Last updated: 2021-02-28

Checks: 7 0

Knit directory: emlr_mod_v_XXX/

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.

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(20200707)

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.

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: 73658ed

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 73658ed. 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/

Unstaged changes:
    Modified:   data/auxillary/params_local.rds

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/config_parameterization_local.Rmd) and HTML (docs/config_parameterization_local.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 73658ed Donghe-Zhu 2021-02-28 local rebuild
html feb991c Donghe-Zhu 2021-02-27 Build site.
html 287123c Donghe-Zhu 2021-02-27 Build site.
Rmd 764a9c2 Donghe-Zhu 2021-02-27 local rebuild
html 54d5b5b Donghe-Zhu 2021-02-27 Build site.
Rmd 2e836bf Donghe-Zhu 2021-02-27 local rebuild
html 330f064 Donghe-Zhu 2021-02-27 Build site.
Rmd f360282 Donghe-Zhu 2021-02-27 local rebuild
html adbc9bc Donghe-Zhu 2021-02-27 Build site.
Rmd a8a8f9c Donghe-Zhu 2021-02-27 local rebuild
html 5937141 Donghe-Zhu 2021-02-27 Build site.
Rmd 5f0bfca Donghe-Zhu 2021-02-27 local rebuild
html 4414bbf Donghe-Zhu 2021-02-27 Build site.
Rmd d24665a Donghe-Zhu 2021-02-27 local rebuild
html a265efb Donghe-Zhu 2021-02-27 Build site.
Rmd b4d5c17 Donghe-Zhu 2021-02-27 local rebuild
html 19edd1e Donghe-Zhu 2021-02-27 Build site.
Rmd 1ae5bb4 Donghe-Zhu 2021-02-27 local rebuild
html f20483f Donghe-Zhu 2021-02-26 Build site.
Rmd b3920b1 Donghe-Zhu 2021-02-26 local rebuild
html 6a2c7b3 Donghe-Zhu 2021-02-25 Build site.
Rmd 25aa736 Donghe-Zhu 2021-02-25 local rebuild
html 02b976d Donghe-Zhu 2021-02-24 Build site.
Rmd 309010e Donghe-Zhu 2021-02-24 local rebuild
html 354c224 Donghe-Zhu 2021-02-24 Build site.
Rmd d910d39 Donghe-Zhu 2021-02-24 local rebuild
html 1a0a88a Donghe-Zhu 2021-02-24 Build site.
Rmd 663e891 Donghe-Zhu 2021-02-24 local rebuild
html 57f701e Donghe-Zhu 2021-02-24 Build site.
Rmd 4d9b2d1 Donghe-Zhu 2021-02-24 local rebuild
html 06f3149 Donghe-Zhu 2021-02-16 Build site.
Rmd 716c041 Donghe-Zhu 2021-02-15 local rebuild
html 401eab3 Donghe-Zhu 2021-02-15 Build site.
Rmd 5a31947 Donghe-Zhu 2021-02-15 local rebuild
html e3bba84 Donghe-Zhu 2021-02-15 Build site.
