In sdtaylor/phenometR: An interface to the Phenomet database

First load the phenometR and tidyverse packages.

library(tidyverse)
library(phenometR)

This will pull data for all mesquites using it's species code. Then filter it to the open flowers (DS_08) and leaves (DS_02) phenophases, then to just three of the sites (GI,P9, and SC), and finally only rows with status 0, or 1 to exclude null (-99) values. If you are running this for the first time it will ask for the database username and password.

pros_glan = get_species_phenophase('PRGL') %>%
  filter(PHENOPHASE %in% c('DS_08','DS_02')) %>%
  filter(SITE_CODE %in% c('GI','P9','SC')) %>%
  filter(STATUS %in% c(0,1))

Add in a week column to get the mean numbers of plants with leaves or flowers per week.

pros_glan = pros_glan %>%
  mutate(week = lubridate::week(DATE)) %>%
  group_by(SITE_CODE, PHENOPHASE, YEAR, week) %>%
  summarise(percent_present = mean(STATUS)) %>%
  ungroup()

And plot it. With sites as rows, the two phenophases as columns, and different colors as years.

ggplot(pros_glan, aes(x=week, y=percent_present, color=as.factor(YEAR))) +
  geom_point() +
  geom_line() + 
  scale_color_viridis_d() + 
  facet_wrap(SITE_CODE~PHENOPHASE, ncol=2) +
  theme_bw(20)