BGC-Argo pH Data
Pasqualina Vonlanthen & Jens Daniel Müller
26 November, 2021
Last updated: 2021-11-26
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Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 5e2b8a5 | pasqualina-vonlanthendinenna | 2021-11-26 | Build site. |
| html | 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 | Build site. |
| Rmd | 9b5df99 | pasqualina-vonlanthendinenna | 2021-11-26 | added oceanSODA page |
| Rmd | f43074c | pasqualina-vonlanthendinenna | 2021-11-23 | switched reccap biomes to loading data |
| html | d3f9eb5 | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | b1706c9 | pasqualina-vonlanthendinenna | 2021-11-22 | updated timeseries plots |
| html | 105630e | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | 82f09d0 | pasqualina-vonlanthendinenna | 2021-11-22 | separated Southern Ocean regions |
| html | e96cc7f | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | 2c5f2e5 | pasqualina-vonlanthendinenna | 2021-11-22 | corrected offset plot |
| Rmd | fb2fb74 | pasqualina-vonlanthendinenna | 2021-11-19 | corrected offset plot |
| html | 13df4f5 | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | fd6ef5a | pasqualina-vonlanthendinenna | 2021-11-19 | changed offset plot |
| html | 578ae8c | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | ae64132 | pasqualina-vonlanthendinenna | 2021-11-19 | added offset pH plot |
| html | ab70649 | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | 171aa37 | pasqualina-vonlanthendinenna | 2021-11-19 | updated loading pH data and color palettes |
| Rmd | c696726 | pasqualina-vonlanthendinenna | 2021-11-17 | updated loading pH data and color palettes |
| html | 9824928 | pasqualina-vonlanthendinenna | 2021-11-16 | Build site. |
| Rmd | 383aa57 | pasqualina-vonlanthendinenna | 2021-11-16 | updated |
| html | b6a26a1 | pasqualina-vonlanthendinenna | 2021-11-16 | Build site. |
| Rmd | b473f72 | pasqualina-vonlanthendinenna | 2021-11-16 | added ggOceanMap for pH |
| html | 0dce554 | pasqualina-vonlanthendinenna | 2021-11-15 | Build site. |
| Rmd | 2c20367 | pasqualina-vonlanthendinenna | 2021-11-15 | added ggOceanMap for pH |
| html | 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 | Build site. |
| Rmd | 59073c1 | pasqualina-vonlanthendinenna | 2021-11-12 | added NE Pacific oxygen |
| html | 273ed2c | pasqualina-vonlanthendinenna | 2021-11-12 | Build site. |
| Rmd | 06b6be7 | pasqualina-vonlanthendinenna | 2021-11-12 | added NE Pacific oxygen |
| html | 284003d | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| Rmd | f7807db | pasqualina-vonlanthendinenna | 2021-11-11 | added oxygen data page |
| html | 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| Rmd | 8baed53 | pasqualina-vonlanthendinenna | 2021-11-11 | added pH data page |
Task
Explore BGC-Argo pH data through timeseries and monthly climatological maps
path_argo <- '/nfs/kryo/work/updata/bgc_argo_r_argodata'
path_emlr_utilities <- "/nfs/kryo/work/jenmueller/emlr_cant/utilities/files/"
path_basin_mask <- "/nfs/kryo/work/updata/reccap2/"Load pH data
Load in delayed-mode adjusted pH data from the data files created in Loading Data
# keep only pH data and associated CTD variables
path_argo_preprocessed <- paste0(path_argo, "/preprocessed_bgc_data")
# load in surface pH data
ph_surface_2x2 <- read_rds(file = paste0(path_argo_preprocessed, '/ph_surface_2x2.rds'))
ph_surface_1x1 <- read_rds(file = paste0(path_argo_preprocessed, "/ph_surface_1x1.rds"))
region_masks_all_seamask_2x2 <- read_rds(file = paste0(
path_argo_preprocessed, "/region_masks_all_seamask_2x2.rds"))
region_masks_all_2x2 <- read_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_2x2.rds"))Southern Ocean surface pH
The focus here is on surface pH (in the top 20 m of the watercolumn), in the region south of 30ºS
# select pH data for the Southern Ocean, as defined by the RECCAP regions
ph_surface_SO <- ph_surface_2x2 %>%
filter(region == 'southern',
value != 0)
# check the correct latitudes, QC flags, and depth levels have been filtered
#max(ph_surface_SO$lat)
#min(ph_surface_SO$lat)
# table(ph_surface_SO$ph_in_situ_total_adjusted_qc)
# max(ph_surface_SO$depth)
# min(ph_surface_SO$date)
# max(ph_surface_SO$date)Data offset with depth
Plot the difference between in-situ observed pH and the profile-mean surface pH for the upper 20 m. This difference represents the variability of the surface pH values with respect to the mean surface pH of the upper 20 m.
