) ggplotObject ``` @@ -92,11 +92,8 @@ Changes in the cold pool habitat can affect species distribution, recruitment, a **Variable definitions** 1) Source: ROMS (bias-corrected ROMS-NWA bottom temperature [@dupontavice_ocean_2022]), GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature), PSY (CMEM’s PSY global forecast bottom temperature) -2) year 3) cold_pool_index: measure of mean temperature within cold pool -4) se_cold_pool_index: standard error of cold_pool_index -5) persistence_index: measure of duration of cold pool -6) se_persistence_index: standard error of persistence_index -7) extent_index: measure of spatial extent of cold pool 8) se_extent_index: standard error of extent_index +2) year 3) cold_pool_index: measure of mean temperature within cold pool 4) se_cold_pool_index: standard error of cold_pool_index 5) persistence_index: measure of duration of cold pool +6) se_persistence_index: standard error of persistence_index 7) extent_index: measure of spatial extent of cold pool 8) se_extent_index: standard error of extent_index ```{r vars_cold_pool} # Pull all var names diff --git a/chapters/comdat.rmd b/chapters/comdat.rmd index 0b7e58a3..aff4bd59 100644 --- a/chapters/comdat.rmd +++ b/chapters/comdat.rmd @@ -28,25 +28,25 @@ Commercial revenue by managed species has generally been down. The exception is ```{r plot_comdatMidAtlanticlandingstotal} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'landings', plottype = 'total') +ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'landings', plottype = 'total',n=10) ggplotObject ``` ```{r plot_comdatMidAtlanticlandingsguild} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'landings', plottype = 'guild') +ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'landings', plottype = 'guild',n=10) ggplotObject ``` ```{r plot_comdatMidAtlanticrevenuetotal} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'revenue', plottype = 'total') +ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'revenue', plottype = 'total',n=10) ggplotObject ``` ```{r plot_comdatMidAtlanticrevenueguild} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'revenue', plottype = 'guild') +ggplotObject <- ecodata::plot_comdat(report= 'MidAtlantic', varName= 'revenue', plottype = 'guild',n=10) ggplotObject ``` @@ -54,25 +54,25 @@ ggplotObject ```{r plot_comdatNewEnglandlandingstotal} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'landings', plottype = 'total') +ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'landings', plottype = 'total',n=10) ggplotObject ``` ```{r plot_comdatNewEnglandlandingsguild} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'landings', plottype = 'guild') +ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'landings', plottype = 'guild',n=10) ggplotObject ``` ```{r plot_comdatNewEnglandrevenuetotal} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'revenue', plottype = 'total') +ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'revenue', plottype = 'total',n=10) ggplotObject ``` ```{r plot_comdatNewEnglandrevenueguild} # Plot indicator -ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'revenue', plottype = 'guild') +ggplotObject <- ecodata::plot_comdat(report= 'NewEngland', varName= 'revenue', plottype = 'guild',n=10) ggplotObject ``` diff --git a/chapters/commercial_div.rmd b/chapters/commercial_div.rmd index b3df79c4..16e11d17 100644 --- a/chapters/commercial_div.rmd +++ b/chapters/commercial_div.rmd @@ -95,8 +95,7 @@ In the Mid-Atlantic, stability in commercial fleet diversity metrics suggests st **Variable definitions** 1) Name: Permit revenue species diversity; Definition: Diversity of revenue across species averaged across permits; Units: effective Shannon. -2) Name: Fleet diversity in revenue; Definition: Diversity of revenue across fleet segments; Units: effective Shannon. -3) Name: Fleet count; Definition: Number of active fleets; Units: number of fleets. +2) Name: Fleet diversity in revenue; Definition: Diversity of revenue across fleet segments; Units: effective Shannon. 3) Name: Fleet count; Definition: Number of active fleets; Units: number of fleets. ```{r vars_commercial_div} # Pull all var names diff --git a/chapters/condition.rmd b/chapters/condition.rmd index 6451817a..e5ac8e08 100644 --- a/chapters/condition.rmd +++ b/chapters/condition.rmd @@ -86,8 +86,7 @@ These changes in condition have direct implications for stock assessments, catch **Variable definitions** -Species: common name for fish species EPU: Ecological Production Unit YEAR: year of condition data -MeanCond: annual mean by EPU and species of relative condition (unitless) +Species: common name for fish species EPU: Ecological Production Unit YEAR: year of condition data MeanCond: annual mean by EPU and species of relative condition (unitless) ```{r vars_condition} # Pull all var names diff --git a/chapters/engagement.rmd b/chapters/engagement.rmd index 78087084..647953af 100644 --- a/chapters/engagement.rmd +++ b/chapters/engagement.rmd @@ -151,16 +151,10 @@ It is also important to note that factor scores and their associated categorical **Variable definitions** -1) Name: Community Name: name of the community. -2) Commercial Engagement Index: commercial engagement factor score. -3) Commercial Reliance Index: commercial reliance factor score. -4) Recreational Engagement Score: recreational engagement factor score. -5) Recreational Reliance Index: recreational reliance factor score. -6) EJ Rating: environmental justice categorical rankings. -7) Personal Disruption Index: personal disruption factor score. -8) Population Composition Index: population composition factor score. -9) Poverty Index: poverty index factor score. 10) 1std: 1 standard deviation. -11) 0.5 std: 0.5 standard deviation. +1) Name: Community Name: name of the community. 2) Commercial Engagement Index: commercial engagement factor score. 