From d245660eeb2ae509c065768d329b111885049a28 Mon Sep 17 00:00:00 2001
From: d-callan <53306535+d-callan@users.noreply.github.com>
Date: Tue, 30 Apr 2024 19:51:14 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?=
 =?UTF-8?q?meDB/microbiomeComputations@73af8659e5f4a75ba20a87e20dc9376702a?=
 =?UTF-8?q?14022=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                         | 2 +-
 LICENSE.html                                     | 2 +-
 authors.html                                     | 6 +++---
 index.html                                       | 2 +-
 pkgdown.yml                                      | 2 +-
 reference/AbsoluteAbundanceData-class.html       | 2 +-
 reference/AbundanceData-class.html               | 2 +-
 reference/Comparator-class.html                  | 2 +-
 reference/Comparator-methods.html                | 2 +-
 reference/DifferentialAbundanceResult-class.html | 2 +-
 reference/alphaDiv-methods.html                  | 2 +-
 reference/betaDiv-methods.html                   | 2 +-
 reference/getAbundances.html                     | 2 +-
 reference/index.html                             | 2 +-
 reference/internalDiffAbund-methods.html         | 2 +-
 reference/microbiomeComputations-package.html    | 2 +-
 reference/rankedAbundance-methods.html           | 2 +-
 reference/removeIncompleteSamples.html           | 2 +-
 reference/selfCorrelation-methods.html           | 2 +-
 search.json                                      | 2 +-
 20 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/404.html b/404.html
index 9f1b7c7..920cd74 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://microbiomedb.github.io/microbiomeComputations/index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 6007c48..ba34d77 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 7d425c3..2d5a7e1 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -59,13 +59,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Callan D, Blevins A (2024).
 <em>microbiomeComputations: Compute Results for Microbiome Analyses</em>.
-R package version 5.1.1, https://microbiomedb.github.io/microbiomeComputations/, <a href="https://github.com/microbiomeDB/microbiomeComputations" class="external-link">https://github.com/microbiomeDB/microbiomeComputations</a>. 
+R package version 5.1.2, https://microbiomedb.github.io/microbiomeComputations/, <a href="https://github.com/microbiomeDB/microbiomeComputations" class="external-link">https://github.com/microbiomeDB/microbiomeComputations</a>. 
 </p>
       <pre>@Manual{,
   title = {microbiomeComputations: Compute Results for Microbiome Analyses},
   author = {Danielle Callan and Ann Blevins},
   year = {2024},
-  note = {R package version 5.1.1, https://microbiomedb.github.io/microbiomeComputations/},
+  note = {R package version 5.1.2, https://microbiomedb.github.io/microbiomeComputations/},
   url = {https://github.com/microbiomeDB/microbiomeComputations},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index a57dfef..2cadd5c 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index b1553c5..1f9ecdc 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-04-30T19:48Z
+last_built: 2024-04-30T19:51Z
 urls:
   reference: https://microbiomedb.github.io/microbiomeComputations/reference
   article: https://microbiomedb.github.io/microbiomeComputations/articles
diff --git a/reference/AbsoluteAbundanceData-class.html b/reference/AbsoluteAbundanceData-class.html
index 6713d47..bde7d20 100644
--- a/reference/AbsoluteAbundanceData-class.html
+++ b/reference/AbsoluteAbundanceData-class.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/AbundanceData-class.html b/reference/AbundanceData-class.html
index e2c0f23..a3e8d77 100644
--- a/reference/AbundanceData-class.html
+++ b/reference/AbundanceData-class.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Comparator-class.html b/reference/Comparator-class.html
index 364a5d1..59b7518 100644
--- a/reference/Comparator-class.html
+++ b/reference/Comparator-class.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Comparator-methods.html b/reference/Comparator-methods.html
index 0f6bb6e..ee2e81f 100644
--- a/reference/Comparator-methods.html
+++ b/reference/Comparator-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/DifferentialAbundanceResult-class.html b/reference/DifferentialAbundanceResult-class.html
index 852bed2..6e283cf 100644
--- a/reference/DifferentialAbundanceResult-class.html
+++ b/reference/DifferentialAbundanceResult-class.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/alphaDiv-methods.html b/reference/alphaDiv-methods.html
index d03356a..3520309 100644
--- a/reference/alphaDiv-methods.html
+++ b/reference/alphaDiv-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/betaDiv-methods.html b/reference/betaDiv-methods.html
index 17a4139..07bb5fd 100644
--- a/reference/betaDiv-methods.html
+++ b/reference/betaDiv-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getAbundances.html b/reference/getAbundances.html
index 5377d3c..a4b03b2 100644
--- a/reference/getAbundances.html
+++ b/reference/getAbundances.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 4fe99f8..98ed12f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/internalDiffAbund-methods.html b/reference/internalDiffAbund-methods.html
index c975874..6f5e670 100644
--- a/reference/internalDiffAbund-methods.html
+++ b/reference/internalDiffAbund-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/microbiomeComputations-package.html b/reference/microbiomeComputations-package.html
index 87bea41..68efe15 100644
