Temporal data coverage
Pasqualina Vonlanthen & Jens Daniel Müller
29 August, 2022
Last updated: 2022-08-29
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Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 8e81570 | pasqualina-vonlanthendinenna | 2022-08-29 | load and add in core-argo data (1 month) |
| html | bdd516d | pasqualina-vonlanthendinenna | 2022-05-23 | Build site. |
| html | 4173c20 | jens-daniel-mueller | 2022-05-12 | Build site. |
| html | dfe89d7 | jens-daniel-mueller | 2022-05-12 | Build site. |
| html | 710edd4 | jens-daniel-mueller | 2022-05-11 | Build site. |
| Rmd | 2f20a76 | jens-daniel-mueller | 2022-05-11 | rebuild all after subsetting AB profiles and code cleaning |
| html | 68eff8b | jens-daniel-mueller | 2022-05-11 | Build site. |
| Rmd | cf4d1b6 | jens-daniel-mueller | 2022-05-11 | rerun with flag A and B subset |
| html | 6531981 | pasqualina-vonlanthendinenna | 2022-05-10 | Build site. |
| Rmd | bbafe7c | pasqualina-vonlanthendinenna | 2022-05-10 | updated profile counts timeseries |
| html | f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 | Build site. |
| Rmd | a66f31c | pasqualina-vonlanthendinenna | 2022-05-09 | updated argo index |
| html | 3f012ba | pasqualina-vonlanthendinenna | 2022-05-06 | Build site. |
| Rmd | 90d5e7c | pasqualina-vonlanthendinenna | 2022-05-06 | added timeseries of flag A dataframe |
| html | 6a6e874 | pasqualina-vonlanthendinenna | 2022-04-29 | Build site. |
| html | 2d44f8a | pasqualina-vonlanthendinenna | 2022-04-29 | Build site. |
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| html | 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 | Build site. |
| Rmd | c4cce1a | pasqualina-vonlanthendinenna | 2021-12-17 | updated cache data |
| html | 123e5db | pasqualina-vonlanthendinenna | 2021-12-07 | Build site. |
| Rmd | f8abe59 | pasqualina-vonlanthendinenna | 2021-12-07 | suppressed output messages and updated plots |
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| html | 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 | Build site. |
| html | 284003d | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| html | 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| html | 358d54e | pasqualina-vonlanthendinenna | 2021-11-05 | Build site. |
| Rmd | 395f3ec | pasqualina-vonlanthendinenna | 2021-11-05 | added total profile count |
| 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 |
| html | b57291a | pasqualina-vonlanthendinenna | 2021-10-26 | Build site. |
| html | bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 | Build site. |
| Rmd | 4bc1859 | pasqualina-vonlanthendinenna | 2021-10-26 | run with full data |
| html | cabaa10 | jens-daniel-mueller | 2021-10-22 | Build site. |
| Rmd | e2a1f9e | jens-daniel-mueller | 2021-10-22 | code revision |
| 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. |
| Rmd | 2b22099 | pasqualina-vonlanthendinenna | 2021-10-22 | edited text |
| html | c81f21c | pasqualina-vonlanthendinenna | 2021-10-21 | Build site. |
| html | b55928d | pasqualina-vonlanthendinenna | 2021-10-21 | Build site. |
| Rmd | 58c24b6 | pasqualina-vonlanthendinenna | 2021-10-21 | timeseries attempt 2, added description |
| html | 62d8519 | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| html | b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| Rmd | b7b1806 | pasqualina-vonlanthendinenna | 2021-10-20 | adding revised code |
| html | 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 | Build site. |
| Rmd | b88a839 | pasqualina-vonlanthendinenna | 2021-10-20 | adding revised code |
Task
Count the number of bgc-argo profiles, and plot their evolution over time.
Load data
BGC-Argo data
Read the files created in loading_data.html:
bgc_metadata <-
read_rds(file = paste0(path_argo_preprocessed, "/bgc_metadata.rds"))Core-Argo data
core_metadata <- read_rds(file = paste0(path_argo_core_preprocessed, "/core_metadata.rds"))Basin data
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 = ""))QC flags
QC flags for values (‘flag’ column) are between 1 and 8, where:
- 1 is ‘good’ data
- 2 is ‘probably good’ data,
- 3 is ‘probably bad’ data,
- 4 is ‘bad’ data,
- 5 is ‘value changed’,
- 8 is ‘estimated value’,
- 9 is ‘missing value’.
