In BenioffOceanInitiative/shipr: ships for whales functions

knitr::opts_chunk$set(echo = TRUE)

library(knitr)
library(kableExtra)
library(tidyverse)
library(leaflet)
library(RColorBrewer)
library(maptools)
library(sf)
library(rgeos)
library(dplyr)
library(RPostgreSQL)
library(dbplyr)
library(lubridate)
library(units)
library(data.table)
library(ggplot2)
library(here)

Source R files

source('~/github/whalesafe4r/R/db.R')
source('~/github/whalesafe4r/R/crawlers.R')
source('~/github/whalesafe4r/R/readers.R')
source('~/github/whalesafe4r/R/utils.R')
source('~/github/whalesafe4r/R/seg_stats.R')

con=db_connect()

ihs_data = dbGetQuery(con, "select * from ihs_data;")

vsr_segs_ihs = merge_ihs_vsr()

ship_stats_2019 = ship_statistics(data= vsr_segs_ihs, date_start = '2019-01-01', date_end = '2019-12-31', tonnage = 300)

operator_stats_2019 = operator_statistics(data= vsr_segs_ihs, date_start = '2019-01-01', date_end = '2019-12-31', tonnage = 300)

# 4160 mmsi total in IHS data
length(unique(ihs_data$mmsi))

# 4094 mmsi's over 300 gt
length(unique(ihs_data$mmsi[ihs_data$gt>=300]))

# 1812 unique mmsi's in vsr_segments database table
dbGetQuery(con, "select count(distinct mmsi) from vsr_segments;")

# 897 unique mmsi's in vsr_segments database table in 2019
dbGetQuery(con, "select count(distinct mmsi) from vsr_segments where year = 2019;")

# 1441 unique mmsi's (merged df) in vsr in 2018 & 2019
length(unique(vsr_segs_ihs$mmsi))

# 706 unique mmsi's in vsr in 2019
length(unique(vsr_segs_ihs$mmsi[vsr_segs_ihs$year==2019]))

# 683 unique mmsi's in vsr in 2019 with gross tonnage >= 300
length(unique(vsr_segs_ihs$mmsi[vsr_segs_ihs$year==2019 & vsr_segs_ihs$gt>=300]))

# DOUBLE CHECKIN'
# 683 unique mmsi's in vsr in 2019
length(unique(ship_stats_2019$mmsi))

# 683 unique mmsi's in vsr in 2019 with gross tonnage >= 300
length(unique(ship_stats_2019$mmsi[ship_stats_2019$gt>=300]))

# 549 unique mmsi's in vsr in 2019 with gross tonnage >= 300 and travelled >= 100 km
length(unique(ship_stats_2019$mmsi[ship_stats_2019$gt>=300 & ship_stats_2019$`total distance (km)`>=100]))

# 1095 operators total in IHS data
length(unique(ihs_data$operator))

# 1062 operators over 300 gt
length(unique(ihs_data$operator[ihs_data$gt>=300]))

# 467 unique operators in vsr in 2018 & 2019
length(unique(vsr_segs_ihs$operator))

# 267 unique operators in vsr in 2019
length(unique(vsr_segs_ihs$operator[vsr_segs_ihs$year==2019]))

# 257 unique operators in vsr in 2019 with gross tonnage >= 300
length(unique(vsr_segs_ihs$operator[vsr_segs_ihs$year==2019 & vsr_segs_ihs$gt>=300]))


# DOUBLE CHECKIN'
# 257 unique operators in vsr in 2019 with gt>=300
length(unique(operator_stats_2019$operator))

# 257 unique operators in vsr in 2019 with vessels gt >= 300
length(unique(ship_stats_2019$operator[ship_stats_2019$gt>=300]))

# 208 operators with over 100 km travelled total
length(unique(operator_stats_2019$operator[operator_stats_2019$`total distance (km)`>=100]))

operator_stats_2019_100k=operator_stats_2019 %>% 
  filter(operator_stats_2019$`total distance (km)`>=100)

theme_set(theme_bw()) 

op_grade <- ggplot(data.frame(operator_stats_2019_100k), aes(x=grade)) +
  geom_bar() +  
  theme(plot.title = element_text(hjust = 0.5)) + 
  ggtitle("Operator VSR Cooperation Grade Distribution: 2019") + 
  labs(caption="Source: Benioff Ocean Initiative",
       x="VSR Cooperation Grade",
       y="Count") +
  geom_text(stat='count', aes(label=..count..), vjust=1.5, color="white")+
      # geom_text(stat='count', aes(label=..count..), position = position_stack(vjust = 0.5),size=4, color = "white") + 
    theme(plot.title = element_text(size = 14))

op_grade

ship_stats_2019_100k=ship_stats_2019 %>% 
  filter(ship_stats_2019$`total distance (km)`>=100)

