Last updated: 2023-10-06
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Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2bd702c | ds2n19 | 2023-10-06 | Changed core Argo location folders and run for 2022 |
| html | c3381d0 | ds2n19 | 2023-10-06 | Build site. |
| Rmd | bc8d46d | ds2n19 | 2023-10-06 | Changed core Argo location folders and run for 2022 |
| html | 8d5c853 | pasqualina-vonlanthendinenna | 2022-08-30 | Build site. |
| Rmd | 9bde106 | pasqualina-vonlanthendinenna | 2022-08-30 | added 6 months of core data (still have to fix the dates |
| html | 7b3d8c5 | pasqualina-vonlanthendinenna | 2022-08-29 | Build site. |
| Rmd | 8e81570 | pasqualina-vonlanthendinenna | 2022-08-29 | load and add in core-argo data (1 month) |
Load core-Argo temperature data for comparison with BGC-Argo temperature data
Directory where the core-Argo profile files are stored
# set cache directory
argo_set_cache_dir(cache_dir = path_argo_core)
# check cache directory
argo_cache_dir()[1] "/nfs/kryo/work/datasets/ungridded/3d/ocean/floats/core_argo_r_argodata"# check argo mirror
argo_mirror()[1] "https://data-argo.ifremer.fr"argo_update_global(max_global_cache_age = Inf) # age argument: age of the cached files to update in hours (Inf means always use the cached file, and -Inf means always download from the server)
# ex: max_global_cache_age = 5 updates files that have been in the cache for more than 5 hours, max_global_cache_age = 0.5 updates files that have been in the cache for more than 30 minutes, etc.
argo_update_data(max_data_cache_age = Inf)Load in delayed-mode core-Argo (CTD) data index file
#------------------------------------------------------------------------------
# Imnportant - file are loaded for the given year and saved in the preprocessed folder with a year prefix.
#------------------------------------------------------------------------------
load_year = "2014"
# core_index <- argo_global_prof() %>%
# argo_filter_data_mode(data_mode = 'delayed') %>% # load in delayed-mode data
# argo_filter_date(date_min = '2013-01-01',
# date_max = Sys.time())
core_index <- argo_global_prof() %>%
argo_filter_data_mode(data_mode = 'delayed') %>%
argo_filter_date(date_min = paste0(load_year, "-01-01"),
date_max = paste0(load_year, "-12-31"))
# 1 month worth of data for test purposes
# check dates
# max(core_index$date, na.rm = TRUE)
# min(core_index$date, na.rm = TRUE)Read in the core CTD variables corresponding to the index defined above
core_data <- argo_prof_levels(
path = core_index,
vars =
c(
'PRES_ADJUSTED',
'PRES_ADJUSTED_QC',
'PSAL_ADJUSTED',
'PSAL_ADJUSTED_QC',
'TEMP_ADJUSTED',
'TEMP_ADJUSTED_QC'),
quiet = TRUE
)
# read in the profiles (takes a while)Read in the corresponding metadata:
core_metadata <- argo_prof_prof(path = core_index)core_merge <- full_join(core_data, core_metadata)
core_merge <- core_merge %>%
rename(lon = longitude,
lat = latitude) %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 1), seq(-89.5, 89.5, 1)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 1), seq(20.5, 379.5, 1)),
lon = as.numeric(as.character(lon))
) %>%
mutate(depth = swDepth(pres_adjusted, latitude = lat),
.before = pres_adjusted)core_metadata <- core_metadata %>%
rename(lon = longitude,
lat = latitude) %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 1), seq(-89.5, 89.5, 1)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 1), seq(20.5, 379.5, 1)),
lon = as.numeric(as.character(lon))
)core_data %>%
write_rds(file = paste0(path_argo_core_preprocessed, "/", load_year, "_core_data.rds"))
core_metadata %>%
write_rds(file = paste0(path_argo_core_preprocessed, "/", load_year, "_core_metadata.rds"))
core_merge %>%
write_rds(file = paste0(path_argo_core_preprocessed, "/", load_year, "_core_merge.rds"))core_merge_flag_A <- core_merge %>%
filter(profile_temp_qc == 'A') %>%
select(lat, lon, date,
depth, temp_adjusted, temp_adjusted_qc,
platform_number, cycle_number,
profile_temp_qc)
core_merge_flag_A %>%
write_rds(file = paste0(path_argo_core_preprocessed, "/", load_year, "_core_merge_flag_A.rds"))core_merge_flag_AB <- core_merge %>%
filter(profile_temp_qc == 'A' | profile_temp_qc == 'B') %>%
filter(temp_adjusted_qc == '1' | temp_adjusted_qc == '8') %>%
select(lat, lon, date,
depth, temp_adjusted, temp_adjusted_qc,
platform_number, cycle_number,
profile_temp_qc)
core_merge_flag_AB %>%
write_rds(file = paste0(path_argo_core_preprocessed, "/", load_year, "_core_merge_flag_AB.rds"))
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.4
Matrix products: default
BLAS: /usr/local/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.2.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] oce_1.7-10 gsw_1.1-1 sf_1.0-9 lubridate_1.9.0
[5] timechange_0.1.1 argodata_0.1.0 forcats_0.5.2 stringr_1.4.1
[9] dplyr_1.0.10 purrr_0.3.5 readr_2.1.3 tidyr_1.2.1
[13] tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] httr_1.4.4 sass_0.4.4 bit64_4.0.5
[4] vroom_1.6.0 jsonlite_1.8.3 modelr_0.1.10
[7] bslib_0.4.1 assertthat_0.2.1 googlesheets4_1.0.1
[10] cellranger_1.1.0 progress_1.2.2 yaml_2.3.6
[13] pillar_1.8.1 backports_1.4.1 glue_1.6.2
[16] digest_0.6.30 promises_1.2.0.1 rvest_1.0.3
[19] colorspace_2.0-3 htmltools_0.5.3 httpuv_1.6.6
[22] pkgconfig_2.0.3 broom_1.0.1 haven_2.5.1
[25] scales_1.2.1 whisker_0.4 later_1.3.0
[28] tzdb_0.3.0 git2r_0.30.1 proxy_0.4-27
[31] googledrive_2.0.0 generics_0.1.3 ellipsis_0.3.2
[34] cachem_1.0.6 withr_2.5.0 cli_3.4.1
[37] magrittr_2.0.3 crayon_1.5.2 readxl_1.4.1
[40] evaluate_0.18 fs_1.5.2 fansi_1.0.3
[43] xml2_1.3.3 class_7.3-20 prettyunits_1.1.1
[46] tools_4.2.2 hms_1.1.2 gargle_1.2.1
[49] lifecycle_1.0.3 munsell_0.5.0 reprex_2.0.2
[52] compiler_4.2.2 jquerylib_0.1.4 e1071_1.7-12
[55] RNetCDF_2.6-1 rlang_1.1.1 classInt_0.4-8
[58] units_0.8-0 grid_4.2.2 rstudioapi_0.14
[61] rmarkdown_2.18 gtable_0.3.1 DBI_1.1.3
[64] R6_2.5.1 knitr_1.41 bit_4.0.5
[67] fastmap_1.1.0 utf8_1.2.2 workflowr_1.7.0
[70] rprojroot_2.0.3 KernSmooth_2.23-20 stringi_1.7.8
[73] parallel_4.2.2 Rcpp_1.0.10 vctrs_0.5.1
[76] dbplyr_2.2.1 tidyselect_1.2.0 xfun_0.35