# INBO CODING CLUB
28 januari 2020

Welcome!

## Deelnemers
Dirk
Patrik
Sander

## 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*)

Your snippets:

### Challenge 1

#### step by step

p1 <-
  ggplot(fit_results, aes(x = year, y = obs)) +
  geom_col() +
  facet_wrap(~scientificName,
             scales = "free_y")
p1
p2 <-
  p1 +
  geom_line(aes(y = fit),
            colour = "red",
            linetype = "dotted")
p2
p3 <-
  p2 +
  geom_ribbon(aes(ymin = lcl,
                  ymax = ucl),
              alpha = 0.3,
              fill = "purple")
p3
p4 <-
  p3 +
  ggtitle("Number of observations in Belgian Natura2000 protected areas",
          subtitle = "Source: GBIF")
p4
p5 <- 
  p4 +
  theme(plot.title = element_text(hjust = 0),
        plot.subtitle = element_text(hjust = 0))        
p5

I like it with points instead of bars:

p <- ggplot(fit_results, aes(x = year)) +
  #geom_bar(aes(y = obs), stat = "identity") + 
  geom_point(aes(y = obs)) + 
  geom_line(aes(y = fit), colour = "red", linetype = "dashed", size = 1) +
  geom_ribbon(aes(ymin = lcl, ymax = ucl), fill = "purple", alpha = 0.3) + 
  facet_wrap(vars(scientificName), scales = "free", nrow = 2, ncol = 2) +
  ggtitle("Number of observations in Belgian Natura2000 protected areas", 
          subtitle = "Source: GBIF") + 
scale_y_continuous("number of observations") +
  theme(plot.title = element_text(hjust = 0), 
        plot.subtitle = element_text(hjust = 0))
print(p)

### Challenge 2

#### alternative only difficult for the subtitle

library(gridExtra)
library(gridGraphics)
p <- ggplot(fit_results_sum, aes(x = year, y = obs)) +
  geom_point()

s <- ggplot(fit_results, aes(x= year, y= obs)) +
  facet_wrap(~scientificName, nrow = 2, ncol = 2, scales = 'free') +
  geom_line(linetype = "dotted", color = "red") +
  geom_ribbon(aes(ymin =lcl, ymax= ucl), colour = "purple", alpha=0.3)

lay <- rbind(c(1,1),
             c(2,2),
             c(2,2))
grid.arrange(p, s, layout_matrix = lay, top = textGrob("Number of observations in Belgian Natura2000 protected areas
                                                       source: GBIF", hjust = 0.65))
...

pgrid <- ggplot(fit_results) +
  geom_line(aes(y = obs, x = year))+
  facet_wrap(.~scientificName, nrow = 2, scales= 'free') +
  geom_line(aes(x=year, y=fit),color='red', linetype='dotted')+
  geom_ribbon(aes(ymin=lcl,ymax=ucl,x=year),alpha=0.3, fill='purple') 
psummary<-ggplot(fit_results_sum)+ 
  geom_line(aes(y = obs, x = year))+ labs(title = 'Number of observations in Belgian Natura2000 protected areas',subtitle = 'Source: GBIF')+
  theme(plot.title = element_text(hjust = 0),plot.subtitle = element_text(hjust = 0))
plot_grid(psummary, pgrid, nrow=2)

p1 <- fit_results %>% 
  ggplot(aes(x = year, y = obs)) +
  geom_bar(stat = "identity") +
  facet_wrap(~scientificName, scales = "free") +
  geom_line(aes(y = fit), color = "red", linetype = "dashed") +
  geom_ribbon(aes(ymin = lcl, ymax = ucl), color = "purple", alpha = 0.3) +
  labs(y = NULL,
       x = NULL)

p2 <- fit_results_sum %>% 
  ggplot(aes(x = year, y = obs)) +
  geom_area(stat = "identity") +
  labs(title = "Number of observations in Belgian Natura2000 protected areas",
       subtitle = "Source: GBIF",
       y = NULL,
       x = NULL) +
  theme(plot.title = element_text(hjust = 0),
        plot.subtitle = element_text(hjust = 0))

ggarrange(p2, p1)

#### one step more

q <- 
  fit_results_sum %>% 
  ggplot(aes(x = year, y = obs)) +
  geom_area() +
  ggtitle("Number of observations in Belgian Natura2000 protected areas",
          subtitle = "Source: GBIF")

egg::ggarrange(q, p3, ncol = 1)

### Challenge 3

#### Option 1

Damiano: I forgot to put link of GBIF logo in R code. I did it now. You can download R script again, or just copy this line in your R script:

link <- "https://github.com/inbo/coding-club/raw/master/docs/assets/images/20191219_logo_gbif.png"

logo<- image_read(link)
library(grid)
pgrid <- ggplot(fit_results) +
  geom_line(aes(y = obs, x = year))+
  facet_wrap(.~scientificName, nrow = 2, scales= 'free') +
  geom_line(aes(x=year, y=fit),color='red', linetype='dotted')+
  geom_ribbon(aes(ymin=lcl,ymax=ucl,x=year),alpha=0.3, fill='purple')
psummary<-ggplot(fit_results_sum)+
  geom_line(aes(y = obs, x = year))+ labs(title = 'Number of observations in Belgian Natura2000 protected areas')+
  theme(plot.title = element_text(hjust = 0))
Pboth <- plot_grid(psummary, pgrid, nrow=2)

#Add figure using cowplot
ggdraw() + 
  draw_plot(Pboth) +
  draw_image(logo, x = 0, hjust = 0, vjust=-4.2,width = 0.1, height = 0.2)

# Add an animated farting chicken to your plot
# Save your plot (the one from fit_results_sum, I called it p1) and load it as a magick image object
ggsave(p1, file="p1.png", width = 7, height = 5, dpi = 100)
plot <- image_read("p1.png")
plot

# Load the chicken gif
kip <- image_read("https://media.giphy.com/media/kGLpbileUNXfdb5SKl/giphy.gif") %>%
  image_scale("100")

# Set the plot as the background of the final image
background <- image_background(image_scale(plot, "500"), "white", flatten = TRUE)

# Combine background and chicken
frames <- image_composite(background, kip, offset = "+150+100")
animation <- image_animate(frames, fps = 5)
print(animation)

#Save gif
image_write(animation, "kip.gif")

#### Option 2

dynamic_plot <-
  ggplot(survey_timestamp) +
  geom_point(aes(weight, hindfoot_length, color = sex),alpha = 0.3) +
  transition_time(timestamp) + 
  shadow_mark()+ 
  labs(title = 'hindfoot length vs weight, \n Time: {frame_time}') 
animate(dynamic_plot)

##### with a nice title

static_plot +
  transition_time(timestamp) +
  shadow_mark() + 
  ggtitle('Showing timestamp {frame_time}',
          subtitle = 'Frame {frame} of {nframes}')