--- a/reference/microbiomeComputations-package.html
+++ b/reference/microbiomeComputations-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rankedAbundance-methods.html b/reference/rankedAbundance-methods.html
index a54eeac..a6b9947 100644
--- a/reference/rankedAbundance-methods.html
+++ b/reference/rankedAbundance-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/removeIncompleteSamples.html b/reference/removeIncompleteSamples.html
index 3c7f59e..2d501b4 100644
--- a/reference/removeIncompleteSamples.html
+++ b/reference/removeIncompleteSamples.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selfCorrelation-methods.html b/reference/selfCorrelation-methods.html
index 5feafc6..f321afc 100644
--- a/reference/selfCorrelation-methods.html
+++ b/reference/selfCorrelation-methods.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">microbiomeComputations</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 4df0faa..63ab45e 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://microbiomedb.github.io/microbiomeComputations/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 <http://www.apache.org/licenses/>","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeComputations/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. 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(Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/microbiomeComputations/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer. Ann Blevins. Author.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D, Blevins (2024). microbiomeComputations: Compute Results Microbiome Analyses. R package version 5.1.1, https://microbiomedb.github.io/microbiomeComputations/, https://github.com/microbiomeDB/microbiomeComputations.","code":"@Manual{,   title = {microbiomeComputations: Compute Results for Microbiome Analyses},   author = {Danielle Callan and Ann Blevins},   year = {2024},   note = {R package version 5.1.1, https://microbiomedb.github.io/microbiomeComputations/},   url = {https://github.com/microbiomeDB/microbiomeComputations}, }"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"microbiomecomputations","dir":"","previous_headings":"","what":"Compute Results for Microbiome Analyses","title":"Compute Results for Microbiome Analyses","text":"microbiomeComputations R package provides helper functions performing common analyses microbiome data. results available json, optionally data.table. package intended compliant API specified VEuPathDB/service-eda-compute.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Compute Results for Microbiome Analyses","text":"Use R package remotes install microbiomeComputations. R command prompt:","code":"remotes::install_github('microbiomeDB/microbiomeComputations')"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Compute Results for Microbiome Analyses","text":"","code":"# df is a data frame of abundance values with samples as rows. One column should hold the sample id, all other columns are assumed to be taxa # the 'recordIdColumn' is the name of the column that contains the sample ids. # 'method' can be 'simpson', 'shannon', or 'evenness'. dt <- alphaDiv(df, recordIdColumn=\"entity.SampleID\", method='simpson')"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"testing","dir":"","previous_headings":"","what":"Testing","title":"Compute Results for Microbiome Analyses","text":"package uses testthat package testing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Compute Results for Microbiome Analyses","text":"Pull requests welcome. major changes, please open issue first discuss like change. Please make sure update unit tests appropriate. making change affects eda-verse, please conduct integration testing possible.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Compute Results for Microbiome Analyses","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbsoluteAbundanceData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Absolute Abundance Data — AbsoluteAbundanceData-class","title":"Absolute Abundance Data — AbsoluteAbundanceData-class","text":"class working count data microbial ecological assay.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbsoluteAbundanceData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Absolute Abundance Data — AbsoluteAbundanceData-class","text":"data data.frame integer abundance counts species columns samples rows sampleMetadata data.frame metadata samples samples rows metadata variables columns recordIdColumn name column containing IDs samples. columns treated abundance values. ancestorIdColumns character vector column names representing parent entities recordIdColumn. imputeZero logical indicating whether NA/ null values replaced zeros.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbundanceData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Abundance Data — AbundanceData-class","title":"Abundance Data — AbundanceData-class","text":"class working microbiome ecological abundance data.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbundanceData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Abundance Data — AbundanceData-class","text":"data data.frame abundance values species columns samples rows sampleMetadata SampleMetadata object metadata samples samples rows metadata variables columns recordIdColumn name column containing IDs samples. columns treated abundance values. ancestorIdColumns character vector column names representing parent entities recordIdColumn. imputeZero logical indicating whether NA/ null values replaced zeros. removeEmptyRecords logical indicating whether empty (NA/ zero) samples removed.