diff --git a/404.html b/404.html
index 920cd74..24e318a 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 ba34d77..4937ad1 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 2d5a7e1..e0d5902 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 5.1.2, https://microbiomedb.github.io/microbiomeComputations/, <a href="https://github.com/microbiomeDB/microbiomeComputations" class="external-link">https://github.com/microbiomeDB/microbiomeComputations</a>. 
+R package version 5.1.3, 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 5.1.2, https://microbiomedb.github.io/microbiomeComputations/},
+  note = {R package version 5.1.3, https://microbiomedb.github.io/microbiomeComputations/},
   url = {https://github.com/microbiomeDB/microbiomeComputations},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 2cadd5c..08f9d08 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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">
@@ -85,8 +85,9 @@ <h2 id="testing">Testing<a class="anchor" aria-label="anchor" href="#testing"></
 <div class="section level2">
 <h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
 </h2>
-<p>Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.</p>
-<p>Please make sure to update unit tests as appropriate. If making a change that affects the eda-verse, please conduct integration testing if possible.</p>
+<p>Pull requests are welcome and should be made to the <strong>dev</strong> branch.</p>
+<p>For major changes, please open an issue first to discuss what you would like to change.</p>
+<p>Please make sure to update unit tests as appropriate.</p>
 </div>
 <div class="section level2">
 <h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
diff --git a/pkgdown.yml b/pkgdown.yml
index 91e6d2f..f41a4cb 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-23T15:50Z
+last_built: 2024-05-30T13:42Z
 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 bde7d20..b301ee1 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 a3e8d77..ff2f16e 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 59b7518..ce2ff28 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 ee2e81f..068fdbb 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 6e283cf..5376720 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 3520309..c921f12 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 07bb5fd..00188c2 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 a4b03b2..09d0545 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 98ed12f..6a00694 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 6f5e670..6865d89 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 68efe15..e1121cc 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 a6b9947..4e45119 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 2d501b4..8c43b33 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 f321afc..f49eae6 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="">5.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">5.1.3</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 63ab45e..4e2be43 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. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://microbiomedb.github.io/microbiomeComputations/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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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":""}]
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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 5.1.3, 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 5.1.3, 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 made dev branch. major changes, please open issue first discuss like change. Please make sure update unit tests appropriate.","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":""}]