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.gitignore

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+*.nc

define_marine_habitat.md

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+# Define a marine habitat
+
+> notebook filename | 07\_turtlewatch\_xtracto.Rmd
+
+The TurleWatch project investigated the thermal habitat of loggerhead
+sea turtles in the Pacific Ocean north of the Hawaiian Islands. Research
+results indicate that most loggerhead turtles stay in water between
+17.5°C and 18.5°C. When the 17.5°C to 18.5°C temperature contour is
+drawn on a map of sea surface temperature conditions, it delineates the
+boundary of the loggerhead’s preferred habitat.
+
+In this exercise you will plot the thermal boundary of loggerhead sea
+turtles using satellite sea surface temperature. The exercise
+demonstrates the following techniques:  
+\* Using xtracto\_3D to extract data from a rectangular area  
+\* Masking a data array  
+\* Plotting maps using
+ggplot
+
+## Install required packages and load libraries
+
+``` r
+# Function to check if pkgs are installed, install missing pkgs, and load
+pkgTest <- function(x)
+{
+  if (!require(x,character.only = TRUE))
+  {
+    install.packages(x,dep=TRUE,repos='http://cran.us.r-project.org')
+    if(!require(x,character.only = TRUE)) stop(x, " :Package not found")
+  }
+}
+
+list.of.packages <- c( "ncdf4", "rerddap", "plotdap", "RCurl",  
+                       "raster", "colorRamps", "maps", "mapdata",
+                       "ggplot2", "RColorBrewer", "rerddapXtracto")
+
+# create list of installed packages
+pkges = installed.packages()[,"Package"]
+
+for (pk in list.of.packages) {
+  pkgTest(pk)
+}
+```
+
+## Select the Satellite Data
+
+  - Use the MUR SST dataset (ID jplMURSST41mday)  
+  - Gather information about the dataset (metadata) using **rerddap**  
+  - Displays the information
+
+<!-- end list -->
+
+``` r
+# CHOOSE DATASET and get information about it 
+
+
+url = "http://coastwatch.pfeg.noaa.gov/erddap/"
+dataInfo <- rerddap::info('jplMURSST41mday',url=url)
+parameter <- 'sst'
+```
+
+## Get Satellite Data
+
+  - Select an area off the coast of California: longitude range of -130
+    to -115 east and latitude range of 25 to 40 north  
+  - Set the time range to days withing one month:
+    tcoord=c(‘2018-06-06’,‘2018-06-08’)). The values do have to be
+    different.
+
+<!-- end list -->
+
+``` r
+# latitude and longitude of the vertices
+ylim<-c(25,40)
+xlim<-c(-130,-115)
+
+# Choose an area off the coast of California
+# Extract the data
+SST <- rxtracto_3D(dataInfo,xcoord=xlim,ycoord=ylim,parameter=parameter, 
+                   tcoord=c('2018-06-06','2018-06-08'))
+```
+
+    ## Registered S3 method overwritten by 'httr':
+    ##   method           from  
+    ##   print.cache_info hoardr
+
+    ## info() output passed to x; setting base url to: http://coastwatch.pfeg.noaa.gov/erddap/
+
+``` r
+# Drop command needed to reduce SST from a 3D variable to a 2D  one  
+SST$sst <- drop(SST$sst) 
+```
+
+## Make a quick plot using plotBBox
+
+``` r
+plotBBox(SST, plotColor = 'thermal',maxpixels=100000)
+```
+
+    ## grid object contains more than 1e+05 pixels
+
+    ## increase `maxpixels` for a finer resolution
+
+    ## Warning in raster::projectRaster(r, crs = crs_string): input and ouput crs are
+    ## the same
+
+![](define_marine_habitat_files/figure-gfm/qplot-1.png)<!-- -->
+
+## Define the Thermal niche of Loggerhead Turtles
+
+\_\_ Set the thermal range to 17.5-18.5 degrees C, as determined by the
+TurtleWatch program.\_\_
+
+``` r
+## Define turtle temperature range
+min.temp <- 17.5
+max.temp <- 18.5
+```
+
+**Create another variable for habitat temperature**
+
+Set the habitat temperature to equal NA
+
+``` r
+SST2 <- SST
+SST2$sst[SST2$sst >= min.temp & SST2$sst <= max.temp] <- NA
+plotBBox(SST2, plotColor = 'thermal',maxpixels=100000)
+```
+
+    ## grid object contains more than 1e+05 pixels
+
+    ## increase `maxpixels` for a finer resolution
+
+    ## Warning in raster::projectRaster(r, crs = crs_string): input and ouput crs are
+    ## the same
+
+![](define_marine_habitat_files/figure-gfm/makeVar-1.png)<!-- -->
+
+It would be nicer to color in the turtle habitat area (the NA values)
+with a different color. If you want to customize graphs its better to
+use `ggplot` than the `plotBBox` that comes with `rerrdapXtracto`
+package. Here we will use `ggplot` to plot the data. But first the data
+is reformatted for use in `ggplot`.
+
+Restructure the data
+
+``` r
+dims <- dim(SST2$sst)
+SST2.lf <- expand.grid(x=SST$longitude,y=SST$latitude)
+SST2.lf$sst<-array(SST2$sst,dims[1]*dims[2])
+```
+
+## Plot the Data using ‘ggplot’
+
+``` r
+coast <- map_data("worldHires", ylim = ylim, xlim = xlim)
+
+par(mar=c(3,3,.5,.5), las=1, font.axis=10)
+
+myplot<-ggplot(data = SST2.lf, aes(x = x, y = y, fill = sst)) +
+  geom_tile(na.rm=T) +
+  geom_polygon(data = coast, aes(x=long, y = lat, group = group), fill = "grey80") +
+  theme_bw(base_size = 15) + ylab("Latitude") + xlab("Longitude") +
+  coord_fixed(1.3,xlim = xlim, ylim = ylim) +
+  ggtitle(unique(as.Date(SST2$time))) +
+  scale_fill_gradientn(colours = rev(rainbow(12)),limits=c(10,22),na.value = "firebrick4") 
+
+myplot
+```
+
+![](define_marine_habitat_files/figure-gfm/plot-1.png)<!-- -->