Rmd 9f346bd Donghe-Zhu 2021-02-15 local rebuild
html 5dce4b1 Donghe-Zhu 2021-02-15 Build site.
Rmd 35b0f2e Donghe-Zhu 2021-02-15 local rebuild
html 4469a0c Donghe-Zhu 2021-02-13 Build site.
Rmd c99d126 Donghe-Zhu 2021-02-13 local rebuild
Rmd 8186d57 Donghe-Zhu 2021-02-10 apply nr_obs
html 5ae6a69 Donghe-Zhu 2021-02-10 Build site.
Rmd 6d6aed8 Donghe-Zhu 2021-02-10 1
html 05385dc Donghe-Zhu 2021-02-10 Build site.
Rmd 67fa8d0 Donghe-Zhu 2021-02-09 local rebuild
html f791ae4 Donghe-Zhu 2021-02-09 Build site.
Rmd b18769b Donghe-Zhu 2021-02-09 local rebuild
html f71ae34 Donghe-Zhu 2021-02-09 Build site.
Rmd f433615 Donghe-Zhu 2021-02-09 local rebuild
html c011832 Donghe-Zhu 2021-02-09 Build site.
Rmd b7a2ab2 Donghe-Zhu 2021-02-09 local rebuild
html a145fa7 Donghe-Zhu 2021-02-09 Build site.
Rmd 37a41c8 Donghe-Zhu 2021-02-09 local rebuild
html c344e42 Donghe-Zhu 2021-02-08 Build site.
Rmd 8f5fa79 Donghe-Zhu 2021-02-08 local rebuild
html 2f095d7 Donghe-Zhu 2021-02-07 Build site.
Rmd a923be1 Donghe-Zhu 2021-02-07 local rebuild
html 2305044 Donghe-Zhu 2021-02-07 Build site.
Rmd c3638c1 Donghe-Zhu 2021-02-07 local rebuild
html 1fad5f1 Donghe-Zhu 2021-02-07 Build site.
Rmd 3ddd358 Donghe-Zhu 2021-02-07 local rebuild
html ca03c39 Donghe-Zhu 2021-02-07 Build site.
Rmd b8981f0 Donghe-Zhu 2021-02-07 local rebuild
html e2ffc14 Donghe-Zhu 2021-02-05 Build site.
Rmd 55cdfe6 Donghe-Zhu 2021-02-05 local rebuild
html cd7c52c Donghe-Zhu 2021-02-04 Build site.
Rmd 8c4ddb3 Donghe-Zhu 2021-02-03 plots
html bcf84f4 Donghe-Zhu 2021-02-02 Build site.
Rmd fad137a Donghe-Zhu 2021-02-02 local rebuild
html a518739 Donghe-Zhu 2021-02-01 Build site.
Rmd ff9c7e6 Donghe-Zhu 2021-02-01 local rebuild
html 61666de Donghe-Zhu 2021-01-31 Build site.
Rmd 647c56d Donghe-Zhu 2021-01-31 local rebuild
html 865b582 Donghe-Zhu 2021-01-31 Build site.
Rmd d35a1fc Donghe-Zhu 2021-01-31 local rebuild
html 3e68089 Donghe-Zhu 2021-01-31 Build site.
Rmd 727f0d9 Donghe-Zhu 2021-01-31 local rebuild
html ecf335c Donghe-Zhu 2021-01-31 Build site.
Rmd 9781315 Donghe-Zhu 2021-01-31 local rebuild
html a618965 Donghe-Zhu 2021-01-31 Build site.
Rmd a815096 Donghe-Zhu 2021-01-31 local rebuild
html 59e006e Donghe-Zhu 2021-01-31 Build site.
Rmd 7829e3c Donghe-Zhu 2021-01-31 local rebuild
html a1c8f87 Donghe-Zhu 2021-01-31 Build site.
Rmd 66daaf4 Donghe-Zhu 2021-01-31 local rebuild
html ae5c18f Donghe-Zhu 2021-01-31 Build site.