- (6 and 7 are not used)
Profile QC flags (‘profile_flag’ column) are QC codes attributed to the entire profile, and indicate the number of depth levels (in %) where the value is considered to be good data (QC flags of 1, 2, 5, and 8):
- ‘A’ means 100% of profile levels contain good data,
- ‘B’ means 75-<100% of profile levels contain good data,
- ‘C’ means 50-75% of profile levels contain good data,
- ‘D’ means 25-50% of profile levels contain good data,
- ‘E’ means >0-50% of profile levels contain good data,
- ‘F’ means 0% of profile levels contain good data.
Number of BGC-profiles
Per parameter
# count the number of profiles per parameter
bgc_profile_counts <- bgc_metadata %>%
select(platform_number, cycle_number, date, profile_temp_qc,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(year, month, parameter, profile_flag) %>% # count the number of occurrences of unique flags for each parameter, in each month of each year
filter(!is.na(profile_flag),
profile_flag != "")
# the 'parameter' column contains character strings of either 'doxy_qc', 'ph_in_situ_total_qc', or 'nitrate_qc', with the corresponding profile QC flag in the 'profile_flag' column
# count the total number of profiles for each parameter and each flag:
bgc_profile_counts_total <- bgc_metadata %>%
select(platform_number, cycle_number, date,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>% # count the number of occurrences of flags for each parameter
filter(!is.na(profile_flag),
profile_flag != "")# bgc_merge <- read_rds(file = paste0(path_argo_preprocessed, "/bgc_merge.rds"))
#
# bgc_profile_counts_test <- bgc_merge %>%
# select(platform_number, cycle_number, date, profile_temp_qc,
# profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
# unite('platform_cycle', platform_number:cycle_number, sep = '_', remove = FALSE) %>%
# mutate(year = year(date),
# month = month(date))
#
# bgc_profile_counts_test_n <- bgc_profile_counts_test %>%
# pivot_longer(cols = profile_temp_qc:profile_nitrate_qc,
# values_to = 'profile_flag',
# names_to = 'parameter',
# names_prefix = 'profile_') %>%
# distinct(year, month, platform_cycle, parameter, profile_flag) %>%
# group_by(year, month, parameter, profile_flag) %>%
# count(platform_cycle) %>%
# group_by(year, month, parameter, profile_flag) %>%
# summarise(n = sum(n)) %>%
# filter(!is.na(profile_flag),
# profile_flag != "")
#
#
# # total number of profiles
# print(sum(bgc_profile_counts_test_n$n))
#
# bgc_profile_counts_test_n %>%
# group_by(parameter) %>%
# group_split(parameter) %>%
# map(
# ~ ggplot(data = .x,
# aes(x = month, y = n, col = profile_flag))+
# geom_line()+
# geom_point()+
# facet_wrap(~year,
# ncol = 10)+
# labs(title = paste0('parameter:', unique(.x$parameter)))
# )
# gives the same result as using bgc_metadata Total number of profiles
Total number of BGC-profiles (all flags A-F)
# count the total number of profiles, regardless of QC flag
total_data_count <- bgc_metadata %>%
select(platform_number, cycle_number, date,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>% # count the number of occurrences of flags for each parameter
filter(!is.na(profile_flag),
profile_flag != "") %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(total_data_count, caption = 'total number of profiles', format = 'markdown')| parameter | n |
|---|---|
| doxy_qc | 133428 |
| nitrate_qc | 42302 |
| ph_in_situ_total_qc | 27538 |
Total number of profiles with usable data (flags A-E)
# count the number of profiles which have QC flags of A, B, C, D, or E (profiles which contain data that can be used)
usable_data_count <- bgc_metadata %>%
select(platform_number, cycle_number, date,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>% # count the number of occurrences of flags for each parameter
filter(!is.na(profile_flag),
profile_flag != "",
profile_flag != 'F') %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(usable_data_count,
