Tivy

# install.packages("devtools")
devtools::install_github("HansTtito/Tivy")

install.packages("Tivy")

library(Tivy)

# Load and process logbook files
data_hauls <- process_hauls(
  data_hauls = calas_bitacora,
  correct_coordinates = TRUE,
  verbose = TRUE
)

data_fishing_trips <- process_fishing_trips(
  data_fishing_trips = faenas_bitacora,
  verbose = TRUE
)

hauls_length <- process_length(
  data_length = tallas_bitacora,
  verbose = TRUE
)

# Combination of length and fishing trip data
data_length_fishing_trips <- merge(
  x = data_fishing_trips,
  y = hauls_length,
  by = 'fishing_trip_code',
  all = TRUE
)

# Complete integration with haul data
data_total <- merge_length_fishing_trips_hauls(
  data_hauls = data_hauls,
  data_length_fishing_trips = data_length_fishing_trips
)

# Add derived variables (juveniles, distance to coast, etc.)
final_data <- add_variables(
  data = data_total,
  JuvLim = 12,  # Juvenile threshold in cm
  distance_type = "haversine",
  unit = "nm"
)

# Define length columns manually
length_cols <- as.character(seq(from = 8, to = 15, by = 0.5))

# Length-weight relationship parameters (for anchoveta)
a <- 0.0001
b <- 2.983

# Create catch column in tons
final_data$catch_t <- final_data$catch_ANCHOVETA / 1000

# Weight length frequencies according to catch
final_data_weighted <- apply_catch_weighting(
  data = final_data,
  length_cols = length_cols,
  catch_col = 'catch_t',
  a = a,  # Length-weight coefficient
  b = b   # Length-weight exponent
)

# Calculate juvenile proportion by group
juvenile_results <- summarize_juveniles_by_group(
  data = final_data_weighted,
  group_cols = c("dc_cat"),  # Distance category
  length_cols = paste0("weighted_", length_cols),
  juvenile_limit = 12,
  a = a,
  b = b
)

print(juvenile_results)

# Create date column for plotting
final_data_weighted$unique_date <- convert_to_date(final_data_weighted$start_date_haul)

# Basic plot of juveniles by date
juvenile_plot <- plot_juvenile_analysis(
  data = final_data_weighted,
  x_var = "unique_date",
  fill_var = "dc_cat",
  length_cols = paste0("weighted_", length_cols),
  a = a,
  b = b,
  reference_line = 10
)

print(juvenile_plot)

# Complete dashboard of juvenile analysis
dashboard <- create_fishery_dashboard(
  data = final_data_weighted,
  date_col = "unique_date",
  length_cols = paste0("weighted_", length_cols),
  a = a,
  b = b,
  latitude_col = "lat_initial",
  longitude_col = "lon_initial",
  catch_col = "catch_t",
  juvenile_col = "juv",
  date_breaks = "1 day"
)

# View individual dashboard components
dashboard$comparison      # Juvenile comparison
dashboard$trends         # Juvenile trends over time
dashboard$catch_trends   # Cumulative catch
dashboard$spatial_map    # Spatial distribution map
dashboard$dashboard      # Complete panel with all plots

# Fetch announcements from PRODUCE website
pdf_announcements <- fetch_fishing_announcements(
  start_date = "01/03/2025",
  end_date = "31/03/2025",  
  download = FALSE  # Set TRUE to download PDF files
)

print(pdf_announcements)

# Extract information from PDF announcements
results <- extract_pdf_data(
  pdf_sources = pdf_announcements$DownloadURL
)

# Format data for visualization
formatted_results <- format_extracted_data(
  data = results,
  convert_coordinates = TRUE
)

# Visualize closed areas with ggplot (static)
static_plot <- plot_fishing_zones(
  data = formatted_results,
  type = "static",
  show_legend = TRUE,
  title = "Fishing Closure Areas"
)

print(static_plot)

# Interactive visualization with leaflet
interactive_map <- plot_fishing_zones(
  data = formatted_results,
  type = "interactive",
  show_legend = TRUE,
  base_layers = TRUE,
  minimap = TRUE
)

interactive_map

# Overview and quick start
vignette("introduction", package = "Tivy")

# Detailed data processing workflows  
vignette("data-processing", package = "Tivy")

# Spatial analysis and mapping
vignette("spatial-analysis", package = "Tivy")

# Fish population analysis
vignette("fish-analysis", package = "Tivy")