Last updated: 2025-02-03

Checks: 7 0

Knit directory: oae_ccs_roms/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(20240919)

The command set.seed(20240919) 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.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 639b38d

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 639b38d. 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:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  code/read_data.Rmd
    Untracked:  oae_ccs_roms.Rproj.RData

Unstaged changes:
    Modified:   analysis/_site.yml
    Deleted:    analysis/read_data.Rmd
    Modified:   code/Workflowr_project_managment.R
    Modified:   code/regrid_cdr_eff_molar.R
    Modified:   code/regrid_dTA_dDIC.R

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/cdreff_plots.Rmd) and HTML (docs/cdreff_plots.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 639b38d vgfroh 2025-02-03 Column integrated plots and hovmoeller plots completed
html ce19057 vgfroh 2025-01-05 Build site.
Rmd 009b735 vgfroh 2025-01-05 Plotted time series of integrated dTA and CDREff data

Read this

Plotting the results of the full-grid integrated time series of dTA and CDR efficiency for each 3 phases

#loading packages
library(tidyverse)
library(data.table)
library(arrow)

# Path to intermediate computation outputs
path_outputs <- "/net/sea/work/vifroh/oae_ccs_roms_data/original_grid/"

# Path to save practice plots when working on them
path_plots <- "/net/sea/work/vifroh/test_plots/"

# loading in previous saved integrated CDR data
lanina_cdreff_sum <- read_feather(
  paste0(path_outputs, "lanina_CDReff_integrated.feather"))
neutral_cdreff_sum <- read_feather(
  paste0(path_outputs, "neutral_CDReff_integrated.feather"))
elnino_cdreff_sum <- read_feather(
  paste0(path_outputs, "elnino_CDReff_integrated.feather"))
# create combined table with "phase" column to identify each of the 3
full_cdreff <- rbindlist(
  list(lanina = lanina_cdreff_sum, neutral = neutral_cdreff_sum,
       elnino = elnino_cdreff_sum),
  idcol = "phase")

# add column for months since oae addition begins for x-axis
full_cdreff <- full_cdreff[, month := seq_len(.N), by = phase]
# plotting dTA
ggplot(full_cdreff, aes(x = month, y = dTA_sum/1e10, color = phase)) +
  geom_line() +
  labs(x = "Months Since OAE Begins",
       y = "Integrated moles of Alk (in 10^10)",
       title = "Total Added Alkalinity") +
  theme_bw()

Version Author Date
ce19057 vgfroh 2025-01-05 
# plotting CDReff
ggplot(full_cdreff, aes(x = month, y = CDR_eff, color = phase)) +
  geom_line() +
  labs(x = "Months Since OAE Begins",
       y = "CDR Efficinecy % (dDIC/dTA)",
       title = "Integrated CDR Efficiency ") +
  theme_bw()

Version Author Date
ce19057 vgfroh 2025-01-05 

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: openSUSE Leap 15.6

Matrix products: default
BLAS/LAPACK: /usr/local/OpenBLAS-0.3.28/lib/libopenblas_haswellp-r0.3.28.so;  LAPACK version 3.12.0

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       

time zone: Europe/Zurich
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] arrow_18.1.0.1    data.table_1.16.2 lubridate_1.9.3   forcats_1.0.0    
 [5] stringr_1.5.1     dplyr_1.1.4       purrr_1.0.2       readr_2.1.5      
 [9] tidyr_1.3.1       tibble_3.2.1      ggplot2_3.5.1     tidyverse_2.0.0  
[13] workflowr_1.7.1  

loaded via a namespace (and not attached):
 [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.4    
 [5] hms_1.1.3         digest_0.6.37     magrittr_2.0.3    timechange_0.3.0 
 [9] evaluate_1.0.1    grid_4.4.2        fastmap_1.2.0     rprojroot_2.0.4  
[13] jsonlite_1.8.9    processx_3.8.4    whisker_0.4.1     ps_1.8.1         
[17] promises_1.3.2    httr_1.4.7        fansi_1.0.6       scales_1.3.0     
[21] jquerylib_0.1.4   cli_3.6.3         rlang_1.1.4       bit64_4.5.2      
[25] munsell_0.5.1     withr_3.0.2       cachem_1.1.0      yaml_2.3.10      
[29] tools_4.4.2       tzdb_0.4.0        colorspace_2.1-1  httpuv_1.6.15    
[33] assertthat_0.2.1  vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4  
[37] git2r_0.35.0      bit_4.5.0         fs_1.6.5          pkgconfig_2.0.3  
[41] callr_3.7.6       pillar_1.9.0      bslib_0.8.0       later_1.4.1      
[45] gtable_0.3.6      glue_1.8.0        Rcpp_1.0.13-1     xfun_0.49        
[49] tidyselect_1.2.1  rstudioapi_0.17.1 knitr_1.49        farver_2.1.2     
[53] htmltools_0.5.8.1 labeling_0.4.3    rmarkdown_2.29    compiler_4.4.2   
[57] getPass_0.2-4