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Comparator — Comparator-class","title":"Comparator — Comparator-class","text":"class representing variable used compare samples two groups. variable's values used split samples groups.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Comparator — Comparator-class","text":"variable VariableMetadata groupA BinList groupB BinList","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get labels from a group in a Comparator — getGroupLabels","title":"Get labels from a group in a Comparator — getGroupLabels","text":"Comparator object, returns bin labels either groupA groupB","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get labels from a group in a Comparator — getGroupLabels","text":"","code":"getGroupLabels(object, group = c(\"groupA\", \"groupB\"))  # S4 method for Comparator getGroupLabels(object, group = c(\"groupA\", \"groupB\"))"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get labels from a group in a Comparator — getGroupLabels","text":"object Comparator group String, either \"groupA\" \"groupB\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get labels from a group in a Comparator — getGroupLabels","text":"charactor vector labels groupA groupB","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/DifferentialAbundanceResult-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential Abundance Result — DifferentialAbundanceResult-class","title":"Differential Abundance Result — DifferentialAbundanceResult-class","text":"DifferentialAbundanceResult object contains results differential abundance analysis.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/DifferentialAbundanceResult-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Differential Abundance Result — DifferentialAbundanceResult-class","text":"effectSizeLabel label effect size metric used. Default 'log2(Fold Change)'. statistics data frame containing statistics pValueFloor p-value floor. p-values less set value. adjustedPValueFloor adjusted p-value floor.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha diversity — alphaDiv","title":"Alpha diversity — alphaDiv","text":"function returns alpha diversity values sample.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha diversity — alphaDiv","text":"data AbundanceData object method string defining alpha diversity method. Accepted values 'shannon','simpson', 'evenness' verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha diversity — alphaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Beta diversity — betaDiv","title":"Beta diversity — betaDiv","text":"function returns pcoa coordinates calculated beta diversity dissimilarity matrix.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beta diversity — betaDiv","text":"","code":"betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beta diversity — betaDiv","text":"data AbundanceData object method string defining beta diversity dissimilarity method. Accepted values 'bray','jaccard', 'jsd' k integer determining number pcoa axes return verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beta diversity — betaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":null,"dir":"Reference","previous_headings":"","what":"Get data.table of abundances from AbundanceData — getAbundances","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"Returns data.table abundances, respecting imputeZero slot.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"","code":"getAbundances(   object,   ignoreImputeZero = c(FALSE, TRUE),   includeIds = c(TRUE, FALSE),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData getAbundances(   object,   ignoreImputeZero = c(FALSE, TRUE),   includeIds = c(TRUE, FALSE),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"object AbundanceData ignoreImputeZero boolean indicating whether respect imputeZero slot includeIds boolean indicating whether include recordIdColumn ancestorIdColumns verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"data.table abundances","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential abundance — internalDiffAbund","title":"Differential abundance — internalDiffAbund","text":"function returns fold change associated p value differential abundance analysis comparing samples two groups.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential abundance — internalDiffAbund","text":"","code":"internalDiffAbund(   data,   comparator,   method = c(\"DESeq2\", \"Maaslin2\"),   pValueFloor = P_VALUE_FLOOR,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData,Comparator internalDiffAbund(   data,   comparator,   method = c(\"DESeq2\", \"Maaslin2\"),   pValueFloor = P_VALUE_FLOOR,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential abundance — internalDiffAbund","text":"data AbsoluteAbundanceData object comparator Comparator object specifying variable values bins used dividing samples groups. method string defining differential abundance method. Accepted values 'DESeq2' 'Maaslin2'. pValueFloor numeric value indicates smallest p value returned. corresponding adjusted p value floor also updated based value, set maximum adjusted p value floored p values. default value uses P_VALUE_FLOOR=1e-200 constant defined package. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential abundance — internalDiffAbund","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/microbiomeComputations-package.html","id":null,"dir":"Reference","previous_headings":"","what":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","title":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","text":"microbiomeComputations provides helper functions performing common analyses microbiome data. results available json, optionally `data.table`. package intended compliant API specified VEuPathDB/service-eda-compute.