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72 changes: 67 additions & 5 deletions SearchPEZ/code/report_pt1_generic_intro_EN.Rmd
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,8 @@ output:
word_document:
toc: yes
---
```{r Clean up environment for new report, echo=FALSE, include=FALSE, cache=FALSE}
rm(list=ls(all=TRUE))
```


```{r setup, echo=FALSE, include=FALSE, cache=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE, fig.align="left")
library(Mar.datawrangling)
Expand Down Expand Up @@ -179,7 +178,70 @@ MARSAR_sci <- listed_species$Scientific_Name
MARSAR_sci_up <- listed_species$Scientific_Name_upper
```

```{r Fig 1 PEZ polygon, fig.height=8, fig.width=11}
```{r Fig 1 PEZ polygon, fig.height=8, fig.width=11, fig.cap="Map showing the defined Potential Exposure Zone (PEZ) polygon (blue) used to search regional databases and summarize recorded species."}
site_map_new(PEZ_poly,PEZ_poly_st,site_sf,land_sf,40)
```
**Fig. 1:** Map showing the defined Potential Exposure Zone (PEZ) polygon (blue) used to search regional databases and summarize recorded species.


<!-- Sections + -->





# **Document Notes**

This synthesis is created using Rmarkdown and therefore this document can be reproduced and reused using the code available in <https://github.com/AtlanticR/MSP/tree/master/SearchPEZ>. The full document can be updated rapidly as more or different information becomes available.

This document was prepared by the Science MSP Team: <Gregory.Puncher@dfo-mpo.gc.ca>, <Catalina.Gomez@dfo-mpo.gc.ca>, <Gordana.Lazin@dfo-mpo.gc.ca>, <Brian.Bower@dfo-mpo.gc.ca>, <Philip.Greyson@dfo-mpo.gc.ca>, and <Tana.Worcester@dfo-mpo.gc.ca>

# **Additional sources of information: to be included in future reports**

For information about seabirds please contact Environment and Climate Change Canada. Link: <https://open.canada.ca/data/en/dataset/f612e2b4-5c67-46dc-9a84-1154c649ab4e>

There are sources of data and information that were not included in this report. These include data from past studies/publications, acoustic detections, prey sampling and tagging. While the value of these data in predicting and describing cetacean occurrence is vital, these types of data are not available for all species and are not yet available for data querying. In the future, as information from other data sources becomes available, it too will help to provide a more comprehensive understanding of cetacean use and occurrence in the search areas.

# **Additional Notes**
Should you receive a request for set-level Observer data (ISDB) and MARFIS, please just forward to Peter Comeau and <XMARComData@dfo-mpo.gc.ca>, respectively. Please feel free to use the email template below. Note that the template includes an attachment which you can download here - Informal Release Guidelines <\\ent.dfo-mpo.ca\ATLShares\Shared\ATIP Information\Informal_Release_Guidelines-eng.docx>.

Hi,

I apologize, but we can not provide you with the level of detail as it has been requested. Fisheries catch and effort information for an individual licence holder is considered personal information and is protected under section 19 of the Access to Information Act. Fisheries catch and effort information for a corporate licence holder is considered to be sensitive, proprietary information and protected under Section 20 of the Access to Information Act. Without written consent, DFO is not permitted to release information or data products (e.g., maps and data layers) that might reveal personal or third party information such as catch, landed values, and vessel-specific fishing locations. All of this is spelled out to DFO staff the attached document (i.e. Appendix B – “Catch and Effort and Quota Information: Do’s and Don’ts for Informal Release”)

# **References**

Gomez, C., Konrad, C.M., Vanderlaan, A., Moors-Murphy, H.B., Marotte, E., Lawson, J., Kouwenberg, A-L., Fuentes-Yaco, C., Buren, A. 2020. Identifying priority areas to enhance monitoring of cetaceans in the Northwest Atlantic Ocean. Can. Tech. Rep.Fish. Aquat. Sci. 3370: vi + 103 p. http://waves-vagues.dfo-mpo.gc.ca/Library/40869155.pdf

Kennedy R.D. 2019. The North Atlantic Right Whale Consortium Database: A Guide for Users and Contributors. Version 6. North Atlantic Right Whale Consortium Reference Document 2019-02.144 pp. <https://www.narwc.org/uploads/1/1/6/6/116623219/narwc_users_guide__v_6_.pdf>

Lesage, V., Gosselin, J-F., Lawson, J. W., McQuinn, I., Moors-Murphy, H., Plourde, S., Sears. R. et Y. Simard. 2018. Habitats important to blue whales (Balaenoptera musculus) in the Western North Atlantic. DFO Can. Sci. Advis. Sec. Res. Doc. 2016/080: iv + 50 p. <https://waves-vagues.dfo-mpo.gc.ca/Library/40687776.pdf>

MacDonald, D., Emery, P., Themelis, D., Smedbol, R.K., Harris, L.E., and McCurdy, Q. 2017. Marine mammal and pelagic animal sightings (Whalesightings) database: a user’s guide. Can. Tech. Rep. Fish. Aquat. Sci. 3244: v + 44 p.<https://waves-vagues.dfo-mpo.gc.ca/Library/40642999.pdf>

# **Acknowledgments**

<Mike.McMahon@dfo-mpo.gc.ca>! for providing code and advice in the use of `Mar.datawrangling`: A suite of tools for extracting, filtering and aggregating data from the Maritimes fisheries science databases <https://github.com/Maritimes/Mar.datawrangling>

The Atlantic R Learning & Development Initiative <https://github.com/AtlanticR>.

