## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  message = FALSE,
  warning = FALSE
)


## ----setup--------------------------------------------------------------------
library(ggplot2)
library(dplyr)
library(emmeans)
library(multcomp)
library(MASS)
library(aanova)


## ----one-way------------------------------------------------------------------
res_one <- one_way_anova(
  data = hilsa_weight, 
  factor_var = "Habitat", 
  numeric_var = "Weight_g", 
  factor_levels = c("River", "Estuary", "Marine"),
  plot_type = "boxplot",
  sig_display = "letters"
)

print(res_one$ANOVA_Summary)
print(res_one$Plot)


## ----two-way------------------------------------------------------------------
res_two <- two_way_anova(
  data = hilsa_two_way,
  factor1_var = "Habitat",
  factor2_var = "Season",
  numeric_var = "Weight_g",
  factor1_levels = c("River", "Estuary", "Marine"),
  factor2_levels = c("Dry", "Monsoon"),
  plot_type = "boxplot"
)

print(res_two$ANOVA_Summary)
print(res_two$Plot)


## ----three-way----------------------------------------------------------------
res_three <- three_way_anova(
  data = hilsa_three_way,
  factor1_var = "Habitat",
  factor2_var = "Season",
  factor3_var = "Size_Class",
  numeric_var = "Weight_g",
  factor1_levels = c("River", "Estuary", "Marine"),
  factor2_levels = c("Dry", "Monsoon"),
  factor3_levels = c("Juvenile", "Adult"),
  y_limits = c(0, 1600),
  plot_type = "boxplot"
)

print(res_three$ANOVA_Summary)
print(res_three$Plot)


## ----manova-------------------------------------------------------------------
res_lda <- manova_analysis(
  data = hilsa_morphology,
  response_vars = c("Body_Depth_cm", "Head_Length_cm", "Fin_Length_cm"),
  factor_var = "Habitat",
  factor_levels = c("River", "Estuary", "Marine"),
  plot_type = "lda",
  color_palette = "Set1"
)

print(res_lda$MANOVA_Summary)
print(res_lda$Plot)


## ----ancova-------------------------------------------------------------------
res_ancova <- ancova_analysis(
  data = hilsa_ancova,
  response_var = "Weight_g",
  factor_var = "Habitat",
  covariate_var = "Total_Length_cm",
  factor_levels = c("River", "Estuary", "Marine"),
  color_palette = "Set1"
)

print(res_ancova$ANCOVA_Table)
print(res_ancova$Adjusted_Means)
print(res_ancova$Plot)


## ----regression---------------------------------------------------------------
res_reg <- regression_analysis(
  data = hilsa_regression,
  x_var = "Total_Length_cm",
  y_var = "Weight_g",
  fit_type = "logarithmic",
  group_var = "Habitat",
  color_palette = "Set1"
)

print(res_reg$Model_Summary)
print(res_reg$Plot)


## ----glm----------------------------------------------------------------------
res_glm <- glm_analysis(
  data = hilsa_catch,
  response_var = "Catch_Count",
  predictor_vars = c("Habitat", "Season", "Fishing_Hours"),
  family_type = "quasipoisson",
  color_palette = "Set1"
)

print(res_glm$Model_Summary)
print(res_glm$Plot)


## ----correlation--------------------------------------------------------------
res_cor <- correlation_heatmap(
  data = hilsa_env,
  method = "pearson",
  shape = "circle",
  view = "lower",
  color_palette = "RdBu"
)

print(res_cor$Correlation_Matrix)
print(res_cor$Plot)


## ----mantel-------------------------------------------------------------------
set.seed(42)
env_test <- data.frame(
  pH = rnorm(40, 7.5, 0.4),
  DO = rnorm(40, 6.2, 0.7),
  Temp = rnorm(40, 27.5, 1.5),
  Salinity = rnorm(40, 14.0, 2.5)
)

comm_test <- data.frame(
  Taxon_A = rpois(40, 12),
  Taxon_B = rpois(40, 18),
  Taxon_C = rpois(40, 7)
)

res_mantel <- mantel_heatmap_analysis(
  comm_data = comm_test,
  env_data = env_test,
  method = "pearson",
  color_palette = "RdBu"
)

print(res_mantel$Plot)