3) Commercial Reliance Index: commercial reliance factor score. +4) Recreational Engagement Score: recreational engagement factor score. 5) Recreational Reliance Index: recreational reliance factor score. 6) EJ Rating: environmental justice categorical rankings. +7) Personal Disruption Index: personal disruption factor score. 8) Population Composition Index: population composition factor score. 9) Poverty Index: poverty index factor score. +10) 1std: 1 standard deviation. 11) 0.5 std: 0.5 standard deviation. **Indicator Category**: diff --git a/chapters/exp_n.rmd b/chapters/exp_n.rmd index 7c00323b..19e41499 100644 --- a/chapters/exp_n.rmd +++ b/chapters/exp_n.rmd @@ -26,13 +26,13 @@ Due to the shift to the NOAA vessel Henry B. Bigelow in 2009 and the inability t ```{r plot_exp_nMidAtlanticfall} # Plot indicator -ggplotObject <- ecodata::plot_exp_n(report= 'MidAtlantic', varName= 'fall') +ggplotObject <- ecodata::plot_exp_n(report= 'MidAtlantic', varName= 'fall',n=10) ggplotObject ``` ```{r plot_exp_nMidAtlanticspring} # Plot indicator -ggplotObject <- ecodata::plot_exp_n(report= 'MidAtlantic', varName= 'spring') +ggplotObject <- ecodata::plot_exp_n(report= 'MidAtlantic', varName= 'spring',n=10) ggplotObject ``` @@ -40,13 +40,13 @@ ggplotObject ```{r plot_exp_nNewEnglandfall} # Plot indicator -ggplotObject <- ecodata::plot_exp_n(report= 'NewEngland', varName= 'fall') +ggplotObject <- ecodata::plot_exp_n(report= 'NewEngland', varName= 'fall',n=10) ggplotObject ``` ```{r plot_exp_nNewEnglandspring} # Plot indicator -ggplotObject <- ecodata::plot_exp_n(report= 'NewEngland', varName= 'spring') +ggplotObject <- ecodata::plot_exp_n(report= 'NewEngland', varName= 'spring',n=10) ggplotObject ``` diff --git a/chapters/forage_index.rmd b/chapters/forage_index.rmd index 0eb54f83..54d3bef2 100644 --- a/chapters/forage_index.rmd +++ b/chapters/forage_index.rmd @@ -27,13 +27,13 @@ Variables plotted are Fall Forage Fish Biomass Estimate and Spring Forage Fish B ```{r plot_forage_indexMidAtlanticindex} # Plot indicator -ggplotObject <- ecodata::plot_forage_index(report= 'MidAtlantic', varName= 'index') +ggplotObject <- ecodata::plot_forage_index(report= 'MidAtlantic', varName= 'index',n=10) ggplotObject ``` ```{r plot_forage_indexMidAtlanticcog} # Plot indicator -ggplotObject <- ecodata::plot_forage_index(report= 'MidAtlantic', varName= 'cog') +ggplotObject <- ecodata::plot_forage_index(report= 'MidAtlantic', varName= 'cog',n=10) ggplotObject ``` @@ -41,13 +41,13 @@ ggplotObject ```{r plot_forage_indexNewEnglandindex} # Plot indicator -ggplotObject <- ecodata::plot_forage_index(report= 'NewEngland', varName= 'index') +ggplotObject <- ecodata::plot_forage_index(report= 'NewEngland', varName= 'index',n=10) ggplotObject ``` ```{r plot_forage_indexNewEnglandcog} # Plot indicator -ggplotObject <- ecodata::plot_forage_index(report= 'NewEngland', varName= 'cog') +ggplotObject <- ecodata::plot_forage_index(report= 'NewEngland', varName= 'cog',n=10) ggplotObject ``` diff --git a/chapters/gom_salmon.rmd b/chapters/gom_salmon.rmd index e418bf7e..2b259ffa 100644 --- a/chapters/gom_salmon.rmd +++ b/chapters/gom_salmon.rmd @@ -23,6 +23,12 @@ GOM Atlantic salmon abundance is tracked through adult counts at traps in large A significant and persistent decrease in marine productivity of North American Atlantic salmon populations occurred around 1990, which impacted U.S. adult spawner abundance (Figure ##). The GOM DPS was listed as Endangered under the ESA in 2000. Primary threats are dams, marine survival and climate change. Decreased productivity was linked to a regime shift that resulted in a cascading effect of ecosystem conditions driven by large scale oceanic changes. Atlantic salmon adult returns in 2022 were estimated at 1,520 with 85% originating from hatchery supplementation and 86% returning to the Penobscot River. Abundance remains critically low relative to recovery targets of 6,000 naturally-reared returns with only an estimated 218 natural returns. Return rate of Penobscot River hatchery origin 2SW salmon was 0.17%, over 2.5 times the rate for 2021 returns (Figure ##). While rates are comparable to the last decade they are significantly lower than in the past. +```{r plot_gom_salmonMAB} +# Plot indicator +ggplotObject <- ecodata::plot_gom_salmon(report='MidAtlantic',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: EPU = Gulf of Maine @@ -49,8 +55,7 @@ These large scale changes have impacted temperature, current patterns, and prima **Variable definitions** -1) Return Year. -2) GoM Salmon Total = number of documented Atlantic salmon returns to Gulf of Maine rivers in number of animals +1) Return Year. 2) GoM Salmon Total = number of documented Atlantic salmon returns to Gulf of Maine rivers in number of animals 3) PSAR -2SW = return rates for 2 sea winter returns from hatchery smolt stockings in percentage. ```{r vars_gom_salmon} diff --git a/chapters/grayseal.rmd b/chapters/grayseal.rmd index 7664886e..15853aa3 100644 --- a/chapters/grayseal.rmd +++ b/chapters/grayseal.rmd @@ -55,12 +55,9 @@ The high level of variability of the annual gray seal estimates may be due in pa **Variable definitions** -1) pbr = Potential Biological Removal level. Unit = n (number of animals) -2) totalest1y = Total bycatch of 1 year annual estimate. Unit = n (number of animals) -3) totalest5y = Total bycatch of 5 year running average estimate. Unit = n (number of animals) -4) total5yLCI = Lower 95% confidence interval of totalest5y. Unit = n (number of animals) -5) total5yUCI= Upper 95% confidence interval of totalest5y. Unit = n (number of animals) -6) Ratio1ytoPBR = ratio of the total bycatch of 1 year annual estimate relative to the corresponding annual pbr. +1) pbr = Potential Biological Removal level. Unit = n (number of animals) 2) totalest1y = Total bycatch of 1 year annual estimate. Unit = n (number of animals) +3) totalest5y = Total bycatch of 5 year running average estimate. Unit = n (number of animals) 4) total5yLCI = Lower 95% confidence