caption = 'total number of profiles with QC flags A, B, C, D, E',
format = 'markdown')| parameter | n |
|---|---|
| doxy_qc | 113126 |
| nitrate_qc | 36606 |
| ph_in_situ_total_qc | 13365 |
Total number of BGC-profiles with flag A (100% good data)
# count the number of profiles with QC flag A
A_data_count <- bgc_metadata %>%
select(platform_number, cycle_number, date, profile_temp_qc,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>% # count the number of occurrences of flags for each parameter
filter(!is.na(profile_flag),
profile_flag != "",
profile_flag == 'A') %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(A_data_count,
caption = 'total number of profiles with QC flag A',
format = 'markdown')| parameter | n |
|---|---|
| doxy_qc | 86243 |
| nitrate_qc | 34668 |
| ph_in_situ_total_qc | 11195 |
| temp_qc | 45117 |
flag_AB <- read_rds(file = paste0(path_argo_preprocessed, "/bgc_merge_flag_AB.rds"))
flag_AB <- flag_AB %>%
unite('platform_cycle', platform_number:cycle_number, sep = '_', remove = FALSE) %>%
mutate(year = year(date),
month = month(date))
flag_AB_n <- flag_AB %>%
distinct(year, month, platform_cycle) %>%
count(year, month)
# total number of profiles
print(sum(flag_AB_n$n))[1] 11802flag_AB_n %>%
ggplot(aes(x = month, y = n))+
geom_point()+
geom_line()+
facet_wrap(~year, ncol = 10)+
labs(title = 'bgc_merge_flag_AB.rds dataframe (temp & pH flag A)')
################################
# using the flag A pH and temperature dataframe which doesn't remove NA values
# flag_A_test <- bgc_merge_flag_A_test %>%
# unite('platform_cycle', platform_number:cycle_number, sep = '_', remove = FALSE) %>%
# mutate(year = year(date),
# month = month(date))
#
# flag_A_test_n <- flag_A_test %>%
# distinct(year, month, platform_cycle) %>%
# group_by(year, month) %>%
# count(platform_cycle) %>%
# group_by(year, month) %>%
# summarise(n = sum(n))
#
#
# # total number of profiles
# print(sum(flag_A_test_n$n))
#
# flag_A_test_n %>%
# ggplot(aes(x = month, y = n))+
# geom_point()+
# geom_line()+
# facet_wrap(~year, ncol = 10)+
# labs(title = 'bgc_merge_flag_AB.rds dataframe (temp & pH flag A)')Total number of F-flag BGC profiles (unusable data)
# count the number of profiles with QC Flag F (not usable data)
F_data_count <- bgc_metadata %>%
select(platform_number, cycle_number, date,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc) %>%
pivot_longer(cols = profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>% # count the number of occurrences of flags for each parameter
filter(!is.na(profile_flag),
profile_flag != "",
profile_flag == 'F') %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(F_data_count,
caption = 'total number of profiles with QC flag F',
format = 'markdown')| parameter | n |
|---|---|
| doxy_qc | 20302 |
| nitrate_qc | 5696 |
| ph_in_situ_total_qc | 14173 |
Plot the evolution of the number of profiles over time
bgc_profile_counts %>%
ggplot(aes(x = month, y = n, col = profile_flag)) +
geom_line() +
geom_point() +
facet_grid(parameter ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,4))+
labs(x = 'month', y = 'number of profiles', title = 'number of profiles per year')# draw separate plots for the separate parameters
bgc_profile_counts %>%
group_split(parameter) %>% # creates a separate flag count for each parameter
map(
~ ggplot(data = .x, # repeats the ggplot for each separate parameter
aes(
x = month, y = n, col = profile_flag
)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
labs(title = paste("Parameter: ", unique(.x$parameter)),
x = 'month', y = 'number of profiles',
col = 'profile QC flag') +
scale_x_continuous(breaks = seq(1,12,4))
)[[1]]
| Version | Author | Date |
|---|---|---|
| f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
| bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 |
| aa7280d | jens-daniel-mueller | 2021-10-22 |
| b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 |
| 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 |
