Code/02_code_for_fig1_function.R

In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests

require(ggthemes)
require(tidyverse)
require(lubridate)
require(extrafont)
#function for theme here for now


# This is currently NOT WORKING
# theme mods
# generating new theme is in this plotting function now


## ----orginal-plot--------------------------------------------------------
output_for_fig_1_func <- function(sim.dat = sim.dat) {

theme_new <- function(base_size = 18,
                        base_family = "Times",
                        base_line_size = base_size / 170,
                        base_rect_size = base_size / 300) {
    theme_bw(
      base_size = base_size,
      base_family = base_family,
      base_line_size = base_line_size
    ) %+replace%
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          # panel.spacing = unit(2, "lines"),
          panel.border = element_blank(),

          axis.title.y = element_text(colour = "black", angle = 90),
          axis.title.x = element_blank(),

          axis.text.y=element_text(colour = "black"),
          axis.text.x = element_blank(),

          axis.ticks.x = element_line(size = 1),
          axis.ticks.y = element_line(size = 1),

          axis.line.x = element_line(size = 1),
          axis.line.y = element_line(size = 1), complete = TRUE) # end of ggplot theme
  }## finishin function

  ##imported data
  sim.dat <- sim.dat

  ## labels
  labels1 <-  c("Summer", "Autumn", "Winter", "Spring", "Summer", "Autumn", "Winter", "Spring")
  labels2 <-  c("", "", "Non-mast year", "", "", "", "Mast year", "")
  points.dat <- tibble(
    prediction = as.factor(c("A", "C", "B", "D")),
    value = as.numeric(c(15, 88, 108, 60)),
    date = as.Date(c("1999-08-20", "2000-05-01", "2000-09-13", "2000-12-25")))

  # reset labels
  # build points data
  # tibble my life
  arrow.length <- 10
  touchoff.distance <- 40 # distance between data and start of arrow
  arrowhead.size <- 3 # in millimeters
  time.loc <- as.character()


  sim.dat.no <- filter(sim.dat, control == "no.stoats") %>%
    droplevels()
  sim.dat.yes <- filter(sim.dat, control == "stoats") %>%
    droplevels()

  #plot seeds
pseed <-
    ggplot(sim.dat, aes(y = beech.seed, x = date)) +

    geom_rect(aes(xmin=ymd("2000-12-31"),
                  xmax = ymd('1999-12-31'),
                  ymin = -Inf, ymax = Inf),
              fill = "grey90") +

    geom_line(aes(y = beech.seed, x = date),
              size = 1.1,
              col = "grey50",
              lty = 3) +

    geom_point(aes(y = beech.seed, x = date, fill = control),
               alpha = 0.7,
               stroke = 1.5,
               shape = 25,
               size = 4.5,
               col = "black",
               fill = "black") +

    geom_point(aes(y = beech.seed, x = date), alpha = 1, stroke = 0.7, shape = 25, size = 1,col = "white", fill = "white") +
    xlab("") +
    ylab(expression(paste("Seed Avaliability "))) +

    scale_y_continuous(expand = c(0.05, 0.05)) +
    scale_x_date(breaks = sim.dat.no$date, date_labels =  labels1, expand = c(0.05, 0.05))+
    # scale_fill_manual(value ss = c("black")) +

    annotate("text", x=as.Date('2000-05-15'), y = 2000,
             label = "Masting year", size = 4, colour = "black") +
    annotate("text", x=as.Date('1999-07-30'), y = 2000,
             label = "Non-mast year", size = 4, colour = "black") +
    annotate("text", x=as.Date('2001-03-30'), y = 2000,
             label = "Non-mast", size = 4, colour = "black") +
theme_classic()+
    theme_new()+
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          # panel.spacing = unit(2, "lines"),
          panel.border = element_blank(),

          axis.title.y = element_text(colour = "black", angle = 90),
          axis.title.x =  element_text(colour = "black", angle = 90),

          axis.text.y=element_text(colour = "black"),
          axis.text.x = element_blank(),

          axis.ticks.x = element_line(size = 1),
          axis.ticks.y = element_line(size = 1),

          axis.line.x = element_line(size = 1),
          axis.line.y = element_line(size = 1))


 pseed

# Imported data
# sim.dat
sim.dat.no <- filter(sim.dat, control == "no.stoats") %>%
    droplevels()
sim.dat.yes <- filter(sim.dat, control == "stoats") %>%
    droplevels()


pmice <- ggplot(sim.dat, aes(y = value, x = date)) +

    geom_rect(aes(xmin=ymd("2000-12-31"),xmax = ymd('1999-12-31'), ymin = -Inf, ymax = Inf), fill = "grey90") +

    geom_line(aes(group = control), size = 0.9, col = "grey50", lty = 3) +

    geom_point(data = sim.dat.yes, aes(y = value, x = date), alpha = 0.7,  shape = 25, size = 5, col = "black", fill = "black") +
    geom_point(data = sim.dat.no, aes(y = value, x = date), alpha = 0.7,  shape = 25, size = 5,col = "black", fill = "white") +

    xlab("Time (t)") +
    ylab(expression(paste("Rodent "," ", "Abundance"))) +

    scale_y_continuous(expand = c(0.05, 0.05)) +
    scale_x_date(breaks = sim.dat.yes$date, date_labels =  labels1, expand = c(0.05, 0.05)) +

    # scale_fill_manual(values = c("white", "black")) +

    scale_colour_manual(name = "Stoat control",
                        labels = c("Yes", "No"),
                        values = c("black","white")) +

    scale_fill_manual(name = "Stoat control",
                      labels = c("Yes", "No"),
                      values = c("black","white")) +


    geom_segment(data = points.dat, aes(x = date, y = value,
                                        xend = date, yend = value + touchoff.distance + arrow.length),
                 arrow = arrow(length = unit(arrowhead.size, "mm"), ends = "last"), size = 1.25, colour = "red") +

    geom_label(data = points.dat, aes(x = date, y = value - touchoff.distance, label = prediction),
               nudge_x = 20,
               nudge_y = 60)  +

  theme_new() +
  theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        # panel.spacing = unit(2, "lines"),
        panel.border = element_blank(),

        axis.title.y = element_text(colour = "black", angle = 90),
        axis.title.x = element_text(colour = "black"),

        axis.text.y=element_text(colour = "black"),
        axis.text.x = element_text(colour = "black"),

        axis.ticks.x = element_line(size = 1),
        axis.ticks.y = element_line(size = 1),

        axis.line.x = element_line(size = 1),
        axis.line.y = element_line(size = 1))

  # pmice
  # makes graphs smaller
  result.plot <- cowplot::plot_grid(pseed, pmice ,nrow = 2,
                                    align="v",
                                    labels = c("a)", "b)"),
                                    rel_heights = c(0.8, 1.2)
                                    )

 # return(result.plot = result.plot)
} #function end

#example
sim.dat <- read_csv(file = "C://data/simulated_data_v2.csv")
result.plot <- output_for_fig_1_func(sim.dat = sim.dat)
result.plot