RCA Tutorial - Revision history

Morgan: /* References */

2013-04-29T15:58:44Z

References

2013-04-29T15:58:21Z

References

2013-04-29T15:53:58Z

2013-04-29T15:39:39Z

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Visualizing Results

2013-04-29T15:10:35Z

Run RCA Plugin

← Older revision		Revision as of 15:58, 29 April 2013
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	==References==		==References==

−	* D. G. Armanini, W. A. Monk, L. Carter, D. Cote & D. J. Baird "Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada" (2012) Environ Monit Assess. [[http://www.ncbi.nlm.nih.gov/pubmed/23250724\|epub]]	+	* D. G. Armanini, W. A. Monk, L. Carter, D. Cote & D. J. Baird "Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada" (2012) Environ Monit Assess. [http://www.ncbi.nlm.nih.gov/pubmed/23250724 epub]

← Older revision		Revision as of 15:58, 29 April 2013
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	[[Image:Rca_tutorial_screenshot3.png\|1500px]]		[[Image:Rca_tutorial_screenshot3.png\|1500px]]
	==References==		==References==
		+
		+	* D. G. Armanini, W. A. Monk, L. Carter, D. Cote & D. J. Baird "Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada" (2012) Environ Monit Assess. [[http://www.ncbi.nlm.nih.gov/pubmed/23250724\|epub]]

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 [[Image:Rca_tutorial_screenshot1.png|1500px]]
 ==Using results with other plugins==
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 [[Image:Rca_tutorial_screenshot3.png|1500px]]
 ==References==

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 * Each of the columns (O/E diversity measures) can be added as location metadata for use by GenGIS and other plugins by clicking on one of the columns and clicking ''Add Selected To GenGIS''.
 * The new location metdata can be viewed by using ''Plugins->Location Table Viewer''.
-[[Image:Rca_tutorial_screenshot2.png|500px]]
+* Other plugins can be used with the RCA results as well such as ''Plugins->Linear Regression''.
 ==Saving results==
 ==References==

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 [[Image:Rca_tutorial_screenshot1.png|1500px]]
 ==Using results with other plugins==
 ==Saving results==
 ==References==

← Older revision		Revision as of 15:26, 29 April 2013
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	* Each of the "O/E" diversity measures can be plotted as a bar plot on the GenGIS map by highlighting a column (e.g. ''O/E Richness'') and clicking 'Plot Selected Data'. The height of the bars can be changed using the ''Bar plot scale factor'' (e.g. setting to a value of 0.5 will make the bars shorter).		* Each of the "O/E" diversity measures can be plotted as a bar plot on the GenGIS map by highlighting a column (e.g. ''O/E Richness'') and clicking 'Plot Selected Data'. The height of the bars can be changed using the ''Bar plot scale factor'' (e.g. setting to a value of 0.5 will make the bars shorter).

−	[[Image:Rca_tutorial_screenshot1.png\|~~1000px~~]]	+	[[Image:Rca_tutorial_screenshot1.png\|1500px]]

← Older revision		Revision as of 15:25, 29 April 2013
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	* Each of the "O/E" diversity measures can be plotted as a bar plot on the GenGIS map by highlighting a column (e.g. ''O/E Richness'') and clicking 'Plot Selected Data'. The height of the bars can be changed using the ''Bar plot scale factor'' (e.g. setting to a value of 0.5 will make the bars shorter).		* Each of the "O/E" diversity measures can be plotted as a bar plot on the GenGIS map by highlighting a column (e.g. ''O/E Richness'') and clicking 'Plot Selected Data'. The height of the bars can be changed using the ''Bar plot scale factor'' (e.g. setting to a value of 0.5 will make the bars shorter).

		+	[[Image:Rca_tutorial_screenshot1.png\|1000px]]

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 ==Visualizing Results==
-* Each
+* The RCA plugin calculates various "expected" diversity measures using metadata ('clim_Trange', 'geo_intr', 'geo_sed', and 'geo_sedvol') from the location file and compares these to the "observed" diversity measures from the sequence data (taxa and counts).
 ==Using results with other plugins==

← Older revision		Revision as of 15:11, 29 April 2013
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	==Visualizing Results==		==Visualizing Results==
		+	* Each

	==Using results with other plugins==		==Using results with other plugins==

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 * Check that the ''Taxon Names'' box has ''Label'' selected (this contains the names of the taxa that were loaded with the sequence file).
 * Check that the ''Taxon Counts'' box has ''Count'' selected (this contains the number of each taxa that were loaded with the sequence file).
-* Click '''Run'''
+* Click '''Run'''. Results should appear in table within a couple of seconds.
 ==Visualizing Results==