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/microbiomeComputations-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu Authors: Ann Blevins annsize@upenn.edu","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Ranked abundance — rankedAbundance","title":"Ranked abundance — rankedAbundance","text":"function returns abundances, ranked selected ranking function","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ranked abundance — rankedAbundance","text":"data AbundanceData object method string defining ranking strategy order taxa. Accepted values 'median','max','q3','variance'. Note taxa return value 0 given method included results. cutoff integer indicating maximium number taxa kept ranking. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ranked abundance — rankedAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"Modifies data sampleMetadata slots AbundanceData object, exclude samples missing SampleMetadata specified column.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"","code":"removeIncompleteSamples(   object,   colName = character(),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData removeIncompleteSamples(   object,   colName = character(),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"object AbundanceData colName String providing column name SampleMetadata check completeness verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"AbundanceData modified data sampleMetadata slots","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Self Correlation — selfCorrelation,AbundanceData-method","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"function returns correlation coefficients variables one AbundanceData object . generally serves convenience wrapper around veupathUtils::correlation, exception additionally supports sparcc.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"","code":"# S4 method for AbundanceData selfCorrelation(   data,   method = c(\"spearman\", \"pearson\", \"sparcc\"),   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   proportionNonZeroThreshold = 0.5,   varianceThreshold = 0,   stdDevThreshold = 0 )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"data AbundanceData object method string defining type correlation run. currently supported values 'spearman','pearson' 'sparcc' format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired proportionNonZeroThreshold numeric threshold filter features proportion non-zero values across samples varianceThreshold numeric threshold filter features variance across samples stdDevThreshold numeric threshold filter features standard deviation across samples","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"ComputeResult object","code":""}]
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(Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/microbiomeComputations/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer. Ann Blevins. Author.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D, Blevins (2024). microbiomeComputations: Compute Results Microbiome Analyses. R package version 5.1.2, https://microbiomedb.github.io/microbiomeComputations/, https://github.com/microbiomeDB/microbiomeComputations.","code":"@Manual{,   title = {microbiomeComputations: Compute Results for Microbiome Analyses},   author = {Danielle Callan and Ann Blevins},   year = {2024},   note = {R package version 5.1.2, https://microbiomedb.github.io/microbiomeComputations/},   url = {https://github.com/microbiomeDB/microbiomeComputations}, }"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"microbiomecomputations","dir":"","previous_headings":"","what":"Compute Results for Microbiome Analyses","title":"Compute Results for Microbiome Analyses","text":"microbiomeComputations R package provides helper functions performing common analyses microbiome data. results available json, optionally data.table. package intended compliant API specified VEuPathDB/service-eda-compute.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Compute Results for Microbiome Analyses","text":"Use R package remotes install microbiomeComputations. R command prompt:","code":"remotes::install_github('microbiomeDB/microbiomeComputations')"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Compute Results for Microbiome Analyses","text":"","code":"# df is a data frame of abundance values with samples as rows. One column should hold the sample id, all other columns are assumed to be taxa # the 'recordIdColumn' is the name of the column that contains the sample ids. # 'method' can be 'simpson', 'shannon', or 'evenness'. dt <- alphaDiv(df, recordIdColumn=\"entity.SampleID\", method='simpson')"},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"testing","dir":"","previous_headings":"","what":"Testing","title":"Compute Results for Microbiome Analyses","text":"package uses testthat package testing.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Compute Results for Microbiome Analyses","text":"Pull requests welcome. major changes, please open issue first discuss like change. Please make sure update unit tests appropriate. making change affects eda-verse, please conduct integration testing possible.