Mapping
Jens Daniel Müller
04 August, 2020
Last updated: 2020-08-04
Checks: 7 0
Knit directory: Cant_eMLR/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200707) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version c834496. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rproj.user/
Ignored: data/GLODAPv2_2016b_MappedClimatologies/
Ignored: data/GLODAPv2_2020/
Ignored: data/WOCE/
Ignored: data/World_Ocean_Atlas_2018/
Ignored: data/dclement/
Ignored: data/eMLR/
Ignored: data/pCO2_atmosphere/
Ignored: dump/
Untracked files:
Untracked: analysis/test_scripts/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/mapping.Rmd) and HTML (docs/mapping.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | c834496 | jens-daniel-mueller | 2020-08-04 | formatting |
| html | e29d39d | jens-daniel-mueller | 2020-08-04 | Build site. |
| Rmd | 1443a30 | jens-daniel-mueller | 2020-08-04 | Included gamma values from Clement based on WOA13 |
| html | 9dc5d7f | jens-daniel-mueller | 2020-07-29 | Build site. |
| html | 21524b4 | jens-daniel-mueller | 2020-07-29 | Build site. |
| html | 4f80a27 | jens-daniel-mueller | 2020-07-28 | Build site. |
| Rmd | c63f537 | jens-daniel-mueller | 2020-07-28 | included model coeffcients in mapping |
| html | 4eebe14 | jens-daniel-mueller | 2020-07-24 | Build site. |
| Rmd | 12f9ef2 | jens-daniel-mueller | 2020-07-24 | started neutral density calculation |
| html | 2e08795 | jens-daniel-mueller | 2020-07-24 | Build site. |
| html | 64978a1 | jens-daniel-mueller | 2020-07-24 | Build site. |
| Rmd | 7cbc7ec | jens-daniel-mueller | 2020-07-24 | first publish |
library(tidyverse)
library(lubridate)
library(oce)1 Required data
Currently we use following data sets for mapping:
- GLODAPv2_2016b_MappedClimatologies
- Salinity
- Temperature
- Phosphate
- Nitrate
- Silicate
- oxygen
- World Ocean Atlas 2013
- Neutral densities calculated by D Clement
- eMLR model coefficients
We aim to use WOA18 instead of WOA13, but still need to implement neutral density calculation.
variables <- c("salinity", "temperature", "NO3", "oxygen", "PO4", "silicate")
for (i_variable in variables) {
# i_variable <- variables[2]
# print(i_variable)
temp <- read_csv(
here::here("data/GLODAPv2_2016b_MappedClimatologies/_summarized_files",
paste(i_variable,".csv", sep = "")))
if (exists("GLODAP_predictors")) {
GLODAP_predictors <- full_join(GLODAP_predictors, temp)
}
if (!exists("GLODAP_predictors")) {
GLODAP_predictors <- temp
}
}
rm(temp, i_variable, variables)
# GLODAP_depths <- unique(GLODAP_predictors$depth)
# GLODAP_lon <- unique(GLODAP_predictors$lon)
# min(GLODAP_lon)
# max(GLODAP_lon)WOA18_predictors <-
read_csv(here::here("data/World_Ocean_Atlas_2018/_summarized_files",
"WOA18_predictors.csv"))
WOA18_predictors <- WOA18_predictors %>%
rename(salinity = s_an, temperature = t_an)
# WOA18_depths <- unique(WOA18_predictors$depth)WOA13 <-
read_csv(here::here("data/World_Ocean_Atlas_2018/_summarized_files",
"WOA13_mask_gamma.csv"))
WOA13_gamma <- WOA13 %>%
select(-mask)
WOA13_gamma <- WOA13_gamma %>%
rename(lat = latitude, lon = longitude) %>%
mutate(lon = if_else(lon > 180, lon - 360, lon))
rm(WOA13)
# WOA13_depths <- unique(WOA13_gamma$depth)
# GLODAP_depths - WOA13_depthsall_lm <- read_csv(here::here("data/eMLR",
"all_lm.csv"))2 Join predictor climatologies
CAVEAT: Coverage of GLODAP climatologies differs slightly for parameters (some are NA in some regions)
2.1 Control plots
Maps of number of observations per horizontal grid cell.