interval of totalest5y. Unit = n (number of animals) +5) total5yUCI= Upper 95% confidence interval of totalest5y. Unit = n (number of animals) 6) Ratio1ytoPBR = ratio of the total bycatch of 1 year annual estimate relative to the corresponding annual pbr. ```{r vars_grayseal} # Pull all var names diff --git a/chapters/gsi.rmd b/chapters/gsi.rmd index 22db3f7d..fbee9584 100644 --- a/chapters/gsi.rmd +++ b/chapters/gsi.rmd @@ -25,13 +25,13 @@ The Gulf Stream Index suggest that recent years (2021-2022) the GS almost mainta ```{r plot_gsiMidAtlanticgsi} # Plot indicator -ggplotObject <- ecodata::plot_gsi(report= 'MidAtlantic', varName= 'gsi') +ggplotObject <- ecodata::plot_gsi(report= 'MidAtlantic', varName= 'gsi',n=10) ggplotObject ``` ```{r plot_gsiMidAtlanticwestgsi} # Plot indicator -ggplotObject <- ecodata::plot_gsi(report= 'MidAtlantic', varName= 'westgsi') +ggplotObject <- ecodata::plot_gsi(report= 'MidAtlantic', varName= 'westgsi',n=10) ggplotObject ``` @@ -39,13 +39,13 @@ ggplotObject ```{r plot_gsiNewEnglandgsi} # Plot indicator -ggplotObject <- ecodata::plot_gsi(report= 'NewEngland', varName= 'gsi') +ggplotObject <- ecodata::plot_gsi(report= 'NewEngland', varName= 'gsi',n=10) ggplotObject ``` ```{r plot_gsiNewEnglandwestgsi} # Plot indicator -ggplotObject <- ecodata::plot_gsi(report= 'NewEngland', varName= 'westgsi') +ggplotObject <- ecodata::plot_gsi(report= 'NewEngland', varName= 'westgsi',n=10) ggplotObject ``` diff --git a/chapters/habs.rmd b/chapters/habs.rmd index 0b49e7a5..074df959 100644 --- a/chapters/habs.rmd +++ b/chapters/habs.rmd @@ -82,12 +82,9 @@ Alexandrium bloom events in the Gulf of Maine can result in Paralytic Shellfish **Variable definitions** -Alexandrium: 1) Year; Definition: calendar year; Units: yyyy. -2) Name: Var; Definition: Gulf of Maine region (West, East, Bay of Fundy, All); Units: categories. -3) Name: Value; Definition: Estimated cyst abundance; Units: numbers of cells * 10 to the 16th power) -PSP: 1) Year; Definition: calendar year; Units: yyyy. -2) Name: State; Definition: MA, NH, or ME ; Units: categories. -3) Name: N_Rows; Definition: Number of sample events represented; Units: integer. +Alexandrium: 1) Year; Definition: calendar year; Units: yyyy. 2) Name: Var; Definition: Gulf of Maine region (West, East, Bay of Fundy, All); Units: categories. +3) Name: Value; Definition: Estimated cyst abundance; Units: numbers of cells * 10 to the 16th power) PSP: 1) Year; Definition: calendar year; Units: yyyy. +2) Name: State; Definition: MA, NH, or ME ; Units: categories. 3) Name: N_Rows; Definition: Number of sample events represented; Units: integer. 4) Name: PSP_Exceed_Threshold_Pct; Definition: Percentage of samples exceeding PSP threshold; Units: decimal number, 0-100. ```{r vars_habs} diff --git a/chapters/harborporpoise.rmd b/chapters/harborporpoise.rmd index 8279cabb..ef5a37bd 100644 --- a/chapters/harborporpoise.rmd +++ b/chapters/harborporpoise.rmd @@ -55,10 +55,8 @@ The high level of variability of the annual gray seal estimates may be due in pa **Variable definitions** -1) pbr = Potential Biological Removal level. Unit = n (number of animals) -2) totalest1y = Total bycatch estimate over all gear types per year -3) totalest5y = Total bycatch estimate over all gear types as a 5-year running average -4) total5yLCI = Lower 95% confidence interval of totalest5y. Unit = n (number of animals) +1) pbr = Potential Biological Removal level. Unit = n (number of animals) 2) totalest1y = Total bycatch estimate over all gear types per year +3) totalest5y = Total bycatch estimate over all gear types as a 5-year running average 4) total5yLCI = Lower 95% confidence interval of totalest5y. Unit = n (number of animals) 5) total5yUCI= Upper 95% confidence interval of totalest5y. Unit = n (number of animals) ```{r vars_harborporpoise} diff --git a/chapters/heatwave.rmd b/chapters/heatwave.rmd index 8b95f286..0246fa83 100644 --- a/chapters/heatwave.rmd +++ b/chapters/heatwave.rmd @@ -47,13 +47,13 @@ In 2023, the Middle Atlantic Bight did not experience any bottom MHWs. The stron ```{r plot_heatwaveMidAtlanticSurface} # Plot indicator -ggplotObject <- ecodata::plot_heatwave(report= 'MidAtlantic', varName= 'Surface') +ggplotObject <- ecodata::plot_heatwave(report= 'MidAtlantic', varName= 'Surface',n=10) ggplotObject ``` ```{r plot_heatwaveMidAtlanticBottom} # Plot indicator -ggplotObject <- ecodata::plot_heatwave(report= 'MidAtlantic', varName= 'Bottom') +ggplotObject <- ecodata::plot_heatwave(report= 'MidAtlantic', varName= 'Bottom',n=10) ggplotObject ``` @@ -61,13 +61,13 @@ ggplotObject ```{r plot_heatwaveNewEnglandSurface} # Plot indicator -ggplotObject <- ecodata::plot_heatwave(report= 'NewEngland', varName= 'Surface') +ggplotObject <- ecodata::plot_heatwave(report= 'NewEngland', varName= 'Surface',n=10) ggplotObject ``` ```{r plot_heatwaveNewEnglandBottom} # Plot indicator -ggplotObject <- ecodata::plot_heatwave(report= 'NewEngland', varName= 'Bottom') +ggplotObject <- ecodata::plot_heatwave(report= 'NewEngland', varName= 'Bottom',n=10) ggplotObject ``` diff --git a/chapters/hms_stock_status.rmd b/chapters/hms_stock_status.rmd index f765b8fe..1bed15b0 100644 --- a/chapters/hms_stock_status.rmd +++ b/chapters/hms_stock_status.rmd @@ -57,21 +57,15 @@ TBD – our assessment team has asked that the Kobe plots be redone, so please d **Variable definitions** -Current Relative Biomass level = finalized biomass estimate provided in latest stock assessments -Bmsy = biomass at maximum sustainable yield +Current Relative Biomass level = finalized biomass estimate provided in latest stock assessments Bmsy = biomass at maximum sustainable yield Threshold = the threshold identified in respective assessments to indicate overfished vs. overfishing -International Stock Status, Domestic Stock Status, Years to Rebuild = estimate if provided in assessments -Rebuilding Start Date (End Date) = estimate if provided in assessments. -Current