Merge pull request #8 from afsc-gap-products/ai-plots

Code used for 2022 bottom temperature maps

.gitignore

@@ -35,3 +35,5 @@ vignettes/*.pdf
 ConnectToOracle.R
 *.log
 /shapefiles/archive
+/code/ftp.R
+

code/run_AI.R

@@ -0,0 +1,249 @@
+#' ---------------------------
+#' title: Survey Daily and Anomaly Temperature Plot
+#' OG author: Jason Conner
+#' maintained: Emily Markowitz and Liz Dawson (May 2022)
+#' purpose: run script
+#' ---------------------------
+
+# Knowns -----------------------------------------------------------------------
+
+maxyr <- 2022 
+data_source <- "gd" # google drive
+dates0 <- "latest" # "all" # latest # "all", #"2021-06-05",# Sys.Date(), # as.character(seq(as.Date("2022-07-30"), as.Date("2022-08-14"), by="days"))
+shapef <- FALSE #set to TRUE to run make_grid_wrapper to run shapefiles for EBS and AI
+var <- "bt"
+
+googledrive_dl <- TRUE
+dir_googledrive_log <- "https://docs.google.com/spreadsheets/d/16CJA6hKOcN1a3QNpSu3d2nTGmrmBeCdmmBCcQlLVqrE/edit#gid=315914502"
+#dir_googledrive_upload_bs = "https://drive.google.com/drive/u/2/folders/1wvLejYW73nd0v_lOejmAdoCBbD2kUsbf" #NULL #"https://drive.google.com/drive/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
+dir_googledrive_upload_ai = "https://drive.google.com/drive/u/0/folders/17rHN6GTkw5ywMXJ6VfyOkKXr7FY7o7B3" #NULL #"https://drive.google.com/drive/folders/1SeNOAh5-muQ2BDgOHWZWwYIoLl68DHWX"
+#dir_googledrive_upload_test = "https://drive.google.com/drive/folders/1rsR0aFfFzrspTBFU48Bb26EJvdhIZSpl"
+
+# The surveys this script will be covering 
+dat_survreg <- data.frame(reg_shapefile = "EBS_SHELF", 
+                          region_long = "Eastern Bering Sea", 
+                          SRVY = "EBS", 
+                          region = "BS", 
+                          vessel_id = c(94, 162), # CHANGE
+                          vessel_shape = c("V", "A"), # CHANGE
+                          reg_dates = "May 25 - Aug 03 2022") # CHANGE
+dat_survreg <- dplyr::bind_rows(dat_survreg, 
+                                data.frame(reg_shapefile = "NBS_SHELF", 
+                                           region_long = "Northern Bering Sea", 
+                                           SRVY = "NBS", 
+                                           region = "BS", 
+                                           vessel_id = c(94, 162), # CHANGE
+                                           vessel_shape = c("V", "A"), # CHANGE
+                                           reg_dates = "Aug 03 - Aug 28 2022")) # CHANGE
+dat_survreg <- dplyr::bind_rows(dat_survreg, 
+                                data.frame(reg_shapefile = "AI",
+                                           region_long = "Aleutian Islands",
+                                           SRVY = "AI",
+                                           region = "AI",
+                                           vessel_id = c(148, 176), # CHANGE
+                                           vessel_shape = c("OEX", "AP"), # CHANGE
+                                           reg_dates = "Jun 07 - Aug 17 2022")) # CHANGE
+# dat_survreg <- dplyr::bind_rows(dat_survreg, 
+#                                data.frame(reg_shapefile = "GOA", 
+#                                           region_long = "Gulf of Alaska", 
+#                                           SRVY = "GOA", 
+#                                           region = "GOA", 
+#                                           vessel_id = c(148, 176), # CHANGE
+#                                           vessel_shape = c("OEX", "SS"), # CHANGE
+#                                           reg_dates = "May 25 - Aug 04")) # CHANGE
+
+# SIGN INTO GOOGLE DRIVE--------------------------------------------------------
+## This sign in needs to be here for the Task Scheduler to run, please do not comment out.
