Anthropogenic CO2 from 1994 to 2007
Jens Daniel Müller
12 May, 2021
Last updated: 2021-05-12
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Knit directory: emlr_obs_preprocessing/
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path_sabine_2004 <- "/nfs/kryo/work/updata/glodapv1_1/GLODAP_gridded.data/"
path_preprocessing <- paste(path_root, "/observations/preprocessing/", sep = "")1 Data source
- Anthropogenic CO2 estimates (1800-1994) by Sabine et al. (2004) downloaded in August 2020 from NOAA/NCEI Ocean Carbon Data System (OCADS)
2 Read nc files
# read text files
AnthCO2_data <-
read_csv(
paste(path_sabine_2004,
"AnthCO2.data/AnthCO2.data.txt",
sep = ""),
col_names = FALSE,
na = "-999",
col_types = list(.default = "d")
)
# read respective depth layers and convert to vector
Depth_centers <-
read_file(paste(path_sabine_2004,
"Depth.centers.txt",
sep = ""))
Depth_centers <- Depth_centers %>%
str_split(",") %>%
as_vector()
# read respective latitudes and convert to vector
Lat_centers <-
read_file(paste(path_sabine_2004, "Lat.centers.txt",
sep = ""))
Lat_centers <- Lat_centers %>%
str_split(",") %>%
as_vector()
# read respective longitudes and convert to vector
Long_centers <-
read_file(paste(path_sabine_2004, "Long.centers.txt",
sep = ""))
Long_centers <- Long_centers %>%
str_split(",") %>%
as_vector()
# match lon, lat and depth vectors with Cant value file
names(AnthCO2_data) <- Lat_centers
Long_Depth <-
expand_grid(depth = Depth_centers, lon = Long_centers) %>%
mutate(lon = as.numeric(lon),
depth = as.numeric(depth))
cant_3d <- bind_cols(AnthCO2_data, Long_Depth)
# adjust file dimensions
cant_3d <- cant_3d %>%
pivot_longer(1:180, names_to = "lat", values_to = "cant") %>%
mutate(lat = as.numeric(lat))
cant_3d <- cant_3d %>%
drop_na()
# harmonize coordinates
cant_3d <- cant_3d %>%
mutate(lon = if_else(lon < 20, lon + 360, lon))
rm(AnthCO2_data,
Long_Depth,
Depth_centers,
Lat_centers,
Long_centers)3 Apply basin mask
# use only three basin to assign general basin mask
# ie this is not specific to the MLR fitting
basinmask <- basinmask %>%
filter(MLR_basins == "2") %>%
select(lat, lon, basin_AIP)
cant_3d <- inner_join(cant_3d, basinmask)4 Calculation
4.1 Column inventory
cant_3d <- cant_3d %>%
mutate(cant_pos = if_else(cant <= 0, 0, cant),
eras = "1800-1994")
cant_inv_layers <- m_cant_inv(cant_3d)
cant_inv <- cant_inv_layers %>%
filter(inv_depth == params_global$inventory_depth_standard)4.2 Zonal mean section
cant_zonal <- m_zonal_mean_section(cant_3d)5 Plots
5.1 Inventory map
p_map_cant_inv(
df = cant_inv,
var = "cant_pos_inv",
breaks = seq(0,max(cant_inv$cant_pos_inv),5))
5.2 Horizontal plane maps
p_map_climatology(
df = cant_3d,
var = "cant",
col = "divergent")
5.3 Global section
p_section_global(
df = cant_3d,
var = "cant",
col = "divergent")
5.4 Sections at regular longitudes
p_section_climatology_regular(
df = cant_3d,
var = "cant",
col = "divergent")
5.5 Write files
cant_3d %>%
write_csv(paste(path_preprocessing,
"S04_cant_3d.csv", sep = ""))
cant_inv %>%
write_csv(paste(path_preprocessing,
"S04_cant_inv.csv", sep = ""))
cant_zonal %>%
write_csv(paste(path_preprocessing,
"S04_cant_zonal.csv", sep = ""))
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
Matrix products: default
BLAS: /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/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] metR_0.9.0 scico_1.2.0 patchwork_1.1.1 collapse_1.5.0
[5] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4
[9] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.3
[13] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lattice_0.20-41 lubridate_1.7.9
[4] assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.27
[7] R6_2.5.0 cellranger_1.1.0 backports_1.1.10
[10] reprex_0.3.0 evaluate_0.14 httr_1.4.2
[13] pillar_1.4.7 rlang_0.4.10 readxl_1.3.1
[16] data.table_1.13.2 rstudioapi_0.13 whisker_0.4
[19] blob_1.2.1 Matrix_1.2-18 checkmate_2.0.0
[22] rmarkdown_2.5 labeling_0.4.2 RcppEigen_0.3.3.7.0
[25] munsell_0.5.0 broom_0.7.5 compiler_4.0.3
[28] httpuv_1.5.4 modelr_0.1.8 xfun_0.18
[31] pkgconfig_2.0.3 htmltools_0.5.0 tidyselect_1.1.0
[34] fansi_0.4.1 crayon_1.3.4 dbplyr_1.4.4
[37] withr_2.3.0 later_1.1.0.1 grid_4.0.3
[40] jsonlite_1.7.1 gtable_0.3.0 lifecycle_1.0.0
[43] DBI_1.1.0 git2r_0.27.1 magrittr_1.5
[46] scales_1.1.1 cli_2.1.0 stringi_1.5.3
[49] farver_2.0.3 fs_1.5.0 promises_1.1.1
[52] RcppArmadillo_0.10.1.2.0 xml2_1.3.2 ellipsis_0.3.1
[55] generics_0.0.2 vctrs_0.3.5 tools_4.0.3
[58] glue_1.4.2 hms_0.5.3 parallel_4.0.3
[61] yaml_2.2.1 colorspace_1.4-1 isoband_0.2.2
[64] rvest_0.3.6 knitr_1.30 haven_2.3.1