[[2]]
| Version | Author | Date |
|---|---|---|
| f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
| bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 |
| aa7280d | jens-daniel-mueller | 2021-10-22 |
| b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 |
| 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 |
[[3]]
| Version | Author | Date |
|---|---|---|
| f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
| bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 |
| aa7280d | jens-daniel-mueller | 2021-10-22 |
| b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 |
| 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 |
[[4]]
ggsave("output/figures/time_series_profiles_per_parameter.png",
width = 7,
height = 4)All flag A
# count the number of profiles which have a QC flag of A for all three BGC parameters
# the if_all(starts_with()) notation allows to filter over a range of columns simultaneously
# this new approach is identical to your previous solution
# except that it filters also the pres, temp, and sal flags
# (plotted below)
bgc_profile_counts_total_A <- bgc_metadata %>%
select(platform_number, cycle_number, date,
profile_pres_qc:profile_ph_in_situ_total_qc) %>%
filter(if_all(starts_with("profile_"), ~. == 'A')) %>%
pivot_longer(cols = starts_with("profile_"),
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month) %>%
count(year, month)bgc_profile_counts_total_A %>%
ggplot(aes(x = month, y = n)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,4)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "All three BGC + core parameters (QC flag A)")
| Version | Author | Date |
|---|---|---|
| 710edd4 | jens-daniel-mueller | 2022-05-11 |
| f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 |
| cabaa10 | jens-daniel-mueller | 2021-10-22 |
| aa7280d | jens-daniel-mueller | 2021-10-22 |
| b55928d | pasqualina-vonlanthendinenna | 2021-10-21 |
| b8feac2 | pasqualina-vonlanthendinenna | 2021-10-20 |
| 701fffa | pasqualina-vonlanthendinenna | 2021-10-20 |
ggsave("output/figures/time_series_flag_A_profiles.png",
width = 7,
height = 4)All pH flag A
# count the number of profiles which have a QC flag of A for all three BGC parameters
# the if_all(starts_with()) notation allows to filter over a range of columns simultaneously
# this new approach is identical to your previous solution
# except that it filters also the pres, temp, and sal flags
# (plotted below)
bgc_profile_counts_total_A_pH <- bgc_metadata %>%
filter(profile_ph_in_situ_total_qc == "A") %>%
select(platform_number, cycle_number, date,
profile_temp_qc) %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month, profile_temp_qc) %>%
count(year, month, profile_temp_qc)bgc_profile_counts_total_A_pH %>%
ggplot(aes(x = month, y = n, col = profile_temp_qc)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,4)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "All three BGC + core parameters (QC flag A)")
| Version | Author | Date |
|---|---|---|
| 710edd4 | jens-daniel-mueller | 2022-05-11 |
ggsave("output/figures/time_series_flag_A_profiles_pH.png",
width = 7,
height = 4)By region
# bgc_metadata <- bgc_metadata %>%
# 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))
# )
bgc_grid <- bgc_metadata %>%
distinct(lat, lon)
bgc_grid <- inner_join(
basinmask, bgc_grid
)
map +
geom_raster(data = basinmask,
aes(lon, lat, fill = basin_AIP)) +
geom_raster(data = bgc_grid,
aes(lon, lat)) +
scale_fill_brewer(palette = "Dark2")
| Version | Author | Date |
|---|---|---|
| f196b7c | pasqualina-vonlanthendinenna | 2022-05-09 |
| 8805f99 | pasqualina-vonlanthendinenna | 2022-04-11 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
| bba33bf | pasqualina-vonlanthendinenna | 2021-10-26 |
| aa7280d | jens-daniel-mueller | 2021-10-22 |
rm(bgc_grid)bgc_profile_counts_total_A_region <-
inner_join(bgc_metadata,
basinmask) %>%
select(platform_number, cycle_number, date,