2.1.1 GLODAP climatology
GLODAP_n <- GLODAP_predictors %>%
drop_na() %>%
group_by(lat, lon) %>%
summarise(n = n()) %>%
ungroup()
GLODAP_n %>%
ggplot(aes(lon, lat, fill = n)) +
geom_raster() +
scale_fill_viridis_c(direction = -1) +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom")
rm(GLODAP_n)2.1.2 WOA13 climatology
WOA13_gamma_n <- WOA13_gamma %>%
drop_na() %>%
group_by(lat, lon) %>%
summarise(n = n()) %>%
ungroup()
WOA13_gamma_n %>%
ggplot(aes(lon, lat, fill = n)) +
geom_raster() +
scale_fill_viridis_c(direction = -1) +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom")
rm(WOA13_gamma_n)2.2 WOA13 + GLODAP
predictors <- full_join(GLODAP_predictors, WOA13_gamma)
rm(GLODAP_predictors, WOA13_gamma)
predictors <- predictors %>%
group_by(lat, lon) %>%
mutate(n_NO3 = sum(!is.na(NO3)),
n_oxygen = sum(!is.na(oxygen)),
n_PO4 = sum(!is.na(PO4)),
n_silicate = sum(!is.na(silicate)),
n_salinity = sum(!is.na(salinity)),
n_temperature = sum(!is.na(temperature)),
n_gamma = sum(!is.na(gamma))) %>%
ungroup()
predictors <- predictors %>%
filter(n_NO3 > 0,
n_oxygen > 0,
n_PO4 > 0,
n_silicate > 0,
n_salinity > 0,
n_temperature > 0,
n_gamma > 0) %>%
select(-c(n_NO3,
n_oxygen,
n_PO4,
n_silicate,
n_salinity,
n_temperature,
n_gamma))
predictors <- predictors %>%
drop_na()
predictors %>%
ggplot(aes(lon, lat)) +
geom_bin2d(binwidth = c(1,1)) +
scale_fill_viridis_c(direction = -1) +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom")
predictors %>%
filter(depth == 0) %>%
ggplot(aes(lon, lat, fill = PO4)) +
geom_raster() +
scale_fill_viridis_c() +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom") +
labs(title = "Surface values")
predictors %>%
filter(depth == 0) %>%
ggplot(aes(lon, lat, fill = gamma)) +
geom_raster() +
scale_fill_viridis_c() +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom") +
labs(title = "Surface values")
2.3 WOA18 + GLODAP
WOA18 data are currently not used. Code chunks in this section are not executed.