extract_data_marine-sanctuary.md

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+# Extract data within a boundary
+
+In this exercise, you will download data from within the boundaries of
+the Monterey Bay National Marine Sanctuary (MBNMS) and visualize the
+data on a map.
+
+The exercise demonstrates the following skills:
+
+  - Using **rerddap** to retrieve information about a dataset from
+    ERDDAP
+  - Using the **rxtractogon** function from **rerdapXtracto** to extract
+    satellite data within an polygon over time  
+  - Mapping satellite data
+
+## Install packages and load libraries
+
+``` r
+pkges = installed.packages()[,"Package"]
+# Function to check if pkgs are installed, install missing pkgs, and load
+pkgTest <- function(x)
+{
+  if (!require(x,character.only = TRUE))
+  {
+    install.packages(x,dep=TRUE,repos='http://cran.us.r-project.org')
+    if(!require(x,character.only = TRUE)) stop(x, " :Package not found")
+  }
+}
+
+# create list of required packages
+list.of.packages <- c("ncdf4", "rerddap","plotdap", "parsedate", 
+                      "sp", "ggplot2", "RColorBrewer", 
+                      "reshape2", "maps", "mapdata", 
+                      "jsonlite", "rerddapXtracto")
+
+# Run install and load function
+for (pk in list.of.packages) {
+  pkgTest(pk)
+}
+
+# create list of installed packages
+pkges = installed.packages()[,"Package"]
+```
+
+## Load sanctuary boundary coordinates
+
+The **rerddapXtracto** package comes with the dataset **mbnms** which
+conatains the longitude and latitude values for the boundary of the
+Monterey Bay National Marine Sanctuary. These coordinates draw the the
+boundary of the sanctuary on a map, like tracing a dot-to-dot drawing.
+Take a quick look at the contents of this data variable.
+
+``` r
+str(mbnms)
+```
+
+    ## 'data.frame':    6666 obs. of  2 variables:
+    ##  $ Longitude: num  -123 -123 -123 -123 -123 ...
+    ##  $ Latitude : num  37.9 37.9 37.9 37.9 37.9 ...
+
+Additional sanctuary boundaries may be obtained at
+<http://sanctuaries.noaa.gov/library/imast_gis.html>.
+
+**The script below:**
+
+  - Extracts the longitude and latitude data into vector variables
+
+<!-- end list -->
+
+``` r
+xcoord <- mbnms$Longitude
+ycoord <- mbnms$Latitude
+```
+
+## Select the chloropyll dataset
+
+For this example we will use a 750 m VIIRS monthly chlorophyll dataset
+(ID erdVHNchlamday)
+
+**The script below:**  
+\* Gathers information about the dataset (metadata) using **rerddap**  
+\* The default source ERDDAP for **rerddap** is
+“<https://upwell.pfeg.noaa.gov/erddap>”. Since we are pulling the data
+from a different ERDDAP at “<http://coastwatch.pfeg.noaa.gov/erddap/>”,
+change the url to url = “<http://coastwatch.pfeg.noaa.gov/erddap/>” \*
+Displays the dataset information
+
+``` r
+# Use rerddap to get dataset metadata 
+url = "http://coastwatch.pfeg.noaa.gov/erddap/"
+dataInfo <- rerddap::info('erdVHNchlamday',url=url)  # N. Pacific 750 m VIIRS chl
+# Display the metadata dataset info
+dataInfo
+```
+
+    ## <ERDDAP info> erdVHNchlamday 
+    ##  Base URL: http://coastwatch.pfeg.noaa.gov/erddap/ 
+    ##  Dataset Type: griddap 
+    ##  Dimensions (range):  
+    ##      time: (2015-03-16T00:00:00Z, 2021-04-16T00:00:00Z) 
+    ##      altitude: (0.0, 0.0) 
+    ##      latitude: (-0.10875, 89.77125) 
+    ##      longitude: (-180.03375, -110.00625) 
+    ##  Variables:  
+    ##      chla: 
+    ##          Units: mg m^-3
+
+## Set the options for the polygon data extract
+
