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Add reference page and vignettes for pkgdown site (#56) #56

Merged
merged 81 commits into from
Jan 5, 2019
Merged

Add reference page and vignettes for pkgdown site (#56) #56

merged 81 commits into from
Jan 5, 2019

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grabear
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@grabear grabear commented Jan 5, 2019 •
edited by sdhutchins
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This is a pretty large change. But git checkout this site and then pkgdown::preview_site()..

❗️ Starts to address #15.

MicrobiomeR 0.2.0

Documentations

  • Added vignettes to package and pkgdown config.
    • About
    • Introduction
    • Data Wrangling
    • Filtering
    • Analysis
  • Added reference sections to pkgdown config corresponding to @family tag.
    • Import
    • Formatting
    • Validation
    • Filtering (Basic, Advanced, Other)
    • Visualization
    • Color Palettes

Functional Changes

  • Renamed sample_filter to sample_id_filter.
  • Renamed get_phyloseq_obj to create_phyloseq.
  • Renamed format_metacoder_object to as_custom_format.
  • Updated vlookup and get_color_palette parameters.
  • Added the root_phyloseq_tree function.
  • Fixed minor bugs in code and docs.

grabear added 30 commits December 28, 2018 12:24
@grabear
Initial commit of package docs.
42d0203
@grabear
Added initial description.
995507a
@grabear
Updated with details section.
d1efc7d
@grabear
Updated bad NAMESPACE imports.
6ec1388
@grabear
Added Other Documentation section to package docs.
d780a4c
@grabear
updated NAMESPACE
df79e96
@grabear
Started vignettes setup.
fbe4d30
@grabear
Started vignettes setup.
a30a949
@grabear
Initialized introduction vignette.
66f4ec7
@grabear
Added MicrobiomeR Formats section to the introduction vignette.
8e56c91
@grabear
Added start to the data-wrangling vignette.
090d7da
@grabear
Updated the data-wrangling vignette.
08dc65e
@grabear
Updated docs.
ee69d3c
@grabear
Made a function for creating a rooted phylogenetic tree from a phylos…
7454fc3 
…eq object.
@grabear
Updated the roxygen documentation for the new function.
7dd0031
@grabear
Updated the get_phyloseq_obj function.
c63bfa5
@grabear
Added an import section to the data-wrangling vignette.
c891168
@grabear
Added a Formatting section to the data-wrangling vignette.
432298f
@grabear
Updated data-wrangling vignette.
c075590
@grabear
Updated introduction vignette.
7783d4a
@grabear
Added initial commit to workflow vignette.
53c8ec3
@grabear
Added a Data Wrangling section to the workflow vignette.
ad4d19a
@grabear
Added a Basic Filtering section to the workflow vignette.
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@grabear
Added the Advanced Filtering section to the workflow vignette.
df25902
@grabear
Renamed workflow vignette to filtering vignette.
345f508
@grabear
Added some minor fixes to vignette docs.
3e3a0fd
@grabear
Updated bug in transposer function.
3b04153
@grabear
Added the Other Filtering section.
b4a633f
@grabear
Added the Transposing subsection.
ed09379
@grabear
Updated transformer function.
5964418
@grabear grabear requested a review from sdhutchins January 5, 2019 00:22
sdhutchins
sdhutchins requested changes Jan 5, 2019
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@sdhutchins sdhutchins left a comment •
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A couple of spelling/grammar changes.

I think the new families are GREAT! We're almost there.

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@grabear grabear merged commit ce74018 into dev-master Jan 5, 2019
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grabear commented Jan 5, 2019

Hooray!! @sdhutchins

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Now...REST! lol @grabear (I know you won't. 😆 )

@sdhutchins sdhutchins changed the title Merge docs branch into dev-master Add reference page and vignettes for pkgdown site (#56) Jan 5, 2019
@grabear grabear deleted the pkg-doc-down-test branch January 7, 2019 17:40
@sdhutchins sdhutchins mentioned this pull request Jan 11, 2019
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Status: In Progress 🚧 🚧 Type: Documentation 📄 Type: Maintenance 🔧
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