+googledrive::drive_deauth()
+googledrive::drive_auth()
+1
+
+# SOURCE SUPPORT SCRIPTS -------------------------------------------------------
+## Actually we cant use the here package, here - it actually causes issues with 
+## the tasks scheduler, which has no concept of a project root folder. 
+#dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
+#dir_wd <- "G:/EBSother/GAPsurveyTemperatureMap/"
+#dir_wd <- paste0(getwd(), "/")
+dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
+#dir_wd <- "C:/Users/caitlin.akselrud/Work/survey-live-temperature-map/"
+
+source(file = paste0(dir_wd,"code/functions.R"))
+# source(file = paste0(dir_wd, "code/data_dl.R")) # you don't unnecessarily run this each time
+source(file = paste0(dir_wd, "code/data.R"))
+if (googledrive_dl == TRUE) {
+  source(file = paste0(dir_wd, "code/ftp.R")) # removed in gitignore - ask for premission
+}
+
+# Map --------------------------------------------------------------------------
+# ## AI --------------------------------------------------------------------------
+SRVY <- "AI"
+region_akgfmaps = "ai"
+plot_subtitle = "NOAA Fisheries Aleutian Islands Bottom Trawl Survey"
+dir_googledrive_upload <- (dir_googledrive_upload_ai)
+plot_anom <- FALSE
+show_planned_stations <- FALSE
+survey_area <- akgfmaps::get_base_layers(select.region = region_akgfmaps, set.crs = "auto")
+survey_area$survey.grid <- rgdal::readOGR(dsn = paste0(dir_wd, '/shapefiles/'),# Prepare map objects
+                                          layer = "aigrid_trawable_thru2018_Emily",
+                                          verbose=F) %>%
+  sp::spTransform(x = ., CRS(survey_area$crs$input)) %>%
+  st_as_sf(x = .) %>%
+  dplyr::rename(station = ID,
+                stratum = STRATUM) %>%
+  dplyr::filter(stratum %in% unique(goa_strata0$stratum) &
+                  stratum != 0) %>% # land
+  sp::merge(
+    x = .,
+    y = goa_strata0 %>%
+      dplyr::filter(survey == "AI") %>%
+      dplyr::mutate(SRVY = "AI",
+                    region = stringr::str_to_title(inpfc_area),
+                    region = dplyr::case_when(
+                      region %in% c("Western Aleutians", "Chirikof") ~ "Western Aleutians",
+                      TRUE ~ region)) %>%
+      dplyr::select(SRVY, stratum, region) %>%
+      dplyr::distinct(),
+    all.x = TRUE)  %>% 
+  dplyr::arrange(region)
+survey_area$survey.grid1 <- survey_area$survey.grid
+
+if(shapef == TRUE)
+{
+  make_grid_wrapper(maxyr = maxyr,                             # Blank grid plot
+                    SRVY = SRVY,
+                    haul = haul,
+                    dat_survreg = dat_survreg,
+                    dir_googledrive_upload = dir_googledrive_upload,
+                    survey_area = survey_area,
+                    data_source = data_source,
+                    plot_subtitle = plot_subtitle,
+                    dir_wd = dir_wd)
+}
+
+make_varplot_wrapper(maxyr = maxyr,                               # Daily plot
+                     SRVY = SRVY,
+                     haul = haul,
+                     dat_survreg = dat_survreg,
+                     var = var,
+                     dir_googledrive_upload = dir_googledrive_upload,
+                     dates0 = dates0,
+                     survey_area = survey_area,
+                     plot_subtitle = plot_subtitle,
+                     show_planned_stations = show_planned_stations,
+                     data_source = data_source,
+                     plot_anom = plot_anom,
+                     dir_wd = dir_wd)
+# make_varplot_wrapper(maxyr = maxyr,                       # Anom and mean plot
+#                   SRVY = SRVY,
+#                   haul = haul,
+#                   dat_survreg = dat_survreg,
+#                   var = var,
+#                   dir_googledrive_upload = dir_googledrive_upload,
+#                   dates0 = "latest",
+#                   survey_area = survey_area,
+#                   plot_subtitle = plot_subtitle,
