## To download package from other sources
library(drat)

## Include 'hyenaproject' as a package source
addRepo("hyenaproject") 

## Download hyenaR
install.packages("hyenaR")

library(hyenaR) ## For our hyena specific functions
library(dplyr) ## For most data wrangling
library(ggplot2) ## For plotting
library(lubridate) ## Working with dates
library(tidyr) ## Extra data wrangling functions
library(stringr) ## Working with text
library(waldo) ## To compare objects
library(skimr) ## Inspect data
library(purrr) ## For loops in the tidyverse

load_package_database.full(
  
  # Location of our database file
  db.path = "example_git/source_data/Fisidata_2022_08_10.sqlite"
  
)

build_vignette_news()

fetch_clan_number.anysex.all(clan = "A", at = "1997-01-01")

# Our function name...
my_function

# Our function name and argument names
my_function <- function(argument1, argument2){}

# Our function name and argument names
my_function <- function(argument1, argument2){
  
  # Code between {}
  argument1 + argument2
  
}

my_function(argument1 = 1, argument2 = 3)

day_of_the_week <- function(){
  format(Sys.Date(), "%A")
}
day_of_the_week()

add <- function(number, addition = 1){
  
  number + addition
  
}
add(number = 10)

add(number = 10, addition = 2)

add <- function(number, addition = 1){
  
  number + addition
  10
  
}

add(20)

add <- function(number, addition = 1){
  
  new_number <- number + addition
  return(new_number)
  10
  
}

add(20)

is_even <- function(object){
  ## Check if a number is 0...
  if (object == 0) {
    output <- NA
  }
  ## THEN check if a number is >0 and even
  if (object > 0 & object %% 2 == 0) {
    output <- "even"
  }
  ## THEN check if a number is >0 and odd
  if (object > 0 & object %% 2 != 0) {
    output <- "odd"
  }
  ## Return the output
  output
}

is_even_new <- function(object){
  ## If number is 0...return NA and stop!!
  if (object == 0) {
    return(NA)
  }
  ## Otherwise...check if a number is >0 and even
  if (object > 0 & object %% 2 == 0) {
    output <- "even"
  }
  ## and check if a number is >0 and odd
  if (object > 0 & object %% 2 != 0) {
    output <- "odd"
  }
  ## Return the output
  output
}

add <- function(number, addition = 1){
  
  number + addition
  
}
add("B")

add <- function(number, addition = 1){
  
  if (is.character(number) | is.character(addition)) {
    stop("The arguments 'number' and 'addition' cannot be characters!")
  }
  number + addition
  
}
add("B")

add <- function(number, addition = 1){
  
  if (is.character(number) | is.character(addition)) {
    stop("The arguments 'number' and 'addition' cannot be characters!")
  }
  
  if (is.logical(number) | is.logical(addition)) {
    warning("Coercing logical value to numeric.\n")
  }
  number + addition
  
}
add(number = 10, addition = TRUE)

day_of_week <- function(date){
  if (is.numeric(date)) {
    stop("Function cannot accept a number")
  }
  day <- format(as.Date(date), "%A")
  paste("You were born on", day)
}
day_of_week("12-03-88")

day_of_week <- function(date){
  browser()
  if (is.numeric(date)) {
    stop("Function cannot accept a number")
  }
  day <- format(as.Date(date), "%A")
  paste("You were born on", day)
}
day_of_week("12-03-88")

transform_numbers <- function(n){
  
  output <- c()
  
  for (i in runif(min = -10, max = 10, n = n)) {
    
    output <- append(output, log(i))
    
  }
  
  return(output)
  
}

set.seed(123)
transform_numbers(10)

transform_numbers <- function(n){
  
  output <- c()
  
  for (i in runif(min = -10, max = 10, n = n)) {
    
    browser(expr = i <= 0)
    output <- append(output, log(i))
    
  }
  
  return(output)
  
}

set.seed(123)
transform_numbers(10)

debug(day_of_week)
day_of_week("12-03-88")

date_time <- lubridate::ymd_hms("1999-01-01 00:00:00", tz = "Africa/Dar_es_Salaam")
as.Date(date_time)

average_age_firstrepro <- function(sex, birth_year, na.rm = FALSE){
  
  ## Create start and end date for the target year
  start_date <- paste('birth_year', "01/01", sep = "_")
  end_date   <- paste('birth_year', "12/31", sep = "_")
  
  ## Extract all individuals born in that year and their age at first birth
  all_births <- create_id_starting.table(from = start_date, to = end_date,
                           sex = sex,
                           lifestage = "cub", lifestage.overlap = "start") %>% 
    dplyr::mutate(firstbirth = fetch_id_date.birth.first(ID)) %>% 
    dplyr::mutate(age = fetch_id_age(ID, at = firstbirth))
  
  ## Determine an average age at first birth
  avg_age <- mean(all_births$age, na.rm = na.rm)
  
  ## Return the number
  return(avg_age)

}

average_age_firstrepro(2019, "male")