View source for Help For Editors

[[File:Title-help.png|link=Help2]]
=Basics=
Welcome to QMRAwiki!  We really appreciate your insights and contributions to this website.   Anyone can freely browse QMRAwiki. To contribute to QMRAwiki, you must create an account. Click log in/create account (top left) and follow the easy steps. Send us an email [mailto:camra@msu.edu camra@msu.edu] with your user name, and we will then allow you to make edits.

It is easy to start editing wiki pages.  Just click on the “edit” tab at the top of a wiki page, or if there are  several sections on one page, you can click on the section-edit link to make edits on that section.  Then it will bring you to a page which contains the editable wiki text of this current page.  In this text box, you can type in text using the wiki markup language which will be illustrated in the following.  You can add tables or upload images to the QMRAwiki as well.

Some pages cannot be edited directly. However, every page has a 'talk' (or 'discussion') page, which you can access by clicking the 'discussion' tab near the top. If you want to change a page but cannot edit it, please mention it the discussion page, and our staff editors will implement it.

QMRAwiki runs on MediaWiki software, just like [http://wikipedia.org Wikipedia]. The full [http://www.mediawiki.org/wiki/Manual:Contents MediaWiki documentation] will help you on QMRAwiki also. Wikipedia also has a very helpful quick reference for [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet editing].

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Be bold!</font></div>
  <div class="NavContent" style="text-align:left">
Remember, 
*Content is more important than formatting.  The wiki system allows more experienced proofreaders to clean up your entries if they don't have perfect formatting.  Go ahead and put something in the wiki, and then [[Help:Asking for help|ask for help]] if you want someone to clean up the formatting or discuss the content with you.  As you gain experience you can help others with their pages.
*You can try out different editing techniques in the [[Sandbox]].
*You can't mess up anything so badly that we can't go back to the previous version.  QMRAwiki saves old versions of every page.
*Use the [[Help:Discussion Pages|discussion pages]] for guidance if you're uncertain about something
*Editing is a collaborative effort that should strive for a neutral point of view ([[Wikipedia:NPOV|NPOV]]).  We want links to your strong opinions, but these should be placed outside the main QMRAwiki site, where others can't edit them.  
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">QMRAwiki style</font></div>
  <div class="NavContent" style="text-align:left">
*Always italicize scientific names (genus and species, e.g., ''Acer rubrum''). If the genus is used by itself, it must also be italicized. The first letter of a genus is capitalized; species names are never capitalized. Note that viruses and prions do not have genus and species designations, so virus names are not italicized.
*Scientific notation should be represented with a capital E representing '10x' and should include either a + or a - for the direction of exponent, followed by 2 digits for its magnitude; for example, 25000 should be written 2.5E+04.

Each pathogen has multiple pages associated with it. Such page titles should lead with the pathogen name, followed by a colon, followed by the type of page. For example: [[Bacillus anthracis: Dose Response Models]]. It is not necessary to italicize scientific names in page titles.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Editing existing pages</font></div>
  <div class="NavContent" style="text-align:left">
To edit a page, click either the edit tab on top of the display, or one of the edit links for a specific subsection.  This will bring up an editing form.  If you are having trouble editing, [[Help:Asking for help|ask for help]] or use the [[Help:Discussion Pages|discussion pages]] located in the tabs at the top of each page to express a problem to our editors.

===Following a Red Link===
Often, you will be reading a page that someone else created that has both Blue and Red text links.  Links in red text are to pages that don't exist yet; whoever put in the link thought a page was needed, but didn't get around to creating one.  If you click on such a link, you'll get an edit page for that page.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Working in edit mode</font></div>
  <div class="NavContent" style="text-align:left">
[[Image:Edit_buttons.jpg|thumb|framed|right|Edit buttons at bottom of a page in Edit mode]]
Adding or editing is just like any other web form.  Click or drag to select an insertion point, and just type away.  Just remember '''don't use the TAB key''' to space your text.  That will take you out of the editing box.

Note that you can preview your changes before saving them.  This is useful, since things don't always come out as expected, but you should also be sure to save at regular intervals.  If you don't, your changes could be lost if your session times out, or if someone else starts editing the page while you're working on it.  The show changes button shows you what parts of the page you've changed.  The Summary box allows you to put in a short description of why you edited the page.  This is optional, but it can be useful for when you, or others, come back and edit the page again.  For example, if you delete a material that you think is inappropriate for a page, you might want to explain that to keep others from adding it back without thinking about it.  Others may disagree with you and add it back anyway, but in that case, you should work out a neutral consensus text with the other editors.  Each page in the wiki has a [[Help:Discussion Pages|discussion page]] which is a good place to work things out.

