Reorganized tutorials book to include vignette section by kimberlyh66 · Pull Request #81 · terraref/tutorials

kimberlyh66 · 2019-01-23T22:03:02Z

Please review changes that I have made to include a vignette section. Some changes are old and for the traits tutorial.

… bash shell.

…SON function.

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

…rence. also updated comment on embedded shiny app (link to traitvis app does work).

… tutorial and terraref bety home page

…not work on Windows

…y_height' -removed geom_smooth layer from ggplot

… results of the 'query-danforth' r chunk

…enotype Analysis.

…bles chunk (running this chunk results in a HTTP 504 Gateway Timeout)

…using options

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

… traits_tutorials

dlebauer · 2019-01-25T19:36:56Z

@kimberlyh66 can you resolve the merge conflicts so that I can finish up my review? I am not sure where the merge conflicts happened, but it seems that for the most part we want what is in the traits_tutorials branch to replace what is in master. You can either do it here: https://github.com/terraref/tutorials/pull/81/conflicts or if you want to take everything from this branch git checkout --ours PATH/FILE https://easyengine.io/tutorials/git/git-resolve-merge-conflicts

dlebauer

What are the steps required to get this to compile now? Are there changes in other branches that I need to merge in? For example, it seems that the file names listed in _bookdown.yml are inconsistent w/ the files in the vignettes folder

kimberlyh66 · 2019-01-28T19:07:55Z

I think you will need to merge in Kristina's branch (#85) as well as Chris' branch (#86). I will change the file names in _bookdown.yml to be consistent with those in the vignettes folder.

Merge branch 'traits_tutorials' of github.com:terraref/tutorials into traits_tutorials # Conflicts: # _bookdown.yml

Co-Authored-By: Chris-Schnaufer <schnaufer@email.arizona.edu>

* set python engine to python3

Images vignette

…g in a query

… traits_tutorials

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

kimberlyh66 and others added 30 commits November 5, 2018 13:58

fixed link to agronomic metadata tutorial

7b8751d

Updated tutorial. Added a summary showing the 3 ways to access API data.

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Further updated the tutorial on how to access API using URL query and…

2c80e2e

… bash shell.

Further updated tutorial. Added short comment on the use of the fromJ…

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…SON function.

Further updated R jsonlite portion of tutorial

b017aa2

Update traits/01-web-access.Rmd

bd4c8f4

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

added comment. link to traitvis webapp not working.

d24928c

fixed links to terraref and pecan sites, betydb schemas, and doi refe…

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…rence. also updated comment on embedded shiny app (link to traitvis app does work).

updated beta user program link, and fixed links to agronomic metadata…

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… tutorial and terraref bety home page

made changes according to previous comments

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Merge branch 'master' of github.com:kimberlyh66/tutorials

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made minor edits - assuming betykey in traits directory since ~ does …

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…not work on Windows

minor edit - removed comment

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-changed trait in sorghum height search from 'canopy_cover' to 'canop…

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…y_height' -removed geom_smooth layer from ggplot

made minor edits. changed api version from 'beta' to 'v1' and hid the…

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… results of the 'query-danforth' r chunk

changed image name from 'betydb-postgis' to 'bety-postgis'

82d34ee

changed ~ (home directory) to . (current directory)

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changed ~ (home directory) to . (current directory)

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Removed YAML metadata header. Added Chapter title.

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Removed YAML header. Added chapter title.

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Changed chapter title to be more specific. Chapter 6 title is also Ph…

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…enotype Analysis.

Removed text comment

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updated chapter title - made more specific

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commented out all chunks that were related to the traits-05-get-varia…

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…bles chunk (running this chunk results in a HTTP 504 Gateway Timeout)

set betydb_query parameters using options

7b1f88d

loaded in some needed packages; set betydb_query function parameters …

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…using options

set options for chunks to improve look of output

b20b78b

changed headers to level 2 so not treated like a chapter title

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set warning option to FALSE

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removed .Rmd files that are not ready to be built into book

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kimberlyh66 and others added 8 commits January 24, 2019 15:00

removed all references to the public key

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Update traits/05-maricopa-field-scanner.Rmd

1ff1006

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

Update traits/05-maricopa-field-scanner.Rmd

5dcecd5

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

removed references to public key and made minor spacing edits

3b7020d

deleted file

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removed "installing database locally" section

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Merge branch 'traits_tutorials' of github.com:terraref/tutorials into…

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… traits_tutorials

changed title and added my draft of traits vignette

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Chris-Schnaufer and others added 4 commits January 25, 2019 15:10

Added in vignette contents

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Reverting my changes

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Fleshed out images vignette

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Merge branch 'master' into traits_tutorials

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dlebauer reviewed Jan 28, 2019

View reviewed changes

kimberlyh66 and others added 7 commits January 28, 2019 12:19

updated file names to match those in the vignettes folder

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updated file names

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Merge branch 'traits_tutorials' of github.com:terraref/tutorials into traits_tutorials # Conflicts: # _bookdown.yml

Update vignettes/03-get-images-python.Rmd

ad5b12c

Co-Authored-By: Chris-Schnaufer <schnaufer@email.arizona.edu>

Added information on getting API keys

ea0874f

* added ending to comment in index.Rmd

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* set python engine to python3

Cleaned up an API key related spot

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Removed some extra words

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dlebauer reviewed Jan 28, 2019

View reviewed changes

Comment thread vignettes/01-get-trait-data-R.Rmd Outdated

Chris-Schnaufer approved these changes Jan 29, 2019

View reviewed changes

Comment thread traits/02-betydb-api-access.Rmd

Comment thread traits/04-danforth-indoor-phenotyping-facility.Rmd

Merge pull request #96 from terraref/images_vignette

bcc4a5b

Images vignette

dlebauer approved these changes Jan 29, 2019

View reviewed changes

dlebauer merged commit 88ea83a into master Jan 29, 2019

kimberlyh66 and others added 3 commits January 29, 2019 15:22

added a clarifying comment on how to use ~ for partial string matchin…

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…g in a query

Merge branch 'traits_tutorials' of github.com:terraref/tutorials into…

187f538

… traits_tutorials

Update vignettes/01-get-trait-data-R.Rmd

4f2e89d

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>

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Reorganized tutorials book to include vignette section#81

Reorganized tutorials book to include vignette section#81
dlebauer merged 96 commits intomasterfrom
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kimberlyh66 commented Jan 23, 2019 •

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