read_data
Victoria Froh & Jens Daniel Müller
05 November, 2024
Last updated: 2024-11-05
Checks: 7 0
Knit directory: oae_ccs_roms/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 77644c3 | vgfroh | 2024-10-02 | Build site. |
| Rmd | e6e5240 | vgfroh | 2024-10-02 | Plots after perturbations |
| html | 95e822c | vgfroh | 2024-10-01 | Build site. |
| Rmd | 7dd8327 | vgfroh | 2024-10-01 | Comparing model and calculated pCO2 |
| html | 1271b4b | vgfroh | 2024-09-30 | Build site. |
| Rmd | 5dd4857 | vgfroh | 2024-09-30 | Running the carb function |
| html | a2f17f6 | vgfroh | 2024-09-25 | Build site. |
| Rmd | 7f8a0c8 | vgfroh | 2024-09-25 | Alk and DIC maps of surface at t=1 |
| html | f421914 | vgfroh | 2024-09-19 | Build site. |
| Rmd | f7fc26f | vgfroh | 2024-09-19 | first map but i cleaned up the code |
| html | 5eca06c | vgfroh | 2024-09-19 | Build site. |
| Rmd | c9f35a0 | vgfroh | 2024-09-19 | first map |
| html | 16549e7 | vgfroh | 2024-09-19 | Build site. |
| Rmd | 210c100 | vgfroh | 2024-09-19 | setup project |
| html | 2e8d326 | jens-daniel-mueller | 2024-09-19 | Build site. |
| html | 7591977 | jens-daniel-mueller | 2024-09-19 | Build site. |
| Rmd | a97392c | jens-daniel-mueller | 2024-09-19 | setup project |
Read this
this is the script to open the data
#loading packages
library(ncdf4)
library(tidync)
library(stars)Loading required package: abindLoading required package: sfLinking to GEOS 3.11.1, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUEWARNING: different compile-time and runtime versions for GEOS found:Linked against: 3.11.1-CAPI-1.17.1 compiled against: 3.9.1-CAPI-1.14.2It is probably a good idea to reinstall sf, and maybe rgeos and rgdal toolibrary(tidyverse)── Attaching packages
───────────────────────────────────────
tidyverse 1.3.2 ──✔ ggplot2 3.4.4 ✔ purrr 1.0.2
✔ tibble 3.2.1 ✔ dplyr 1.1.3
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()#For the regridded standard files, path:
path_ROMSv2RG_results <-
"/net/sea/work/loher/ROMS/Alk_enh_formatted_2024_08/"
#opening specific nc file to get overview (Columbia site, 1x)
view_nc <- nc_open(paste0(path_ROMSv2RG_results,
"ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"))
print(view_nc)File /net/sea/work/loher/ROMS/Alk_enh_formatted_2024_08/ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc (NC_FORMAT_NETCDF4):
9 variables (excluding dimension variables):
float Alk[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged Alkalinity
units: mMol m-3
missing_value: NaN
_FillValue: NaN
float DIC[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged Dissolved inorganic carbon
units: mMol C m-3
missing_value: NaN
_FillValue: NaN
float PO4[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged Phosphate
units: mMol P m-3
missing_value: NaN
_FillValue: NaN
float SiO3[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged Silicate
units: mMol Si m-3
missing_value: NaN
_FillValue: NaN
float salt[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged salinity
units: PSU
missing_value: NaN
_FillValue: NaN
float temp[lon,lat,depth,time] (Chunking: [96,88,1,1])