Relative Fishing Mortality Rate = finalized mortality rates provided in latest stock assessment -Maximum Fishing Mortality Threshold = reference point identified in latest stock assessment -International Stock Status, Domestic Stock Status. Stock = the name of the stock assessed -Last Assessment Year = the year in which the latest assessment was finalized -Upcoming Assessment = Year that the next assessment is anticipated (if scheduled) -Notes = additional information. Shark Stock = the name of the stock assessed +International Stock Status, Domestic Stock Status, Years to Rebuild = estimate if provided in assessments Rebuilding Start Date (End Date) = estimate if provided in assessments. +Current Relative Fishing Mortality Rate = finalized mortality rates provided in latest stock assessment Maximum Fishing Mortality Threshold = reference point identified in latest stock assessment +International Stock Status, Domestic Stock Status. Stock = the name of the stock assessed Last Assessment Year = the year in which the latest assessment was finalized +Upcoming Assessment = Year that the next assessment is anticipated (if scheduled) Notes = additional information. Shark Stock = the name of the stock assessed Last Assessment Year = the year the latest assessment was finalized Last Assessment Type = unless otherwise indicated, this identifies the type of SEDAR assessment used (typically “Benchmark”, “Standard”, or “Update”). This is subject to change as SEDAR adjusts their assessment types. -Upcoming Assessment = year of upcoming assessment, if scheduled. -Upcoming Assessment Type = unless otherwise indicated this identifies the type of SEDAR assessment used. +Upcoming Assessment = year of upcoming assessment, if scheduled. Upcoming Assessment Type = unless otherwise indicated this identifies the type of SEDAR assessment used. Notes = Relevant information concerning the domestic assessments. ```{r vars_hms_stock_status} diff --git a/chapters/long_term_sst.rmd b/chapters/long_term_sst.rmd index 65a2426b..b91d5b73 100644 --- a/chapters/long_term_sst.rmd +++ b/chapters/long_term_sst.rmd @@ -21,6 +21,12 @@ The data presented here are average annual sea-surface temperatures from the NOA ## Key Results and Visualizations Since the 1860’s, the Northeast US shelf sea surface temperature (SST) has exhibited an overall warming trend, with the past decade measuring well above the long term average. +```{r plot_long_term_sstMAB} +# Plot indicator +ggplotObject <- ecodata::plot_long_term_sst(report='MidAtlantic',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: Full shelf diff --git a/chapters/mab_inshore_survey.rmd b/chapters/mab_inshore_survey.rmd index 2c3c3ef0..805d0a3c 100644 --- a/chapters/mab_inshore_survey.rmd +++ b/chapters/mab_inshore_survey.rmd @@ -27,6 +27,14 @@ Indicators from these inshore surveys are analagous to those produced by the NEF ## Key Results and Visualizations Each survey shows trends by aggregate group. +### MAB + +```{r plot_mab_inshore_surveyMAB} +# Plot indicator +ggplotObject <- ecodata::plot_mab_inshore_survey(report='MidAtlantic',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: Nearshore regions of the MAB and GOM diff --git a/chapters/mass_inshore_survey.rmd b/chapters/mass_inshore_survey.rmd index 58c6bc9b..2195f49f 100644 --- a/chapters/mass_inshore_survey.rmd +++ b/chapters/mass_inshore_survey.rmd @@ -27,6 +27,14 @@ Indicators from these inshore surveys are analagous to those produced by the NEF ## Key Results and Visualizations Each survey shows trends by aggregate group. +### NE + +```{r plot_mass_inshore_surveyNE} +# Plot indicator +ggplotObject <- ecodata::plot_mass_inshore_survey(report='NewEngland',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: Nearshore regions of the MAB and GOM diff --git a/chapters/narw.rmd b/chapters/narw.rmd index 7efccd4a..6b55add8 100644 --- a/chapters/narw.rmd +++ b/chapters/narw.rmd @@ -85,12 +85,9 @@ The UMEs are under investigation and are likely the result of multiple drivers. **Variable definitions** -NARW Abundance 1) Year 2) lower95 = lower 95% confidence interval value in number of animals. -3) Median=median estimate of right whale abundance in number of animals. -4) Upper95= upper 95% confidence interval value in number of animals. -5) Mean= mean estimate of right whale abundance in number of animals. -6) SD=standard deviation of estimate of right whale abundance in number of animals. NARW Calves 1) Year -2) Tot.Calves = total number of right whale calves born that year in number of animals. +NARW Abundance 1) Year 2) lower95 = lower 95% confidence interval value in number of animals. 3) Median=median estimate of right whale abundance in number of animals. +4) Upper95= upper 95% confidence interval value in number of animals. 5) Mean= mean estimate of right whale abundance in number of animals. +6) SD=standard deviation of estimate of right whale abundance in number of animals. NARW Calves 1) Year 2) Tot.Calves = total number of right whale calves born that year in number of animals. ```{r vars_narw} # Pull all var names diff --git a/chapters/ocean_acidification.rmd b/chapters/ocean_acidification.rmd index 3f15769a..88d644b7 100644 --- a/chapters/ocean_acidification.rmd +++ b/chapters/ocean_acidification.rmd @@ -102,8 +102,7 @@ The seasonal level resolution of data collected in the Mid-Atlantic Bight in 202 **Variable definitions** -1) depth_interpolated meters 2) temperature degrees Celsius 3) chlorophyll_a µg L-1 -4) oxygen_concentration_shifted_mgL mg L-1 5) pH_shifted 6) aragonite_saturation_state +1) depth_interpolated meters 2) temperature degrees Celsius 3) chlorophyll_a µg L-1 4) oxygen_concentration_shifted_mgL mg L-1 5) pH_shifted 6) aragonite_saturation_state No Data diff --git a/chapters/ppr.rmd b/chapters/ppr.rmd index 56d03e89..4b92f2f8 100644 --- a/chapters/ppr.rmd +++ b/chapters/ppr.rmd @@ -132,8 +132,7 @@ There is insufficient evidence to determine