profile_doxy_qc, profile_ph_in_situ_total_qc, profile_nitrate_qc,
basin_AIP) %>%
filter(if_all(starts_with("profile_"), ~. == 'A')) %>%
pivot_longer(cols = profile_doxy_qc:profile_nitrate_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month, basin_AIP) %>%
count(year, month, basin_AIP)bgc_profile_counts_total_A_region %>%
ggplot(aes(x = month, y = n, col = basin_AIP)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,2)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "All three BGC + core parameters (QC flag A)")
ggsave("output/figures/time_series_profiles_per_region.png",
width = 7,
height = 4)Remove BGC data
rm(list = ls(pattern = 'bgc_'))
rm(list = ls(pattern = '_count'))Number of Core-Profiles
Core- temperature and salinity
core_profile_counts <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(year, month, parameter, profile_flag) %>% # count the number of occurrences of unique flags for each parameter, in each month of each year
filter(!is.na(profile_flag),
profile_flag != "")
core_profile_counts_total <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>%
filter(!is.na(profile_flag),
profile_flag != "")Total number of profiles
Total number of profiles, regardless of QC flags
# count the total number of core profiles, regardless of QC flag
total_data_count_core <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = 'parameter',
values_to = 'profile_flag',
names_prefix = 'profile_') %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>%
filter(!is.na(profile_flag),
profile_flag != "") %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(total_data_count_core, caption = 'total number of profiles', format = 'markdown')| parameter | n |
|---|---|
| psal_qc | 15241 |
| temp_qc | 15934 |
Number of core profiles with usable data (flags A, B, C, D, and E)
# count the number of core tempa and sal profiles which have QC flags of A, B, C, D, or E (profiles which contain data that can be used)
usable_data_count_core <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>%
filter(!is.na(profile_flag),
profile_flag !="",
profile_flag != "F") %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(usable_data_count_core,
caption = 'total number of core profiles with QC flags A, B, C, D, E',
format = 'markdown')| parameter | n |
|---|---|
| psal_qc | 13733 |
| temp_qc | 15558 |
Total number of core-profiles with flag A (best data)
# count the number of core profiles with QC flag A
A_data_count_core <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>%
filter(!is.na(profile_flag),
profile_flag != "",
profile_flag == 'A') %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(A_data_count_core,
caption = 'total number of core profiles with QC flag A',
format = 'markdown')| parameter | n |
|---|---|
| psal_qc | 11084 |
| temp_qc | 11811 |
Total number of F-flag core profiles (0% good data)
# count the number of core profiles with QC Flag F (not usable data)
F_data_count_core <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
count(parameter, profile_flag) %>%
filter(!is.na(profile_flag),
profile_flag !="",
profile_flag == 'F') %>%
group_by(parameter) %>%
summarise(n = sum(n))
knitr::kable(F_data_count_core,
caption = 'total number of core profiles with QC flag F',
format = 'markdown')| parameter | n |
|---|---|
| psal_qc | 1508 |
| temp_qc | 376 |
Plot the evolution of the total number of core profiles over time
# draw separate plots for the separate parameters
core_profile_counts %>%
group_split(parameter) %>% # creates a separate flag count for each parameter
map(
~ ggplot(data = .x, # repeats the ggplot for each separate parameter
aes(
x = month, y = n, col = profile_flag
)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
labs(title = paste("Parameter: ", unique(.x$parameter)),
x = 'month', y = 'number of profiles',
col = 'profile QC flag') +
scale_x_continuous(breaks = seq(1,12,4))
)[[1]]
[[2]]
ggsave("output/figures/time_series_core_profiles_per_parameter.png",
width = 7,
