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kimberly-bastille committed Mar 24, 2022
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2 changes: 1 addition & 1 deletion chapters/Wind_area_fisheries_revenue.Rmd
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Expand Up @@ -34,7 +34,7 @@ Data were formatted for inclusion in the `ecodata` R package using the R code fo
The plot below was built using the code found
[here](https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/human_dimensions_MAB.Rmd-wea-spp-rev.R).

```{r, code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/human_dimensions_MAB.Rmd-wea-spp-rev.R"), eval = T, echo = F, fig.cap = "Top five species revenue found in wind development areas."}
```{r, code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/human_dimensions_MAB.Rmd-wea-spp-rev.R"), eval = T, echo = F, fig.cap = "Top five MAFMC species revenue found in wind development areas."}
```

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6 changes: 3 additions & 3 deletions chapters/protected_species_hotspots.Rmd
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Expand Up @@ -2,7 +2,7 @@

**Description**: Integrated persistent annual hotspots derived from at-sea observations of seabirds, cetaceans and sea turtles collected on systematic ship and aerial surveys

**Found in**: State of the Ecosystem - Mid-Atlantic (2021), State of the Ecosystem - New England (2021)
**Found in**: State of the Ecosystem - Mid-Atlantic (2022), State of the Ecosystem - New England (2022)

**Indicator category**: Extensive analysis, not yet published, Database pull with analysis

Expand Down Expand Up @@ -30,11 +30,11 @@ Persistent hotspots were computed with the sf and raster R packages.

### Plotting

```{r, fig.cap="North Atlantic Right Whale hotspot maps."}
```{r, fig.cap="North Atlantic Right Whale hotspot map."}
knitr::include_graphics(file.path(image.dir, "NARW_hotpsot_persistence_2_1_2022_TPW.png"))
```

```{r, fig.cap="Hotspot maps for all protected groups (Seabirds, Cetaceans, and Turtles."}
```{r, fig.cap="Hotspot map for all protected groups (Seabirds, Cetaceans, and Turtles)."}
knitr::include_graphics(file.path(image.dir, "seabirds_cetaceans_turtles_hotspot_persistence_2_1_2022_TPW.png"))
```

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6 changes: 3 additions & 3 deletions chapters/sandlance.Rmd
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Expand Up @@ -33,16 +33,16 @@ Code for processing salinity data can be found [here](https://github.com/NOAA-ED

Code use to build the plot below can be found [here](https://github.com/NOAA-EDAB/ecodata/blob/master/chunk-scripts/macrofauna_NE.Rmd-sandlance-colocation.R).

```{r , code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/macrofauna_NE.Rmd-sandlance.R"), echo = F, fig.align="center", eval = T, fig.cap=""}
```{r , code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/macrofauna_NE.Rmd-sandlance.R"), echo = F, fig.align="center", eval = T, fig.cap="These four line graphs (Mean Sandlance, Number of Samples, Number of Samples with Fish, and Proportion of Non-Zero Samples) are metrics derived directly from the raw survey data (SBNMS 2021). Collectively they illustrate a cyclical pattern of abundance, with higher abundance 2014-2016, and lower abundance 2017-2019. Since the data set has many zero-capture samples, the Proportion of Non-Zero Samples may be a useful metric as a proxy for abundance."}
```

```{r , code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/macrofauna_NE.Rmd-sandlance-colocation.R"), echo = F, fig.align="center", eval = T, fig.cap=""}
```{r , code = readLines("https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/chunk-scripts/macrofauna_NE.Rmd-sandlance-colocation.R"), echo = F, fig.align="center", eval = T, fig.cap="The multi-line plot labeled Sandlance illustrates the collocation of sandlance with humpback whale and great shearwater. Data are taken directly from Table 1 of Silva et al. 2020. Although it may not be visually evident from the annual-summed values, there is strong spatial collocation among sand lance, humpbacks and shearwaters across seasons and years."}
```


```{r, fig.cap=""}
```{r, fig.cap="This map graphic depicts the grab sample locations in SBNMS, with cumulative catch at each from 2013 through 2019."}
image.dir <- here::here("images")
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