 Here's a common unintended effect: 
 If your text winds up in a box like this, it's because you started it on a line beginning with <br/> one or more blank spaces.  So don't try to indent your paragraphs!

This is all you need to know to start editing.  If you're just adding text or fixing typos, you can just go ahead and skip the rest of this tutorial.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Basic formatting</font></div>
  <div class="NavContent" style="text-align:left">
One of the most common edits will be to change E. coli to ''E. coli'', or to italicize a gene name.  Occasionally, you may want to make '''bold''' text, or '''''bold italic''''' text.  Here's how:
{|{{Prettytable}}
|-
|''italics'' ||<nowiki>''italics''</nowiki> Text is surrounded by two single quote (') marks on each side.
|-
|'''bold''' ||<nowiki>'''bold'''</nowiki> Text is surrounded by three single quote (') marks on each side.
|-
|'''''bold italics''''' ||<nowiki>'''''bold italics'''''</nowiki> Text is surrounded by five (three for bold, two for italics) single quote (') marks on each side.
|-
|'' 'italicized single quoted' '' ||<nowiki>'' 'italicized single quoted' ''</nowiki> Put a blank space in between the marks for italics and the single quotes you want to appear in the text.
|-
|<s>Strikethrough Text</s> ||<nowiki><s>Strikethrough Text</s></nowiki> 
|}
Most of the time on QMRAwiki, you should not need anything besides italics. However the bold font can draw attention to areas that the editor wants to emphasize.

A fast way to get special characters, such as Greek letters (α), accented characters (á), and math symbols (±), is to go here [[http://meta.wikimedia.org/wiki/Help:Special_characters#Important_special_characters Special Characters]] and simply copy & paste them directly into the wikitext you are writing or editing.

[http://www.mediawiki.org/wiki/Images Adding images] can be tricky. The easiest way is to: 1) create the tag for the image file in the page you're editing, 2) save your edits, and then 3) click on the filename (which will be displayed in red inside a box); this will allow you to upload the file to the wiki.

</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Layout: headings, bullets, numbering</font></div>
  <div class="NavContent" style="text-align:left">
<pre>
----                     <!-- This will add a horizontal line across the page -->
== Heading 1 ==          <!-- This will allow media wiki to make the default TOC -->
=== Heading 2 ===        <!-- Subheading: still a heading, but smaller than Heading 1 -->
====Heading 3 ====       <!-- Mediawiki will only recognize three headings levels
<center> center the text </center>
<br />                   <!-- Line breaks -->

* Bulleted lists are easy
** more asterisks make more levels
*** and making <br/> new lines does not alter alignment

# numbered lists are easy as well
## numbered lists obey the same rules <br/> as the bulleted lists
### There is a limit to the number of
### levels you can go down

# You can also use numbers and bullets together
#* Thus you can mix and make interesting ordered lists
#* quite easily as well
# and continue numbering

: indenting without bullet or number
:: obeys the same <br/> rules as well
: and uses a different symbol

</pre>
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Referencing</font></div>
  <div class="NavContent" style="text-align:left">
All references in QMRAwiki should be formatted according to 'Harvard - Oxford Brookes University' style in Zotero. Zotero is free software for managing references, bibliographies, and research paper collections. Download Zotero at zotero.org [http://zotero.org]; it works best as a Firefox extension, but there is also a stand-alone version. To install the style, open Zotero, click the little gear icon, and then click Preferences > Cite > Styles > Get Additional Styles.

Example of a properly formatted reference (Zotero can automatically format references so you don't have to do it manually):

Akinbami FO, Erinoso O and Akinwolere OA (1995) Defaecation pattern and intestinal transit in Nigerian children. African Journal of Medicine and Medical Sciences. 24 (4), 337–341.

All references in QMRAwiki should also be properly formatted using standard wiki markup (using <code><nowiki> <ref> </nowiki></code> tags) to automatically generate bibliographies for each page. This is very straightforward; see the documentation [https://www.mediawiki.org/wiki/Extension:Cite/Cite.php#Usage] to see how it's done.