long_name: averaged potential temperature
units: Celsius
missing_value: NaN
_FillValue: NaN
float FG_CO2[lon,lat,time] (Chunking: [96,88,1])
long_name: averaged Air-sea flux of CO2
units: mmol/m2/s
missing_value: NaN
_FillValue: NaN
float PCO2OC[lon,lat,time] (Chunking: [96,88,1])
long_name: averaged PCO2OC
units: not looked up yet
missing_value: NaN
_FillValue: NaN
float pCO2air[lon,lat,time] (Chunking: [96,88,1])
long_name: averaged Atmospheric pCO2
units: ppm
missing_value: NaN
_FillValue: NaN
4 dimensions:
time Size:1096 *** is unlimited ***
standard_name: time
calendar: 365_day
axis: T
long_name: Averaged time since 2010-01-01
units: days since 2010-01-01
lon Size:96
standard_name: longitude
long_name: longitude
units: degrees_east
axis: X
lat Size:88
standard_name: latitude
long_name: latitude
units: degrees_north
axis: Y
depth Size:16
axis: Z
long_name: depth
units: m
remark: positive down
5 global attributes:
CDI: Climate Data Interface version 2.2.1 (https://mpimet.mpg.de/cdi)
Conventions: CF-1.6
history: Tue Aug 20 20:38:27 2024: cdo --history -s -P 12 -f nc4 -selvar,Alk,DIC,PO4,salt,SiO3,temp -remapbil,/net/sea/work/loher/ROMS/Alk_enh_formatted_2024_08/griddes_ColumbiaRiver /nfs/sea/work/loher/ROMS/Pactcs30_Alk_enhanced_2024_08/Pactcs30_Alk_enhanced_ColumbiaRiver_1x/avg/z_pactcs30_2010-2015_avg.00000.nc /net/sea/work/loher/ROMS/Alk_enh_formatted_2024_08/ColumbiaRiver/pactcs30_2010-2015_avg.00000_1x.nc
CDO: Climate Data Operators version 2.2.0 (https://mpimet.mpg.de/cdo)
cdo_openmp_thread_number: 12#filtering for just one variable w/ stars package + time and depth slice
nc_alk <- read_ncdf(paste0(path_ROMSv2RG_results,
"ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"),
var = "Alk",
ncsub = cbind(start = c(1, 1, 1, 1), count = c(96, 88, 1, 1)
),
proxy = FALSE #need this on to override the proxy format
)Warning: ignoring unrecognized unit: mMol m-3No projection information found in nc file.
Coordinate variable units found to be degrees,
assuming WGS84 Lat/Lon.nc_dic <- read_ncdf(paste0(path_ROMSv2RG_results,
"ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"),
var = "DIC",
ncsub = cbind(start = c(1, 1, 1, 1), count = c(96, 88, 1, 1)
),
proxy = FALSE #need this on to override the proxy format
)Warning: ignoring unrecognized unit: mMol C m-3No projection information found in nc file.
Coordinate variable units found to be degrees,
assuming WGS84 Lat/Lon.#creating a blank plot and loading in the nc data layers
ggplot() +
geom_stars(data = nc_alk, aes(fill = Alk)) +
labs(title = "Columbia River Surface Alkalinity @ T1",
x = "Longitude",
y = "Latitude") +
theme_minimal() +
scale_fill_viridis_c() +
coord_quickmap()
ggplot() +
geom_stars(data = nc_dic, aes(fill = DIC)) +
labs(title = "Columbia River Surface DIC @ T1",
x = "Longitude",
y = "Latitude") +
theme_minimal() +
scale_fill_viridis_c() +
coord_quickmap()
###################
#using tidync instead
nc <- tidync(paste0(path_ROMSv2RG_results,
"ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"))
