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

install.packages("Tivy")

library(Tivy)# Load and process logbook filesdata_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 datadata_length_fishing_trips<-merge(x = data_fishing_trips,y = hauls_length,by ='fishing_trip_code',all =TRUE)# Complete integration with haul datadata_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 cmdistance_type ="haversine",unit ="nm")

# Define length columns manuallylength_cols<-as.character(seq(from =8,to =15,by =0.5))# Length-weight relationship parameters (for anchoveta)a<-0.0001b<-2.983# Create catch column in tonsfinal_data$catch_t<- final_data$catch_ANCHOVETA/1000# Weight length frequencies according to catchfinal_data_weighted<-apply_catch_weighting(data = final_data,length_cols = length_cols,catch_col ='catch_t',a = a,# Length-weight coefficientb = b# Length-weight exponent)# Calculate juvenile proportion by groupjuvenile_results<-summarize_juveniles_by_group(data = final_data_weighted,group_cols =c("dc_cat"),# Distance categorylength_cols =paste0("weighted_", length_cols),juvenile_limit =12,a = a,b = b)print(juvenile_results)

# Create date column for plottingfinal_data_weighted$unique_date<-convert_to_date(final_data_weighted$start_date_haul)# Basic plot of juveniles by datejuvenile_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 analysisdashboard<-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 componentsdashboard$comparison# Juvenile comparisondashboard$trends# Juvenile trends over timedashboard$catch_trends# Cumulative catchdashboard$spatial_map# Spatial distribution mapdashboard$dashboard# Complete panel with all plots

# Fetch announcements from PRODUCE websitepdf_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 announcementsresults<-extract_pdf_data(pdf_sources = pdf_announcements$DownloadURL)# Format data for visualizationformatted_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 leafletinteractive_map<-plot_fishing_zones(data = formatted_results,type ="interactive",show_legend =TRUE,base_layers =TRUE,minimap =TRUE)interactive_map

# Overview and quick startvignette("introduction",package ="Tivy")# Detailed data processing workflowsvignette("data-processing",package ="Tivy")# Spatial analysis and mappingvignette("spatial-analysis",package ="Tivy")# Fish population analysisvignette("fish-analysis",package ="Tivy")