If you find an improperly formatted reference in QMRAwiki, please fix it.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Basic link examples</font></div>
  <div class="NavContent" style="text-align:left">
<pre>
[http://camra.msu.edu/ CAMRA Website]
[[Dose response assessment | Internal linking to Pages like Dose Response]]
</pre>
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Links: more details</font></div>
  <div class="NavContent" style="text-align:left">
One of the most important aspects of making a page useful are the links to other pages.  These can be links to other pages in QMRAwiki or links to pages on other websites
===Internal Links===
To insert a link to another page in QMRAwiki, put the name of the page inside a pair of brackets.  
:<nowiki>[[Main Page]]</nowiki>
creates
:[[Main Page]]
Note that this is case-sensitive.  [[Main page]] and [[main page]] create red links, indicating no pages with those names.  However, if you want different capitalization to all lead to the same page you can create those pages and have them contain only a [[#What if I don't like the Page Name after I've saved it?|REDIRECT]] statement that points to the original page.
===Piped Links===
Often, it is useful to have link to a page using different text than the page name.  For example, at the top of this page, there is a sentence that starts with:
:Use the [[Help:Discussion Pages|discussion pages]] or...
This actually links to [[Help:Discussion Pages]], not [[discussion pages]].  The link as made using a pipe character (|) between the PageName and the text for the link:
:<nowiki>[[Help:Discussion Pages|discussion pages]]</nowiki>
===Linking to a Subsection===
To link to a subsection in the middle of the page, use the # sign after the PageName, followed by a subsection name.  For example:
:<nowiki>[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]</nowiki>
gives
:[[Help:Editing:Basics#Italics, Bold, and Bold Italics]]
which links to a subsection on this Help page.  Of course, this can be used in a piped link too, as in [[Help:Editing:Basics#Italics, Bold, and Bold Italics|how to make italics]].

===Linking to a header tab===
Pages that are using the 'Header Tabs' extension use section headings to represent tabs. However, linking to section headings does not actually change tabs; a special syntax is required.[https://www.mediawiki.org/wiki/Extension:Header_Tabs#Linking_to_tabs]

<nowiki>{{#switchtablink:Tab name|Link text|Page name}}</nowiki>

This will create a link to the tab with the name "Tab name", and the text of the link will read "Link text". If you want the link to a point to a tab on another page, you can optionally add the third parameter, "Page name".

===Linking to Category Indices===
Pages can be placed into categories, and the index pages for different categories are very useful for finding content.  The PageName for a Category index is Category:CategoryName, but making a link as
:<nowiki>[[Category:Help]]</nowiki>
Doesn't link to the Help index, it adds the page to that category.  To make a link to an index page, add a colon (:) before the PageName, like this:
:<nowiki>[[:Category:Help]]</nowiki>
to get
:[[:Category:Help]]
Again, you can pipe this to give a link to a [[:Category:Help|list of help pages]].

===External Links===
If you just place a URL in the text, it will be converted to a link:
http://example.com
However, usually you want the linked text to be something other than the raw URL. To do that, put the URL and the link text, separated by a space, inside square brackets like this:
:<nowiki>[http://wiki.camra.msu.edu QMRAwiki home page]</nowiki>
becomes
:[http://wiki.camra.msu.edu QMRAwiki home page]
This external link method will also work for links to other pages inside QMRAwiki.  However, the internal link methods described above are preferred, because they allow the system to count how the pages link to each other.

===Interwiki Links===
There are some external sites that we will be linking to so often that it is useful to have shortcuts for them.  These are called interwiki links.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Images or other files</font></div>
  <div class="NavContent" style="text-align:left">
{{Help:Images}}
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Subheadings</font></div>
  <div class="NavContent" style="text-align:left">
One of the reasons you should not need to do much beyond italics is that you don't need '''bold''' or different font sizes to make subheadings.  Subheadings at different levels are made by putting different numbers of '=' signs around text on a line, where the string of equals signs are the first thing on the line.

On QMRAwiki pages, the Page Title is a level 1 heading, so start any headings with two = signs, and increase the number for subheadings and sub-subheadings.  Headings made in this way are automatically used to generate a table of contents for each page in outline format, like the one for this page:

Note that QMRA wiki uses the [http://www.mediawiki.org/wiki/Extension:Header_Tabs Headertabs extension] on certain pages (for example, [[Control Measures]]).  On those pages, any heading using one '=' will be converted into a tab with the heading text as the tab label.