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Compute Results for Microbiome Analyses","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbsoluteAbundanceData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Absolute Abundance Data — AbsoluteAbundanceData-class","title":"Absolute Abundance Data — AbsoluteAbundanceData-class","text":"class working count data microbial ecological assay.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbsoluteAbundanceData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Absolute Abundance Data — AbsoluteAbundanceData-class","text":"data data.frame integer abundance counts species columns samples rows sampleMetadata data.frame metadata samples samples rows metadata variables columns recordIdColumn name column containing IDs samples. columns treated abundance values. ancestorIdColumns character vector column names representing parent entities recordIdColumn. imputeZero logical indicating whether NA/ null values replaced zeros.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbundanceData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Abundance Data — AbundanceData-class","title":"Abundance Data — AbundanceData-class","text":"class working microbiome ecological abundance data.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/AbundanceData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Abundance Data — AbundanceData-class","text":"data data.frame abundance values species columns samples rows sampleMetadata SampleMetadata object metadata samples samples rows metadata variables columns recordIdColumn name column containing IDs samples. columns treated abundance values. ancestorIdColumns character vector column names representing parent entities recordIdColumn. imputeZero logical indicating whether NA/ null values replaced zeros. removeEmptyRecords logical indicating whether empty (NA/ zero) samples removed.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Comparator — Comparator-class","title":"Comparator — Comparator-class","text":"class representing variable used compare samples two groups. variable's values used split samples groups.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Comparator — Comparator-class","text":"variable VariableMetadata groupA BinList groupB BinList","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get labels from a group in a Comparator — getGroupLabels","title":"Get labels from a group in a Comparator — getGroupLabels","text":"Comparator object, returns bin labels either groupA groupB","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get labels from a group in a Comparator — getGroupLabels","text":"","code":"getGroupLabels(object, group = c(\"groupA\", \"groupB\"))  # S4 method for Comparator getGroupLabels(object, group = c(\"groupA\", \"groupB\"))"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get labels from a group in a Comparator — getGroupLabels","text":"object Comparator group String, either \"groupA\" \"groupB\"","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/Comparator-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get labels from a group in a Comparator — getGroupLabels","text":"charactor vector labels groupA groupB","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/DifferentialAbundanceResult-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential Abundance Result — DifferentialAbundanceResult-class","title":"Differential Abundance Result — DifferentialAbundanceResult-class","text":"DifferentialAbundanceResult object contains results differential abundance analysis.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/DifferentialAbundanceResult-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Differential Abundance Result — DifferentialAbundanceResult-class","text":"effectSizeLabel label effect size metric used. Default 'log2(Fold Change)'. statistics data frame containing statistics pValueFloor p-value floor. p-values less set value. adjustedPValueFloor adjusted p-value floor.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha diversity — alphaDiv","title":"Alpha diversity — alphaDiv","text":"function returns alpha diversity values sample.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha diversity — alphaDiv","text":"data AbundanceData object method string defining alpha diversity method. Accepted values 'shannon','simpson', 'evenness' verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/alphaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha diversity — alphaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Beta diversity — betaDiv","title":"Beta diversity — betaDiv","text":"function returns pcoa coordinates calculated beta diversity dissimilarity matrix.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beta diversity — betaDiv","text":"","code":"betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beta diversity — betaDiv","text":"data AbundanceData object method string defining beta diversity dissimilarity method. Accepted values 'bray','jaccard', 'jsd' k integer determining number pcoa axes return verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/betaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beta diversity — betaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":null,"dir":"Reference","previous_headings":"","what":"Get data.table of abundances from AbundanceData — getAbundances","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"Returns data.table abundances, respecting imputeZero slot.