GLODAPv2_2020 subsetting
Jens Daniel Müller
23 December, 2020
Last updated: 2020-12-23
Checks: 7 0
Knit directory: emlr_mod_v_XXX/
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1 Read files
Main data source for this project is the synthetic cmorized model subset based on preprocessed version of the GLODAPv2.2020_Merged_Master_File.csv downloaded from glodap.info in June 2020.
CAVEAT: This file still contains neutral densities gamma calculated with a preliminary method. However, this is consistent with the way gamma is currently calculated in this script and should therefore be maintained until changed on all levels.
GLODAP <-
read_csv(paste(path_preprocessing,
"GLODAPv2.2020_preprocessed_model_runA_final.csv",
sep = ""))2 Data preparation
2.1 Reference eras
Samples were assigned to following eras:
# create labels for era
labels <- bind_cols(
start = params_local$era_breaks+1,
end = lead(params_local$era_breaks))
labels <- labels %>%
filter(!is.na(end)) %>%
mutate(end = if_else(end == Inf, max(GLODAP$year), end),
label = paste(start, end, sep = "-")) %>%
select(label) %>%
pull()
# cut observation years into era applying the labels
GLODAP <- GLODAP %>%
filter(year > params_local$era_breaks[1]) %>%
mutate(era = cut(year,
params_local$era_breaks,
labels = labels))
levels(GLODAP$era)[1] "1982-1999" "2000-2012" "2013-2019"rm(labels)2.2 Spatial boundaries
2.2.1 Basin mask
The basin mask from the World Ocean Atlas was used. For details consult the data base subsection for WOA18 data.
Please note that some GLODAP-based subsetting model data were outside the WOA18 basin mask (i.e. in marginal seas) and will be removed for further analysis.
# use only data inside basinmask
GLODAP <- inner_join(GLODAP, basinmask)2.2.2 Depth
GLODAP-based subsetting model data with depth shallower than:
- minimum sampling depth: 150m
were excluded from the analysis to avoid seasonal bias.
GLODAP <- GLODAP %>%
filter(depth >= params_local$depth_min)2.2.3 Bottomdepth
GLODAP-based subsetting model data in an area with a:
- minimum bottom depth: 0m
were excluded from the analysis to avoid coastal impacts. Please note that minimum bottom depth criterion of 0m means that no filtering was applied here.
GLODAP <- GLODAP %>%
filter(bottomdepth >= params_local$bottomdepth_min)2.2.4 Neutral density threshold
GLODAP-based subsetting model data in an area with:
- neutral density below: 0m
were excluded from the analysis due to expected high seasonality, except when:
- minimum sampling depth: 150m
was fulfilled
GLODAP <- GLODAP %>%
filter(gamma > params_local$gamma_min | depth >= params_local$depth_min)2.3 Flags and missing data
Only rows (samples) for which all relevant parameters are available were selected, ie NA’s were removed.
According to Olsen et al (2020), flags within the merged master file identify:
f:
- 2: Acceptable
- 0: Interpolated (nutrients/oxygen) or calculated (CO[2] variables)
- 9: Data not used (so, only NA data should have this flag)
qc:
- 1: Adjusted or unadjusted data
- 0: Data appear of good quality but have not been subjected to full secondary QC
- data with poor or uncertain quality are excluded.
Following flagging criteria were taken into account:
- flag_f: 2, 0
- flag_qc: 1
The cleaning process was performed successively and the maps below represent the data coverage at various cleaning levels.
Summary statistics were calculated during cleaning process.
2.3.1 tco2
2.3.1.1 NA
Rows with missing tco2 in GLODAP-based subsetting model data were already removed in the preprocessing. The map below shows the coverage of preprocessed GLODAP-based subsetting model data.