whether ecosystem overfishing in occ **Variable definitions** -1. Ryther; The Ryther index; mt km^-2 y^-1 2. Fogarty; The Fogarty Index; Parts per thousand 0/00 -3. PP; Primary Production; mtC region^-1 year^-1 +1. Ryther; The Ryther index; mt km^-2 y^-1 2. Fogarty; The Fogarty Index; Parts per thousand 0/00 3. PP; Primary Production; mtC region^-1 year^-1 ```{r vars_ppr} # Pull all var names diff --git a/chapters/productivity_anomaly.rmd b/chapters/productivity_anomaly.rmd index b3b56c2d..fa08f30b 100644 --- a/chapters/productivity_anomaly.rmd +++ b/chapters/productivity_anomaly.rmd @@ -89,12 +89,9 @@ The apparent decline in productivity across multiple managed species in the MAB, **Variable definitions** -Variable names are organized using this format: [region] stock name - variable type and source -Variables ending with "_Survey" are survey derived recruits/spawner anomalies -Variables ending with "-Assessment" are assessment derived quantities Survey stock names are in ALL CAPS -NE LME prepended to a survey stock name means the anomalies are coastwide -Assessment stock names are in Sentence case -Units for survey variables are the Z score of (number of recruits in year+1/biomass of adults in year) +Variable names are organized using this format: [region] stock name - variable type and source Variables ending with "_Survey" are survey derived recruits/spawner anomalies +Variables ending with "-Assessment" are assessment derived quantities Survey stock names are in ALL CAPS NE LME prepended to a survey stock name means the anomalies are coastwide +Assessment stock names are in Sentence case Units for survey variables are the Z score of (number of recruits in year+1/biomass of adults in year) Units for plotted assessment variables are the Z score of (numbers of recruits per kg spawning biomass with recruits aligned to spawning biomass year using age at recruitment) Other variables are available in the assessment derived dataset but are not plotted. To be added later. diff --git a/chapters/recdat.rmd b/chapters/recdat.rmd index 9d939830..49b016e3 100644 --- a/chapters/recdat.rmd +++ b/chapters/recdat.rmd @@ -30,25 +30,25 @@ In New England, recreational species catch diversity has been above the time ser ```{r plot_recdatMidAtlanticlandings} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'landings') +ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'landings',n=10) ggplotObject ``` ```{r plot_recdatMidAtlanticeffortdiversity} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'effortdiversity') +ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'effortdiversity',n=10) ggplotObject ``` ```{r plot_recdatMidAtlanticcatchdiversity} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'catchdiversity') +ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'catchdiversity',n=10) ggplotObject ``` ```{r plot_recdatMidAtlanticeffort} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'effort') +ggplotObject <- ecodata::plot_recdat(report= 'MidAtlantic', varName= 'effort',n=10) ggplotObject ``` @@ -56,25 +56,25 @@ ggplotObject ```{r plot_recdatNewEnglandlandings} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'landings') +ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'landings',n=10) ggplotObject ``` ```{r plot_recdatNewEnglandeffortdiversity} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'effortdiversity') +ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'effortdiversity',n=10) ggplotObject ``` ```{r plot_recdatNewEnglandcatchdiversity} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'catchdiversity') +ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'catchdiversity',n=10) ggplotObject ``` ```{r plot_recdatNewEnglandeffort} # Plot indicator -ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'effort') +ggplotObject <- ecodata::plot_recdat(report= 'NewEngland', varName= 'effort',n=10) ggplotObject ``` @@ -110,9 +110,8 @@ The increase in recreational species catch diversity in New England is due to re **Variable definitions** -Ex: 1) Name: piscivore_biomass; Definition: Biomass of piscivores; Units: kg tow^-1. 2) Name: forage_biomass; Definition: Biomass of forage fish; Units: kg tow^-1. - 1) Name: Recreational Seafood; Definition: Recreational Harvest; Units: lbs -2) Name: Recreational Effort; Definition: Recreational Trips; Units: Angler Trips +Ex: 1) Name: piscivore_biomass; Definition: Biomass of piscivores; Units: kg tow^-1. 2) Name: forage_biomass; Definition: Biomass of forage fish; Units: kg tow^-1. +1) Name: Recreational Seafood; Definition: Recreational Harvest; Units: lbs 2) Name: Recreational Effort; Definition: Recreational Trips; Units: Angler Trips 3) Name: Recreational Effort Diversity; Definition: Recreational fleet effort diversity across modes; Units: Effective Shannon Metric 4) Name: Recreational Catch Diversity; Definition: Recreational Diversity of Catch across managed species; Units: Effective Shannon Metric diff --git a/chapters/seabird_ne.rmd b/chapters/seabird_ne.rmd index 703be0bf..ae259053 100644 --- a/chapters/seabird_ne.rmd +++ b/chapters/seabird_ne.rmd @@ -25,19 +25,19 @@ GOM common tern average productivity (fledglings per nest) across 7 colonies has ```{r plot_seabird_neMidAtlanticdiversity} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'diversity') +ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'diversity',n=10) ggplotObject ``` ```{r plot_seabird_neMidAtlanticproductivity} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'productivity') +ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'productivity',n=10) ggplotObject ``` ```{r plot_seabird_neMidAtlanticprey} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'prey') +ggplotObject <- ecodata::plot_seabird_ne(report= 'MidAtlantic', varName= 'prey',n=10) ggplotObject ``` @@ -45,19 +45,19 @@ ggplotObject ```{r plot_seabird_neNewEnglanddiversity} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'diversity') +ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'diversity',n=10) ggplotObject ``` ```{r plot_seabird_neNewEnglandproductivity} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'productivity') +ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'productivity',n=10) ggplotObject ``` ```{r plot_seabird_neNewEnglandprey} # Plot indicator -ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'prey') +ggplotObject <- ecodata::plot_seabird_ne(report= 'NewEngland', varName= 'prey',n=10) ggplotObject ``` diff --git a/chapters/seasonal_oisst_anom.rmd b/chapters/seasonal_oisst_anom.rmd index b1f205fd..ecfbe602 100644 --- a/chapters/seasonal_oisst_anom.rmd +++ b/chapters/seasonal_oisst_anom.rmd @@ -22,6 +22,30 @@ Sea surface temperature can be used as a proxy for overall thermal conditions in ## Key Results and Visualizations Since 1982, SST has been increasing in all seasons in all three EPUs. 2023 was the warmest winter SST in the GOM and MAB on record. All record warmest seasonal SST years have occurred on or after 2012. 2023 also saw relatively cooler summer temperatures in GB and the GOM and fall temperatures in all regions. +### MAB + +```{r plot_seasonal_oisst_anomMAB} +# Plot indicator +ggplotObject <- ecodata::plot_seasonal_oisst_anom(report='MidAtlantic',n=10) +ggplotObject +``` + +### GB + +```{r plot_seasonal_oisst_anomNEGB} +# Plot indicator +ggplotObject <- ecodata::plot_seasonal_oisst_anom(report='NewEngland',EPU='GB',n=10) +ggplotObject +``` + +### GOM + +```{r plot_seasonal_oisst_anomNEGOM} +# Plot indicator +ggplotObject <- ecodata::plot_seasonal_oisst_anom(report='NewEngland',EPU='GOM',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: EPU diff --git a/chapters/spawn_timing.rmd b/chapters/spawn_timing.rmd index ebadda30..48bd6836 100644 --- a/chapters/spawn_timing.rmd +++ b/chapters/spawn_timing.rmd @@ -63,43 +63,43 @@ The multinomial model indicated significant effects of bottom temperature, week ```{r plot_spawn_timingMidAtlanticResting} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Resting') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Resting',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticRipe} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Ripe') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Ripe',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticSpent} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Spent') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Spent',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticDeveloping} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Developing') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'Developing',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticMF} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'MF') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'MF',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticmeanTEMP} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'meanTEMP') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'meanTEMP',n=10) ggplotObject ``` ```{r plot_spawn_timingMidAtlanticmeanJDAY} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'meanJDAY') +ggplotObject <- ecodata::plot_spawn_timing(report= 'MidAtlantic', varName= 'meanJDAY',n=10) ggplotObject ``` @@ -107,43 +107,43 @@ ggplotObject ```{r plot_spawn_timingNewEnglandResting} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Resting') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Resting',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandRipe} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Ripe') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Ripe',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandSpent} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Spent') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Spent',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandDeveloping} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Developing') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'Developing',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandMF} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'MF') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'MF',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandmeanTEMP} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'meanTEMP') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'meanTEMP',n=10) ggplotObject ``` ```{r plot_spawn_timingNewEnglandmeanJDAY} # Plot indicator -ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'meanJDAY') +ggplotObject <- ecodata::plot_spawn_timing(report= 'NewEngland', varName= 'meanJDAY',n=10) ggplotObject ``` @@ -179,13 +179,9 @@ The post spawning Yellowtail Flounder would be expected to have lower relative c **Variable definitions** -Variable names follow the convention "SEASON_Species_STOCK_Variable" where Variable and Units are: -meanTEMP: mean sampled bottom temperature in degrees C MF: number of mature females sampled -meanJDAY: mean julian day of year sampled -Developing: percent of mature females at developing (pre-spawning) stage -Ripe: percent of mature females at ripe (spawning) stage -Spent: percent of mature females at spent (immediately post-spawning) stage -Resting: percent of mature females at resting (non-spawning) stage +Variable names follow the convention "SEASON_Species_STOCK_Variable" where Variable and Units are: meanTEMP: mean sampled bottom temperature in degrees C MF: number of mature females sampled +meanJDAY: mean julian day of year sampled Developing: percent of mature females at developing (pre-spawning) stage Ripe: percent of mature females at ripe (spawning) stage +Spent: percent of mature females at spent (immediately post-spawning) stage Resting: percent of mature females at resting (non-spawning) stage ```{r vars_spawn_timing} # Pull all var names diff --git a/chapters/species_dist.rmd b/chapters/species_dist.rmd index