canopycover.R

library(tidyverse)
library(wesanderson)
library(cowplot)
library(lubridate)
allfields <- read_csv('~/Downloads/canopycover_ratiomask.csv') %>% 
  mutate(method = 'French')
field3 <- read_csv('~/Downloads/canopycover_ratiomask_field3.csv') %>% 
  mutate(method = 'French')
all_tr <- read_csv('~/Downloads/allcanopycover (1).csv') %>% select(-X1) %>% 
  mutate(method = 'Li')

field3_mean <- field3 %>% group_by(local_datetime) %>% 
  summarise(canopy_cover = mean(canopy_cover))
field3_ortho <- allfields %>% filter(site == 3)
f3 <- ggplot(data = field3, aes(local_datetime, canopy_cover)) +
  geom_point(aes(group = site), alpha = 0.1, size = 0.4) +
  geom_line(aes(group = site), alpha = 0.1, size = 0.4) + theme_bw() + ggtitle("Field 3; \n red  = mean across plots \n blue = integrated over full field") + ylim(0,100) +
  geom_line(data = field3_mean, color = 'red') +
  geom_line(data = field3_ortho, color = 'blue')

af <- ggplot(data = allfields, aes(local_datetime, canopy_cover, color = site)) +
  geom_point() +
  geom_line() + theme_bw() + ggtitle("All fields, integrated over each field") + ylim(0,100) + theme(legend.position = c(0.1, 0.6), legend.box.background = element_rect(fill = "transparent"))


cowplot::plot_grid(f3,af, ncol = 1)

allall <- bind_rows(all_tr, allfields)

alljoin <- all_tr %>% full_join(allfields, by = c("local_datetime",  "species", "site"), suffix = c('_li', '_french')) %>% 
  mutate(dap = as.integer(as_date(local_datetime) - min(as_date(local_datetime))))

z1 <- wes_palette(name="Zissou1", n=5, type = "continuous")
ggplot(alljoin) +
  geom_point(aes(canopy_cover_li, canopy_cover_french, color = dap), size = 0.4) +
  geom_abline() + theme_bw() +
  scale_color_gradientn(colours = z1)

ggplot(alljoin) +
  geom_histogram(aes(canopy_cover_li - canopy_cover_french)) 

dj1 <- wes_palette(name="Darjeeling2", n=5, type = "continuous")

compare_methods <- 
  
  ggplot(data = allall, 
                          aes(local_datetime, canopy_cover, color = site)) +
  geom_point() +
  geom_line(aes(linetype = method)) + 
  theme_bw() + ggtitle("All fields, integrated over each field, comparing methods") + ylim(0,100) + theme(legend.position = c(0.1, 0.5), legend.box.margin = margin(0,0,0,0)) +
    scale_color_manual(values = dj1)

cowplot::plot_grid(f3, compare_methods, ncol = 1)