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caitlin's working main code for run.R
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Caitlin Akselrud authored and Caitlin Akselrud committed Jun 13, 2022
1 parent 708ae3b commit 18f73d1
Showing 1 changed file with 3 additions and 99 deletions.
102 changes: 3 additions & 99 deletions code/run.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ 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/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
dir_googledrive_upload_ai = "https://drive.google.com/drive/folders/1SeNOAh5-muQ2BDgOHWZWwYIoLl68DHWX"
dir_googledrive_upload_test = "https://drive.google.com/drive/folders/1rsR0aFfFzrspTBFU48Bb26EJvdhIZSpl"
# 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",
Expand Down Expand Up @@ -61,7 +61,7 @@ dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
dir_wd <-"C:/Users/caitlin.akselrud/Work/survey-live-temperature-map/"
#dir_wd <- "G:/EBSother/GAPsurveyTemperatureMap/"
# dir_wd <-"C:/Users/emily.markowitz/Work/Projects/GAPSurveyTemperatureMap/"
dir_wd <- paste0(getwd(), "/")
# dir_wd <- paste0(getwd(), "/")

sink(file=paste0(dir_wd , "/output/", Sys.Date(), "_log.txt"))

Expand Down Expand Up @@ -135,89 +135,6 @@ make_varplot_wrapper(maxyr = maxyr, # Daily plot
# plot_anom = FALSE, # anom plot here doesnt make sense to print until the end
# plot_mean = TRUE,
# dir_wd = dir_wd)
<<<<<<< HEAD
#
## AI --------------------------------------------------------------------------
# maxyr <- 2022 #CHANGE
# data_source <- "gd" # google drive
# SRVY <- "AI"
# plot_anom <- FALSE
# plot_subtitle = "NOAA Fisheries Aleutian Islands Bottom Trawl Survey"
# region_akgfmaps = "ai"
# dir_googledrive_upload <- googledrive::as_id(dir_googledrive_upload_ai)
# #dir_googledrive_upload <- googledrive::as_id(dir_googledrive_upload_test)
# var = "bt"
# dates0 <- "latest" # latest # "all", #"2021-06-05",# Sys.Date(), # as.character(seq(as.Date("2022-07-30"), as.Date("2022-08-14"), by="days"))
# 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) %>% # , duplicateGeoms = TRUE
# dplyr::arrange(region)
# survey_area$survey.grid1 <- survey_area$survey.grid
#
# # 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)
# #
# # ### past years -----------------------------------------------------------------
# data_source = "oracle"
# plot_anom = FALSE
# dates0 <- "all" # latest # "all", #"2021-06-05",# Sys.Date(), # as.character(seq(as.Date("2022-07-30"), as.Date("2022-08-14"), by="days"))
#
# dat_survreg <- dplyr::bind_rows(dat_survreg,
# data.frame(reg_shapefile = "AI",
# region_long = "Aleutian Islands",
# SRVY = "AI",
# region = "AI",
# vessel_id = c(148, 143), # CHANGE
# vessel_shape = c("OEX", "SS"), # CHANGE
# reg_dates = "\n(June 07-Aug 17 2022)")) # CHANGE
#
# maxyr <- 2018
# dir_googledrive_upload <- googledrive::as_id("https://drive.google.com/drive/folders/1dzWwb3bXnPXlSy_JIaY4BKo6WDshru_d")
# make_grid_wrapper(maxyr = maxyr, # Blank grid plot
=======


# ## AI --------------------------------------------------------------------------
maxyr <- 2022 #CHANGE
data_source <- "gd" # google drive
Expand Down Expand Up @@ -257,7 +174,6 @@ survey_area$survey.grid <- rgdal::readOGR(dsn = paste0(dir_wd, '/shapefiles/'),#
survey_area$survey.grid1 <- survey_area$survey.grid

# make_grid_wrapper(maxyr = maxyr, # Blank grid plot
>>>>>>> 936837bd8408c7e81501abb1a4013b0060d168dd
# SRVY = SRVY,
# haul = haul,
# dat_survreg = dat_survreg,
Expand All @@ -266,9 +182,7 @@ survey_area$survey.grid1 <- survey_area$survey.grid
# data_source = data_source,
# plot_subtitle = plot_subtitle,
# dir_wd = dir_wd)
<<<<<<< HEAD
# make_varplot_wrapper(maxyr = maxyr, # Daily plot
=======

make_varplot_wrapper(maxyr = maxyr, # Daily plot
SRVY = SRVY,
haul = haul,
Expand All @@ -283,30 +197,20 @@ make_varplot_wrapper(maxyr = maxyr, # Daily plot
plot_anom = plot_anom,
dir_wd = dir_wd)
# make_varplot_wrapper(maxyr = maxyr, # Anom and mean plot
>>>>>>> 936837bd8408c7e81501abb1a4013b0060d168dd
# SRVY = SRVY,
# haul = haul,
# dat_survreg = dat_survreg,
# var = var,
# dir_googledrive_upload = dir_googledrive_upload,
<<<<<<< HEAD
# dates0 = dates0,
=======
# dates0 = "latest",
>>>>>>> 936837bd8408c7e81501abb1a4013b0060d168dd
# survey_area = survey_area,
# plot_subtitle = plot_subtitle,
# show_planned_stations = show_planned_stations,
# data_source = data_source,
<<<<<<< HEAD
# plot_anom = plot_anom,
# dir_wd = dir_wd)
=======
# plot_daily = FALSE,
# plot_anom = TRUE,
# plot_mean = TRUE,
# dir_wd = dir_wd)
#

sink()
>>>>>>> 936837bd8408c7e81501abb1a4013b0060d168dd

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