GLODAP_stats <- GLODAP %>%
summarise(tco2_values = n())
GLODAP_obs_grid <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "tco2_values")GLODAP_obs <- GLODAP %>%
group_by(lat, lon) %>%
summarise(n = n()) %>%
ungroup()
map +
geom_raster(data = basinmask, aes(lon, lat, fill = basin)) +
geom_raster(data = GLODAP_obs, aes(lon, lat)) +
scale_fill_brewer(palette = "Dark2") +
theme(legend.position = "top",
legend.title = element_blank())
rm(GLODAP_obs)2.3.1.2 f flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, tco2f)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ tco2f) +
theme(legend.position = "top")
rm(GLODAP_obs_grid_temp)
GLODAP <- GLODAP %>%
filter(tco2f %in% params_local$flag_f)2.3.1.3 qc flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, tco2qc)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ tco2qc) +
theme(legend.position = "top")
##
GLODAP <- GLODAP %>%
filter(tco2qc %in% params_local$flag_qc)
GLODAP_stats_temp <- GLODAP %>%
summarise(tco2_flag = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "tco2_flag")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)2.3.2 talk
2.3.2.1 NA
GLODAP <- GLODAP %>%
mutate(talkna = if_else(is.na(talk), "NA", "Value"))
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, talkna)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ talkna) +
theme(legend.position = "top")
GLODAP <- GLODAP %>%
select(-talkna) %>%
filter(!is.na(talk))
##
GLODAP_stats_temp <- GLODAP %>%
summarise(talk_values = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "talk_values")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)2.3.2.2 f flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, talkf)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ talkf) +
theme(legend.position = "top",
legend.title = element_blank())
# ###
GLODAP <- GLODAP %>%
filter(talkf %in% params_local$flag_f)2.3.2.3 qc flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, talkqc)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ talkqc) +
theme(legend.position = "top",
legend.title = element_blank())
###
GLODAP <- GLODAP %>%
filter(talkqc %in% params_local$flag_qc)
##
GLODAP_stats_temp <- GLODAP %>%
summarise(talk_flag = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "talk_flag")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)2.3.3 Phosphate
2.3.3.1 NA
GLODAP <- GLODAP %>%
mutate(phosphatena = if_else(is.na(phosphate), "NA", "Value"))
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, phosphatena)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era ~ phosphatena) +
theme(legend.position = "top")
GLODAP <- GLODAP %>%
select(-phosphatena) %>%
filter(!is.na(phosphate))
##
GLODAP_stats_temp <- GLODAP %>%
summarise(phosphate_values = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "phosphate_values")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)2.3.3.2 f flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, phosphatef)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era~phosphatef) +
theme(legend.position = "top",
legend.title = element_blank())
###
GLODAP <- GLODAP %>%
filter(phosphatef %in% params_local$flag_f)2.3.3.3 qc flag
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era, phosphateqc)
map +
geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_grid(era~phosphateqc) +
theme(legend.position = "top",
legend.title = element_blank())
###
GLODAP <- GLODAP %>%
filter(phosphateqc %in% params_local$flag_qc)
##
GLODAP_stats_temp <- GLODAP %>%
summarise(phosphate_flag = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "phosphate_flag")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)2.3.4 eMLR variables
Variables required as predictors for the MLR fits, are subsetted for NAs and flags.
if ("temp" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(temp))
}
##
if ("sal" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(sal))
GLODAP <- GLODAP %>%
filter(salinityf %in% params_local$flag_f)
GLODAP <- GLODAP %>%
filter(salinityqc %in% params_local$flag_qc)
}
##
if ("silicate" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(silicate))
GLODAP <- GLODAP %>%
filter(silicatef %in% params_local$flag_f)
GLODAP <- GLODAP %>%
filter(silicateqc %in% params_local$flag_qc)
}
##
if ("oxygen" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(oxygen))
GLODAP <- GLODAP %>%
filter(oxygenf %in% params_local$flag_f)
GLODAP <- GLODAP %>%
filter(oxygenqc %in% params_local$flag_qc)
}
##
if ("aou" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(aou))
GLODAP <- GLODAP %>%
filter(aouf %in% params_local$flag_f)
}
##
if ("nitrate" %in% params_local$MLR_predictors) {
GLODAP <- GLODAP %>%
filter(!is.na(nitrate))
GLODAP <- GLODAP %>%
filter(nitratef %in% params_local$flag_f)
GLODAP <- GLODAP %>%
filter(nitrateqc %in% params_local$flag_qc)
}
##
GLODAP <- GLODAP %>%
filter(!is.na(depth))
GLODAP <- GLODAP %>%
filter(!is.na(gamma))
##
GLODAP_stats_temp <- GLODAP %>%
summarise(eMLR_variables = n())
GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)
##
GLODAP_obs_grid_temp <- GLODAP %>%
count(lat, lon, era) %>%
mutate(cleaning_level = "eMLR_variables")
GLODAP_obs_grid <-
bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)
rm(GLODAP_obs_grid_temp)GLODAP <- GLODAP %>%
select(-ends_with(c("f", "qc")))2.4 Manual adjustment A16 cruise
For harmonization with Gruber et al. (2019), cruises 1041 (A16N) and 1042 (A16S) were grouped into the 2000-2012 era despite taking place in 2013/14.
