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index.md

@@ -13,7 +13,7 @@ devtools::install_github('mverbyla/pathogenflows')
 
 ## About
 
-The 'getLoadings' function allows you to predict annual loadings of water pathogens from the onsite sanitation system technologies used in a given region of the world. 
+The `getLoadings` function allows you to predict annual loadings of water pathogens from the onsite sanitation system technologies used in a given region of the world. 
 
 | Pathogen Loadings               | Description          |
 |:--------------------------|:---------------------------|
@@ -25,6 +25,17 @@ The 'getLoadings' function allows you to predict annual loadings of water pathog
 | Conveyed in fecal sludge to treatment   | Number of pathogens conveyed each year to treatment in fecal sludge |
 | Conveyed in sewerage to treatment   | Number of pathogens conveyed each year to treatment in sewerage | 
 
+The `getloadings` function requires the following three inputs:
+
+### Inputs:
+
+*   onsiteData
+*   by
+*   pathogenType
+
+The input `onsiteData` should refer to a data input file from the K2P Data Portal (data.waterpathogens.org). This file must be in a very specific format. An example file can be found [here](http://data.waterpathogens.org/dataset/5374462b-5bb5-456f-bfc0-816ea572666d/resource/4d9e5fba-9280-4b8b-acce-d1c87952acc1/download/onsitedata_example.csv).
+
+
 ## Example
 
 The following shows the use of the getLoadings function for data from Kampala, Uganda, grouping the data by 'region' and showing results for the 'Virus' group.
@@ -38,112 +49,9 @@ getLoadings(onsiteData,by="region",group="Virus")
 #> 3 Makindye 2.115370e+17   5.784264e+15 7.404292e+15     5.205838e+16 1.396717e+17    1.877473e+14 6.042660e+15 1.941896e+16       1.04    0.9082
 #> 4   Nakawa 1.740476e+17   4.848475e+15 5.834954e+15     4.363628e+16 1.023125e+17    1.109438e+14 1.716174e+16 2.795611e+16       0.79    0.8394
 #> 5   Rubaga 2.103805e+17   4.278101e+15 5.257688e+15     3.850291e+16 1.602164e+17    2.221318e+14 9.808800e+14 1.073880e+16       1.29    0.9490
-```
-
-## Header 2
-
-> This is a blockquote following a header.
->
-> When something is important enough, you do it even if the odds are not in your favor.
-
-### Header 3
 
-```js
-// Javascript code with syntax highlighting.
-var fun = function lang(l) {
-  dateformat.i18n = require('./lang/' + l)
-  return true;
-}
 ```
 
-```ruby
-# Ruby code with syntax highlighting
-GitHubPages::Dependencies.gems.each do |gem, version|
-  s.add_dependency(gem, "= #{version}")
-end
-```
-
-#### Header 4
-
-*   This is an unordered list following a header.
-*   This is an unordered list following a header.
-*   This is an unordered list following a header.
-
-##### Header 5
-
-1.  This is an ordered list following a header.
-2.  This is an ordered list following a header.
-3.  This is an ordered list following a header.
-
-###### Header 6
-
-| head1        | head two          | three |
-|:-------------|:------------------|:------|
-| ok           | good swedish fish | nice  |
-| out of stock | good and plenty   | nice  |
-| ok           | good `oreos`      | hmm   |
-| ok           | good `zoute` drop | yumm  |
-
-### There's a horizontal rule below this.
-
-* * *
+## Learn More
 
-### Here is an unordered list:
-
-*   Item foo
-*   Item bar
-*   Item baz
-*   Item zip
-
-### And an ordered list:
-
-1.  Item one
-1.  Item two
-1.  Item three
-1.  Item four
-
-### And a nested list:
-
-- level 1 item
-  - level 2 item
-  - level 2 item
-    - level 3 item
-    - level 3 item
-- level 1 item
-  - level 2 item
-  - level 2 item
-  - level 2 item
-- level 1 item
-  - level 2 item
-  - level 2 item
-- level 1 item
-
-### Small image
-
-![Octocat](https://github.githubassets.com/images/icons/emoji/octocat.png)
-
-### Large image
-
-![Branching](https://guides.github.com/activities/hello-world/branching.png)
-
-
-### Definition lists can be used with HTML syntax.
-
-<dl>
-<dt>Name</dt>
-<dd>Godzilla</dd>
-<dt>Born</dt>
-<dd>1952</dd>
-<dt>Birthplace</dt>
-<dd>Japan</dd>
-<dt>Color</dt>
-<dd>Green</dd>
-</dl>
-
-```
-Long, single-line code blocks should not wrap. They should horizontally scroll if they are too long. This line should be long enough to demonstrate this.
-```
-
-```
-The final element.
-```
+For more information, please see [our website](https://www.waterpathogens.org/).