+#                   show_planned_stations = show_planned_stations,
+#                   data_source = data_source,
+#                   plot_daily = FALSE,
+#                   plot_anom = TRUE,
+#                   plot_mean = TRUE,
+#                   dir_wd = dir_wd)
+
+## send all current files to the FTP -------------------------------------------
+# vars here defined in ftp.R
+dir_out <- paste0(dir_wd,"/output/",maxyr,"_",SRVY,"/")
+temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
+dest <- dev_ai
+
+for (iiii in 1:length(temp)) {
+  print(temp[iiii])
+
+  RCurl::ftpUpload(
+    what = paste0(dir_out, "/", temp[iiii]),
+    asText = FALSE,
+    to = paste0(glue::glue("{protocol}://STOR@{server}/{dest}/", temp[iiii])),
+    userpwd = paste0(user,":", pass),
+    .opts=curlOptions(verbose=TRUE))
+}
+
+
+# NBS + EBS Maps --------------------------------------------------------------
+# 
+# SRVY <- "BS"
+# region_akgfmaps = "bs.all"
+# plot_subtitle <- "NOAA Fisheries Bering Sea Bottom Trawl Survey"
+# dir_googledrive_upload <- (dir_googledrive_upload_bs)
+# survey_area <- akgfmaps::get_base_layers(select.region = region_akgfmaps, set.crs = "auto")
+# show_planned_stations <- TRUE
+# plot_anom <- TRUE
+# survey_area$survey.grid <- survey_area$survey.grid %>% 
+#   sf::st_transform(x = ., survey_area$crs$input) %>%
+#   dplyr::rename(station = STATIONID) %>%
+#   sp::merge(x = ., 
+#             y = haul %>%
+#               dplyr::rename(station = stationid) %>% 
+#               dplyr::select(station, stratum) %>% 
+#               dplyr::distinct(), 
+#             all.x = TRUE) %>% 
+#   dplyr::mutate(region = "Bering Sea")
+# survey_area$place.labels$y[survey_area$place.labels$lab == "200 m"] <- -60032.7
+# 
+# if(shapef == TRUE)
+# {
+# make_grid_wrapper(maxyr = maxyr,                             # Blank grid plot
+#                   SRVY = SRVY,
+#                   haul = haul,
+#                   dat_survreg = dat_survreg,
+#                   dir_googledrive_upload = dir_googledrive_upload,
+#                   survey_area = survey_area,
+#                   data_source = data_source,
+#                   plot_subtitle = plot_subtitle,
+#                   dir_wd = dir_wd)
+# }
+# 
+# make_varplot_wrapper(maxyr = maxyr,                               # Daily plot
+#                      SRVY = SRVY,
+#                      haul = haul,
+#                      dat_survreg = dat_survreg,
+#                      var = var,
+#                      dir_googledrive_upload = dir_googledrive_upload,
+#                      dates0 = dates0,
+#                      survey_area = survey_area,
+#                      plot_subtitle = plot_subtitle,
+#                      show_planned_stations = show_planned_stations,
+#                      data_source = data_source,
+#                      plot_anom = plot_anom,
+#                      dir_wd = dir_wd)
+# # make_varplot_wrapper(maxyr = maxyr,                       # Anom and mean plot
+# #                   SRVY = SRVY,
+# #                   haul = haul,
+# #                   dat_survreg = dat_survreg,
+# #                   var = var,
+# #                   dir_googledrive_upload = dir_googledrive_upload,
+# #                   dates0 = "latest",
+# #                   survey_area = survey_area,
+# #                   plot_subtitle = plot_subtitle,
+# #                   show_planned_stations = show_planned_stations,
+# #                   data_source = data_source,
+# #                   plot_daily = FALSE,
+# #                   plot_anom = FALSE, # anom plot here doesnt make sense to print until the end
+# #                   plot_mean = TRUE,
+# #                   dir_wd = dir_wd)
+# 
+## send all current files to the FTP -------------------------------------------
+# vars here defined in ftp.R
+# dir_out <- paste0(dir_wd, "/output/", maxyr, "_",SRVY,"/")
+# temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