f9ad6c45..c8b5a7d6 100644 --- a/chapters/species_dist.rmd +++ b/chapters/species_dist.rmd @@ -28,13 +28,13 @@ The center of distribution for a suite of 48 commercially or ecologically import ```{r plot_species_distMidAtlanticalong} # Plot indicator -ggplotObject <- ecodata::plot_species_dist(report= 'MidAtlantic', varName= 'along') +ggplotObject <- ecodata::plot_species_dist(report= 'MidAtlantic', varName= 'along',n=10) ggplotObject ``` ```{r plot_species_distMidAtlanticdepth} # Plot indicator -ggplotObject <- ecodata::plot_species_dist(report= 'MidAtlantic', varName= 'depth') +ggplotObject <- ecodata::plot_species_dist(report= 'MidAtlantic', varName= 'depth',n=10) ggplotObject ``` @@ -42,13 +42,13 @@ ggplotObject ```{r plot_species_distNewEnglandalong} # Plot indicator -ggplotObject <- ecodata::plot_species_dist(report= 'NewEngland', varName= 'along') +ggplotObject <- ecodata::plot_species_dist(report= 'NewEngland', varName= 'along',n=10) ggplotObject ``` ```{r plot_species_distNewEnglanddepth} # Plot indicator -ggplotObject <- ecodata::plot_species_dist(report= 'NewEngland', varName= 'depth') +ggplotObject <- ecodata::plot_species_dist(report= 'NewEngland', varName= 'depth',n=10) ggplotObject ``` @@ -78,8 +78,7 @@ Temperature change is a major driver of changing fish distributions [@friedland_ **Variable definitions** -"along-shelf distance" "depth" "distance to coast" "Latitude" -"Longitude" +"along-shelf distance" "depth" "distance to coast" "Latitude" "Longitude" ```{r vars_species_dist} # Pull all var names diff --git a/chapters/species_groupings.rmd b/chapters/species_groupings.rmd index 50b5823b..07514128 100644 --- a/chapters/species_groupings.rmd +++ b/chapters/species_groupings.rmd @@ -66,10 +66,8 @@ We changed species groupings in response to comments over the years. The table s **Variable definitions** -1. SOE.24 = Feeding guild definitions for State of the Ecosystem report (2024) -2. MAFMC = Mid Atlantic Fishery Management Council - list of managed species by feeding guild -3. NEFMC = New England Fishery Management Council - list of managed species by feeding guild -4. Joint = Jointly managed species by feeding guild +1. SOE.24 = Feeding guild definitions for State of the Ecosystem report (2024) 2. MAFMC = Mid Atlantic Fishery Management Council - list of managed species by feeding guild +3. NEFMC = New England Fishery Management Council - list of managed species by feeding guild 4. Joint = Jointly managed species by feeding guild 5. State or Other = Species managed by other bodies listed by feeding guild **Indicator Category**: diff --git a/chapters/stock_status.rmd b/chapters/stock_status.rmd index 54029ca8..4db90600 100644 --- a/chapters/stock_status.rmd +++ b/chapters/stock_status.rmd @@ -72,12 +72,10 @@ In New England, stock status and associated management constraints are likely co **Variable definitions** -Variables in `ecodata::stock_status` **Stock:** Name of stock -**Last assessment:** Most recent assessment year for stock status -**Council:** "MAFMC" (Mid Atlantic Fishery Management Council), "NEFMC" (New England Fishery Management Council), or "Both" - **Code:** Short stock name for plotting corresponding to **Stock** -**Var:** "F.Fmsy" (Current year fishing mortality F relative to FMSY) "B.Bmsy" (Current year biomass B relative to BMSY) - **Value:** Decimal value of Var **Units:** Unitless +Variables in `ecodata::stock_status` **Stock:** Name of stock **Last assessment:** Most recent assessment year for stock status +**Council:** "MAFMC" (Mid Atlantic Fishery Management Council), "NEFMC" (New England Fishery Management Council), or "Both" **Code:** Short stock name for plotting corresponding to **Stock** +**Var:** "F.Fmsy" (Current year fishing mortality F relative to FMSY) "B.Bmsy" (Current year biomass B relative to BMSY) **Value:** Decimal value of Var +**Units:** Unitless ```{r vars_stock_status} # Pull all var names diff --git a/chapters/thermal_habitat_area.rmd b/chapters/thermal_habitat_area.rmd index d9bd79a1..7c7358e6 100644 --- a/chapters/thermal_habitat_area.rmd +++ b/chapters/thermal_habitat_area.rmd @@ -72,9 +72,8 @@ If a large proportion of species current habitat become thermally inhospitable, **Variable definitions** -Time: Date EPU: EPU name Depth: Depth category Var: Temperature Category -Value: Proportion of area above temp.threshold -Source: GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature) year: year Units: Proportion +Time: Date EPU: EPU name Depth: Depth category Var: Temperature Category Value: Proportion of area above temp.threshold Source: GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature) +year: year Units: Proportion ```{r vars_thermal_habitat_area} # Pull all var names diff --git a/chapters/thermal_habitat_gridded.rmd b/chapters/thermal_habitat_gridded.rmd index e8ff9efe..3332779a 100644 --- a/chapters/thermal_habitat_gridded.rmd +++ b/chapters/thermal_habitat_gridded.rmd @@ -54,10 +54,8 @@ Using a high resolution bottom temperature product allows for localized heat str **Variable definitions** -Source: GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature) and PSY (CMEM’s PSY global forecast bottom temperature) -min.depth: minimum of depth band max.depth: maximum of depth band -temp.threshold: cutoff temperature for thermal area calculations (all areas greater than or equal to this temperature) -longitude: longitude of cell center point latitude: latitude of cell center point +Source: GLORYS (CMEM’s GLORYS12V1 global reanalysis bottom temperature) and PSY (CMEM’s PSY global forecast bottom temperature) min.depth: minimum of depth band max.depth: maximum of depth band +temp.threshold: cutoff temperature for thermal area calculations (all areas greater than or equal to this temperature) longitude: longitude of cell center point latitude: latitude of cell center point Ndays: number of days exceeding temp.threshold ```{r vars_thermal_habitat_gridded} diff --git