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DeAD- day2007 - #239

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vaasukimarupaka wants to merge 34 commits into
ktoddbrown:mainfrom
bcheser:DeAD_Day2007
Open

DeAD- day2007#239
vaasukimarupaka wants to merge 34 commits into
ktoddbrown:mainfrom
bcheser:DeAD_Day2007

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@vaasukimarupaka

@vaasukimarupaka vaasukimarupaka commented Apr 20, 2026

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Data Rescue Plan

  • Lead
    • Read the article or data resource and the discription of the target project
    • Create a fresh fork of the primary repository https://github.com/ktoddbrown/SoilDRaH/tree/main, it might be useful to rename it 'SoilDRaH_AuthorYYYY'
    • Create a copy of this template folder and rename it to AuthorYYYY
    • Fill out Data summary section (except for the Files), the Data Rescue Plan (here!), and update the author section of the yml to reflect who is working on the rescue
    • Create a GitHub issue from the Data Rescue template and get feedback from a reviewer on the project (Dr Todd-Brown or a grad student typically).
    • Add the reviewer to the author list in the yml
  • Do
    • Create a spreadsheet with TableN and export it to csv
    • Extract points from FigureM and export it to csv
    • Transcribe or copy the method section
    • Insert references to bib entries
    • reformat equations and mathematical symbols as LaTex
    • reformat text using Markdown
    • Create a bib file with the citations from the methods section
    • Push to your local fork and get a second transcription pushed to your local fork by someone else on the project
  • Measure
    • cross check with second transcriber for tables and methods, and resolve any differences
    • compile or render this ReadMe with all chunks up through the Level 0 data rescue section with eval: true
    • push to your local fork and create a pull request to the main branch of the primary repository
    • address any revisions in your pull request review
    • celebrate!

bcheser and others added 30 commits April 3, 2026 16:31
@bcheser
adding data rescue files to this folder
e576458
@JennavieveK
Transcribed tables 1 (secondary) and 2 (primary)
bc45458
@JennavieveK
Fixing .csv
f520808
@bcheser
transcribe table 2 and 3 (primary 3, secondary 2)
ed64633
@vaasukimarupaka
adding the transcribed files: methods.md primary citation.bib and tab…
44af9fb 
…le 3 csv
@JennavieveK
Fixed table 1 and table 2
a4f84b0
@JennavieveK
Renamed table 2
d1560d7
@bcheser
crosscheck table 2 done
81ce142
@angelacanini-a11y
Table 1 for Day2007 - issue updated too
0be479d
@angelacanini-a11y
test push
fb063fe
@angelacanini-a11y
added AC to name
1649a62
@angelacanini-a11y
test commit
b566e80
@angelacanini-a11y
adding table1 transcription (primary)
1a923fd
@angelacanini-a11y
added period
8c08d83
@angelacanini-a11y
Merge branch 'DeAD_Day2007' of https://github.com/bcheser/SoilDRaH_bc …
2a4c6f8 
…into DeAD_Day2007

t #
@angelacanini-a11y
space removed
3e4e4e2
@angelacanini-a11y
removed more whitespaces
7cb3791
@angelacanini-a11y
remove "
7da74af
@angelacanini-a11y
changed "leaves" to "litter" to match og paper
f2cc50a
@angelacanini-a11y
added newline to the end
3f756bf
@JennavieveK
Pushing methods.bib (secondary)
b6606b6
@angelacanini-a11y
added rmd methods_ac (missing a citation)
c8adeae
@vaasukimarupaka
cross-checks complete for methods.md!
8423b5a
@vaasukimarupaka
changed it to .md format
cca4aa1
@vaasukimarupaka
cross-checks done!
4a39fb5
@bcheser
methods citation
c6e833e
@vaasukimarupaka
cross checks!
fd2cf4f
@vaasukimarupaka
Renaming files and having a common naming convention for README
e3610d2
@vaasukimarupaka
just some coding practice with the markdown!
2ef92b0
@JennavieveK
Added table 2
1dae3a5
ktoddbrown
ktoddbrown requested changes Jul 21, 2026
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@ktoddbrown ktoddbrown left a comment

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Some things to tighten up here before integrating into the main branch. Let me know if you have questions.

Comment thread 01_DataRescue/Data2007/AuthorYYYY.bib

@ktoddbrown ktoddbrown Jul 21, 2026

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I think the Data2007 files need to be removed using git rm. These appear to be an incomplete draft.

Comment thread 01_DataRescue/Data2007/README_AuthorYYYY.qmd

@ktoddbrown ktoddbrown Jul 21, 2026

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Remove this file using git rm

Comment thread 01_DataRescue/Data2007/AuthorYYYY_TableN.csv

@ktoddbrown ktoddbrown Jul 21, 2026

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Remove this file using git rm

Comment thread 01_DataRescue/Data2007/AuthorYYYY_Methods.md

@ktoddbrown ktoddbrown Jul 21, 2026

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Remove this file using git rm

Comment thread 01_DataRescue/Data2007/AuthorYYYY_Methods.bib

@ktoddbrown ktoddbrown Jul 21, 2026

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Remove this file using git rm

Comment thread 01_DataRescue/Day2007/README_Day2007.qmd

```{bash}
#| label: compareTableN
#| eval: false

@ktoddbrown ktoddbrown Jul 21, 2026

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Set to True

Comment thread 01_DataRescue/Day2007/README_Day2007.qmd
# You will want to repeat the line below to cross check each csv and md file in the
#... data rescue. Having no lines flagged by this command will ensure that each character matches exactly.

diff --strip-trailing-cr --suppress-common-lines -y temp/AuthorYYYY_TableN_ABC.md AuthorYYYY_TableN.md

@ktoddbrown ktoddbrown Jul 21, 2026

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Update file names

Comment thread 01_DataRescue/Day2007/README_Day2007.qmd
diff --strip-trailing-cr --suppress-common-lines -y temp/AuthorYYYY_Methods_ABC.md AuthorYYYY_Methods.md
```

```{bash eval=FALSE, echo=FALSE}

@ktoddbrown ktoddbrown Jul 21, 2026

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evaluate and echo.

Comment thread 01_DataRescue/Day2007/README_Day2007.qmd

Any different to the cross check for the methods section will be output after this line.

```{bash}

@ktoddbrown ktoddbrown Jul 21, 2026

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Evaluate this chunk.

Comment thread 01_DataRescue/Day2007/README_Day2007.qmd
#| eval: false
# You will want to repeat the line below to cross check each csv and md file in the
#... data rescue. Having no lines flagged by this command will ensure that each character matches exactly.
diff --strip-trailing-cr --suppress-common-lines -y temp/AuthorYYYY_Methods_ABC.md AuthorYYYY_Methods.md

@ktoddbrown ktoddbrown Jul 21, 2026

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Update fiel names

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5 participants

@vaasukimarupaka @ktoddbrown @bcheser @JennavieveK @angelacanini-a11y