+# dest <- dev_bs
+# 
+# for (iiii in 1:length(temp)) {
+#   print(temp[iiii])
+# 
+#   RCurl::ftpUpload(
+#     what = paste0(dir_out, "/", temp[iiii]),
+#     asText = FALSE,
+#     to = paste0(glue::glue("{protocol}://STOR@{server}/{dest}/", temp[iiii])),
+#     userpwd = paste0(user,":", pass),
+#     .opts=curlOptions(verbose=TRUE))
+# }
+# 

code/run_BS.R

@@ -0,0 +1,135 @@
+#' ---------------------------
+#' title: Survey Daily and Anomaly Temperature Plot
+#' OG author: Jason Conner
+#' maintained: Emily Markowitz and Liz Dawson (May 2022)
+#' purpose: run script
+#' ---------------------------
+
+# Knowns -----------------------------------------------------------------------
+maxyr <- 2022 
+data_source <- "gd" # google drive
+dates0 <- "latest" # "all" # latest # "all", #"2021-06-05",# Sys.Date(), # as.character(seq(as.Date("2022-07-30"), as.Date("2022-08-14"), by="days"))
+shapef <- FALSE #set to TRUE to run make_grid_wrapper to run shapefiles for EBS and AI
+var <- "bt"
+
+googledrive_dl <- TRUE
+dir_googledrive_log <- "https://docs.google.com/spreadsheets/d/16CJA6hKOcN1a3QNpSu3d2nTGmrmBeCdmmBCcQlLVqrE/edit#gid=315914502"
+dir_googledrive_upload_bs = "https://drive.google.com/drive/u/0/folders/1wvLejYW73nd0v_lOejmAdoCBbD2kUsbf" #NULL #"https://drive.google.com/drive/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
+#dir_googledrive_upload_ai = "https://drive.google.com/drive/u/2/folders/17rHN6GTkw5ywMXJ6VfyOkKXr7FY7o7B3" #NULL #"https://drive.google.com/drive/folders/1SeNOAh5-muQ2BDgOHWZWwYIoLl68DHWX"
+#dir_googledrive_upload_test = "https://drive.google.com/drive/folders/1rsR0aFfFzrspTBFU48Bb26EJvdhIZSpl"
+
+# The surveys this script will be covering 
+dat_survreg <- data.frame(reg_shapefile = "EBS_SHELF", 
+                          region_long = "Eastern Bering Sea", 
+                          SRVY = "EBS", 
+                          region = "BS", 
+                          vessel_id = c(94, 162), # CHANGE
+                          vessel_shape = c("V", "A"), # CHANGE
+                          reg_dates = "May 25 - Aug 03 2022") # CHANGE
+dat_survreg <- dplyr::bind_rows(dat_survreg, 
+                                data.frame(reg_shapefile = "NBS_SHELF", 
+                                           region_long = "Northern Bering Sea", 
+                                           SRVY = "NBS", 
+                                           region = "BS", 
+                                           vessel_id = c(94, 162), # CHANGE
+                                           vessel_shape = c("V", "A"), # CHANGE
+                                           reg_dates = "Aug 03 - Aug 28 2022")) # CHANGE
+dat_survreg <- dplyr::bind_rows(dat_survreg, 
+                                data.frame(reg_shapefile = "AI",
+                                           region_long = "Aleutian Islands",
+                                           SRVY = "AI",
+                                           region = "AI",
+                                           vessel_id = c(148, 176), # CHANGE
+                                           vessel_shape = c("OEX", "AP"), # CHANGE
+                                           reg_dates = "Jun 07 - Aug 17 2022")) # CHANGE
+# dat_survreg <- dplyr::bind_rows(dat_survreg, 
+#                                data.frame(reg_shapefile = "GOA", 
+#                                           region_long = "Gulf of Alaska", 
+#                                           SRVY = "GOA", 
+#                                           region = "GOA", 
+#                                           vessel_id = c(148, 176), # CHANGE
+#                                           vessel_shape = c("OEX", "SS"), # CHANGE
+#                                           reg_dates = "May 25 - Aug 04")) # CHANGE
+
+# SIGN INTO GOOGLE DRIVE--------------------------------------------------------
+## This sign in needs to be here for the Task Scheduler to run, please do not comment out.