#filtering nc file for just the surface @ the first time index, outputting tbl_df
alk_surface_t1 <- nc %>%
hyper_filter(depth = index == 1, time = index == 1) %>%
hyper_tibble(select_var = c("Alk")
) %>%
mutate(lon = as.numeric(lon), lat = as.numeric(lat))
dic_surface_t1 <- nc %>%
hyper_filter(depth = index == 1, time = index == 1) %>%
hyper_tibble(select_var = c("DIC"),
) %>%
mutate(lon = as.numeric(lon), lat = as.numeric(lat))
#plotting variables
ggplot(data = alk_surface_t1) +
geom_tile(aes(lon, lat, fill = Alk)) +
labs(title = "Columbia River Surface Alkalinity @ T1",
x = "Longitude", y = "Latitude") +
theme_minimal() +
scale_fill_viridis_c() +
coord_quickmap()
ggplot(data = dic_surface_t1) +
geom_tile(aes(lon, lat, fill = DIC)) +
labs(title = "Columbia River Surface DIC @ T1",
x = "Longitude", y = "Latitude") +
theme_minimal() +
scale_fill_viridis_c() +
coord_quickmap()
| Version | Author | Date |
|---|---|---|
| 95e822c | vgfroh | 2024-10-01 |
##########################
# Using sea carb:
library(seacarb)Loading required package: oce
Loading required package: gsw
Loading required package: SolveSAPHElibrary(metR)
Attaching package: 'metR'
The following object is masked from 'package:oce':
coriolis
The following object is masked from 'package:purrr':
cross#load in data from tidync file in main active grid w/ T1 surface slice
surface_data <- nc %>%
hyper_filter(depth = index == 1, time = index == 1) %>%
hyper_tibble(force = TRUE) %>%
mutate(lon = as.numeric(lon), lat = as.numeric(lat))
#loading in data in other grid ie surface variables
surface_data_pco2 <- nc %>%
activate("D1,D2,D0") %>% #activating surface grid for PCO2OC variable
hyper_filter(time = index == 1) %>%
hyper_tibble(select_var = c("PCO2OC"), # produces a tibble object
force = TRUE) %>%
mutate(lon = as.numeric(lon), lat = as.numeric(lat))
merged_surface <- full_join(surface_data, surface_data_pco2)Joining with `by = join_by(lon, lat)`#running carb to produce the pCO2 values
merged_surface_orig <-
merged_surface %>%
#head(6) %>% #testing subsset
drop_na() %>% #drops all rows with an NA
mutate(
pco2_calc = carb(
flag = 15,
var1 = Alk * 1e-6 / 1.02518,
var2 = DIC * 1e-6 / 1.02518,
S = salt,
T = temp,
P = 0,
#surface = 0
Pt = PO4 * 1e-6 / 1.02518,
Sit = SiO3 * 1e-6 / 1.02518,
kf="dg",
k1k2="m06",
ks="d"
)$pCO2 #to just save the pco2 output
)
#plotting pco2
ggplot(data = merged_surface_orig) +
geom_tile(aes(lon, lat, fill = pco2_calc)) +
labs(title = "Columbia River Calculated PCO2 @ T1",
x = "Longitude", y = "Latitude", fill = "pCO2 (ppm)") +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_fill_viridis_c(na.value = "red") + #will show any tiles w/ var=NA
coord_quickmap()
######################
#Comparing Outputs
#New dataframe w/ reorganized pCO2 data
pco2_compare <- merged_surface_orig %>%
select(lon, lat, pco2_calc, PCO2OC) %>%
pivot_longer(
cols = c(pco2_calc, PCO2OC),
names_to = "Variant",
values_to = "pCO2"
)
#Plotting side-by-side comparison
ggplot(data = pco2_compare) +
geom_tile(aes(lon, lat, fill = pCO2)) +
facet_grid(cols = vars(Variant)) +
labs(title = "Calculated pCO2 vs Model pCO2",