# calculate the mean pH for each surface profile
mean_profile_ph <- ph_surface_SO %>%
group_by(float_serial_no, cycle_number) %>%
mutate(mean_prof_ph = mean(ph_in_situ_total_adjusted, na.rm = TRUE),
.before = depth) %>%
ungroup() %>%
mutate(offset = ph_in_situ_total_adjusted-mean_prof_ph,
.after = mean_prof_ph) # subtract the mean profile pH from the measured in situ pH
mean_profile_ph %>%
ggplot()+
geom_point(aes(x = offset, y = depth, col = as.character(year)), size = 0.3, pch = 19) +
scale_y_reverse()+
geom_vline(xintercept = 0, col = 'red', size = 0.6)+
labs(x = 'offset (pH units)',
y = 'depth (m)',
col = 'year',
title = 'in situ pH - mean profile pH')
Bin the pH data into 2m-depth intervals and calculate the offset for each pH observation in each depth interval relative to the profile-mean pH
# bin the ph values into 2m bins and calculate the offset for each 2m bin
mean_profile_ph_binned <- ph_surface_SO %>%
mutate(depth = cut(depth, seq(0, 20, 2), seq(1, 19, 2)),
depth = as.numeric(as.character(depth))) %>%
group_by(float_serial_no, cycle_number) %>%
mutate(mean_prof_ph = mean(ph_in_situ_total_adjusted, na.rm = TRUE),
.before = depth) %>%
ungroup() %>%
mutate(offset = ph_in_situ_total_adjusted-mean_prof_ph,
.after = mean_prof_ph)
# plot the offset of the depth-binned values
mean_profile_ph_binned %>%
ggplot()+
geom_point(aes(x = offset, y = depth, col = as.character(year)), size = 0.3, pch = 19) +
scale_y_reverse()+
geom_vline(xintercept = 0, col = 'red', size = 0.6)+
labs(x = 'offset (pH units)',
y = 'depth (m)',
col = 'year',
title = 'in situ pH - mean profile pH (2m depth bins)')
| Version | Author | Date |
|---|---|---|
| 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 |
Monthly climatological map
Create a climatological monthly map of surface pH, in a 2x2º longitude/latitude grid, for the region south of 30ºS (monthly pH averaged over April 2014-August 2021)
# average pH values in the top 20 m for each month in each 2 x 2º longitude/latitude grid
ph_clim_SO <- ph_surface_SO %>%
group_by(lat, lon, month) %>%
summarise(ph_clim_month = mean(ph_in_situ_total_adjusted))`summarise()` has grouped output by 'lat', 'lon'. You can override using the `.groups` argument.# read in the map from updata
map <-
read_rds(paste(path_emlr_utilities,
"map_landmask_WOA18.rds",
sep = ""))
# map a monthly climatology of pH (April 2014 - August 2021)
map +
geom_tile(data = ph_clim_SO,
aes(lon, lat, fill = ph_clim_month)) +
lims(y = c(-85, -25)) +
scale_fill_viridis_c() +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly climatological \nArgo pH (Apr 2014 - Aug 2021)') +
theme(legend.position = 'right') +
facet_wrap(~month, ncol = 2)Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.Warning: Removed 153708 rows containing missing values (geom_raster).