predictors <- full_join(GLODAP_predictors, WOA18_predictors)
rm(GLODAP_predictors, WOA18_predictors)
predictors <- predictors %>%
group_by(lat, lon) %>%
mutate(n_NO3 = sum(!is.na(NO3)),
n_oxygen = sum(!is.na(oxygen)),
n_PO4 = sum(!is.na(PO4)),
n_silicate = sum(!is.na(silicate)),
n_salinity = sum(!is.na(salinity)),
n_temperature = sum(!is.na(temperature))) %>%
ungroup()
predictors <- predictors %>%
filter(n_NO3 > 1,
n_oxygen > 1,
n_PO4 > 1,
n_silicate > 1,
n_salinity > 1,
n_temperature > 1) %>%
select(-c(n_NO3 , n_oxygen , n_PO4 , n_silicate , n_salinity , n_temperature))
predictors %>%
ggplot(aes(lon, lat)) +
geom_bin2d(binwidth = c(1,1)) +
scale_fill_viridis_c(direction = -1) +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom")
predictors %>%
filter(depth == 0) %>%
ggplot(aes(lon, lat, fill = PO4)) +
geom_raster() +
scale_fill_viridis_c() +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom") +
labs(title = "Surface values")
predictors %>%
filter(depth == 0) %>%
ggplot(aes(lon, lat, fill = temperature)) +
geom_raster() +
scale_fill_viridis_c() +
coord_quickmap(expand = 0) +
theme(legend.position = "bottom") +
labs(title = "Surface values")predictors <- predictors %>%
group_by(lat, lon) %>%
arrange(depth) %>%
mutate(temperature = approxfun(depth, temperature, rule = 2)(depth),
salinity = approxfun(depth, salinity, rule = 2)(depth)) %>%
ungroup()
predictors <- predictors %>%
filter(depth %in% GLODAP_depths)2.3.1 Predictor profiles
N_Atl <- predictors %>%
filter(lat == 40.5, lon == -20.5)
N_Atl <- N_Atl %>%
pivot_longer(salinity:gamma, names_to = "parameter", values_to = "value")
N_Atl %>%
ggplot(aes(value, depth)) +
geom_path() +
geom_point() +
scale_y_reverse() +
facet_wrap(~parameter, scales = "free_x")
rm(N_Atl)3 Prepare model coefficients
all_lm <- all_lm %>%
select(term, estimate, basin, era, gamma_slab, model)
all_lm_wide <- all_lm %>%
pivot_wider(values_from = estimate, names_from = term)4 Neutral density calculation
GLODAP <- read_csv(here::here("data/GLODAPv2_2020/_summarized_data_files",
"GLODAP_MLR_fitting_ready.csv"))
cruises_meridional <- c("1041")
GLODAP_cruise <- GLODAP %>%
filter(cruise %in% cruises_meridional)
GLODAP_cruise <- GLODAP_cruise %>%
mutate(gamma_calc = swRho(salinity = salinity,
temperature = temperature,
pressure = depth,
longitude = lon,
latitude = lat,
eos = "gsw"))
GLODAP_cruise <- GLODAP_cruise %>%
mutate(gamma_calc = gamma_calc - 1000,
delta_gamma = gamma - gamma_calc)
lat_section <-
GLODAP_cruise %>%
ggplot(aes(lat, depth)) +
scale_y_reverse() +
scale_color_viridis_c() +
theme(legend.position = "bottom")
lat_section +
geom_point(aes(col = gamma))
lat_section +
geom_point(aes(col = gamma_calc))
lat_section +
geom_point(aes(col = delta_gamma))
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] oce_1.2-0 gsw_1.0-5 testthat_2.3.2 lubridate_1.7.9
[5] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4
[9] readr_1.3.1 tidyr_1.1.0 tibble_3.0.3 ggplot2_3.3.2
[13] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 here_0.1 assertthat_0.2.1 rprojroot_1.3-2
[5] digest_0.6.25 R6_2.4.1 cellranger_1.1.0 backports_1.1.8
[9] reprex_0.3.0 evaluate_0.14 httr_1.4.2 pillar_1.4.6
[13] rlang_0.4.7 readxl_1.3.1 rstudioapi_0.11 whisker_0.4
[17] blob_1.2.1 rmarkdown_2.3 labeling_0.3 munsell_0.5.0
[21] broom_0.7.0 compiler_4.0.2 httpuv_1.5.4 modelr_0.1.8
[25] xfun_0.16 pkgconfig_2.0.3 htmltools_0.5.0 tidyselect_1.1.0
[29] fansi_0.4.1 viridisLite_0.3.0 crayon_1.3.4 dbplyr_1.4.4
[33] withr_2.2.0 later_1.1.0.1 grid_4.0.2 jsonlite_1.7.0
[37] gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0 git2r_0.27.1
[41] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6
[45] farver_2.0.3 fs_1.4.2 promises_1.1.1 xml2_1.3.2
[49] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 tools_4.0.2
[53] glue_1.4.1 hms_0.5.3 yaml_2.2.1 colorspace_1.4-1
[57] rvest_0.3.6 knitr_1.29 haven_2.3.1