From 2493676835dc12ceeeb09fe94b93abfc44403455 Mon Sep 17 00:00:00 2001 From: Aubrey Odom Date: Thu, 25 Jan 2024 14:02:08 -0500 Subject: [PATCH] Update site --- docs/404.html | 7 +-- docs/LICENSE-text.html | 7 +-- docs/LICENSE.html | 7 +-- docs/articles/LegATo_vignette.html | 7 +-- .../docs/animalcules_MAE_formatting.html | 7 +-- docs/articles/index.html | 7 +-- docs/authors.html | 7 +-- docs/index.html | 7 +-- docs/news/index.html | 7 +-- docs/pkgdown.yml | 2 +- docs/reference/LegATo-package.html | 7 +-- docs/reference/clean_animalcules_MAE.html | 7 +-- docs/reference/filter_animalcules_MAE.html | 7 +-- docs/reference/get_long_data.html | 7 +-- docs/reference/get_stacked_data.html | 7 +-- docs/reference/get_summary_table.html | 7 +-- docs/reference/get_top_taxa.html | 7 +-- docs/reference/index.html | 61 ++++++++++++++----- docs/reference/parse_MAE_SE.html | 7 +-- docs/reference/plot_alluvial.html | 7 +-- docs/reference/plot_spaghetti.html | 7 +-- docs/reference/plot_stacked_area.html | 7 +-- docs/reference/plot_stacked_bar.html | 7 +-- docs/reference/run_gee_model.html | 7 +-- docs/reference/test_hotelling_t2.html | 7 +-- 25 files changed, 117 insertions(+), 107 deletions(-) diff --git a/docs/404.html b/docs/404.html index bba2d37..ff5faab 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,8 +39,7 @@
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    diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f87b57c..0bd472e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -24,8 +24,7 @@
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    diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 8b94a06..93c0d5f 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -24,8 +24,7 @@
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    diff --git a/docs/articles/LegATo_vignette.html b/docs/articles/LegATo_vignette.html index 0b656d2..9579fa4 100644 --- a/docs/articles/LegATo_vignette.html +++ b/docs/articles/LegATo_vignette.html @@ -41,8 +41,7 @@
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    diff --git a/docs/articles/docs/animalcules_MAE_formatting.html b/docs/articles/docs/animalcules_MAE_formatting.html index a807876..c77238b 100644 --- a/docs/articles/docs/animalcules_MAE_formatting.html +++ b/docs/articles/docs/animalcules_MAE_formatting.html @@ -41,8 +41,7 @@
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    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 1f7c550..093045a 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: LegATo_vignette: LegATo_vignette.html animalcules_MAE_formatting: docs/animalcules_MAE_formatting.html -last_built: 2024-01-25T18:42Z +last_built: 2024-01-25T19:00Z urls: reference: https://aubreyodom.github.io/LegATo-docs/reference article: https://aubreyodom.github.io/LegATo-docs/articles diff --git a/docs/reference/LegATo-package.html b/docs/reference/LegATo-package.html index 82dde63..7d7c7e2 100644 --- a/docs/reference/LegATo-package.html +++ b/docs/reference/LegATo-package.html @@ -24,8 +24,7 @@
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    diff --git a/docs/reference/clean_animalcules_MAE.html b/docs/reference/clean_animalcules_MAE.html index 364e0fc..d428037 100644 --- a/docs/reference/clean_animalcules_MAE.html +++ b/docs/reference/clean_animalcules_MAE.html @@ -30,8 +30,7 @@
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    diff --git a/docs/reference/filter_animalcules_MAE.html b/docs/reference/filter_animalcules_MAE.html index c1bd6b6..e4e80c4 100644 --- a/docs/reference/filter_animalcules_MAE.html +++ b/docs/reference/filter_animalcules_MAE.html @@ -34,8 +34,7 @@
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    diff --git a/docs/reference/get_long_data.html b/docs/reference/get_long_data.html index 42c2728..0c0828f 100644 --- a/docs/reference/get_long_data.html +++ b/docs/reference/get_long_data.html @@ -28,8 +28,7 @@
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    diff --git a/docs/reference/get_stacked_data.html b/docs/reference/get_stacked_data.html index 62155ae..ca64ab5 100644 --- a/docs/reference/get_stacked_data.html +++ b/docs/reference/get_stacked_data.html @@ -30,8 +30,7 @@
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    diff --git a/docs/reference/get_summary_table.html b/docs/reference/get_summary_table.html index 03fa7d2..5e176fb 100644 --- a/docs/reference/get_summary_table.html +++ b/docs/reference/get_summary_table.html @@ -26,8 +26,7 @@
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    diff --git a/docs/reference/get_top_taxa.html b/docs/reference/get_top_taxa.html index 379302e..79d74cd 100644 --- a/docs/reference/get_top_taxa.html +++ b/docs/reference/get_top_taxa.html @@ -28,8 +28,7 @@
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    All functions +

    +

    Reformat MAEs into data frames

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    Take a animalcules-formatted MAE and reformat for visualizationa and analysis.

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    get_long_data() @@ -95,12 +110,18 @@

    All functionsget_top_taxa()

    Obtain a data.frame of ordered taxa abundances at a given level
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    Parse a MultiExperimentAssay object and extract the elements as data.frames
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    Plot and Visualize Longitudinal Microbial Data

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    All functionsplot_stacked_bar()
    Plot a stacked bar chart of microbial relative abundance
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    Analyze Longitudinal Microbial Data

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    Conduct Hotelling’s T-squared tests, NMIT, and model data.

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    run_gee_model()
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