| Version | Author | Date |
|---|---|---|
| 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 |
| 105630e | pasqualina-vonlanthendinenna | 2021-11-22 |
| e96cc7f | pasqualina-vonlanthendinenna | 2021-11-22 |
| ab70649 | pasqualina-vonlanthendinenna | 2021-11-19 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
basemap(limits = -32, data = ph_clim_SO) + # change to polar projection
geom_spatial_tile(data = ph_clim_SO,
aes(x = lon,
y = lat,
fill = ph_clim_month),
linejoin = 'mitre',
col = 'transparent',
detail = 60)+
scale_fill_viridis_c()+
theme(legend.position = 'bottom')+
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'monthly climatological \nArgo pH (Apr 2014 - Aug 2021)')+
facet_wrap(~month)Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Assuming `crs = 4326` in stat_spatial_rect()
Monthly timeseries
Timeseries of monthly mean pH values, over the three different Southern Ocean regions (separated based on RECCAP biomes):
# plot the region separations on a map
ggplot() +
geom_raster(data = region_masks_all_seamask_2x2 %>%
filter(seamask == 0),
aes(x = lon, y = lat)) +
geom_raster(data = region_masks_all_2x2 %>%
filter(region == 'southern',
value != 0),
aes(x = lon,
y = lat,
fill = value)) +
coord_quickmap(expand = 0) +
labs(title = 'Southern Ocean RECCAP regions',
fill = 'region')Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
# plot a timeseries of monthly values over the whole southern ocean south of 30ºS
ph_month_SO <- ph_surface_SO %>%
group_by(year, month, value) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))`summarise()` has grouped output by 'year', 'month'. You can override using the `.groups` argument.# timeseries of monthly pH values over 2014-2021 (separate panels for each month)
ph_month_SO %>%
ggplot(aes(x = year,
y = ph_ave,
group = value,
col = value)) +
facet_wrap(~month) +
geom_line() +
geom_point() +
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'monthly mean Argo pH (Apr 2014-Aug 2021, Southern Ocean)',
col = 'region')
#all months on one plot in different colors (not very nice plot)
# ph_month_SO %>%
# ggplot(aes(x = year, y = ph_ave, group = month, col = as.character(month))) +
# geom_line() +
# geom_point() +
# labs(x = 'year', y = 'pH in situ (total scale)', title = 'monthly mean pH (Apr 2014-Aug 2021)')Plot the monthly average pH, per year (from Jan 2015 - Dec 2020), for each Southern Ocean RECCAP region (1, 2, 3)
# timeseries of monthly pH values for each year (separate years on the same plot)
ph_month_SO %>%
filter(year != 2014,
year != 2021,
value != 0) %>% # remove the two years that are missing data (keep only data for full years)
ggplot(aes(x = month,
y = ph_ave,
group = year,
col = as.character(year)))+
geom_line()+
geom_point()+
scale_x_continuous(breaks = seq(1, 12, 2))+
facet_wrap(~value)+
labs(x = 'month',
y = 'pH in situ (total scale)',
title = 'monthly mean Argo pH (Jan 2015-Dec 2020, Southern Ocean)',
col = 'year')
# calculate a yearly average ph (one ph value per year, for the whole domain)
ph_year_SO <- ph_surface_SO %>%
group_by(year, value) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))
# plot a timeseries of the yearly average pH value (one value per year)
ph_year_SO %>%
ggplot(aes(x = year, y = ph_ave, group = value, col = value))+
geom_line()+
geom_point()+
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'yearly mean Argo pH (Apr 2014-Aug 2021, south of 30ºS)',
col = 'region')Northeast Pacific surface pH
Focus on surface pH in the northeast Pacific Ocean (10ºN - 70ºN, -190ºE - -140ºE)
# select only best pH data (with QC flag 1) between 10 and 70ºN, and 190 and 140ºW, for the top 20 m of the watercolumn
ph_nepacific <- ph_surface_2x2 %>%
mutate(depth = swDepth(pres_adjusted, latitude = lat), .before = pres_adjusted) %>%
filter(ph_in_situ_total_adjusted_qc == '1', # keep only 'good' data
between(lat, 10, 70),
between(lon, 190, 240), # NE Pacific
depth <= 20) %>% # keep only data above or at 20 m depth
mutate(
year = year(date), # separate the year and month from the date column
month = month(date), .after = n_prof
)
# longitudes larger than -180ºE are lon-380Monthly climatological map
Create a map of climatological monthly surface pH values, in the north-west Pacific ocean (10ºN - 70ºN, -190ºE, -140ºE), for
# average pH values in the top 20 m for each month in each 2 x 2º longitude/latitude grid
ph_mean_nepacific <- ph_nepacific %>%
group_by(lat, lon, month) %>%
summarise(ph_ave_month = mean(ph_in_situ_total_adjusted))`summarise()` has grouped output by 'lat', 'lon'. You can override using the `.groups` argument.# map a monthly climatology of surface pH (Jan 2013 - August 2021)
map +
geom_tile(data = ph_mean_nepacific,
aes(lon, lat, fill = ph_ave_month)) +
lims(y = c(5, 60),
x = c(180, 250)) +
scale_fill_viridis_c() +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly average pH (Jan 2013-Aug 2021)') +
theme(legend.position = 'right')+
facet_wrap(~month)Warning: Removed 219516 rows containing missing values (geom_raster).