# png("/Users/seangoral/Library/Mobile Documents/com~apple~CloudDocs/_Benioff_SRA_Limited/100kHighRes150dpi2.png", units="px", width=1200, height=800, res=150)

ggplot(data.frame(ship_stats_2019_100k), aes(x=noaa_grade)) +
  geom_bar() +  
  theme(plot.title = element_text(hjust = 0.5)) + 
    theme(plot.subtitle = element_text(hjust = 0.5)) +
  ggtitle("Ship VSR Cooperation Grade Distribution: 2019", subtitle = "Modified NOAA Rubric") + 
  labs(caption="Source: Benioff Ocean Initiative",
       x="VSR Cooperation Grade",
       y="Count") +
    geom_text(stat='count', aes(label=..count..), vjust=1.5, color="white")

# dev.off()

t = operator_stats_2019 %>% 
  kable(escape = F) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "responsive")) 

t

summary_stats = data.table(  
  nm_0_10=sum(ship_stats_2019$`distance (nautcal miles) 0-10 knots`),
    nm_10_12=sum(ship_stats_2019$`distance (nautcal miles) 10-12 knots`),
    nm_12_15=sum(ship_stats_2019$`distance (nautcal miles) 12-15 knots`),
    nm_over_15=sum(ship_stats_2019$`distance (nautcal miles) over 15 knots`))

summary_stats_percents = data.table(  
  `% Travelled 0-10 kn` = (sum(ship_stats_2019_100k$`distance (nautcal miles) 0-10 knots`)/sum(ship_stats_2019_100k$`total distance (nautcal miles)`)*100),
  `% Travelled 10-12 kn`= sum(ship_stats_2019_100k$`distance (nautcal miles) 10-12 knots`)/sum(ship_stats_2019_100k$`total distance (nautcal miles)`)*100,
  `% Travelled 12-15 kn` = sum(ship_stats_2019_100k$`distance (nautcal miles) 12-15 knots`)/sum(ship_stats_2019_100k$`total distance (nautcal miles)`)*100,
  `% Travelled over 15 kn` = sum(ship_stats_2019_100k$`distance (nautcal miles) over 15 knots`)/sum(ship_stats_2019_100k$`total distance (nautcal miles)`)*100)

sum_stats=melt(summary_stats_percents)

pie <- ggplot(sum_stats, aes(x="", y=value, fill=variable)) + geom_bar(stat="identity", width=1) + 
  coord_polar("y", start=0) +
   geom_text(aes(label = paste0(round(value), "%")), position = position_stack(vjust = 0.5)) +
  scale_fill_manual(values=c("palegreen1", "skyblue1", "gold1" ,"coral2")) + 
  labs(x = NULL, y = NULL, fill = NULL, title = "Summary of VSR cooperation for 2019") + 
  theme_classic() + theme(axis.line = element_blank(),
          axis.text = element_blank(),
          axis.ticks = element_blank(),
          plot.title = element_text(hjust = 0.5, color = "#666666")) +  theme(plot.title = element_text(hjust = -0.5)) + theme(plot.title = element_text(size = 16))

pie

ggplot(data.frame(operator_stats_2019_100k), aes(x=operator_stats_2019_100k$number_of_distinct_mmsi)) +
  geom_bar() +  
  theme(plot.title = element_text(hjust = 0.5)) + 
  ggtitle("Vessels per Operator: 2019") + 
  labs(caption="Source: Benioff Ocean Initiative",
       x="Number of Vessels (MMSI)",
       y="Number of Operators") +
   geom_text(stat='count', aes(label=..count..), vjust=-0.18, color="black")+
      # geom_text(stat='count', aes(label=..count..), position = position_stack(vjust = 0.5),size=4, color = "white") + 
    theme(plot.title = element_text(size = 16)) + scale_x_continuous(breaks = scales::pretty_breaks(n = 22)) +
scale_y_continuous(breaks = scales::pretty_breaks(n = 8))