+The **rxtractogon** function will need the parameter and coordinates for
+the extract \* For the parameter: Use the name of the chlorophyll
+parameter that was displayed above in dataInfo: **parameter \<- “chla”**
+\* For the coordinates: determine your selctions for x, y, z, and time.
+\* z coordinate: The metadata from dataInfo shows that this variable has
+a altitude coordinate that equals zero. So set the value of the z
+coordinate to zero: **zcoord \<- 0.**  
+\* time coordinate: The time variable passed to xtracogon must contain
+two elements, the start and endpoints of the desired time period. This
+example uses ERDDAP’s **last** option to retrieve data from the most
+recent time step. The **last** option also accepts the minus **-**
+operator. To request the time step with the second most recent data use
+“last-1”. In the script below the time variable (tcoord) is defined as
+**tcoord \<- c(“last-1”, “last”)**
+
+``` r
+# set the parameter to extract
+parameter <- 'chla'
+# set the time range
+tcoord <- c("last-1", "last")
+# Assign longitude and latitude vectors from the CSV file to variables
+xcoord <- mbnms$Longitude
+ycoord <- mbnms$Latitude
+# set the altitude variable to zero
+zcoord <- 0. 
+```
+
+## Extract data and mask it using rxtractogon
+
+  - Run **rxtractogon** to extract data from the “erdVHNchlamday”
+    dataset and mask out any data outside the MBNMS boundary.  
+  - List the data
+
+<!-- end list -->
+
+``` r
+## Request the data
+sanctchl <- rxtractogon (dataInfo, parameter=parameter, xcoord=xcoord, ycoord=ycoord,tcoord=tcoord,zcoord=zcoord)
+```
+
+    ## Registered S3 method overwritten by 'httr':
+    ##   method           from  
+    ##   print.cache_info hoardr
+
+    ## info() output passed to x; setting base url to: http://coastwatch.pfeg.noaa.gov/erddap/
+
+``` r
+## List the returned data
+str(sanctchl)
+```
+
+    ## List of 6
+    ##  $ chla       : num [1:272, 1:311, 1:2] NA NA NA NA NA NA NA NA NA NA ...
+    ##  $ datasetname: chr "erdVHNchlamday"
+    ##  $ longitude  : num [1:272(1d)] -123 -123 -123 -123 -123 ...
+    ##  $ latitude   : num [1:311(1d)] 35.6 35.6 35.6 35.6 35.6 ...
+    ##  $ altitude   : num [1(1d)] 0
+    ##  $ time       : POSIXlt[1:2], format: "2021-03-16" "2021-04-16"
+    ##  - attr(*, "class")= chr [1:2] "list" "rxtracto3D"
+
+## Choose Time to Plot
+
+The extracted data contains two time periods of chlorophyll data within
+the sanctuary boundaries. For this example we will show how to select
+just one time period from the options and map it, here we choose the
+second time stamp.
+
+``` r
+sanctchl1 <- sanctchl
+sanctchl1$chla <- sanctchl1$chla[, , 2]
+sanctchl1$time <- sanctchl1$time[2]
+```
+
+### Plot the data
+
+  - Use the plotBBox function in rerddapXtracto to quickly plot the
+    data
+
+<!-- end list -->
+
+``` r
+plotBBox(sanctchl1, plotColor = 'algae',maxpixels=100000)
+```
+
+    ## Warning in raster::projectRaster(r, crs = crs_string): input and ouput crs are
+    ## the same
+
+![](extract_data_marine-sanctuary_files/figure-gfm/map-1.png)<!-- -->
+
+### Apply a function to the data
+
+  - Here we apply a log function to the chlorophyll data and plot it
+    again.
+
+<!-- end list -->
+
+``` r
+myFunc <- function(x) log(x) 
+plotBBox(sanctchl1, plotColor = 'algae',maxpixels=100000, myFunc=myFunc)
+```
+
+    ## Warning in raster::projectRaster(r, crs = crs_string): input and ouput crs are
+    ## the same
+
+![](extract_data_marine-sanctuary_files/figure-gfm/addfunc-1.png)<!-- -->