From 752af08a1ebdff68292367d6705e993219f15dd8 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 26 Aug 2024 22:28:55 +0200
Subject: [PATCH] Add challenges script 20240827

---
 src/20240827/20240827_challenges.R | 179 +++++++++++++++++++++++++++++
 1 file changed, 179 insertions(+)
 create mode 100644 src/20240827/20240827_challenges.R

diff --git a/src/20240827/20240827_challenges.R b/src/20240827/20240827_challenges.R
new file mode 100644
index 0000000..49b7c24
--- /dev/null
+++ b/src/20240827/20240827_challenges.R
@@ -0,0 +1,179 @@
+library(tidyverse)
+
+## CHALLENGE 1
+
+# Use debug techniques to find the bug in the function evenOdd()
+
+#' Function evenOdd() takes an integer n and returns a list containing two integers
+#' that respectively indicate how many even and odd digits occur in n
+#'
+#' @examples
+#' evenOdd(398473234) -> (4, 5)
+#' evenOdd(459) -> (1, 2)
+evenOdd <- function(n) {
+  char_n <- as.character(n)
+  counter_even <- 0
+  counter_odd <- 0
+  for (i in char_n) {
+    digit <- as.integer(i)
+    if (digit %% 2 == 0) {
+      counter_even <- counter_even + 1
+    } else {
+      counter_odd <- counter_odd + 1
+    }
+  }
+  return(list(n_even = counter_even,
+              n_odd = counter_odd))
+}
+
+
+## CHALLENGE 2
+
+# Using debug techniques find what is going wrong in functions step() and steps()
+
+#' Function step() takes a positive integer:
+#' 886328712442992
+#'
+#' Write down a positive integer:
+#' 398473234
+#' Count up the number of even and odd digits, and the total number of digits:
+#' 4 5 9
+#' String the digits of those three numbers together to make a new number:
+#' 459
+#' Return it as a number
+#' @examples
+#' step(398473234)
+#' 459
+#' step(459)
+#' 123
+step <- function(n) {
+  n_odd_even <- evenOdd(n)
+  total_digits <- nchar(n)
+  n_odd_even_total <- n_odd_even
+  n_odd_even_total$n_total <- total_digits
+  return(n_odd_even_total)
+}
+
+
+#' Function `steps` takes an integer and return how
+#' many steps you need before the number 123 is reached.
+#' @examples
+#' steps(398473234)
+#' 2
+#' steps(1)
+#' 5
+#' steps(2)
+#' 2
+steps <- function(n) {
+  while (n != 123) {
+    n <- step(n)
+    n_steps <- n_steps + 1
+  }
+  return(n_steps)
+}
+
+
+## INTERMEZZO
+
+#' Customized `min()` function for numeric vectors to avoid warning while
+#' calculating minimum of empty vectors
+#'
+#' `custom_min()` should fail if a not numeric vector is passed
+#'
+#' @examples
+#' custom_min(c(8, 4, 2, 5)) # this works
+#' custom_min(c("e", "r", "a")) # this should return an error
+custom_min <- function(x) {
+  if (length(x)>0) min(x) else NA
+}
+
+
+# Improve version with assertion
+
+#' Customized `min()` function for numeric vectors to avoid warning while
+#' calculating minimum of empty vectors
+#'
+#' `custom_min()` should fail if a not numeric vector is passed
+#'
+#' @examples
+#' custom_min(c(8, 4, 2, 5)) # this works
+#' custom_min(c("e", "r", "a")) # this should return an error
+custom_min <- function(x) {
+  # Check x argument (assertion)
+  assertthat::assert_that(
+    is.numeric(x),
+    msg = "Invalid type of input: only numeric vectors allowed."
+  )
+  # Function core follows
+  if (length(x)>0) min(x) else NA
+}
+
+## CHALLENGE 3
+
+
+#' Core function to find migration periods of a tagged eel
+#' @examples
+#' library(readr)
+#' library(dplyr)
+#' library(lubridate)
+#' library(ggplot2)
+#'
+#' ## Example 1
+#'
+#' # Read eel tagging data
+#' eel_emma <- read_csv("./data/20240827/20240827_eel_Emma.txt", na = "")
+#' # Define thresholds
+#' distance_threshold <- 5000 # Threshold in meter
+#' migration_speed_threshold <- 0.1 # Speed threshold in m/s
+#' # Run migration detection
+#' eel_emma_migration_info <- get_migrations(
+#'   eel_emma,
+#'   dist_threshold = distance_threshold,
+#'   speed_threshold = migration_speed_threshold
+#' )
+#' # Plot result (this chunk is not included in following examples)
+#' ggplot(eel_emma_migration_info, aes(x = arrival, y = totaldistance_m)) +
+#'   geom_point(aes(color = downstream_migration)) +
+#'   geom_line() +
+#'   scale_y_reverse()
+#'
+#' ## Example 2
+#' eel_rhea <- read_csv("./data/20240827/20240827_eel_Rhea.txt", na = "")
+#' # Define thresholds
+#' dist_thresh <- "5000" # Threshold in meter
+#' speed_thresh <- 0.1 # Speed threshold in m/s
+#' # Run migration detection
+#' get_migrations(eel_rhea,
+#'                dist_threshold = dist_thresh,
+#'                speed_threshold = speed_thresh)
+#'
+#' ## Example 3
+#' eel_amber <- read_csv("./data/20240827/20240827_eel_Amber.txt", na = "")
+#' # Define thresholds
+#' dist_thresh <- 5000 # Threshold in meter
+#' speed_thresh <- 0.1 # Speed threshold in m/s
+#' # Run migration detection
+#' get_migrations(eel_amber,
+#'                dist_threshold = dist_thresh,
+#'                speed_threshold = speed_thresh)
+get_migrations <- function(df,
+                           dist_threshold,
+                           speed_threshold) {
+  df %>%
+    mutate(dist_threshold = totaldistance_m + dist_threshold) %>%
+    rowwise() %>%
+    mutate(first_dist_to_use = custom_min(
+      df$totaldistance_m[df$totaldistance_m >= dist_threshold])) %>%
+    mutate(row_first_dist_to_use = if_else(
+      !is.na(first_dist_to_use),
+      which(df$totaldistance_m == first_dist_to_use)[1],
+      NA)) %>%
+    ungroup() %>%
+    mutate(time_first_dist_to_use = if_else(!is.na(row_first_dist_to_use),
+                                            df$arrival[row_first_dist_to_use],
+                                            NA)) %>%
+    mutate(delta_totdist = first_dist_to_use - totaldistance_m) %>%
+    mutate(delta_t = as.numeric(as.duration(time_first_dist_to_use - departure))) %>%
+    mutate(migration_speed = (delta_totdist / delta_t)) %>%
+    mutate(downstream_migration = migration_speed >= speed_threshold)
+}