GLODAP_cruises <- GLODAP %>%
filter(basin_AIP == "Atlantic",
year %in% c(2013, 2014)) %>%
count(lat, lon, cruise)
map +
geom_raster(data = GLODAP_cruises, aes(lon, lat, fill = as.factor(cruise))) +
scale_fill_brewer(palette = "Dark2") +
theme(legend.position = "top",
legend.title = element_blank())
| Version | Author | Date |
|---|---|---|
| c8b76b3 | jens-daniel-mueller | 2020-12-19 |
rm(GLODAP_cruises)GLODAP <- GLODAP %>%
mutate(era = if_else(cruise %in% c(1041, 1042),
sort(unique(GLODAP$era))[2], era))2.5 Create clean observations grid
Grid containing all grid cells where at least one observation remains available after cleaning.
GLODAP_obs_grid_clean <- GLODAP %>%
count(lat, lon) %>%
select(-n)2.6 Write summary file
GLODAP_obs_grid_clean %>% write_csv(paste(path_version_data,
"GLODAPv2.2020_clean_model_runA_obs_grid.csv",
sep = ""))
# select relevant columns for further analysis
GLODAP <- GLODAP %>%
select(year, date, era, basin, basin_AIP, lat, lon, cruise,
bottomdepth, depth,
temp, sal, gamma,
tco2, talk, phosphate,
oxygen, aou, nitrate, silicate)
GLODAP %>% write_csv(paste(path_version_data,
"GLODAPv2.2020_clean_model_runA.csv",
sep = ""))3 Overview plots
3.1 Cleaning stats
Number of GLODAP-based subsetting model data at various steps of data cleaning.
GLODAP_stats_long <- GLODAP_stats %>%
pivot_longer(1:length(GLODAP_stats),
names_to = "parameter",
values_to = "n")
GLODAP_stats_long <- GLODAP_stats_long %>%
mutate(parameter = fct_reorder(parameter, n))
GLODAP_stats_long %>%
ggplot(aes(parameter, n/1000)) +
geom_col() +
coord_flip() +
theme(axis.title.y = element_blank())
rm(GLODAP_stats_long)3.2 Assign coarse spatial grid
For the following plots, the cleaned data set was re-opened and GLODAP-based subsetting data were gridded spatially to intervals of:
- 5° x 5°
GLODAP <- m_grid_horizontal_coarse(GLODAP)3.3 Histogram Zonal coverage
GLODAP_histogram_lat <- GLODAP %>%
group_by(era, lat_grid, basin) %>%
tally() %>%
ungroup()
GLODAP_histogram_lat %>%
ggplot(aes(lat_grid, n, fill = era)) +
geom_col() +
scale_fill_brewer(palette = "Dark2") +
facet_wrap( ~ basin) +
coord_flip() +
theme(legend.position = "top",
legend.title = element_blank())
rm(GLODAP_histogram_lat)3.4 Median years (tref)
Median years of each era (tref) were determined as:
era_median_year <- GLODAP %>%
group_by(era) %>%
summarise(t_ref = median(year)) %>%
ungroup()
era_median_year# A tibble: 3 x 2
era t_ref
<fct> <dbl>
1 1982-1999 1994
2 2000-2012 2007
3 2013-2019 20153.5 Histogram temporal coverage
GLODAP_histogram_year <- GLODAP %>%
group_by(year, basin) %>%
tally() %>%
ungroup()
GLODAP_histogram_year %>%
ggplot() +
geom_vline(xintercept = c(
params_local$era_breaks + 0.5
)) +
geom_col(aes(year, n, fill = basin)) +
geom_point(
data = era_median_year,
aes(t_ref, 0, shape = "Median year"),
size = 2,
fill = "white"
) +
scale_fill_brewer(palette = "Dark2") +
scale_shape_manual(values = 24, name = "") +
scale_y_continuous() +
coord_cartesian() +
theme(
legend.position = "top",
legend.direction = "vertical",
legend.title = element_blank(),
axis.title.x = element_blank()
)
rm(GLODAP_histogram_year,
era_median_year)3.6 Zonal temporal coverage (Hovmoeller)
GLODAP_hovmoeller_year <- GLODAP %>%
group_by(year, lat_grid, basin) %>%
tally() %>%
ungroup()
GLODAP_hovmoeller_year %>%
ggplot(aes(year, lat_grid, fill = n)) +
geom_tile() +
geom_vline(xintercept = c(1999.5, 2012.5)) +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10") +
facet_wrap( ~ basin, ncol = 1) +
theme(legend.position = "top",
axis.title.x = element_blank())
rm(GLODAP_hovmoeller_year)3.7 Coverage maps by era
3.7.1 Subsetting process
The following plots show the remaining data after individual cleaning steps, separately for each era.
