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Update index.rst #2533

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1c87f00
fix Keemei (#2510)
stephanieorch Feb 21, 2018
ef02593
Keemei fix (#2517)
stephanieorch Feb 26, 2018
88fe616
Update index.rst
stephanieorch Apr 4, 2018
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30 changes: 15 additions & 15 deletions qiita_pet/support_files/doc/source/analyzingsamples/index.rst
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Expand Up @@ -95,7 +95,7 @@ Calculating Alpha Diversity
.. figure:: alpha_diversity.png
:align: center

* **Calculate alpha diversity** :ref:`[99]<reference99>`: Measures the diversity within a sample
* **Calculate alpha diversity** :ref:`[99]<reference99>` : Measures the diversity within a sample

* **BIOM table** (required): Feature table containing the samples for which alpha diversity should be computed

Expand All @@ -109,13 +109,13 @@ Calculating Alpha Diversity

* Relative richness of the abundant species

* **Brillouin’s index** :ref:`[73]<reference73>`: Calculates Brillouin’s index
* **Brillouin’s index** :ref:`[73]<reference73>` : Calculates Brillouin’s index

* Measures the diversity of the species present

* Use when randomness can’t be guaranteed

* **Chao1 index** :ref:`[15]<reference15>`: Calculates Chao1 index
* **Chao1 index** :ref:`[15]<reference15>` : Calculates Chao1 index

* Estimates diversity from abundant data
* Estimates number of rare taxa missed from undersampling
Expand Down Expand Up @@ -159,7 +159,7 @@ Calculating Alpha Diversity

* Measures species richness in a given area or community

* **Mcintosh dominance index D** :ref:`[62]<reference62>`: Calculates McIntosh dominance index D
* **Mcintosh dominance index D** :ref:`[62]<reference62>` : Calculates McIntosh dominance index D

* Affected by the variation in dominant taxa and less affected by the variation in less abundant or rare taxa

Expand Down Expand Up @@ -205,7 +205,7 @@ Calculating Alpha Diversity

* Measures the relative abundance of the different species making up the sample richness

* **Strong’s dominance index (Dw)** :ref:`[89]<reference89>`: Calculates Strong’s dominance index
* **Strong’s dominance index (Dw)** :ref:`[89]<reference89>` : Calculates Strong’s dominance index

* Measures species abundance unevenness

Expand All @@ -219,7 +219,7 @@ Calculating Beta Diversity
.. figure:: beta_diversity.png
:align: center

* **Calculate beta diversity** :ref:`[99]<reference99>`: Measured the diversity between samples
* **Calculate beta diversity** :ref:`[99]<reference99>` : Measured the diversity between samples

* **BIOM table** (required): Feature table containing the samples for which beta diversity should be computed
* **Adjust variance** :ref:`[14]<reference14>` (phylogenetic only): Performs variance adjustment
Expand Down Expand Up @@ -249,7 +249,7 @@ Calculating Beta Diversity

* Similar to the Euclidean distance but the effect of a large difference in a single dimension is reduced

* **Correlation coefficient** :ref:`[29]<reference29>`: Measures Correlation coefficient
* **Correlation coefficient** :ref:`[29]<reference29>` : Measures Correlation coefficient

* Measure of strength and direction of linear relationship between samples

Expand Down Expand Up @@ -282,7 +282,7 @@ Calculating Beta Diversity

* Describes the dissimilarity between two samples

* **Matching components** :ref:`[42]<reference42>`: Measures Matching components
* **Matching components** :ref:`[42]<reference42>` : Measures Matching components

* Compares indices under all possible situations

Expand All @@ -294,7 +294,7 @@ Calculating Beta Diversity

* Equal weight is given to matches and non-matches

* **Sokal-Michener coefficient** :ref:`[85]<reference85>`: Measures Sokal-Michener coefficient
* **Sokal-Michener coefficient** :ref:`[85]<reference85>` : Measures Sokal-Michener coefficient

