Oceana
Colby Kresge
2024-06-06
OCEANA Demo
This is an R Markdown document of the Oceana demo data from Anne & Katie
Basic Stuff loaded + data clean
# Load all
libraries <- c("sp", "devtools", "ggplot2", "dplyr",
"scales", "rgeos", "rgdal", "ggalt",
"grid", "cowplot", "raster", "plyr", "sf",
"ggspatial", "readr", "lubridate")
lapply(libraries, library, character.only = TRUE)## The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
## which was just loaded, will retire in October 2023.
## Please refer to R-spatial evolution reports for details, especially
## https://r-spatial.org/r/2023/05/15/evolution4.html.
## It may be desirable to make the sf package available;
## package maintainers should consider adding sf to Suggests:.
## The sp package is now running under evolution status 2
## (status 2 uses the sf package in place of rgdal)## Loading required package: usethis##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
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## intersect, setdiff, setequal, union## rgeos version: 0.6-4, (SVN revision 699)
## GEOS runtime version: 3.11.0-CAPI-1.17.0
## Please note that rgeos will be retired during October 2023,
## plan transition to sf or terra functions using GEOS at your earliest convenience.
## See https://r-spatial.org/r/2023/05/15/evolution4.html for details.
## GEOS using OverlayNG
## Linking to sp version: 2.0-0
## Polygon checking: TRUE##
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## symdiff## Please note that rgdal will be retired during October 2023,
## plan transition to sf/stars/terra functions using GDAL and PROJ
## at your earliest convenience.
## See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
## rgdal: version: 1.6-7, (SVN revision 1203)
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## Loaded GDAL runtime: GDAL 3.5.3, released 2022/10/21
## Path to GDAL shared files: /Users/colby_kresge/Library/R/arm64/4.3/library/rgdal/gdal
## GDAL does not use iconv for recoding strings.
## GDAL binary built with GEOS: TRUE
## Loaded PROJ runtime: Rel. 9.1.0, September 1st, 2022, [PJ_VERSION: 910]
## Path to PROJ shared files: /Users/colby_kresge/Library/R/arm64/4.3/library/rgdal/proj
## PROJ CDN enabled: FALSE
## Linking to sp version:1.6-1
## To mute warnings of possible GDAL/OSR exportToProj4() degradation,
## use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.## Registered S3 methods overwritten by 'ggalt':
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## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
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########## SECTION 1: COMPLETE THE CODE ##########
#' This section involves plotting a vessel's activity using the ggplot package.
## Read in data for vessel tracks (tracks.csv) and events (voyage_events.csv)
vessel_events<- read_csv("short_map_ex_debug/voyage_events.csv")## New names:
## • `` -> `...1`## Rows: 64 Columns: 11
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): event_type, anchorage_name, anchorage_country
## dbl (5): ...1, vessel_1_id, lat, lon, event_duration_hr
## lgl (1): vessel_2_id
## dttm (2): event_start, event_end
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.tracks<- read_csv("short_map_ex_debug/tracks.csv")## New names:
## Rows: 24299 Columns: 5
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): timestamp dbl (4): ...1, mmsi, lat, lon
