Spatial data coverage
Pasqualina Vonlanthen & Jens Daniel Müller
12 November, 2021
Last updated: 2021-11-12
Checks: 7 0
Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 284003d | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| html | 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| html | a103f60 | pasqualina-vonlanthendinenna | 2021-11-05 | Build site. |
| Rmd | 31576f9 | pasqualina-vonlanthendinenna | 2021-11-05 | changed QC flag maps |
| html | fbd5bac | pasqualina-vonlanthendinenna | 2021-11-04 | Build site. |
| html | 68977a1 | pasqualina-vonlanthendinenna | 2021-10-26 | Build site. |
| Rmd | 062b272 | pasqualina-vonlanthendinenna | 2021-10-26 | added ggsave |
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| html | bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 | Build site. |
| Rmd | 4bc1859 | pasqualina-vonlanthendinenna | 2021-10-26 | run with full data |
| html | f7ef44f | jens-daniel-mueller | 2021-10-22 | Build site. |
| Rmd | ee2b3f3 | jens-daniel-mueller | 2021-10-22 | code revision |
| html | aa7280d | jens-daniel-mueller | 2021-10-22 | Build site. |
| Rmd | ca7ba6b | jens-daniel-mueller | 2021-10-22 | adding revised code |
| html | d84c904 | pasqualina-vonlanthendinenna | 2021-10-22 | Build site. |
| html | 8ecdb43 | pasqualina-vonlanthendinenna | 2021-10-22 | Build site. |
| html | c81f21c | pasqualina-vonlanthendinenna | 2021-10-21 | Build site. |
| html | 62d8519 | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| html | b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| html | 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| Rmd | b88a839 | pasqualina-vonlanthendinenna | 2021-10-20 | adding revised code |
Task
Map the location of oxygen, pH, and nitrate observations recorded by BGC-Argo floats
Load data
Read the metadata file created in loading_data.html:
path_argo_preprocessed <- paste0(path_argo, "/preprocessed_bgc_data")
bgc_metadata <-
read_rds(file = paste0(path_argo_preprocessed, "/bgc_metadata.rds"))basinmask <-
read_csv(paste(path_emlr_utilities,
"basin_mask_WOA18.csv",
sep = ""),
col_types = cols("MLR_basins" = col_character()))
basinmask <- basinmask %>%
filter(MLR_basins == unique(basinmask$MLR_basins)[1]) %>%
select(lon, lat, basin_AIP)
map <-
read_rds(paste(path_emlr_utilities,
"map_landmask_WOA18.rds",
sep = ""))Spatial data coverage
Count profiles
bgc_metadata <- inner_join(
bgc_metadata,
basinmask
)Joining, by = c("lat", "lon")bgc_profile_counts_year <- bgc_metadata %>%
select(platform_number, cycle_number, date, lon, lat,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date)) %>%
filter(!is.na(profile_flag),
profile_flag != "") %>%
count(lat, lon, year, parameter) # count the number of profiles per year in each lon/lat grid for each parameter
# count the number of profiles which have flags A, B, C, D, or E (count the number of profiles which have usable data)
bgc_profile_counts_usable <- bgc_metadata %>%
select(platform_number, cycle_number, date, lon, lat,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date)) %>%
filter(!is.na(profile_flag),
profile_flag != "",
profile_flag != 'F') %>%
count(lat, lon, parameter, profile_flag) # count the number of profiles for flags A, B, C, D, and E (usable data) for each lon/lat grid
# count the number of profiles which have QC flag A (100% of levels contain good data)
bgc_profile_counts_A <- bgc_metadata %>%
select(platform_number, cycle_number, date, lon, lat,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date)) %>%
filter(profile_flag == 'A') %>%
count(lat, lon, parameter)
# count the number of profiles which have a QC flag of F (100% of levels contain good data)
bgc_profile_counts_F <- bgc_metadata %>%
select(platform_number, cycle_number, date, lon, lat,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date)) %>%
filter(profile_flag == 'F') %>%
count(lat, lon, parameter)By Year
Map of profile locations for each parameter, per year
map +
geom_tile(data = bgc_profile_counts_year,
aes(lon, lat, fill = n)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
facet_grid(year ~ parameter)
# bgc_profile_counts_year %>%
# ggplot() +
# geom_sf(data = ne_countries(returnclass = "sf"),
# fill = "gray90",
# color = NA) +
# geom_sf(data = ne_coastline(returnclass = "sf")) +
# geom_tile(aes(x = lon, y = lat, fill = n)) +
# scale_fill_gradient(low="blue", high="red",
# trans = "log10") +
# theme_bw() +
# facet_grid(year ~ parameter)# map the location of profiles for each parameter in each year
bgc_profile_counts_year %>%
group_split(parameter) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste('Parameter:', unique(.x$parameter))
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_wrap(~year, ncol = 3)
)[[1]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[2]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[3]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
ggsave("output/figures/maps_per_year.png",
width = 7,
height = 4)Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.# bgc_profile_counts_year %>%