Rmd 7385f2e Donghe-Zhu 2021-01-31 local rebuild
html b50fe52 Donghe-Zhu 2021-01-31 Build site.
Rmd a543fb2 Donghe-Zhu 2021-01-31 local rebuild
Rmd ac99ae5 jens-daniel-mueller 2021-01-29 code review
html ac99ae5 jens-daniel-mueller 2021-01-29 code review
Rmd 74d4c5f Donghe-Zhu 2021-01-29 1
html b5bdcaf Donghe-Zhu 2021-01-29 Build site.
Rmd b234505 Donghe-Zhu 2021-01-29 MLR approach across all depth
html 442010d Donghe-Zhu 2021-01-29 Build site.
Rmd e67e7dd Donghe-Zhu 2021-01-29 surface equilibrium approach across all latitudes irrespective of gamma
Rmd 8d1f5b5 Donghe-Zhu 2021-01-29 para
html 372adf5 Donghe-Zhu 2021-01-29 Build site.
Rmd 016597a Donghe-Zhu 2021-01-29 local rebuild after revision
html af8788e Donghe-Zhu 2021-01-29 Build site.
Rmd f5886d8 Donghe-Zhu 2021-01-29 no aou
html 21c91c9 Donghe-Zhu 2021-01-29 Build site.
Rmd 81cae7e Donghe-Zhu 2021-01-29 no p_star
html eded038 Donghe-Zhu 2021-01-29 Build site.
Rmd e943c60 Donghe-Zhu 2021-01-29 no nitrate
html 541d4dd Donghe-Zhu 2021-01-29 Build site.
Rmd 4fc08bc Donghe-Zhu 2021-01-28 no phosphate
html 6a75576 Donghe-Zhu 2021-01-28 Build site.
Rmd 3e2209f Donghe-Zhu 2021-01-28 no silicate
html 16fba40 Donghe-Zhu 2021-01-28 Build site.
Rmd ec42957 Donghe-Zhu 2021-01-28 local rebuild
Rmd 4584be9 Donghe-Zhu 2021-01-28 latest
html 12bc567 Donghe-Zhu 2021-01-27 Build site.
Rmd 9655866 Donghe-Zhu 2021-01-27 SO with lat random
html ceed31b Donghe-Zhu 2021-01-27 Build site.
Rmd 0098207 Donghe-Zhu 2021-01-27 SO with grid random
html 342402d Donghe-Zhu 2021-01-27 Build site.
Rmd 946d676 Donghe-Zhu 2021-01-27 local rebuild after revision
html 5bad5c2 Donghe-Zhu 2021-01-27 Build site.
Rmd c2c9529 Donghe-Zhu 2021-01-27 random subsetting based on lat
html 61efb56 Donghe-Zhu 2021-01-25 Build site.
Rmd 1f42a92 Donghe-Zhu 2021-01-25 2 x slabs
html 48f638e Donghe-Zhu 2021-01-25 Build site.
Rmd 17a7d1a Donghe-Zhu 2021-01-25 MLR = SO
html c1cec47 Donghe-Zhu 2021-01-25 Build site.
Rmd 560dcf7 Donghe-Zhu 2021-01-25 no temp
html 05ffb0c Donghe-Zhu 2021-01-25 Build site.
Rmd bc7b183 Donghe-Zhu 2021-01-25 no sal
html 8b97165 Donghe-Zhu 2021-01-25 Build site.
Rmd c41c01f Donghe-Zhu 2021-01-25 OXYGEN REPLACE AOU
html c569946 Donghe-Zhu 2021-01-24 Build site.
Rmd 846bfc0 Donghe-Zhu 2021-01-24 no nitrate
html a2f0d56 Donghe-Zhu 2021-01-23 Build site.
