nekton index to fw5, replace old fim plot

R/dat_proc.R

@@ -74,65 +74,73 @@ sgdat <- sgdat |>
 
 save(sgdat, file = here::here('data/sgdat.RData'))
 
-# FIM data from FTP ---------------------------------------------------------------------------
-
-ftp_url <- "ftp://ftp.floridamarine.org/users/fim/DataMgt/Inshore_SAS_Data/FIM_inshore_SAS_database_library_20240222.zip"
-
-temp_dir <- tempdir()
-
-# Download the zip file from FTP to temporary directory
-temp_file <- paste0(temp_dir, "/", basename(ftp_url))
-download.file(url = ftp_url, destfile = temp_file, mode = "wb", quiet = FALSE)
-
-# Unzip the file
-unzip(temp_file, exdir = temp_dir)
-
-# extracted file path
-file_path <- paste0(temp_dir, "/", gsub('\\.zip$', '/', basename(ftp_url)))
-
-# import original SAS data
-phyraw <- read_sas(paste0(file_path, 'tbm_physical.sas7bdat'))
-bioraw <- read_sas(paste0(file_path, 'tbm_biology_number.sas7bdat'))
-sppraw <- read_sas(paste0(file_path, 'species_codes.sas7bdat'))
-
-unlink(temp_dir, recursive = TRUE)
-
-# physical (site) data
-# filter zones A-E for TB proper
-# filter gear type 20 (21.3-m seine)
-# filter by stratum (if wanted) to return shoreline ('S') and/or offshore (>5 m from shore, 'A','B'), we can include both, but will need to add to methods section
-# filter reference with loc info
-# filter by project "AM" to return standard monitoring sites, others are special projects - may not change the output much
-phydat <- phyraw |> 
-  mutate(
-    date = ymd(date)
-  ) |> 
-  filter(Zone %in% c('A', 'B', 'C', 'D', 'E')) |> 
-  #filter(Project =='AM') 
-  filter(Gear == 20) |> 
-  #filter (Stratum %in% c('A','B')) |> 
-  select(Reference, date)
-
-# species codes
-sppdat <- sppraw |> 
-  select(NODCCODE, Commonname) 
-
-# species count data
-biodat <- bioraw |> 
-  select(Reference, Species_record_id, NODCCODE, Number) |> 
-  left_join(sppdat, by = 'NODCCODE')
-
-# filter by species of interest
-sppdat <- biodat |> 
-  filter(Commonname %in% c('Pink Shrimp', 'Red Drum', 'Spotted Seatrout')) |> 
-  select(Reference, Number, Commonname)
-
-# join all an create complete
-fimdat <- left_join(phydat, sppdat, by = 'Reference', relationship = 'one-to-many') |> 
-  complete(Commonname, nesting(Reference, date), fill = list(Number = 0)) |> 
-  na.omit()
-
-save(fimdat, file = here('data/fimdat.RData'))
+# nekton data ---------------------------------------------------------------------------------
+
+data('fimdata', package = 'tbeptools')
+
+tbniscr <- anlz_tbniscr(fimdata)
+
+save(tbniscr, file = here::here('data/tbniscr.RData'))
+
+# # FIM data from FTP ---------------------------------------------------------------------------
+# 
+# ftp_url <- "ftp://ftp.floridamarine.org/users/fim/DataMgt/Inshore_SAS_Data/FIM_inshore_SAS_database_library_20240222.zip"
+# 
+# temp_dir <- tempdir()
+# 
+# # Download the zip file from FTP to temporary directory
+# temp_file <- paste0(temp_dir, "/", basename(ftp_url))
+# download.file(url = ftp_url, destfile = temp_file, mode = "wb", quiet = FALSE)
+# 
+# # Unzip the file
+# unzip(temp_file, exdir = temp_dir)
+# 
+# # extracted file path
+# file_path <- paste0(temp_dir, "/", gsub('\\.zip$', '/', basename(ftp_url)))
+# 
+# # import original SAS data
+# phyraw <- read_sas(paste0(file_path, 'tbm_physical.sas7bdat'))
+# bioraw <- read_sas(paste0(file_path, 'tbm_biology_number.sas7bdat'))
+# sppraw <- read_sas(paste0(file_path, 'species_codes.sas7bdat'))
+# 
+# unlink(temp_dir, recursive = TRUE)
+# 
+# # physical (site) data
+# # filter zones A-E for TB proper
+# # filter gear type 20 (21.3-m seine)
+# # filter by stratum (if wanted) to return shoreline ('S') and/or offshore (>5 m from shore, 'A','B'), we can include both, but will need to add to methods section
+# # filter reference with loc info
+# # filter by project "AM" to return standard monitoring sites, others are special projects - may not change the output much
+# phydat <- phyraw |> 
+#   mutate(
+#     date = ymd(date)
+#   ) |> 
+#   filter(Zone %in% c('A', 'B', 'C', 'D', 'E')) |> 
+#   #filter(Project =='AM') 
+#   filter(Gear == 20) |> 
+#   #filter (Stratum %in% c('A','B')) |> 
+#   select(Reference, date)
+# 
+# # species codes
+# sppdat <- sppraw |> 
+#   select(NODCCODE, Commonname) 
+# 
+# # species count data
+# biodat <- bioraw |> 
+#   select(Reference, Species_record_id, NODCCODE, Number) |> 
+#   left_join(sppdat, by = 'NODCCODE')
+# 
+# # filter by species of interest
+# sppdat <- biodat |> 
+#   filter(Commonname %in% c('Pink Shrimp', 'Red Drum', 'Spotted Seatrout')) |> 
+#   select(Reference, Number, Commonname)
+# 
+# # join all an create complete
+# fimdat <- left_join(phydat, sppdat, by = 'Reference', relationship = 'one-to-many') |> 
+#   complete(Commonname, nesting(Reference, date), fill = list(Number = 0)) |> 
+#   na.omit()
+# 
+# save(fimdat, file = here('data/fimdat.RData'))
 
 # epc ph data ---------------------------------------------------------------------------------
 

_site/site_libs/crosstalk-1.1.1/css/crosstalk.css

@@ -0,0 +1,27 @@
+/* Adjust margins outwards, so column contents line up with the edges of the
+   parent of container-fluid. */
+.container-fluid.crosstalk-bscols {
+  margin-left: -30px;
+  margin-right: -30px;
+  white-space: normal;
+}
+
+/* But don't adjust the margins outwards if we're directly under the body,
+   i.e. we were the top-level of something at the console. */
+body > .container-fluid.crosstalk-bscols {
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+  display: inline-block;
+  padding-right: 12px;
+  vertical-align: top;
+}
+
+@media only screen and (max-width:480px) {
+  .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+    display: block;
+    padding-right: inherit;
+  }
+}