# group_split(parameter) %>%
# map(
# ~ ggplot() +
# geom_sf(data = ne_countries(returnclass = "sf"),
# fill = "gray90",
# color = NA) +
# geom_sf(data = ne_coastline(returnclass = "sf")) +
# geom_tile(data = .x, aes(x = lon, y = lat, fill = n)) +
# scale_fill_gradient(low="blue", high="red",
# trans = "log10") +
# theme_bw() +
# labs(x = 'lon', y = 'lat', fill = 'number of profiles',
# title = paste('Parameter:', unique(.x$parameter)))+
# facet_grid(. ~ year)
# )By QC Flag
Map the profile locations for each profile QC flag of each parameter
bgc_profile_counts_flag %>%
ggplot() +
geom_sf(data = ne_countries(returnclass = "sf"),
fill = "gray90",
color = NA) +
geom_sf(data = ne_coastline(returnclass = "sf")) +
geom_tile(aes(x = lon, y = lat, fill = n)) +
scale_fill_gradient(low="blue", high="red",
trans = "log10") +
theme_bw() +
facet_grid(profile_flag ~ parameter)Flags A, B, C, D, and E
# map the location of profiles which contain usable data (profile QC flags A, B, C, D, and E)
# create a separate plot for each parameter
bgc_profile_counts_usable %>%
group_split(parameter) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste(unique(.x$parameter), 'Profile Flags A, B, C, D, E')
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_wrap(~ parameter)
)[[1]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[2]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[3]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
ggsave("output/figures/maps_usable_data.png",
width = 7,
height = 4)Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.Flag A
# map the location of profiles with QC flag A for each parameter
# only the highest-quality data, with 100% of levels with good data
bgc_profile_counts_A %>%
group_split(parameter) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste(unique(.x$parameter), 'Profile Flag A')
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_wrap(~ parameter)
)[[1]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[2]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[3]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
ggsave("output/figures/maps_A_flag.png",
width = 7,
height = 4)Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.Flag F
# map the location of profiles with QC flag F (not usable data)
bgc_profile_counts_F %>%
group_split(parameter) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste(unique(.x$parameter), 'Profile Flag F')
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_wrap(~ parameter)
)[[1]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[2]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
[[3]]Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.
ggsave("output/figures/maps_flag_F.png",
width = 7,
height = 4)Warning: Raster pixels are placed at uneven vertical intervals and will be
shifted. Consider using geom_tile() instead.# create a separate plot for each QC flag (instead of multiple panels in one plot)
bgc_profile_counts_flag %>%
group_split(profile_flag) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste('Profile QC flag', unique(.x$profile_flag))
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_grid(parameter ~ .)
)
ggsave("output/figures/maps_per_flag.png",
width = 7,
height = 4)ph_profile_counts_year <- bgc_metadata %>% # count the number of A-flag pH profiles
select(platform_number, cycle_number, date, lon, lat,
profile_ph_in_situ_total_qc) %>%
pivot_longer(profile_ph_in_situ_total_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date)) %>%
filter(profile_flag == "A") %>%
count(lat, lon, year, parameter)
# map the location of pH profiles with QC flag A each year
ph_profile_counts_year %>%
group_split(parameter) %>%
map(
~ map +
geom_tile(data = .x, aes(
x = lon, y = lat, fill = n
)) +
scale_fill_gradient(low = "blue", high = "red",
trans = "log10") +
labs(
x = 'lon',
y = 'lat',
fill = 'number of\nprofiles',
title = paste('Parameter:', unique(.x$parameter), 'flag A')
) +
theme(
legend.position = "bottom",
axis.text = element_blank(),
axis.ticks = element_blank()
) +
facet_wrap(~year, ncol = 3)
)
ggsave("output/figures/map_pH_flag_A_per_year.png",
width = 7,
height = 4)
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] lubridate_1.7.9 argodata_0.0.0.9000 forcats_0.5.0
[4] stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4
[7] readr_1.4.0 tidyr_1.1.3 tibble_3.1.3
[10] ggplot2_3.3.5 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.27
[5] utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 backports_1.1.10
[9] reprex_0.3.0 evaluate_0.14 highr_0.8 httr_1.4.2
[13] pillar_1.6.2 rlang_0.4.11 readxl_1.3.1 rstudioapi_0.13
[17] whisker_0.4 jquerylib_0.1.4 blob_1.2.1 rmarkdown_2.10
[21] labeling_0.4.2 munsell_0.5.0 broom_0.7.9 compiler_4.0.3
[25] httpuv_1.6.2 modelr_0.1.8 xfun_0.25 pkgconfig_2.0.3
[29] htmltools_0.5.1.1 tidyselect_1.1.0 fansi_0.5.0 crayon_1.4.1
[33] dbplyr_1.4.4 withr_2.4.2 later_1.3.0 grid_4.0.3
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
[41] git2r_0.27.1 magrittr_2.0.1 scales_1.1.1 cli_3.0.1
[45] stringi_1.5.3 farver_2.1.0 fs_1.5.0 promises_1.2.0.1
[49] xml2_1.3.2 bslib_0.2.5.1 ellipsis_0.3.2 generics_0.1.0
[53] vctrs_0.3.8 tools_4.0.3 glue_1.4.2 RNetCDF_2.4-2
[57] hms_0.5.3 yaml_2.2.1 colorspace_2.0-2 rvest_0.3.6
[61] knitr_1.33 haven_2.3.1 sass_0.4.0