Cetacean section: Shelley Lang, Hilary Moors-Murphy, Susan Heaslip, Emma Marotte, Amanda Babin, Nick Jeffery, Angelia Vanderlaan

# **Future databases and data products to be included**

Examples:

Global Biodiversity Information Facility (GBIF) <https://www.gbif.org/>
Intertidal vegetation maps derived from remote sensing.
Ecosystem Management interactive ArcGIS maps -developed for 1) Regulatory Review projects and 2) SAR program. Currently, maps are for internal use only by Maritimes SARP.
Province's data is openx <https://data.novascotia.ca/w/jgyj-d4fh/default?cur=8JS4clBZaD9&from=l6_um6e8ufx>
Tracking data, OTN <https://obis.org/dataset/80997ac3-87cb-411c-ab1f-334adec45050> via ERDDAP and R package rerdda
Electrofishing (Jeremy Bloome)
eDNA
Lobster and scallop programs
Salmon





<!-- Appendix -->
119 changes: 0 additions & 119 deletions SearchPEZ/code/report_pt2_SAR_dist_crithab_EN.Rmd
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@@ -1,122 +1,3 @@
---
title: "Reproducible Report for Species in Maritimes Region - for Internal DFO use only"
author: Synthesis prepared by the Reproducible Reporting Team, steering committee and advisors.
date: '`r format(Sys.time(), "%d %B, %Y")`'
output:
html_document:
theme: paper
toc: yes
pdf_document:
toc: yes
word_document:
toc: yes
---
```{r Clean up environment for new report, echo=FALSE, include=FALSE, cache=FALSE}
rm(list=ls(all=TRUE))
```
```{r setup, echo=FALSE, include=FALSE, cache=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE, fig.align="left")
library(Mar.datawrangling)
library(Mar.utils)
library(knitr)
library(kableExtra)
library(rgdal)
library(maps)
library(lubridate)
library(raster)
library(RCurl)
library(sf)
library(stringr)
library(ggplot2)
library(data.table)
library(gridExtra)
library(dplyr)
library(stars)
library(ggspatial)
#install.packages("remotes")
#remotes::install_github("terminological/standard-print-output")
library(standardPrintOutput)
#These next two lines are necessary for the generation of the water mark on all plots.
#install.packages("devtools")
#devtools::install_github("JosephCrispell/basicPlotteR")
#library(basicPlotteR)
```
```{r source functions, echo=FALSE, include=FALSE, cache=FALSE}
# the .Rmd file sets the working directory based on where it resides and ignores the wd set by the .RProj file
source("site_map.r")
source("site_map_new.r")
source("plot_wsdb.r")
source("filter_wsdb.r")
source("plot_narwc.r")
source("plot_narwc.r")
source("filter_narwc_new.r")
# ## Another option is to load directly from the web and read in using Rcurl
#function_urls <- c("https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/site_map.r",
# "https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/plot_wsdb.r",
# "https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/filter_wsdb.r")
#for (i in function_urls){eval(parse(text = RCurl::getURL(i, ssl.verifypeer = FALSE)),envir=.GlobalEnv)}
source("EBSA.R")
source("plot_EBSA.R")
source("leatherback.R")
source("plot_leatherback.R")
source("plot_obis.R")
source("plot_cws.R")
source("plot_crithab.R")
source("plot_crithab_zoom.R")
source("plot_inat.R")
source("cetacean_priority_areas.R")
source("plot_cetaceans_4grid.R")
source("Blue_Whale_habitat.R")
source("plot_bw_hab.R")
source("plot_bw_hab_zoom.R")
```
```{r Define Site, echo=FALSE, include=FALSE, cache=FALSE}
#HTML output of code is automatically generated in Catalina's computer: RProjects/MSP/SearchPEZ/code
#output of get.data.R should be manually moved to RProjects/MSP/SearchPEZ/outputs/sitenamexkm
#AquaSiteName <- "TestGully"
#PEZversion <- "Polygon"
AquaSiteName <- "FarmersLedge"
PEZversion <- "4748m"
UserComments <- "Example - First search effort for suitability of a site for a project planned for 2025. Project is expected to have positive/negative impacts on surrounding area. It is likely that some kind of monitoring will be required during operations. Make sure to follow up on all sections pertaining to a particular taxonomic group as this seems to be a concern of the stakeholders."
