# 1. Load libraries
library(ggplot2)
library(dplyr)
library(tidyr)

# 2. Load and Combine Data
y1 <- read.csv("Lime_Year1_Data.csv")
y2 <- read.csv("Lime_Year2_Data.csv")
df_combined <- rbind(y1, y2)

# 3. Reshape and Rename Metrics
df_long <- df_combined %>%
  select(Year, Light, PBZ, DaysToFlower, NoFlowers, NoFruits, FruitWt_g) %>%
  pivot_longer(
    cols = c(DaysToFlower, NoFlowers, NoFruits, FruitWt_g),
    names_to = "Metric",
    values_to = "Value"
  ) %>%
  mutate(
    Metric = recode(Metric,
                    "DaysToFlower" = "Days to Flower",
                    "NoFlowers"    = "No. of Flowers",
                    "NoFruits"     = "No. of Fruits",
                    "FruitWt_g"    = "Fruit Weight (g)")
  )

# 4. Set Factor Levels
df_long <- df_long %>%
  mutate(
    PBZ = factor(PBZ, levels = c("P0", "P1", "P2", "P3")),
    Light = factor(Light, levels = c("L1", "L2", "L3")),
    Metric = factor(Metric, levels = c("Days to Flower",
                                       "No. of Flowers",
                                       "No. of Fruits",
                                       "Fruit Weight (g)")),
    Year = factor(Year)
  )

# 5. Calculate Mean and SEM
plot_summary <- df_long %>%
  group_by(Year, Light, PBZ, Metric) %>%
  summarise(
    mean_val = mean(Value, na.rm = TRUE),
    se_val = sd(Value, na.rm = TRUE) / sqrt(n()),
    .groups = "drop"
  )

# 6. Generate Multi-Variable Plot
ggplot(plot_summary, aes(x = PBZ, y = mean_val, color = Light,
                         group = interaction(Light, Year))) +
  geom_line(aes(linetype = Year), linewidth = 0.8) +
  geom_point(aes(shape = Year), size = 2) +
  geom_errorbar(aes(ymin = mean_val - se_val, ymax = mean_val + se_val),
                width = 0.2, alpha = 0.7) +
  facet_grid(Metric ~ Light, scales = "free_y") +
  labs(
    title = "Lime Phenology & Yield: PBZ and Light Intensity Effects",
    x = "PBZ Concentration",
    y = "Mean Value",
    color = "Light Intensity",
    linetype = "Study Year",
    shape = "Study Year"
  ) +
  theme_bw() +
  theme(
    legend.position = "bottom",
    strip.text = element_text(face = "bold", size = 10),
    strip.background = element_blank(),  # removes boxes around facet titles
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    axis.line = element_line(colour = "black")
  )