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `` -> `...1`#####
## Some of the points in tracks.csv contain nonsensical values in the lat and lon columns.
## WITHOUT manually inspecting the csv file, please describe below how you would identify these points
## and remove them from the tracks dataframe. Please note that you do not need to do actually remove these
## data points, but just need to provide an short explanation (commented below here) of what you would want to look for
# check it out
glimpse(tracks)## Rows: 24,299
## Columns: 5
## $ ...1 <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1…
## $ mmsi <dbl> 224892000, 224892000, 224892000, 224892000, 224892000, 22489…
## $ lat <dbl> -22.45102, -22.43392, -22.39616, -22.38539, -22.38088, -22.3…
## $ lon <dbl> -78.13587, -78.13313, -78.12646, -78.12450, -78.12363, -78.1…
## $ timestamp <chr> "6/2/2017 0:08", "6/2/2017 0:16", "6/2/2017 0:34", "6/2/2017…sum(is.na(tracks$lat))## [1] 1sum(is.na(tracks$lon))## [1] 2# Omit NA lat // lon
tracks_clean <- tracks %>%
filter(!is.na(lat) & !is.na(lon))
# summary(tracks)
min(tracks_clean$lat)## [1] -60max(tracks_clean$lon)## [1] -74.33777summary(tracks_clean)## ...1 mmsi lat lon
## Min. : 1 Min. :224892000 Min. :-60.00 Min. :-100.00
## 1st Qu.: 6077 1st Qu.:224892000 1st Qu.:-21.83 1st Qu.: -78.04
## Median :12151 Median :224892000 Median :-21.41 Median : -77.87
## Mean :12151 Mean :224892000 Mean :-20.57 Mean : -77.24
## 3rd Qu.:18225 3rd Qu.:224892000 3rd Qu.:-20.88 3rd Qu.: -77.16
## Max. :24299 Max. :224892000 Max. :100.00 Max. : -74.34
## timestamp
## Length:24297
## Class :character
## Mode :character
##
##
## plot(tracks_clean$lat~tracks_clean$lon)
# Couple that are far out, lat = > 50 and less than -50 nonsensical
tracks_clean <- tracks %>%
filter(lat <= 50 & lat >= -50)
plot(tracks_clean$lat~tracks_clean$lon)
# Looks fine now
## Read in land and eez shapefiles from working directory (nothing for you to do in this section)
#
land <- st_read(
"short_map_ex_debug/ne_10m_land.shp")## Reading layer `ne_10m_land' from data source
## `/Users/colby_kresge/Desktop/Working R /short_map_ex_debug/ne_10m_land.shp'
## using driver `ESRI Shapefile'
## Simple feature collection with 10 features and 3 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -180 ymin: -90 xmax: 180 ymax: 83.6341
## Geodetic CRS: WGS 84eez<- st_read(
"short_map_ex_debug/World_EEZ_v8_20140228_LR/World_EEZ_v8_2014.shp")## Reading layer `World_EEZ_v8_2014' from data source
## `/Users/colby_kresge/Desktop/Working R /short_map_ex_debug/World_EEZ_v8_20140228_LR/World_EEZ_v8_2014.shp'
## using driver `ESRI Shapefile'
## Simple feature collection with 249 features and 15 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -180 ymin: -85.47029 xmax: 180 ymax: 87.02394
## Geodetic CRS: WGS 84land_df <- fortify(land)
eez_df <- fortify(eez)
## Fill in code on right side of '<-' to create new dataframes that are subset from vessel_events
## dataframe for 'fishing' and 'anchorage' events
View(vessel_events)
fishing <- vessel_events %>%
filter(event_type == "fishing")
# Subset the data frame for anchorage events
anchorage <- vessel_events %>%
filter(event_type == "anchorage")
cols<-c('tracks'='#696969','fishing'='green','anchorage'='red')
## Create list of shapes so that tracks has no shape, and fishing and anchorage are both solid circles
#shps<-
shps <- list(
tracks = NA, # No shape for tracks
fishing = 16, # Solid circle for fishing
anchorage = 16 # Solid circle for anchorage
)
## Create list of line types below so that tracks is a solid line and fishing
## and anchorage events are blank lines
# Create a list of line types
ln <- c('solid', 'blank', 'blank')
# Assign labels to line types
names(ln) <- c('tracks', 'fishing', 'anchorage')
label=c('tracks','fishing','anchorage')