#make sure you delete all shp.xml files in the folder to be able to run this code
minYear <- 1970
maxYear <- 2020
```
```{r Set up paths, echo=FALSE, include=FALSE, cache=FALSE}
mspPath <- "../"
data.dir = "../../../Data/mar.wrangling"
#create a folder in outputs with the name of the site and buffer area search
dataPath <- file.path("../../../Data/outputs",paste0(AquaSiteName,PEZversion))
# setwd(dataPath) #not needed?
polyPath <- "../../../Data/Zones/SearchPEZpolygons"
site <- readOGR(polyPath,layer=paste0("Site_",AquaSiteName))
site_sf <- st_as_sf(site)
opendataPath = "../../../Data/mar.wrangling/RVSurvey_OpenData"
#wsdbFile <- file.path("../inputs","WSDB_GLazin_AllSpecies_2018.csv")
wsdbFile <- file.path("../../../Data/NaturalResources/Species/Cetaceans/WSDB","MarWSDBSightingsForCGomez_27Oct2020.csv")
narwcFile <- file.path("../../../Data/NaturalResources/Species/Cetaceans/NARWC","NARWC_09-18-2020.csv")
```
```{r read baseline data for maps, echo=FALSE, include=FALSE, cache=FALSE}
landGDB <- "../../../Data/Boundaries/Coast50K/Coastline50k.gdb"
land <- readOGR(dsn=landGDB,layer="Land50k_Maritimes",stringsAsFactors=F)
land_sf <- st_as_sf(land)
```
```{r Define PEZ!, echo=FALSE, include=FALSE, cache=FALSE}
pl <- list.files(polyPath,"*.shp")
pl <- pl[-grep("xml",pl)]
PEZ_poly <- readOGR(file.path(polyPath,pl[grep(paste0("PEZ_",AquaSiteName,PEZversion),pl)]))
#PEZ_poly_st<-st_read(../../../Data/Zones/SearchPEZpolygons/PEZ_TestGullyPolygon.shp", quiet=TRUE)
PEZ_poly_st<-st_as_sf(PEZ_poly)
```
```{r Species listed by Wildspecies, COSEWIC and SARA in the Maritime Region, echo=FALSE, include=FALSE, cache=FALSE}

listed_species<-read.csv("../../../Data/NaturalResources/Species/MAR_listed_species.csv")
MARSAR_com <- listed_species$Common_Name
MARSAR_com_up <- listed_species$Common_Name_upper
MARSAR_sci <- listed_species$Scientific_Name
MARSAR_sci_up <- listed_species$Scientific_Name_upper
```

# **Search Results for Species at Risk**

## **National Aquatic Species at Risk Section**
Expand Down
119 changes: 0 additions & 119 deletions SearchPEZ/code/report_pt7_generic_END_EN.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,122 +1,3 @@
---
title: "Reproducible Report for Species in Maritimes Region - for Internal DFO use only"
author: Synthesis prepared by the Reproducible Reporting Team, steering committee and advisors.
date: '`r format(Sys.time(), "%d %B, %Y")`'
output:
html_document:
theme: paper
toc: yes
pdf_document:
toc: yes
word_document:
toc: yes
---
```{r Clean up environment for new report, echo=FALSE, include=FALSE, cache=FALSE}
rm(list=ls(all=TRUE))
```
```{r setup, echo=FALSE, include=FALSE, cache=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE, fig.align="left")
library(Mar.datawrangling)
library(Mar.utils)
library(knitr)
library(kableExtra)
library(rgdal)
library(maps)
library(lubridate)
library(raster)
library(RCurl)
library(sf)
library(stringr)
library(ggplot2)
library(data.table)
library(gridExtra)
library(dplyr)
library(stars)
library(ggspatial)
#install.packages("remotes")
#remotes::install_github("terminological/standard-print-output")
#library(standardPrintOutput)
#These next two lines are necessary for the generation of the water mark on all plots.
