# INBO CODING CLUB

25 April 2023

Welcome!

## Share your code snippet

If you want to share your code snippet, copy paste your snippet within a section of three backticks (```):

As an **example**:

library(tidyverse)

(*you can copy paste this example and add your code further down*)

## Yellow sticky notes

No yellow sticky notes online. Put your name + " | " and add a "*" each time you solve a challenge (see below).

## Participants

Name | Challenges
--- | ---
Damiano Oldoni | ***
Emma Cartuyvels|
Dirk Maes | **
Ward Langeraert | **
Marijke Thoonen |
Amber Mertens | **
Oberon Geunens |**
Jonas Bertels | **
Raïsa Carmen | ***

## Challenge 1

### Solution Ward

library(INBOtheme)

# 1
ias_first_obs_be + ias_first_obs_reg

# 2
ias_first_obs_be / ias_first_obs_reg

# 3
ias_first_obs_reg_facets <- ias_first_obs_reg +
  facet_wrap(~locationId) +
  theme(legend.position = "bottom")

ias_first_obs_be / ias_first_obs_reg_facets

# 4
ias_first_obs_be_facets <- ias_first_obs_be + 
  facet_wrap(~kingdom)

ias_first_obs_reg_facets2 <- ias_first_obs_reg_facets +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

(ias_first_obs_be / ias_first_obs_reg_facets2) | ias_first_obs_be_facets

# 5
tab <- ias_regions %>%
  count(locationId) %>%
  arrange(locationId)

ias_first_obs_reg_facets2 + gridExtra::tableGrob(tab)

### Solution Emma:

ias_first_obs_be | ias_first_obs_reg

ias_first_obs_be / ias_first_obs_reg

ias_first_obs_reg_facets <- ias_first_obs_reg + facet_grid(cols = vars(locationId))
ias_first_obs_be / ias_first_obs_reg_facets

ias_first_obs_be_facets <- ias_first_obs_be + facet_wrap(vars(kingdom))
(ias_first_obs_be / ias_first_obs_reg_facets) | ias_first_obs_be_facets

table <- ias_regions %>% 
  group_by(locationId) %>% 
  summarise(sum = n())
ias_first_obs_reg_facets | gridExtra::tableGrob(table)

### Solution Jonas:

#
ias_first_obs_be + ias_first_obs_reg

#
ias_first_obs_be / ias_first_obs_reg

#
ias_first_obs_reg_facet <- ias_first_obs_reg +
  facet_grid(.~locationId)

ias_first_obs_reg_facet
  
ias_first_obs_be / ias_first_obs_reg_facet

#
ias_first_obs_be_facet <- ias_first_obs_be +
  facet_grid(kingdom~.)

ias_first_obs_be_facet

ias_first_obs_reg_facet_2 <- ias_first_obs_reg +
  facet_grid(locationId~.) +
  theme(legend.position = "none")

ias_first_obs_reg_facet_2 + ias_first_obs_be_facet

#
ias_first_obs_reg_facet +
  theme(legend.position = "none") + 
  gridExtra::tableGrob(count(ias_regions, locationId))

## Challenge 2
### Solution Ward

# 1
ias_first_obs_paths +
  facet_zoom(xlim = c(1980, 2000), ylim = c(0, 100))

# 2
ias_first_obs_reg +
  facet_wrap_paginate(~kingdom, strip.position = "bottom") +
  theme(legend.position = "top") +
  labs(x = "", y = "aantal", fill = "locatie")

### Solution Marijke
'''
#1
ias_first_obs_paths + facet_zoom(xlim = c(1980, 2000))
'''

### Solution Jonas:

# 

ias_first_obs_paths +
  facet_zoom(x = first_observed >= 1980 & 
               first_observed <= 2000)

ias_first_obs_paths +
  facet_zoom(x = first_observed >= 1980 & 
               first_observed <= 2000,
             y = n < 50,
             split = TRUE) 

# 
ias_first_obs_reg_facet_force <- ias_first_obs_reg +
  facet_col(~locationId, scales = 'free', strip.position = 'bottom')

ias_first_obs_reg_facet_force

## Challenge 3

Solution Raisa

#1
ggplotly(ias_first_obs_paths)
#2
ggplotly(ias_first_obs_paths, dynamicTcisk = TRUE)
#3
ias_first_obs_paths_labelled <-
  ggplot(ias_pathways,
         aes(text = paste('year: ', first_observed,
                          '\nintroduction pathway:', pathway,
                          '\nnumber of taxa: ', n))) +
  geom_point(mapping = aes(x = first_observed,
                           y = n,
                           color = pathway),
             shape = 1,
             size = 3) +
  geom_line(mapping = aes(x = first_observed,
                          y = n,
                          # group argument tells R  which points have to be linked together to form a line
                          group = pathway,
                          color = pathway)) +
  labs(x = "year of introduction", y = "number of taxa") +
  theme(axis.text.x = element_text(angle = 70, vjust = 0.5))

ggplotly(ias_first_obs_paths_labelled, dynamicTcisk = TRUE,
         tooltip = "text")

### Solution Ward

# challenge 3A
p <- area_biotopes %>%
  ggplot(aes(x = species, y = meanArea)) +
    geom_point(aes(colour = biotope, size = meanArea)) +
    facet_wrap(~region) +
    theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
    labs(title = 'Year: {frame_time}') +
    transition_time(year) +
    ease_aes("cubic-in-out")

# Save as GIF
library(gifski)
anim_save("area_biotopes.GIF", animation = p, renderer = gifski_renderer(),
          width = 1000, height = 300, path = "src/20230425")
# Save as mp4
library(av)
anim_save("area_biotopes.mp4", animation = p, renderer = av_renderer(),
          width = 1000, height = 300, path = "src/20230425")