Last updated: 2024-09-25

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Knit directory: oae_ccs_roms/

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File Version Author Date Message
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: abind
Loading required package: sf
Linking to GEOS 3.11.1, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
WARNING: different compile-time and runtime versions for GEOS found:
Linked against: 3.11.1-CAPI-1.17.1 compiled against: 3.9.1-CAPI-1.14.2
It is probably a good idea to reinstall sf, and maybe rgeos and rgdal too
library(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()
library(dplyr)

#For the regridded standard files, path:
path_ROMSv2RG_results <- 
 "/net/sea/work/loher/ROMS/Alk_enh_formatted_2024_08/"

#opening specific nc file (Columbia site, 1x)
# nc <- nc_open(paste0(path_ROMSv2RG_results,
#                      "ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"))
# 
# print(nc)

#filtering for just one variable w/ stars package
# nc_alk <- read_ncdf(paste0(path_ROMSv2RG_results,
#                      "ColumbiaRiver/ColumbiaRiver_2010-2015_1x.nc"),
#            var = "Alk")

#problem here with Alk and DIC: include the depth dimension; getting weird error
# when trying to slice for this since the value is 0
# nc_surface_alk <- nc_alk %>%
#   filter(depth == 0)

#slicing for just one timepoint
# nc_surface_alk_1 <- nc_surface_alk %>%
#   slice(time, 1)

###################
#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 for both 
# DIC and Alk variable
alk_surface_t1 <- nc %>%
  hyper_filter(depth = index == 1, time = index == 1) %>% 
  hyper_tibble(select_var = c("Alk"), #  produces a tibble object
               force = TRUE)
dic_surface_t1 <- nc %>%
  hyper_filter(depth = index == 1, time = index == 1) %>% 
  hyper_tibble(select_var = c("DIC"), # produces a tibble object
               force = TRUE)

#plotting
alk_surface_t1_sf <- st_as_sf(alk_surface_t1, coords = c("lon", "lat"), crs = 4326)
ggplot(data = alk_surface_t1_sf) + geom_sf(aes(color = Alk)) +
  labs(title = "Columbia River Surface Alkalinity @ T1", 
       x = "Longitude", y = "Latitude")

Version Author Date
5eca06c vgfroh 2024-09-19 
#plotting
dic_surface_t1_sf <- st_as_sf(dic_surface_t1, coords = c("lon", "lat"), crs = 4326)
ggplot(data = dic_surface_t1_sf) + geom_sf(aes(color = DIC)) +
  labs(title = "Columbia River Surface DIC @ T1", 
       x = "Longitude", y = "Latitude")

#why do they look like dots?

##########################
#i tried something else so i could get the data but i can't plot this w/ ggplot
# lon <- ncvar_get(nc, "lon", verbose = FALSE) # read lon variable
# lat <- ncvar_get(nc, "lat", verbose = FALSE) # read lat variable
# time <- ncvar_get(nc, "time", verbose = FALSE) # read t (time) variable
# depth <- ncvar_get(nc, "depth", verbose = FALSE) # read depth variable
# print(c(length(lon), length(lat), length(t), length(depth))) # show vector lengths
# 
# alk_array <- ncvar_get(nc, "Alk") #pull the alk values from the ncdf4 file
# 
# alk_surface_time_1 <- alk_array[, , 1, 1] #pull only the first time point and surface layer


##################
#creating a blank plot and loading in the nc data layer using stars package  
# ggplot(data = alk_surface_time_1) 
#  geom_stars(data = alk_surface_time_1)


#

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] forcats_0.5.2   stringr_1.5.0   dplyr_1.1.3     purrr_1.0.2    
 [5] readr_2.1.3     tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.4  
 [9] tidyverse_1.3.2 stars_0.6-0     sf_1.0-9        abind_1.4-5    
[13] 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          scales_1.2.1       
[25] classInt_0.4-8      callr_3.7.3         proxy_0.4-27       
[28] digest_0.6.30       rmarkdown_2.18      pkgconfig_2.0.3    
[31] htmltools_0.5.3     highr_0.9           dbplyr_2.2.1       
[34] fastmap_1.1.0       rlang_1.1.1         readxl_1.4.1       
[37] rstudioapi_0.15.0   jquerylib_0.1.4     generics_0.1.3     
[40] farver_2.1.1        jsonlite_1.8.3      googlesheets4_1.0.1
[43] magrittr_2.0.3      ncmeta_0.3.5        Rcpp_1.0.10        
[46] munsell_0.5.0       fansi_1.0.3         lifecycle_1.0.3    
[49] stringi_1.7.8       whisker_0.4         yaml_2.3.6         
[52] grid_4.2.2          parallel_4.2.2      promises_1.2.0.1   
[55] crayon_1.5.2        CFtime_1.4.0        haven_2.5.1        
[58] hms_1.1.2           knitr_1.41          ps_1.7.2           
[61] pillar_1.9.0        reprex_2.0.2        glue_1.6.2         
[64] evaluate_0.18       getPass_0.2-2       modelr_0.1.10      
[67] vctrs_0.6.4         tzdb_0.3.0          httpuv_1.6.6       
[70] cellranger_1.1.0    gtable_0.3.1        assertthat_0.2.1   
[73] cachem_1.0.6        xfun_0.35           lwgeom_0.2-10      
[76] broom_1.0.5         e1071_1.7-12        later_1.3.0        
[79] class_7.3-20        googledrive_2.0.0   gargle_1.2.1       
[82] units_0.8-0         timechange_0.1.1    ellipsis_0.3.2