In ReseauBiodiversiteQuebec/tableauphenologie: Séries chronologiques de la biodiversité québécoise

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(tableauphenologie)
library(tidyverse)

# top species in each region



top10species <- tableauphenologie::inatqc %>%
  group_by(region, taxon_species_name) %>%
  tally %>%
  arrange(region,desc(n)) %>%
  nest %>%
  mutate(top10 = map(data, head, 10)) %>%
  select(-data) %>%
  unnest(top10)


count_taxa <- tableauphenologie::inatqc %>% mutate(julianday = lubridate::yday(observed_on)) %>%
  group_by(region, taxon_species_name, julianday) %>% tally

count_taxa %>%
  semi_join(top10species %>% select(-n)) %>%
  ggplot(aes(x = julianday, y = n)) +
  geom_point() +
  facet_wrap(~region)

chosen_species_range_days <- count_taxa %>%
  semi_join(top10species %>% select(-n)) %>%
  filter(region == "Mauricie") %>%
  summarize(jday = range(julianday)) %>%
  mutate(dayname = if_else(jday == min(jday), "start", "end")) %>%
  ungroup



# count days in the "range" for each species
nper_day <- chosen_species_range_days %>%
  pivot_wider(names_from = dayname, values_from = jday) %>%
  mutate(dayrange = map2(start, end, ~.x:.y)) %>%
  select(dayrange) %>%
  unnest(cols = c(dayrange)) %>%
  group_by(dayrange) %>% tally %>%
  # fill in missing days:
  right_join(tibble(dayrange = 1:365)) %>%
  replace_na(list(n = 0)) %>%
  arrange(dayrange)

p1 <- chosen_species_range_days %>%
  ggplot(aes(x = jday, y = taxon_species_name)) +
  geom_line(size = 10, col = "darkgreen") +
  theme_minimal() +
  coord_cartesian(xlim = c(0,365)) + 
  labs(x = "Jour de l'année", 
       y = NULL)
p1

p2 <- nper_day %>%
  ggplot(aes(x = dayrange, y = n)) + geom_polygon() + theme_minimal()

p1

p2

tableauphenologie::nper_day

Here's another idea

ten_count <- count_taxa %>%
  semi_join(top10species %>% select(-n),
            by = c("region", "taxon_species_name")) 


ten_count_complete <- ten_count %>% 
  complete(nesting(region, taxon_species_name), julianday=1:365)

ten_count_complete %>% 
  ggplot(aes(x = julianday, y = taxon_species_name, fill = is.na(n))) + 
  geom_tile() + 
  facet_wrap(~region, scales = "free_y") + 
  theme(axis.text.y = element_blank())

ReseauBiodiversiteQuebec/tableauphenologie documentation built on Dec. 31, 2020, 4:24 p.m.