# using the ggOceanMaps package
basemap(limits = c(-180, -110, 7, 60), data = ph_mean_nepacific) +
geom_spatial_tile(data = ph_mean_nepacific,
aes(x = lon,
y = lat,
fill = ph_ave_month))+
scale_fill_viridis_c()+
facet_wrap(~month) +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly average pH (Jan 2013-Aug 2021)')
# haven't figured out why the data isn't being plotted Monthly timeseries
Timeseries of monthly mean pH, averaged over the whole NE-Pacific region (10ºN - 70ºN, -190ºE - -140ºE), in the upper 20 m of the watercolumn.
# plot a timeseries of monthly values over the whole southern ocean south of 30ºS
ph_month_nepacific <- ph_nepacific %>%
group_by(year, month) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))`summarise()` has grouped output by 'year'. You can override using the `.groups` argument.# timeseries of monthly pH values over 2014-2021 (separate panels for each month)
ph_month_nepacific %>%
ggplot(aes(x = year, y = ph_ave)) +
facet_wrap(~month) +
scale_x_continuous(breaks = seq(2013, 2021, 2)) +
geom_line() +
geom_point() +
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'monthly mean pH (Jan 2013-Aug 2021, NE Pacific)')
Monthly average pH, per year, over the NE Pacific region
# timeseries of monthly pH values for each year (separate years on the same plot)
ph_month_nepacific %>%
filter(year != 2016,
year != 2021) %>% # remove the two years that are missing data (keep only data for full years)
ggplot(aes(x = month, y = ph_ave, group = year, col = as.character(year)))+
geom_line()+
geom_point()+
scale_x_continuous(breaks = seq(1, 12, 1))+
labs(x = 'month',
y = 'pH in situ (total scale)',
title = 'monthly mean pH (Jan 2013-Dec 2020, NE Pacific)',
col = 'year')
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] ggOceanMaps_0.4.3 ggspatial_1.1.5 oce_1.4-0
[4] testthat_3.0.4 sf_1.0-2 gsw_1.0-6
[7] lubridate_1.7.9 argodata_0.0.0.9000 forcats_0.5.0
[10] stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4
[13] readr_1.4.0 tidyr_1.1.3 tibble_3.1.3
[16] ggplot2_3.3.5 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] smoothr_0.1.2 fs_1.5.0 httr_1.4.2
[4] rprojroot_2.0.2 tools_4.0.3 backports_1.1.10
[7] bslib_0.2.5.1 utf8_1.2.2 rgdal_1.5-18
[10] R6_2.5.1 KernSmooth_2.23-17 rgeos_0.5-5
[13] DBI_1.1.1 colorspace_2.0-2 raster_3.4-5
[16] withr_2.4.2 sp_1.4-4 tidyselect_1.1.0
[19] compiler_4.0.3 git2r_0.27.1 cli_3.0.1
[22] rvest_0.3.6 RNetCDF_2.4-2 xml2_1.3.2
[25] labeling_0.4.2 sass_0.4.0 scales_1.1.1
[28] classInt_0.4-3 ggOceanMapsData_1.0.1 proxy_0.4-26
[31] digest_0.6.27 rmarkdown_2.10 pkgconfig_2.0.3
[34] htmltools_0.5.1.1 highr_0.8 dbplyr_1.4.4
[37] rlang_0.4.11 readxl_1.3.1 rstudioapi_0.13
[40] farver_2.1.0 jquerylib_0.1.4 generics_0.1.0
[43] jsonlite_1.7.2 magrittr_2.0.1 Rcpp_1.0.7
[46] munsell_0.5.0 fansi_0.5.0 abind_1.4-5
[49] lifecycle_1.0.0 stringi_1.5.3 whisker_0.4
[52] yaml_2.2.1 grid_4.0.3 blob_1.2.1
[55] parallel_4.0.3 promises_1.2.0.1 crayon_1.4.1
[58] lattice_0.20-41 stars_0.5-2 haven_2.3.1
[61] hms_0.5.3 knitr_1.33 pillar_1.6.2
[64] codetools_0.2-16 reprex_0.3.0 glue_1.4.2
[67] evaluate_0.14 modelr_0.1.8 vctrs_0.3.8
[70] httpuv_1.6.2 cellranger_1.1.0 gtable_0.3.0
[73] assertthat_0.2.1 xfun_0.25 lwgeom_0.2-5
[76] broom_0.7.9 e1071_1.7-8 later_1.3.0
[79] viridisLite_0.4.0 class_7.3-17 units_0.7-2
[82] ellipsis_0.3.2