+googledrive::drive_deauth()
+googledrive::drive_auth()
+1
+
+# SOURCE SUPPORT SCRIPTS -------------------------------------------------------
+## Actually we cant use the here package, here - it actually causes issues with 
+## the tasks scheduler, which has no concept of a project root folder. 
+#dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
+#dir_wd <- "G:/EBSother/GAPsurveyTemperatureMap/"
+#dir_wd <- paste0(getwd(), "/")
+dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
+#dir_wd <- "C:/Users/caitlin.akselrud/Work/survey-live-temperature-map/"
+
+source(file = paste0(dir_wd,"code/functions.R"))
+# source(file = paste0(dir_wd, "code/data_dl.R")) # you don't unnecessarily run this each time
+source(file = paste0(dir_wd, "code/data.R"))
+if (googledrive_dl == TRUE) {
+  source(file = paste0(dir_wd, "code/ftp.R")) # removed in gitignore - ask for premission
+}
+
+SRVY <- "BS"
+region_akgfmaps = "bs.all"
+plot_subtitle <- "NOAA Fisheries Bering Sea Bottom Trawl Survey"
+dir_googledrive_upload <- (dir_googledrive_upload_bs)
+survey_area <- akgfmaps::get_base_layers(select.region = region_akgfmaps, set.crs = "auto")
+show_planned_stations <- TRUE
+plot_anom <- FALSE
+survey_area$survey.grid <- survey_area$survey.grid %>% 
+  sf::st_transform(x = ., survey_area$crs$input) %>%
+  dplyr::rename(station = STATIONID) %>%
+  sp::merge(x = ., 
+            y = haul %>%
+              dplyr::rename(station = stationid) %>% 
+              dplyr::select(station, stratum) %>% 
+              dplyr::distinct(), 
+            all.x = TRUE) %>% 
+  dplyr::mutate(region = "Bering Sea")
+survey_area$place.labels$y[survey_area$place.labels$lab == "200 m"] <- -60032.7
+
+if(shapef == TRUE)
+{
+  make_grid_wrapper(maxyr = maxyr,                             # Blank grid plot
+                    SRVY = SRVY,
+                    haul = haul,
+                    dat_survreg = dat_survreg,
+                    dir_googledrive_upload = dir_googledrive_upload,
+                    survey_area = survey_area,
+                    data_source = data_source,
+                    plot_subtitle = plot_subtitle,
+                    dir_wd = dir_wd)
+}
+
+make_varplot_wrapper(maxyr = maxyr,                               # Daily plot
+                     SRVY = SRVY,
+                     haul = haul,
+                     dat_survreg = dat_survreg,
+                     var = var,
+                     dir_googledrive_upload = dir_googledrive_upload,
+                     dates0 = dates0,
+                     survey_area = survey_area,
+                     plot_subtitle = plot_subtitle,
+                     show_planned_stations = show_planned_stations,
+                     data_source = data_source,
+                     plot_anom = plot_anom,
+                     dir_wd = dir_wd)
+
+dir_out <- paste0(dir_wd,"/output/",maxyr,"_",SRVY,"/")
+temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
+dest <- dev_bs
+
+for (iiii in 1:length(temp)) {
+  print(temp[iiii])
+
+  RCurl::ftpUpload(
+    what = paste0(dir_out, "/", temp[iiii]),
+    asText = FALSE,
+    to = paste0(glue::glue("{protocol}://STOR@{server}/{dest}/", temp[iiii])),
+    userpwd = paste0(user,":", pass),
+    .opts=curlOptions(verbose=TRUE))
+}