Rmd 0819197 Donghe-Zhu 2021-01-23 local rebuild after revision
html 28509fc Donghe-Zhu 2021-01-23 Build site.
Rmd 550f399 Donghe-Zhu 2021-01-23 local rebuild after revision
html 4c28e4a Donghe-Zhu 2021-01-22 Build site.
Rmd a703e37 Donghe-Zhu 2021-01-22 local rebuild after revision
html 24cc264 jens-daniel-mueller 2021-01-22 cleaned /docs before creating copies
html 88eb28f Donghe-Zhu 2021-01-21 Build site.
Rmd 14827d0 Donghe-Zhu 2021-01-21 generate diagnostic plots
html 2679490 Donghe-Zhu 2021-01-21 Build site.
html 7891955 Donghe-Zhu 2021-01-21 Build site.
Rmd 13c3031 Donghe-Zhu 2021-01-21 Test with nitrate replace oxygen as predictor, atmospheric equilibrium and plot set to n
html d4cf1cb Donghe-Zhu 2021-01-21 Build site.
Rmd 167eeec Donghe-Zhu 2021-01-21 surface DIC calculation with atmospheric equilibrium option
html 1f3e5b6 jens-daniel-mueller 2021-01-20 Build site.
Rmd 30afcd9 jens-daniel-mueller 2021-01-20 local rebuild after revision
Rmd d76b436 Donghe-Zhu 2021-01-19 model quality check
html 0e7bdf1 jens-daniel-mueller 2021-01-15 cleaning template repository
html 73cbef3 jens-daniel-mueller 2021-01-15 Build site.
html 4571843 jens-daniel-mueller 2021-01-14 revision and html deleted for template copying
html 23151cd jens-daniel-mueller 2021-01-14 Build site.
html b3564aa jens-daniel-mueller 2021-01-14 Build site.
Rmd 88db051 jens-daniel-mueller 2021-01-14 local rebuild after revision
html 8d032c3 jens-daniel-mueller 2021-01-14 Build site.
Rmd 8931f13 Donghe-Zhu 2021-01-13 rebuild web
html 022871c Donghe-Zhu 2021-01-13 Build site.
Rmd d44f36f Donghe-Zhu 2021-01-13 reorder analysis final
html 17dee1d jens-daniel-mueller 2021-01-13 Build site.
html a076226 Donghe-Zhu 2021-01-11 Build site.
Rmd 52eff18 Donghe-Zhu 2021-01-09 Implemet model_run and subsetting
html 7cdea0c jens-daniel-mueller 2021-01-06 Build site.
html fa85b93 jens-daniel-mueller 2021-01-06 Build site.
html e5cb81a Donghe-Zhu 2021-01-05 Build site.
Rmd 608cc45 Donghe-Zhu 2021-01-05 modification of analysis
html a499f10 Donghe-Zhu 2021-01-05 Build site.
Rmd 715bdb4 Donghe-Zhu 2021-01-02 model modification
html fb8a752 Donghe-Zhu 2020-12-23 Build site.
html 8fae0b2 Donghe-Zhu 2020-12-21 Build site.
html c8b76b3 jens-daniel-mueller 2020-12-19 Build site.
Rmd b5fedce jens-daniel-mueller 2020-12-19 first build after creating model template
Rmd 8e8abf5 Jens Müller 2020-12-18 Initial commit