## Create a string for the chart title with a line break between the ship name and MMSI
# Example ship name and MMSI
ship_name <- "Ship Name"
mmsi <- "123456789"
# Create the chart title string with a line break
chart_title <- paste(ship_name, "\n", mmsi)
print(chart_title)## [1] "Ship Name \n 123456789"## Use ggplot to create the map. geom_polygon are used to the land and EEZ dataframes,
## geom_path is used for track data, and geom_point is used for anchorage and fishing events
## The tracks, fishing points, and anchorage points are missing from the below map, add them
glimpse(fishing)## Rows: 63
## Columns: 11
## $ ...1 <dbl> 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18…
## $ event_type <chr> "fishing", "fishing", "fishing", "fishing", "fishing…
## $ vessel_1_id <dbl> 224892000, 224892000, 224892000, 224892000, 22489200…
## $ vessel_2_id <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ anchorage_name <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ anchorage_country <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ lat <dbl> -22.2848, -21.8146, -21.8264, -21.7447, -21.7393, -2…
## $ lon <dbl> -78.3230, -78.3637, -78.1114, -77.9397, -77.9582, -7…
## $ event_start <dttm> 2017-06-01 00:20:27, 2017-06-01 09:08:06, 2017-06-0…
## $ event_end <dttm> 2017-06-01 03:08:37, 2017-06-02 04:16:52, 2017-06-0…
## $ event_duration_hr <dbl> 2.80277778, 19.14611111, 19.69722222, 0.68222222, 6.…glimpse(tracks_clean)## Rows: 24,296
## Columns: 5
## $ ...1 <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1…
## $ mmsi <dbl> 224892000, 224892000, 224892000, 224892000, 224892000, 22489…
## $ lat <dbl> -22.45102, -22.43392, -22.39616, -22.38539, -22.38088, -22.3…
## $ lon <dbl> -78.13587, -78.13313, -78.12646, -78.12450, -78.12363, -78.1…
## $ timestamp <chr> "6/2/2017 0:08", "6/2/2017 0:16", "6/2/2017 0:34", "6/2/2017…tracks_clean <- tracks_clean %>%
mutate(timestamp = mdy_hm(timestamp),
date = as.Date(timestamp))
# set up
library(rnaturalearth)## Support for Spatial objects (`sp`) will be deprecated in {rnaturalearth} and will be removed in a future release of the package. Please use `sf` objects with {rnaturalearth}. For example: `ne_download(returnclass = 'sf')`library(rnaturalearthdata)##
## Attaching package: 'rnaturalearthdata'## The following object is masked from 'package:rnaturalearth':
##
## countries110bg = ne_countries(scale = 'medium', returnclass = 'sf')
#
library(ggplot2)
library(plotly)##
## Attaching package: 'plotly'## The following objects are masked from 'package:plyr':
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## layoutlibrary(leaflet)
library(htmlwidgets)
# Define the ggplot without the legend
plot1 <- ggplot() +
geom_sf(data = eez_df, aes(color = "EEZ")) +
geom_sf(data = land_df, aes(color = "Land")) +
geom_path(data = tracks_clean, aes(x = lon, y = lat, color = "Tracks"), size = 1) +
geom_point(data = fishing, aes(x = lon, y = lat, color = "Fishing"), shape = 20, size = 1) +
geom_point(data = anchorage, aes(x = lon, y = lat, color = "Anchorage"), shape = 20, size = 3) +
geom_sf(data = bg, fill = "cornsilk3") +
coord_sf(xlim = c(-87, -60), ylim = c(-30, 0)) +
labs(title = chart_title, x = 'Longitude', y = 'Latitude') +
scale_color_manual(values = c("EEZ" = "lightgrey", "Land" = "cornsilk3", "Tracks" = "green",
"Fishing" = "red", "Anchorage" = "yellow", "Background" = "cornsilk3")) +
theme(panel.grid.major = element_line(color = gray(0.5), linetype = "blank", size = 0.3),
panel.background = element_rect(color = gray(0.5), fill = 'lightblue2'),
legend.position = "none") #+ # Remove the legend## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated. #annotation_north_arrow(which_north = "true", height = unit(0.5, 'cm'),
# width = unit(0.5, 'cm'))
# Convert ggplot to interactive plotly object
plotly_map <- ggplotly(plot1)
leaflet_map <- as_widget(plotly_map)
leaflet_map