a/chapters/trans_dates.rmd b/chapters/trans_dates.rmd index c67e6bf7..e5e73cbe 100644 --- a/chapters/trans_dates.rmd +++ b/chapters/trans_dates.rmd @@ -25,13 +25,13 @@ Ocean summer length in Mid-Atlantic: the annual total number of days between the ```{r plot_trans_datesMidAtlantictiming} # Plot indicator -ggplotObject <- ecodata::plot_trans_dates(report= 'MidAtlantic', varName= 'timing') +ggplotObject <- ecodata::plot_trans_dates(report= 'MidAtlantic', varName= 'timing',n=10) ggplotObject ``` ```{r plot_trans_datesMidAtlanticlength} # Plot indicator -ggplotObject <- ecodata::plot_trans_dates(report= 'MidAtlantic', varName= 'length') +ggplotObject <- ecodata::plot_trans_dates(report= 'MidAtlantic', varName= 'length',n=10) ggplotObject ``` @@ -39,13 +39,13 @@ ggplotObject ```{r plot_trans_datesNewEnglandtiming} # Plot indicator -ggplotObject <- ecodata::plot_trans_dates(report= 'NewEngland', varName= 'timing') +ggplotObject <- ecodata::plot_trans_dates(report= 'NewEngland', varName= 'timing',n=10) ggplotObject ``` ```{r plot_trans_datesNewEnglandlength} # Plot indicator -ggplotObject <- ecodata::plot_trans_dates(report= 'NewEngland', varName= 'length') +ggplotObject <- ecodata::plot_trans_dates(report= 'NewEngland', varName= 'length',n=10) ggplotObject ``` diff --git a/chapters/wind_revenue.rmd b/chapters/wind_revenue.rmd index b3a46860..3e015442 100644 --- a/chapters/wind_revenue.rmd +++ b/chapters/wind_revenue.rmd @@ -101,8 +101,7 @@ Plots of annual landings and revenue within existing and proposed offshore wind **Variable definitions** 1) Managed species; Definition: Fishery species managed by the New England and Mid-Atlantic Fishery Management Councils or the Atlantic States Marine Fisheries Commission -2) Year; Definition: Calendar year in which fishery landings occurred -3) Landings; Definition: Weight of each species landed, as reported in dealer reports; Units: pounds +2) Year; Definition: Calendar year in which fishery landings occurred 3) Landings; Definition: Weight of each species landed, as reported in dealer reports; Units: pounds 4) Revenue; Definition: Total amount paid to the vessel for each species landed; Units: 2022 dollars 5) Percent GARFO Landings; Definition: Proportion of landings of each managed species from within existing/proposed offshore wind lease areas relative to the total landings of that species reported annually to the Greater Atlantic Regional Fisheries Office; Units: Percentage 6) Percent GARFO Revenue; Definition: Proportion of revenue of each managed species from within existing/proposed offshore wind lease areas relative to the total revenue of that species reported annually to the Greater Atlantic Regional Fisheries Office; Units: Percentage diff --git a/chapters/zoo_abundance_anom.rmd b/chapters/zoo_abundance_anom.rmd index 599efe14..731a7929 100644 --- a/chapters/zoo_abundance_anom.rmd +++ b/chapters/zoo_abundance_anom.rmd @@ -27,13 +27,13 @@ Large bodied copepods and euphausiids show no significant trend in any EPU. ```{r plot_zoo_abundance_anomMidAtlanticcopepod} # Plot indicator -ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'MidAtlantic', varName= 'copepod') +ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'MidAtlantic', varName= 'copepod',n=10) ggplotObject ``` ```{r plot_zoo_abundance_anomMidAtlanticeuphausid} # Plot indicator -ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'MidAtlantic', varName= 'euphausid') +ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'MidAtlantic', varName= 'euphausid',n=10) ggplotObject ``` @@ -41,13 +41,13 @@ ggplotObject ```{r plot_zoo_abundance_anomNewEnglandcopepod} # Plot indicator -ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'NewEngland', varName= 'copepod') +ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'NewEngland', varName= 'copepod',n=10) ggplotObject ``` ```{r plot_zoo_abundance_anomNewEnglandeuphausid} # Plot indicator -ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'NewEngland', varName= 'euphausid') +ggplotObject <- ecodata::plot_zoo_abundance_anom(report= 'NewEngland', varName= 'euphausid',n=10) ggplotObject ``` @@ -77,10 +77,8 @@ Check these. If they are correct, we could be seeing the less energy dense zoopl **Variable definitions** -All are unitless anomalies from the 1977-2020 mean abundance for each taxon. -Variables are taxa names: (to be described by contributors) "Calfin" "LgCopepods" -"SmCopepods" "Cyclopoida" "Diplostraca" "Ostracoda" "Cirripedia" "Euphausiacea" -"Gammaridea" "Hyperiidea" "Mysidacea" "Decapoda" "Polychaeta" "Echinodermata" +All are unitless anomalies from the 1977-2020 mean abundance for each taxon. Variables are taxa names: (to be described by contributors) "Calfin" "LgCopepods" "SmCopepods" +"Cyclopoida" "Diplostraca" "Ostracoda" "Cirripedia" "Euphausiacea" "Gammaridea" "Hyperiidea" "Mysidacea" "Decapoda" "Polychaeta" "Echinodermata" "Mollusca" "Pteropod" "Chaetognatha" "Cnidaria" "Tunicate" "Protozoa" ```{r vars_zoo_abundance_anom} diff --git a/chapters/zoo_diversity.rmd b/chapters/zoo_diversity.rmd index a8c51be7..cf155fea 100644 --- a/chapters/zoo_diversity.rmd +++ b/chapters/zoo_diversity.rmd @@ -21,6 +21,22 @@ Zooplankton represent a critical trophic link from primary producers to fish in ## Key Results and Visualizations Zooplankton diversity is increasing in the Mid-Atlantic and on Georges Bank, but shows no trend in the Gulf of Maine. There is no vessel correction for this metric, so indices collected aboard the research vessel Albatross IV (up to 2008) and the research vessel Henry B. Bigelow (2009 - Present) are calculated separately (Fig. ). +### MAB + +```{r plot_zoo_diversityMAB} +# Plot indicator +ggplotObject <- ecodata::plot_zoo_diversity(report='MidAtlantic',n=10) +ggplotObject +``` + +### NE + +```{r plot_zoo_diversityNE} +# Plot indicator +ggplotObject <- ecodata::plot_zoo_diversity(report='NewEngland',n=10) +ggplotObject +``` + ## Indicator statistics Spatial scale: by EPU