outliers.Rmd

---
title: "Mark outliers in Movebank formatted data"
author:
- Tanja Milotic
- Peter Desmet
date: "`r Sys.Date()`"
output:
  html_document:
    toc: true
    toc_depth: 3
    toc_float: true
    number_sections: true
---

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

Load libraries:

```{r}
library(tidyverse)
library(here)
library(lubridate)
library(sp)
library(trip)
library(geosphere)
```

Set values:

```{r}
project_id <- "O_WESTERSCHELDE"
```

Load custom function to mark outliers:

```{r}
source(here::here("src", "functions", "mark_outliers.R"))
```

Process files:

```{r}
files <- list.files(here::here("data", "processed", project_id, "gps"), full.names = TRUE)
for (file in files) {
  data <- readr::read_csv(file, col_types = readr::cols(
    timestamp = readr::col_datetime(),
    `location-lat` = readr::col_double(),
    `location-long` = readr::col_double(),
    .default = readr::col_character() # Don't interpret/alter the other columns
  ))
  print(file)
  
  # Mark outliers when speed is above 45 m/s or at a sharp angle (30°) at 15 m/s
  processed_data <- mark_outliers(
    data,
    max_speed = 45,
    min_angle_above_speed = c(30, 15),
    max_runs = 10
  )
  
  # Change output dir
  file <- stringr::str_replace(file, "/gps", "/gps_outliers")
  readr::write_csv(processed_data, file, na = "")
}
```