In richardjtelford/seedclim-analysis: Code for Cleaning SeedClim data

#load packages
library("tidyverse")
library("DBI")# also needs RMySQL installed
theme_set(theme_bw())

source("start_here.R")

hogsete_plot <- function(target, comm = cover.thin, trace = 0){
  treat_colour <- c("black", "grey50", "red", "blue", "purple") 
  comm <- cover.thin %>% 
    filter(destSiteID == target) %>% 
    spread(key = species, value = cover, fill = 0)
  ord <- vegan::metaMDS(select(comm, -(siteID:destSiteID)), trace = trace)
  ford <- ggvegan:::fortify.cca(ord, display = "sites")
  dat <- ford %>%
    bind_cols(select(comm, siteID:destSiteID)) %>% 
    arrange(year)

  ggplot(dat, aes(x = NMDS1, y = NMDS2, group = turfID, colour = TTtreat)) + 
    geom_path() +
    geom_point(aes(size = if_else(year == 2009, 1, NA_real_)), show.legend = FALSE) +
    scale_colour_manual(values = treat_colour, limits = paste0("TT", c("C", 1:4))) +
    coord_equal() +
    ggtitle(target) 

}
cover.thin %>% 
  distinct(destSiteID) %>% 
  pull(destSiteID) %>% 
  map(hogsete_plot) %>% 
  walk(print)