remove DRAKE

chapters/Comm_climate_vuln_indicator.Rmd

@@ -196,7 +196,7 @@ If a community received a dominant score (50% or more) for any of the above cate
 ### Plotting
 
 ```{r species-vulnerability, fig.cap="Commercial species vulnerability to climate change in in New England fishing communities.",fig.align = 'center', echo = F, eval = T}
-knitr::include_graphics(file.path(image.dir, 'Species_vulnerability_NE.jpg'))
+knitr::include_graphics(file.path(image.dir, 'Species_vulnerability_NE.JPG'))
 ```
 
 

chapters/bottom_temperature.Rmd

@@ -29,7 +29,7 @@ Ocean temperature on the Northeast U.S. Shelf varies significantly on seasonal t
 
 ### Data processing
 
-Source data were formatted for inclusion in the ecodata R package using the following R code.
+Derived bottom temperature data were formatted for inclusion in the ecodata R package using the following R code. 
 
 ```{r, code = readLines(here::here("source/get_oceantemp_insitu.R")), eval =F, echo = T}
 ```

chapters/erddap_query_and_build.Rmd

@@ -5,11 +5,11 @@
 The Technical Documentation for the State of the Ecosystem reports is a [bookdown](https://bookdown.org) document; hosted on the NOAA Northeast Fisheries Science Center Ecosystems Dynamics and Assessment Branch [Github page](https://github.com/NOAA-EDAB), and developed in R. Derived data used to populate figures in this document are queried directly from the [ecodata](https://github.com/NOAA-EDAB/ecodata) R package or the NEFSC [ERDDAP server](https://comet.nefsc.noaa.gov/erddap/info/index.html?page=1&itemsPerPage=1000). ERDDAP queries are made using the R package [rerddap](https://cran.r-project.org/web/packages/rerddap/vignettes/Using_rerddap.html).  
 
 
-### Accessing source data and build code
+### Accessing data and build code
 
-In this technical documentation, we hope to shine a light on the processing and analytical steps involved to get from source data to final product. This means that whenever possible, we have included the code involved in source data extraction, processing, and analyses. We have also attempted to thoroughly describe all methods in place of or in supplement to provided code. Example plotting code for each indicator is presented in sections titled "Plotting", and these code chunks can be used to recreate the figures presented in State of the Ecosystem reports[^1].
+In this technical documentation, we hope to shine a light on the processing and analytical steps involved to get from source data to final product. This means that whenever possible, we have included the code involved in source data extraction, processing, and analyses. We have also attempted to thoroughly describe all methods in place of or in supplement to provided code. Example plotting code for each indicator is presented in sections titled "Plotting", and these code chunks can be used to recreate the figures found in ecosystem reporting documents where each respective indicator was included[^1].
 
-Source data for the derived indicators in this document are linked to in the text unless there are privacy concerns involved. In that case, it may be possible to access source data by reaching out to the Point of Contact associated with that data set. Derived data sets make up the majority of the indicators present in the State of the Ecosystem reports, and these data sets are available for download through the [ecodata](https://github.com/NOAA-EDAB/ecodata) R package. 
+Source data for the derived indicators in this document are linked to in the text unless there are privacy concerns involved. In that case, it may be possible to access source data by reaching out to the Point of Contact associated with that data set. Derived data sets make up the majority of the indicators presented in ecosystem reporting documents, and these data sets are available for download through the [ecodata](https://github.com/NOAA-EDAB/ecodata) R package. 
 
 ### Building the document
 

chapters/seabird_diet_and_productivity.Rmd

@@ -14,6 +14,11 @@
 
 **Public availability statement**: Please email [email protected] for further information and queries on this indicator source data.
 
+
+The purpose of this document is to collate the methods used to access, collect, process, and analyze derived data ("indicators") used to describe the status and trend of social, economical, ecological, and biological conditions in the Northeast Shelf Large Marine Ecosystem (see figure, below). These indicators are further synthesized in State of the Ecosystem Reports produced annually by the [Northeast Fisheries Science Center](https://www.nefsc.noaa.gov/) for the [New England Fisheries Management Council](https://www.nefmc.org/) and the [Mid-Atlantic Fisheries Management Council](http://www.mafmc.org/). The metadata for each indicator (in accordance with the [Public Access to Research Results (PARR) directive](http://obamawhitehouse.archives.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf)) and the methods used to construct each indicator are described in the subsequent chapters, with each chapter title corresponding to an indicator or analysis present in State of the Ecosystem Reports.
+
+Indicators included in this document were selected to clearly align with management objectives, which is required for integrated ecosystem assessment [@levin_integrated_2009], and has been advised many times in the literature [@degnbol_review_2004; @jennings_indicators_2005; @rice_framework_2005; @link_translating_2005]. A difficulty with pratical implementation of this in ecosystem reporting can be the lack of clearly specified ecosystem-level management objectives (although some have been suggested [@murawski_definitions_2000]). In our case, considerable effort had already been applied to derive both general goals and operational objectives from both US legislation such as the Magnuson-Stevens Fisheries Conservation and Management Act (MSA) and regional sources [@depiper_operationalizing_2017]. These objectives are somewhat general and would need refinement together with managers and stakeholders, however, they serve as a useful starting point to structure ecosystem reporting.
+
 ## Methods
 
