---
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)

# required libraries
library(tidyverse)
library(lubridate)
library(sf)
library(rnaturalearth)
library(knitr)

# read in data
track         <- readRDS("data/processed/track.rds")
sightings     <- readRDS("data/processed/sightings.rds")
environmental <- readRDS("data/processed/environmental.rds")

# summarize track data
track_summary <- track |>
  summarise(
    date = unique(as.Date(datetime_edt)),
    lat_min = min(latitude),
    lat_max = max(latitude),
    lon_min = min(longitude),
    lon_max = max(longitude),
    start_time = min(datetime_edt),
    end_time = max(datetime_edt),
    duration_hrs = difftime(end_time, start_time, units = "hours") |>
      as.numeric() |> round(2),
    mean_speed_kts  = mean(speed_kts, na.rm = TRUE) |> round(1),
    total_dist_nm = max(cum_dist_nm) |> round(2)
  )

# select only definite sightings
def_sightings <- sightings |>
  filter(id_reliability == 3)

# summarize sightings data
sightings_summary <- def_sightings |>
  group_by(speccode) |>
  summarise(
    n_sightings    = n(),
    n_total        = sum(number, na.rm = TRUE),
    n_calves       = sum(numcalf, na.rm = TRUE),
    .groups = "drop"
  ) |>
  arrange(desc(n_sightings))

# summarize right whale data
rw_sightings <- def_sightings |>
  filter(speccode == 'RIWH') |>
  select(datetime_edt, sight_no, latitude, longitude, number, numcalf)

```

# NEAq Vessel Survey on `r format(track_summary$date, '%b %d %Y')`

## Summary Map

```{r map}

# import the coastline sf object from my website
coastline_sf <- readRDS(url('https://hansenjohnson.org/files/data/sf-coastline.rds'))

# define the plot limits
buffer = 0.05
min_lon = min(track$longitude, na.rm = T) - buffer
min_lat = min(track$latitude, na.rm = T) - buffer
max_lon = max(track$longitude, na.rm = T) + buffer
max_lat = max(track$latitude, na.rm = T) + buffer

# plot
ggplot() +
  geom_sf(data = coastline_sf) +
  geom_path(data = track, aes(x = longitude, y = latitude), alpha = 0.5) +
  geom_point(data = def_sightings, aes(x = longitude, y = latitude, color = speccode), alpha = 0.7) +
  scale_color_viridis_d() +
  coord_sf(xlim = c(min_lon, max_lon), ylim = c(min_lat, max_lat)) +
  labs(x = NULL, 
       y = NULL,
       color = 'SPECCODE')+
  theme_bw()

```

## Overview

The New England Aquarium conducted a survey aboard the vessel *R/V Nereid* on `r format(track_summary$date, '%b %d %Y')`. We left the dock at `r format(track_summary$start_time, '%H:%M %p')` and returned at `r format(track_summary$end_time, '%H:%M %p %Z')` (approximately `r round(track_summary$duration_hrs,1)` hours), during which time we covered approximately `r track_summary$total_dist_nm` nautical miles. Sea state ranged from `r min(environmental$beaufort)` to `r max(environmental$beaufort)`. We recorded `r sum(sightings_summary$n_sightings)` sightings of `r nrow(sightings_summary)` species, including `r nrow(rw_sightings)` right whale sightings. See below for more details.

## Sightings Tally

```{r sightings_tally}
kable(sightings_summary)
```


## Right whale sightings

```{r rw_sightings}
kable(rw_sightings)
```

## Effort summary

```{r effort_summary}
kable(track_summary)
```