height = 4)All flag A
# count the number of profiles which have a QC flag of A for all three BGC parameters
# the if_all(starts_with()) notation allows to filter over a range of columns simultaneously
core_profile_counts_total_A <- core_metadata %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc) %>%
filter(if_all(starts_with("profile_"), ~. == 'A')) %>%
pivot_longer(cols = starts_with("profile_"),
names_to = "parameter",
values_to = "profile_flag",
names_prefix = "profile_") %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month) %>%
count(year, month)
core_profile_counts_total_A %>%
ggplot(aes(x = month, y = n)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,4)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "Core temp + sal profiles (QC flag A)")
ggsave("output/figures/time_series_flag_A_core_profiles.png",
width = 7,
height = 4)All Core-temp flag A
core_profile_counts_total_A_temp <- core_metadata %>%
filter(profile_temp_qc == 'A') %>%
select(platform_number, cycle_number, date,
profile_temp_qc) %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month, profile_temp_qc) %>%
count(year, month, profile_temp_qc)
# timeseries plot
core_profile_counts_total_A_temp %>%
ggplot(aes(x = month, y = n, col = profile_temp_qc)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,4)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "Core-temp (QC flag A)")
ggsave("output/figures/time_series_flag_A_core_profiles_temp.png",
width = 7,
height = 4)By Region
Number of A-Flag Core profiles by region
core_profile_counts_total_A_region <-
inner_join(core_metadata, basinmask) %>%
select(platform_number, cycle_number, date,
profile_temp_qc, profile_psal_qc, basin_AIP) %>%
filter(if_all(starts_with("profile_"), ~. == 'A')) %>%
pivot_longer(cols = profile_temp_qc:profile_psal_qc,
names_to = 'parameter',
values_to = 'profile_flag',
names_prefix = 'profile_') %>%
mutate(year = year(date),
month = month(date)) %>%
distinct(platform_number, cycle_number, year, month, basin_AIP) %>%
count(year, month, basin_AIP)
core_profile_counts_total_A_region %>%
ggplot(aes(x = month, y = n, col = basin_AIP)) +
geom_line() +
geom_point() +
facet_grid(. ~ year,
scales = "free_y") +
scale_x_continuous(breaks = seq(1,12,2)) +
labs(x = 'month', y = 'number of profiles',
title = "Number of profiles",
subtitle = "Core temp + sal (QC flag A)")
ggsave("output/figures/time_series_core_profiles_per_region.png",
width = 7,
height = 4)rm(list = ls(pattern = 'core_'))
rm(list = ls(pattern = '_core'))
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3
Matrix products: default
BLAS: /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/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] lubridate_1.8.0 argodata_0.1.0 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.7 purrr_0.3.4 readr_2.1.1 tidyr_1.1.4
[9] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] httr_1.4.2 sass_0.4.0 bit64_4.0.5 vroom_1.5.7
[5] jsonlite_1.7.3 modelr_0.1.8 bslib_0.3.1 assertthat_0.2.1
[9] getPass_0.2-2 highr_0.9 cellranger_1.1.0 yaml_2.2.1
[13] pillar_1.6.4 backports_1.4.1 glue_1.6.0 digest_0.6.29
[17] RColorBrewer_1.1-2 promises_1.2.0.1 rvest_1.0.2 colorspace_2.0-2
[21] htmltools_0.5.2 httpuv_1.6.5 pkgconfig_2.0.3 broom_0.7.11
[25] haven_2.4.3 scales_1.1.1 processx_3.5.2 whisker_0.4
[29] later_1.3.0 tzdb_0.2.0 git2r_0.29.0 generics_0.1.1
[33] farver_2.1.0 ellipsis_0.3.2 withr_2.4.3 cli_3.1.1
[37] magrittr_2.0.1 crayon_1.4.2 readxl_1.3.1 evaluate_0.14
[41] ps_1.6.0 fs_1.5.2 fansi_1.0.2 xml2_1.3.3
[45] tools_4.1.2 hms_1.1.1 lifecycle_1.0.1 munsell_0.5.0
[49] reprex_2.0.1 callr_3.7.0 compiler_4.1.2 jquerylib_0.1.4
[53] RNetCDF_2.5-2 rlang_1.0.2 grid_4.1.2 rstudioapi_0.13
[57] labeling_0.4.2 rmarkdown_2.11 gtable_0.3.0 DBI_1.1.2
[61] R6_2.5.1 knitr_1.37 fastmap_1.1.0 bit_4.0.4
[65] utf8_1.2.2 rprojroot_2.0.2 stringi_1.7.6 parallel_4.1.2
[69] Rcpp_1.0.8 vctrs_0.3.8 dbplyr_2.1.1 tidyselect_1.1.1
[73] xfun_0.29