x = "Longitude", y = "Latitude", fill = "pCO2 (ppm)") +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
coord_quickmap() +
scale_fill_viridis_c()
#New df w/ the difference between model and calculated pCO2
pco2_delta <- merged_surface_orig %>%
select(lon, lat, pco2_calc, PCO2OC) %>%
mutate(dpco2 = PCO2OC - pco2_calc)
#Plotting difference
ggplot(data = pco2_delta) +
geom_tile(aes(lon, lat, fill = dpco2)) +
labs(title = "Model pCO2 - Calculated pCO2",
x = "Longitude", y = "Latitude", fill = "dpCO2 (ppm)") +
scale_fill_divergent() +
#scale_fill_viridis_c() +
coord_quickmap() +
theme(plot.title = element_text(hjust = 0.5)) +
theme_minimal()
#####################
#Perturbation of 10 mmol Alk/m^3 in all grid cells
surface_pert <-
surface_data %>%
#head(6) %>% #testing subsset
drop_na() %>% #drops all rows with an NA
mutate(
pco2_calc_pert = carb(
flag = 15,
var1 = (Alk + 10) * 1e-6 / 1.02518,
var2 = DIC * 1e-6 / 1.02518,
S = salt,
T = temp,
P = 0,
#surface = 0
Pt = PO4 * 1e-6 / 1.02518,
Sit = SiO3 * 1e-6 / 1.02518,
kf="dg",
k1k2="m06",
ks="d"
)$pCO2 #to just save the pco2 output
)
#New dataframe w/ reorganized pCO2_pert data to compare
pco2_pert_compare <- full_join(surface_pert, pco2_delta) %>%
select(lon, lat, pco2_calc_pert, pco2_calc) %>%
pivot_longer(
cols = c(pco2_calc_pert, pco2_calc),
names_to = "Variant",
values_to = "pCO2"
)Joining with `by = join_by(lon, lat)`#Plotting side-by-side comparison
ggplot(data = pco2_pert_compare) +
geom_tile(aes(lon, lat, fill = pCO2)) +
facet_grid(cols = vars(Variant)) +
labs(title = "Initial pCO2 vs pCO2 after Added Alkalinity",
x = "Longitude", y = "Latitude", fill = "pCO2 (ppm)") +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
coord_quickmap() +
scale_fill_viridis_c()
#New df w/ the difference in pCO2 after Alk perturbation
pco2_pert_delta <- full_join(surface_pert, pco2_delta) %>%
select(lon, lat, pco2_calc_pert, pco2_calc) %>%
mutate(dpco2 = pco2_calc_pert - pco2_calc)Joining with `by = join_by(lon, lat)`#Plotting difference
ggplot(data = pco2_pert_delta) +
geom_tile(aes(lon, lat, fill = dpco2)) +
labs(title = "Difference in pCO2 after Added Alkalinity",
x = "Longitude", y = "Latitude", fill = "dpCO2 (ppm)") +
#scale_fill_divergent() +
scale_fill_viridis_c() +
coord_quickmap() +
theme(plot.title = element_text(hjust = 0.5)) +
theme_minimal()
####################
#Alkalinity Perturbation, looking at how DIC changes with constant pCO2
surface_pert_dic <-
merged_surface %>%
#head(6) %>% #testing subsset
drop_na() %>% #drops all rows with an NA
mutate(
DIC_pert = carb(
flag = 24,
var1 = PCO2OC,
var2 = (Alk + 10) * 1e-6 / 1.02518,
S = salt,
T = temp,
P = 0,
#surface = 0
Pt = PO4 * 1e-6 / 1.02518,
Sit = SiO3 * 1e-6 / 1.02518,
kf="dg",
k1k2="m06",
ks="d"
)$DIC #to just save the pco2 output
* 1.02518 * 1e6 #converting back to model units of mmol/m^3
)
#New dataframe w/ reorganized DIC data to compare
dic_pert_compare <- full_join(surface_pert_dic, merged_surface) %>%
select(lon, lat, DIC_pert, DIC) %>%
pivot_longer(
cols = c(DIC_pert, DIC),
names_to = "Variant",