#install.packages("devtools")
#devtools::install_github("JosephCrispell/basicPlotteR")
library(basicPlotteR)
```
```{r source functions, echo=FALSE, include=FALSE, cache=FALSE}
# the .Rmd file sets the working directory based on where it resides and ignores the wd set by the .RProj file
source("site_map.r")
source("site_map_new.r")
source("plot_wsdb.r")
source("filter_wsdb.r")
source("plot_narwc.r")
source("plot_narwc.r")
source("filter_narwc_new.r")
# ## Another option is to load directly from the web and read in using Rcurl
#function_urls <- c("https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/site_map.r",
# "https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/plot_wsdb.r",
# "https://raw.githubusercontent.com/AtlanticR/MSP/master/SearchPEZ/code/filter_wsdb.r")
#for (i in function_urls){eval(parse(text = RCurl::getURL(i, ssl.verifypeer = FALSE)),envir=.GlobalEnv)}
source("EBSA.R")
source("plot_EBSA.R")
source("leatherback.R")
source("plot_leatherback.R")
source("plot_obis.R")
source("plot_cws.R")
source("plot_crithab.R")
source("plot_crithab_zoom.R")
source("plot_inat.R")
source("cetacean_priority_areas.R")
source("plot_cetaceans_4grid.R")
source("Blue_Whale_habitat.R")
source("plot_bw_hab.R")
source("plot_bw_hab_zoom.R")
```
```{r Define Site, echo=FALSE, include=FALSE, cache=FALSE}
#HTML output of code is automatically generated in Catalina's computer: RProjects/MSP/SearchPEZ/code
#output of get.data.R should be manually moved to RProjects/MSP/SearchPEZ/outputs/sitenamexkm
#AquaSiteName <- "TestGully"
#PEZversion <- "Polygon"
AquaSiteName <- "FarmersLedge"
PEZversion <- "4748m"
UserComments <- "Example - First search effort for suitability of a site for a project planned for 2025. Project is expected to have positive/negative impacts on surrounding area. It is likely that some kind of monitoring will be required during operations. Make sure to follow up on all sections pertaining to a particular taxonomic group as this seems to be a concern of the stakeholders."
#make sure you delete all shp.xml files in the folder to be able to run this code
minYear <- 1970
maxYear <- 2020
```
```{r Set up paths, echo=FALSE, include=FALSE, cache=FALSE}
mspPath <- "../"
data.dir = "../../../Data/mar.wrangling"
#create a folder in outputs with the name of the site and buffer area search
dataPath <- file.path("../../../Data/outputs",paste0(AquaSiteName,PEZversion))
# setwd(dataPath) #not needed?
polyPath <- "../../../Data/Zones/SearchPEZpolygons"
site <- readOGR(polyPath,layer=paste0("Site_",AquaSiteName))
site_sf <- st_as_sf(site)
opendataPath = "../../../Data/mar.wrangling/RVSurvey_OpenData"
#wsdbFile <- file.path("../inputs","WSDB_GLazin_AllSpecies_2018.csv")
wsdbFile <- file.path("../../../Data/NaturalResources/Species/Cetaceans/WSDB","MarWSDBSightingsForCGomez_27Oct2020.csv")
narwcFile <- file.path("../../../Data/NaturalResources/Species/Cetaceans/NARWC","NARWC_09-18-2020.csv")
```
```{r read baseline data for maps, echo=FALSE, include=FALSE, cache=FALSE}
landGDB <- "../../../Data/Boundaries/Coast50K/Coastline50k.gdb"
land <- readOGR(dsn=landGDB,layer="Land50k_Maritimes",stringsAsFactors=F)
land_sf <- st_as_sf(land)
```
```{r Define PEZ!, echo=FALSE, include=FALSE, cache=FALSE}
pl <- list.files(polyPath,"*.shp")
pl <- pl[-grep("xml",pl)]
PEZ_poly <- readOGR(file.path(polyPath,pl[grep(paste0("PEZ_",AquaSiteName,PEZversion),pl)]))
#PEZ_poly_st<-st_read(../../../Data/Zones/SearchPEZpolygons/PEZ_TestGullyPolygon.shp", quiet=TRUE)
PEZ_poly_st<-st_as_sf(PEZ_poly)
```
```{r Species listed by Wildspecies, COSEWIC and SARA in the Maritime Region, echo=FALSE, include=FALSE, cache=FALSE}

listed_species<-read.csv("../../../Data/NaturalResources/Species/MAR_listed_species.csv")
MARSAR_com <- listed_species$Common_Name
MARSAR_com_up <- listed_species$Common_Name_upper
MARSAR_sci <- listed_species$Scientific_Name
MARSAR_sci_up <- listed_species$Scientific_Name_upper
```

# **Document Notes**

This synthesis is created using Rmarkdown and therefore this document can be reproduced and reused using the code available in <https://github.com/AtlanticR/MSP/tree/master/SearchPEZ>. The full document can be updated rapidly as more or different information becomes available.
Expand Down