R/graph_metrics/input_data.R

In d2gex/seabasstfm: What the Package Does (One Line, Title Case)

source("R/utils.R")
source("R/detections/detection_views.R")
source("R/graph_utils.R")
source("R/graph_metrics/graph_metrics.R")
source("R/graph_metrics/metric_heatmapping.R")
source("R/graph_metrics/metric_stats.R")
library(logger)

# individuals <- c(
#   # "DICLAB-16215",
#   # "DICLAB-16225",
#   # "DICLAB-54173",
#   # "DICLAB-40162",
#   "DICLAB-40690"
#   # "DICLAB-40186",
#   # "DICLAB-16204",
#   # "DICLAB-40163",
#   # "DICLAB-40702"
# )

rbind_av_path_length <-
  function(av_data,
           monthly_av_data_vector,
           individual_name,
           month_name) {
    df <-
      data.frame(mean_distance = monthly_av_data_vector,
                 ind_name = individual_name,
                 period = month_name)
    av_data <-
      rbind(av_data, df) %>% mutate_if(is.numeric, round, 2)
    return(av_data)
    
  }

INPUT_DATA_PATH <- INPUT_DATA_2020_2022
OUTPUT_DATA_PATH <- OUTPUTPUT_METRICS_2020_2022
GENERATE_COORD_GRAPHS <- TRUE
HEAT_MAP_ORDER = TRUE
suffix <- paste(ifelse(HEAT_MAP_ORDER, "_heatmaps_sorted.pdf", "_heatmaps.pdf"))

coast_path <- file.path(GIS_DATA_PATH, "coast/coast_cat_fr.shp")
river_path <- file.path(GIS_DATA_PATH, "coast/coast_cat_fr_rivers_3.shp")
port_path <- file.path(GIS_DATA_PATH, "coast/coast_cat_fr_port_3.shp")
receiver_loc_path <- file.path(INPUT_DATA_PATH, "resmed_receiver_locations.csv")
fish_database_path <- file.path(INPUT_DATA_PATH, "resmed_fish_database.csv")
lubina_detection_path <- file.path(INPUT_DATA_PATH, "lubina_detections.csv")
OUTPUT <- file.path(OUTPUT_DATA_PATH, "centrality")

coast <- st_read(coast_path)
river <- st_read(river_path)
port <- st_read(port_path)
locs = prepare_gis_receiver_locations(receiver_loc_path, coast)
data <- read.csv(lubina_detection_path)
data <- data %>% mutate(station=ifelse(station == "",  station_folder, station))


paper_type <- "a4r"
paper_height <- 8.268
paper_width <- 11.693

# start <- "2020-02-01 00:00"
# end <- "2021-07-31 23:59"

start <- "2020-09-01 00:00"
end <- "2022-04-04 23:59"
granularity <- 'months'