* Proportion of matches between samples

Expand Down Expand Up @@ -380,7 +380,7 @@ Calculating Beta Group Significance
* **Method** (required): Correlation test being applied

* **Anosim** :ref:`[20]<reference20>` : Describes the strength and significance that a category has in determining the distances between points and can accept either categorical or continuous variables in the metadata mapping file
* **Permanova** :ref:`[4]<reference4>`: Describes the strength and significance that a category has in determining the distances between points and can accept categorical variables
* **Permanova** :ref:`[4]<reference4>` : Describes the strength and significance that a category has in determining the distances between points and can accept categorical variables

* **Number of permutations** (required): Number of permutations to be run when computing p-values

Expand All @@ -395,8 +395,8 @@ Calculating Beta Correlation
* **Distance-matrix** (required): Matrix of distances between pairs of samples
* **Correlation method** (required): Correlation test being applied

* **Spearman** :ref:`[88]<reference88>`: Measures if there is a linear relationship between 2 variables
* **Pearson** :ref:`[70]<reference70>`: Measures how strong the linear relationship is between 2 variables
* **Spearman** :ref:`[88]<reference88>` : Measures if there is a linear relationship between 2 variables
* **Pearson** :ref:`[70]<reference70>` : Measures how strong the linear relationship is between 2 variables

* **Metadata-category** (required): Category from metadata file or artifact viewable as metadata
* **Number of permutations** (required): Number of permutations to be run when computing p-values
Expand Down Expand Up @@ -432,7 +432,7 @@ Alpha Diversity Box Plots and Statistics

* **Boxplot**: Shows how different measures of alpha diversity correlate with different metadata categories
* **Category**: Choose the metadata category you would like to analyze
* **Kruskal-Wallis** :ref:`[49]<reference49>`: Result of Kruskal-Wallis tests
* **Kruskal-Wallis** :ref:`[49]<reference49>` : Result of Kruskal-Wallis tests

* Says if the differences are statistically significant

Expand Down Expand Up @@ -504,7 +504,7 @@ Beta Correlation

* Gives the Spearman or Pearson result (rho and p-value)

* **Spearman** [88](../references.rst): Measures if there is a linear relationship between 2 variables
* **Pearson** [70](../references.rst): Measures how strong the linear relationship is between 2 variables
* **Spearman** :ref:`[88]<reference88>` : Measures if there is a linear relationship between 2 variables
* **Pearson** :ref:`[70]<reference70>` : Measures how strong the linear relationship is between 2 variables

* Gives scatterplot of the distance matrix on the x-axis and the variable being tested on the y-axis
13 changes: 0 additions & 13 deletions qiita_pet/support_files/doc/source/gettingstartedguide/index.rst
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Expand Up @@ -126,13 +126,6 @@ Required fields for EBI submission

In order to submit your data to EBI, certain fields are required in your sample information file. You can download a spread sheet containing these required fields on the `Knight Lab website <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__ under "MetaData Template".

Checking for Errors In Sample information
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* `Keemei <https://keemei.qiime2.org/>`__ is a Google Sheets add-on for validating sample metadata. Validation of sample metadata is important before beginning any analysis. Install Keemei and follow the instructions on its website to validate your sample information spread sheet.

**Remember that spelling and capitalization matters in Qiita**

Attaching the Sample Information to the Study
---------------------------------------------

Expand Down Expand Up @@ -318,12 +311,6 @@ additional column is required.
| | | and ``my-data.fastq`` becomes ``my-data``). |
+------------------+-------------+--------------------------------------------------------------------------------------------+

Checking for Errors In Preparation information
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* `Keemei <https://keemei.qiime2.org/>`__ is a Google Sheets add-on for validating sample metadata. Validation of sample metadata is important before beginning any analysis. Install Keemei and follow the instructions on its website to validate your sample information spread sheet.

**Remember that spelling and capitalization matters in Qiita**

Attaching Preparation Information to the Study
----------------------------------------------
Expand Down