server_analysis/Serveur_timespan_sp2.R

In CmlMagneville/SmaxNanalysis: What the Package Does (One Line, Title Case)

###########################################################################
##
## Script to launch on the server to compute SmaxN and other metrics for
## ... a given species and combination of cameras: Gomphosus caeruleus
##
## Serveur_combcam_sp2.R
##
## 21/06/2022
##
## Camille Magneville
##
###########################################################################



## 0 - 1 Load data ####

abund_list <- readRDS(here::here("..", "transformed_data", "all_abund_list.rds"))
dist_df <- read.csv(here::here("..", "data", "dist_df.csv"), row.names = 1)

# ICRS: keep only 9 cameras (6 LD and 3 SD):
dist_df <- dist_df[c(2, 4, 6, 7, 8, 9, 10, 11, 12), c(2, 4, 6, 7, 8, 9, 10, 11, 12)]

# call the functions needed:
source(here::here("..", "R", "6_SmaxN_across_camnb_functions.R"))
source(here::here("..", "R", "7_SmaxN_time_functions.R"))
source(here::here("..", "R", "3_Compute_combinaisons_functions.R"))


# load SmaxN pkge:
remotes::install_github("CmlMagneville/SmaxN", build_vignettes = TRUE, force = TRUE)



## 1 - Prepare data for computing ####

# PREPARE DATA: clean abund list:
clean_abund_list <- abund_list

# ICRS: keep only 9 cameras:
for (i in (1:length(clean_abund_list))) {
  for (j in (1:length(clean_abund_list[[i]]))) {
    clean_abund_list[[i]][[j]] <- clean_abund_list[[i]][[j]][, which(colnames(clean_abund_list[[i]][[j]]) %in%
                                                                       c("A1", "A2", "B1", "B2",
                                                                         "C1", "C2", "D", "F", "H"))]
  }
}

abund_list <- clean_abund_list

# Get the timespans to work on:
spans_set <- c(600, 1200, 1800, 2400, 3000, 3600)

# get the names of cameras for which combinaisns must be computed:
# ICRS 9 cameras:
cam_set <- c("A1", "A2", "B1", "B2",
             "C1", "C2", "D", "F", "H")


## 3 - Compute SmaxN for all timespans


# create a list of abund df with all cam (even if the species ...
# ... is not seen by several cam thus the abund df has 9 (ICRS) 12 (paper) columns).
# ... the list is build as follow:

# be careful for paper, change create.abundlist.allcam.poses() function because 12 cam
abund_allcam_list_GC <- create.abundlist.allcam.poses(cam_set = cam_set,
                                                          species_nm = "Gomphosus_caeruleus",
                                                          abund_list = abund_list)


# create a list of abund df for timespan
abund_timespan_list_GC <- create.abund.list.timespan(spans_set = spans_set,
                                                         abund_allcam_list = abund_allcam_list_GC)


# create the df for plot (really long process so uncomment if want to run again):
maxN_timespan_GC <- compute.maxN.combcam(abund_combcam_list = abund_timespan_list_GC,
                                             dist_df = dist_df,
                                             fish_speed = 0.5,
                                             analysis_type = "timespan")

# save
saveRDS(maxN_timespan_GC, "maxN_timespan_raw_GC.rds")