1 Definition

The following local parametrisations (i.e. relevant for this sensitivity run) were defined to run the analysis:

# neutral density thresholds to cut the Atlantic ocean into slabs
slabs_Atl <-
  c(
    -Inf,
    26.00,
    26.50,
    26.75,
    27.00,
    27.25,
    27.50,
    27.75,
    27.85,
    27.95,
    28.05,
    28.10,
    28.15,
    28.20,
    Inf
  )

# neutral density thresholds to cut the Indo-Pacific ocean into slabs
slabs_Ind_Pac <-
  c(-Inf,
    26.00,
    26.50,
    26.75,
    27.00,
    27.25,
    27.50,
    27.75,
    27.85,
    27.95,
    28.05,
    28.10,
    Inf)

# Predictors for MLR model
MLR_predictors <- c(
                "sal",
                "temp",
                "oxygen",
                "aou",
                "nitrate",
                "silicate",
                "silicate_star",
                "phosphate",
                "phosphate_star")

params_local <-
  lst(
    # model climate forcing with options of variable ("AD") or constant ("CB")
    model_runs = "CB",
    # model subsetting with options of "GLODAP" or "random"
    subsetting = "random",
    # random subsetting with options of "grid" or "lat"
    random = "lat",
    # ID of current sensitivity run
    Version_ID = "v_XXX",
    # f flags accepted for GLODAP data
    flag_f = c(2),
    # qc flags accepted for GLODAP data
    flag_qc = c(1),
    # Should A16 cruise from 2013/14 be included in middle era (y/n)
    A16_GO_SHIP = "y",
    # Shallowest depth for data to be included in MLR fitting
    depth_min = 150,
    # Shallowest water depth for data to be included in MLR fitting
    bottomdepth_min = 0,
    # Lowest neutral density to map Cant with eMLR approach (in surface layer?)
    gamma_min = 26,
    # break years for eras, numbers indicate the upper end of the respective era
    era_breaks_GLODAP = c(1981, 1999, 2012, Inf),
    era_breaks_random = c(1981, 1999, 2012, Inf),
    # ID for basins for MLR fits: 2, 5, SO, AIP
    MLR_basins = "2",
    # Select the target variable for MLR, either "tco2", "cstar" or "cstar_tref"
    MLR_target = "cstar_tref",
    # see above
    MLR_predictors = MLR_predictors,
    # Maxmimum number of MLR predictors
    MLR_predictors_max = 9,
    # Minimum number of MLR predictors
    MLR_predictors_min = 3,
    # Total number of MLR fits taken into account
    MLR_number = 10,
    # Fitted model type rlm or lm
    MLR_type = "lm",
    # Criterion to select best MLR fits, either "rmse" or "aic"
    MLR_criterion = "aic",
    # see above
    slabs_Atl = slabs_Atl,
    # see above
    slabs_Ind_Pac = slabs_Ind_Pac,
    # Stoichiometric ratio of C to P
    rCP = 117,
    # Stoichiometric ratio of N to P
    rNP = 16,
    # Stoichiometric ratio of P to O (PO4* calculation)
    rPO = 170,
    # Offset P to O (PO4* calculation)
    rPO_offset = 1.95,
    # surface DIC calculation with options of "revelle factor" or "atmospheric equilibrium" or "atmospheric pCO2 increase"
    surface_DIC_calculation = "atmospheric pCO2 increase",
    # Preindustrial atmospheric pCO2
    preind_atm_pCO2 = 280,
    # generate a high number of diagnostic plots while running the analysis (y/n)
    plot_all_figures = "n"
  )

2 Write file

Parameterization criteria are locally stored and used throughout this sensitivty case.

params_local %>%
  write_rds(here::here("data/auxillary",
                       "params_local.rds"))

3 Create folders

Folders for each new sensitivity run are automatically created.


sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2

Matrix products: default
BLAS:   /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/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_0.5.0   stringr_1.4.0   dplyr_1.0.2     purrr_0.3.4    
 [5] readr_1.4.0     tidyr_1.1.2     tibble_3.0.4    ggplot2_3.3.3  
 [9] tidyverse_1.3.0 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0 xfun_0.20        haven_2.3.1      colorspace_2.0-0
 [5] vctrs_0.3.6      generics_0.1.0   htmltools_0.5.0  yaml_2.2.1      
 [9] blob_1.2.1       rlang_0.4.10     later_1.1.0.1    pillar_1.4.7    
[13] withr_2.3.0      glue_1.4.2       DBI_1.1.0        dbplyr_1.4.4    
[17] modelr_0.1.8     readxl_1.3.1     lifecycle_0.2.0  munsell_0.5.0   
[21] gtable_0.3.0     cellranger_1.1.0 rvest_0.3.6      evaluate_0.14   
[25] knitr_1.30       httpuv_1.5.4     fansi_0.4.1      broom_0.7.5     
[29] Rcpp_1.0.5       promises_1.1.1   backports_1.1.10 scales_1.1.1    
[33] jsonlite_1.7.2   fs_1.5.0         hms_0.5.3        digest_0.6.27   
[37] stringi_1.5.3    rprojroot_2.0.2  grid_4.0.3       here_1.0.1      
[41] cli_2.2.0        tools_4.0.3      magrittr_2.0.1   crayon_1.3.4    
[45] whisker_0.4      pkgconfig_2.0.3  ellipsis_0.3.1   xml2_1.3.2      
[49] reprex_0.3.0     lubridate_1.7.9  assertthat_0.2.1 rmarkdown_2.5   
[53] httr_1.4.2       rstudioapi_0.13  R6_2.5.0         git2r_0.27.1    
[57] compiler_4.0.3