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"","code":"getAbundances(   object,   ignoreImputeZero = c(FALSE, TRUE),   includeIds = c(TRUE, FALSE),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData getAbundances(   object,   ignoreImputeZero = c(FALSE, TRUE),   includeIds = c(TRUE, FALSE),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"object AbundanceData ignoreImputeZero boolean indicating whether respect imputeZero slot includeIds boolean indicating whether include recordIdColumn ancestorIdColumns verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/getAbundances.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get data.table of abundances from AbundanceData — getAbundances","text":"data.table abundances","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential abundance — internalDiffAbund","title":"Differential abundance — internalDiffAbund","text":"function returns fold change associated p value differential abundance analysis comparing samples two groups.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential abundance — internalDiffAbund","text":"","code":"internalDiffAbund(   data,   comparator,   method = c(\"DESeq2\", \"Maaslin2\"),   pValueFloor = P_VALUE_FLOOR,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData,Comparator internalDiffAbund(   data,   comparator,   method = c(\"DESeq2\", \"Maaslin2\"),   pValueFloor = P_VALUE_FLOOR,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential abundance — internalDiffAbund","text":"data AbsoluteAbundanceData object comparator Comparator object specifying variable values bins used dividing samples groups. method string defining differential abundance method. Accepted values 'DESeq2' 'Maaslin2'. pValueFloor numeric value indicates smallest p value returned. corresponding adjusted p value floor also updated based value, set maximum adjusted p value floored p values. default value uses P_VALUE_FLOOR=1e-200 constant defined package. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/internalDiffAbund-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential abundance — internalDiffAbund","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/microbiomeComputations-package.html","id":null,"dir":"Reference","previous_headings":"","what":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","title":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","text":"microbiomeComputations provides helper functions performing common analyses microbiome data. results available json, optionally `data.table`. package intended compliant API specified VEuPathDB/service-eda-compute.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/microbiomeComputations-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"microbiomeComputations: Compute Results for Microbiome Analyses — microbiomeComputations-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu Authors: Ann Blevins annsize@upenn.edu","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Ranked abundance — rankedAbundance","title":"Ranked abundance — rankedAbundance","text":"function returns abundances, ranked selected ranking function","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ranked abundance — rankedAbundance","text":"data AbundanceData object method string defining ranking strategy order taxa. Accepted values 'median','max','q3','variance'. Note taxa return value 0 given method included results. cutoff integer indicating maximium number taxa kept ranking. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/rankedAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ranked abundance — rankedAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"Modifies data sampleMetadata slots AbundanceData object, exclude samples missing SampleMetadata specified column.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"","code":"removeIncompleteSamples(   object,   colName = character(),   verbose = c(TRUE, FALSE) )  # S4 method for AbundanceData removeIncompleteSamples(   object,   colName = character(),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"object AbundanceData colName String providing column name SampleMetadata check completeness verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/removeIncompleteSamples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop samples with incomplete SampleMetadata — removeIncompleteSamples","text":"AbundanceData modified data sampleMetadata slots","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Self Correlation — selfCorrelation,AbundanceData-method","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"function returns correlation coefficients variables one AbundanceData object . generally serves convenience wrapper around veupathUtils::correlation, exception additionally supports sparcc.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"","code":"# S4 method for AbundanceData selfCorrelation(   data,   method = c(\"spearman\", \"pearson\", \"sparcc\"),   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   proportionNonZeroThreshold = 0.5,   varianceThreshold = 0,   stdDevThreshold = 0 )"},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"data AbundanceData object method string defining type correlation run. currently supported values 'spearman','pearson' 'sparcc' format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired proportionNonZeroThreshold numeric threshold filter features proportion non-zero values across samples varianceThreshold numeric threshold filter features variance across samples stdDevThreshold numeric threshold filter features standard deviation across samples","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/reference/selfCorrelation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self Correlation — selfCorrelation,AbundanceData-method","text":"ComputeResult object","code":""}]