 **Chick diet**
@@ -111,7 +116,7 @@ diet_div <- ecodata::common_tern %>%
 ```
 
 
-```{r tern-prod-div, fig.cap = "a. Mean common tern productivity at nesting sites in Gulf of Maine. Error bars show +/- 1 SE of the mean. b. Shannon diversity of common tern diets observed at nesting sites in Gulf of Maine. Diversity of common tern diets has been predominantly above the long-term mean since 2006.",fig.width = 8, fig.asp = 0.25, echo = T}
+```{r tern-prod-div, fig.cap = "a. Mean common tern productivity at nesting sites in Gulf of Maine. Error bars show +/- 1 SE of the mean. b. Shannon diversity of common tern diets observed at nesting sites in Gulf of Maine. Diversity of common tern diets has been predominantly above the long-term mean since 2006.",fig.width = 8, fig.asp = 0.25, echo = T, fig.align='center'}
 aggregate_prod <- ecodata::common_tern %>% 
     filter(!str_detect(Var, "Diet|Sum"))  %>% 
   mutate(Island = word(Var, 1),
@@ -151,8 +156,7 @@ prodplot <- aggregate_prod %>% ggplot() +
            alpha = hline.alpha,
            linetype = hline.lty) +
   labs(tag = "a")  +
-  theme_ts() +
-  theme(title = element_text(size = 7))
+  theme_ts()
 
 shannon <- diet_div %>% 
   filter(Var == "shannon") %>% 
@@ -172,15 +176,14 @@ ggplot(aes(x = Time, y = Value)) +
            alpha = hline.alpha,
            linetype = hline.lty) +
   labs(tag = "b")  +
-  theme_ts() +
-  theme(title = element_text(size = 7))
+  theme_ts()
 
 prodplot + shannon + plot_layout(ncol = 2, widths=c(4,4))
 ```
 
 Along with nest productivity and diet diversity indices, we presented maps of sampling sites in Gulf of Maine and mean prey frequencies across sites. Prey occurring in less than 5\\% of common tern diets was excluded for visual clarity. 
 
-```{r map-and-prey, fig.cap = "Common terns: a. Locations of the seven sampled common tern nesting sites in Gulf of Maine (EER = Eastern Egg Rock, JI = Jenny Island, MR = Matinicus Rock, OGI = Outer Green Island, PINWR = Pond Island National Wildlife Refuge, SINWR = Seal Island National Wildlife Refuge, STI = Stratton Island), and b. Prey frequencies in the diets of common tern observed across the seven colonies in Gulf of Maine. Prey occurring in <5\\% of common tern diets were excluded for clarity.", fig.height = 4}
+```{r map-and-prey, fig.cap = "Common terns: a. Locations of the seven sampled common tern nesting sites in Gulf of Maine (EER = Eastern Egg Rock, JI = Jenny Island, MR = Matinicus Rock, OGI = Outer Green Island, PINWR = Pond Island National Wildlife Refuge, SINWR = Seal Island National Wildlife Refuge, STI = Stratton Island), and b. Prey frequencies in the diets of common tern observed across the seven colonies in Gulf of Maine. Prey occurring in <5\\% of common tern diets were excluded for clarity.", fig.height = 4, fig.align='center'}
 
 #Map subfig
 # Set lat/lon window for maps
@@ -213,8 +216,7 @@ islands <- ggplot() +
         axis.title = element_text(size = 11),
         strip.background = element_blank(),
         strip.text=element_text(hjust=0),
-        axis.text = element_text(size = 6),
-        title = element_text(size = 7))
+        axis.text = element_text(size = 6))
 # inset_states <- new_england %>% filter(STATE_NAME %in% c("Maine",
 #                                                          "New Hampshire",
 #                                                          "Massachusetts"))
@@ -271,8 +273,7 @@ diet_freq_bar <- prey_freq %>%
   ggtitle("Prey composition") +
   ylab("Proportion of prey items") +
   labs(tag = "b")  +
-  theme_ts() +
-  theme(title = element_text(size = 7))
+  theme_ts()
 
 
 # diet_freq_bar <- girafe(ggobj = diet_freq_bar)

index.Rmd

@@ -111,7 +111,7 @@ Map of Northeast U.S. Continental Shelf Large Marine Ecosystem from @Hare2016.
 
 
 ```{r neusmap, fig.align='center', fig.height=6, echo = F}
-knitr::include_graphics("images/journal.pone.0146756.g002.png")
+knitr::include_graphics("images/journal.pone.0146756.g002.PNG")
 
 ```