values_to = "DIC"
)Joining with `by = join_by(Alk, DIC, PO4, SiO3, salt, temp, lon, lat, PCO2OC)`#Plotting side-by-side comparison
ggplot(data = dic_pert_compare) +
geom_tile(aes(lon, lat, fill = DIC)) +
facet_grid(cols = vars(Variant)) +
labs(title = "Initial Model DIC vs DIC after Added Alkalinity",
x = "Longitude", y = "Latitude", fill = "DIC (mmol/m^3)") +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
coord_quickmap() +
scale_fill_viridis_c()
| Version | Author | Date |
|---|---|---|
| 77644c3 | vgfroh | 2024-10-02 |
#New df w/ the difference in DIC after Alk perturbation
dic_pert_delta <- full_join(surface_pert_dic, merged_surface) %>%
select(lon, lat, DIC_pert, DIC) %>%
mutate(dDIC = DIC_pert - DIC)Joining with `by = join_by(Alk, DIC, PO4, SiO3, salt, temp, lon, lat, PCO2OC)`#Plotting difference
ggplot(data = dic_pert_delta) +
geom_tile(aes(lon, lat, fill = dDIC)) +
labs(title = "Difference in DIC after Added Alkalinity",
x = "Longitude", y = "Latitude", fill = "dDIC (mmol/m^3)") +
#scale_fill_divergent() +
scale_fill_viridis_c() +
coord_quickmap() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5))
| Version | Author | Date |
|---|---|---|
| 77644c3 | vgfroh | 2024-10-02 |
vhjgvj
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.5
Matrix products: default
BLAS: /usr/local/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.2.2/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] metR_0.13.0 seacarb_3.3.3 SolveSAPHE_2.1.0 oce_1.7-10
[5] gsw_1.1-1 forcats_0.5.2 stringr_1.5.0 dplyr_1.1.3
[9] purrr_1.0.2 readr_2.1.3 tidyr_1.3.0 tibble_3.2.1
[13] ggplot2_3.4.4 tidyverse_1.3.2 stars_0.6-0 sf_1.0-9
[17] abind_1.4-5 tidync_0.4.0 ncdf4_1.19 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.2 lubridate_1.9.0 httr_1.4.4
[4] rprojroot_2.0.3 tools_4.2.2 backports_1.4.1
[7] bslib_0.4.1 utf8_1.2.2 R6_2.5.1
[10] KernSmooth_2.23-20 DBI_1.1.3 colorspace_2.0-3
[13] withr_2.5.0 tidyselect_1.2.0 processx_3.8.0
[16] compiler_4.2.2 git2r_0.30.1 cli_3.6.1
[19] rvest_1.0.3 RNetCDF_2.6-1 xml2_1.3.3
[22] labeling_0.4.2 sass_0.4.4 checkmate_2.1.0
[25] scales_1.2.1 classInt_0.4-8 callr_3.7.3
[28] proxy_0.4-27 digest_0.6.30 rmarkdown_2.18
[31] pkgconfig_2.0.3 htmltools_0.5.3 highr_0.9
[34] dbplyr_2.2.1 fastmap_1.1.0 rlang_1.1.1
[37] readxl_1.4.1 rstudioapi_0.15.0 PCICt_0.5-4.3
[40] farver_2.1.1 jquerylib_0.1.4 generics_0.1.3
[43] jsonlite_1.8.3 googlesheets4_1.0.1 magrittr_2.0.3
[46] ncmeta_0.3.5 Rcpp_1.0.10 munsell_0.5.0
[49] fansi_1.0.3 lifecycle_1.0.3 stringi_1.7.8
[52] whisker_0.4 yaml_2.3.6 grid_4.2.2
[55] parallel_4.2.2 promises_1.2.0.1 crayon_1.5.2
[58] CFtime_1.4.0 haven_2.5.1 hms_1.1.2
[61] knitr_1.41 ps_1.7.2 pillar_1.9.0
[64] reprex_2.0.2 glue_1.6.2 evaluate_0.18
[67] getPass_0.2-2 data.table_1.14.6 modelr_0.1.10
[70] vctrs_0.6.4 tzdb_0.3.0 httpuv_1.6.6
[73] cellranger_1.1.0 gtable_0.3.1 assertthat_0.2.1
[76] cachem_1.0.6 xfun_0.35 lwgeom_0.2-10
[79] broom_1.0.5 e1071_1.7-12 later_1.3.0
[82] class_7.3-20 googledrive_2.0.0 viridisLite_0.4.1
[85] gargle_1.2.1 memoise_2.0.1 units_0.8-0
[88] timechange_0.1.1 ellipsis_0.3.2