GLODAP_obs_grid <- GLODAP_obs_grid %>%
mutate(cleaning_level = factor(
cleaning_level,
unique(GLODAP_obs_grid$cleaning_level)
))
map +
geom_raster(data = GLODAP_obs_grid %>%
filter(cleaning_level == "tco2_values") %>%
select(-cleaning_level),
aes(lon, lat, fill = "tco2_values")) +
geom_raster(data = GLODAP_obs_grid %>%
filter(cleaning_level != "tco2_values"),
aes(lon, lat, fill = "subset")) +
scale_fill_brewer(palette = "Set1", name = "") +
facet_grid(cleaning_level ~ era) +
theme(legend.position = "top",
axis.title = element_blank())
3.7.2 Final input data
The following plots show the remaining data density in each grid cell after all cleaning steps, separately for each era.
GLODAP_tco2_grid <- GLODAP %>%
count(lat, lon)
map +
# geom_raster(data = GLODAP_tco2_grid, aes(lon, lat), fill = "grey80") +
geom_bin2d(data = GLODAP,
aes(lon, lat),
binwidth = c(1,1)) +
scale_fill_viridis_c(option = "magma", direction = -1, trans = "log10") +
facet_wrap(~era, ncol = 1) +
labs(title = "Cleaned GLODAP observations",
subtitle = paste("Version:", params_local$Version_ID)) +
theme(axis.title = element_blank())
ggsave(path = path_version_figures,
filename = "data_distribution_era.png",
height = 8,
width = 5)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.1
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] lubridate_1.7.9 metR_0.8.0 scico_1.2.0 patchwork_1.1.0
[5] collapse_1.4.2 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2
[9] purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.0.4
[13] ggplot2_3.3.2 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 viridisLite_0.3.0
[4] here_0.1 modelr_0.1.8 assertthat_0.2.1
[7] blob_1.2.1 cellranger_1.1.0 yaml_2.2.1
[10] pillar_1.4.7 backports_1.2.1 lattice_0.20-41
[13] glue_1.4.2 RcppEigen_0.3.3.9.1 digest_0.6.27
[16] RColorBrewer_1.1-2 promises_1.1.1 checkmate_2.0.0
[19] rvest_0.3.6 colorspace_2.0-0 htmltools_0.5.0
[22] httpuv_1.5.4 Matrix_1.2-18 pkgconfig_2.0.3
[25] broom_0.7.3 haven_2.3.1 scales_1.1.1
[28] whisker_0.4 later_1.1.0.1 git2r_0.27.1
[31] generics_0.1.0 farver_2.0.3 ellipsis_0.3.1
[34] withr_2.3.0 cli_2.2.0 magrittr_2.0.1
[37] crayon_1.3.4 readxl_1.3.1 evaluate_0.14
[40] fs_1.5.0 fansi_0.4.1 xml2_1.3.2
[43] RcppArmadillo_0.10.1.2.0 tools_4.0.3 data.table_1.13.4
[46] hms_0.5.3 lifecycle_0.2.0 munsell_0.5.0
[49] reprex_0.3.0 compiler_4.0.3 rlang_0.4.9
[52] grid_4.0.3 rstudioapi_0.13 labeling_0.4.2
[55] rmarkdown_2.5 gtable_0.3.0 DBI_1.1.0
[58] R6_2.5.0 knitr_1.30 utf8_1.1.4
[61] rprojroot_2.0.2 stringi_1.5.3 parallel_4.0.3
[64] Rcpp_1.0.5 vctrs_0.3.6 dbplyr_1.4.4
[67] tidyselect_1.1.0 xfun_0.19