A few notes about pages using Headertabs:
*Tab-specific reference lists can be implemented by using the <nowiki><references/></nowiki> tag at the end of each section/tab.
*Subheadings can still be used within Headertabs pages. <nowiki>=Heading=</nowiki> creates a heading, i.e., a new tab. To create a subheading under that tab, do this: <nowiki>==Subheading==</nowiki>
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Categories</font></div>
  <div class="NavContent" style="text-align:left">
To add a page to a category, use
:<nowiki>[[Category:CategoryName]]</nowiki>
This will not be rendered on the page, but will add a category link to the bottom of the page.  For example, this page is in the Help category.  A list of categories can be found at [[Special:Categories]].  Using a new CategoryName creates a new Category.  Any given page can belong to multiple categories.

</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">FAQ</font></div>
  <div class="NavContent" style="text-align:left">
===What do I do if someone changes what I wrote?===
This is a wiki and so the information you add to the wiki may be changed by other users, just as you may change other users' entries.  If you find the correction to be inaccurate, you may discuss the subject with other users in the '''Notes''' section available below each main section, or on the '''Discussion''' page.  To add a note on the same page at the bottom of the section, click the '''Edit''' link to the right of the '''Notes''' heading.  To initiate or view a discussion on a particular topic, click the '''discussion''' tab located on the top left hand side of the page.  To add additional comments, you can click the '''+''' to add your comment to the end of the list.  OR, you may click the '''edit''' tab and type your comments there.  As you can see, there are plenty of places to make your voice heard.

===Is there any way to keep people from editing my entries?===
Yes.  When you add data to a table, you have the opportunity to select '''public''' or '''private'''.  The '''public''' selection  allows any registered user to change your entries, whereas the '''private''' selection allows only you and the QMRAwiki staff to edit your entries.
  
===Can I import data from an Excel spreadsheet?===
No.  We are working on creating a way to do that, but that option is currently unavailable.

===How do I add categories?===
Categories are ways of grouping pages together by some common thread. To add a page to a category page, you'll need to know the category you want to add your page to.  Once you know the Category, use the following wiki mark-up to add the category:<nowiki>[[Category:Name of Category]]</nowiki>. 

===How do I make suggestions?===
There are two ways to make suggestions to the QMRAwiki staff.  Click on the '''Suggestions''' on the main page and you will be taken to the Suggestions page.  Click the '''edit''' tab at the top of the page and let us have it.  The other way to do this is to email the QMRAwiki staff at [mailto:camra@msu.edu Email Camra!].  Either option will get your suggestions to us.

===How do I know if it's right?===
You can't break the wiki.  If you're unsure of the formatting, markup, etc. someone else can fix it. Email the QMRAwiki staff at [mailto:camra@msu.edu Email Camra!] and inform them of your concern.  The staff will then format the page.
</div>
</div>

=Advanced=

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Tables</font></div>
  <div class="NavContent" style="text-align:left">
<pre>
<!-- For tables this is the border arrangement that we use all of the | symbols need to line up -->
<!-- {| starts the table   || defines new columns  |- defines that a new row is starting or the other one is finsihing -->
<!-- |} closes the table

{|                                                    <!-- These top 3 lines will not change other than renaming the caption -->
{| border = "1"
|+ '''Table Caption'''                                <!-- for a link use  [http://link.to.file.uploaded.xls '''Table caption''' -->
! Column A 
! Column B					      <!-- Headers are defined thusly and are automatically bolded and centered -->
|-
| A1                                                  <!-- Two ways to define cell entries -->
| B1
|-
| ''A2'' || '''''B2'''''
|-
| text or numbers go in (1,2,3,4,5) || rows adapt size to fit values <br/> starting a new line is easy too
|-
| colspan = "2" align="center"| merged columns
|-
| colspan = "2" align="right"| Right alignment
|-
| colspan = "2" | left alignment
|-
| rowspan = "2" | merged rows
| only for that column
|-
| Thus thus column is normal
|-
| And you can add Greek letters || <center> &alpha; &Alpha; &delta; &Delta; </center>
|}
|}
</pre>
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Templates</font></div>
  <div class="NavContent" style="text-align:left">
===About===
We use templates to control the layout of our pages. 

===Creating a template===
Template names are prefixed with <code>Template:</code>, you create them like any other wiki page.

===Using a template===
Templates are wiki pages which can be used in other pages in three ways:
*<code><nowiki>{{Name}}</nowiki></code> includes the content of the template at the moment the page containing it is fetched <nowiki>"[[Template:Name]]"</nowiki>. 
*<code><nowiki>{{subst:Name}}</nowiki></code> inserts the content of the template into the code of the page in a form that is editable normally <nowiki>"[[Template:Name]]"</nowiki> after you have saved your text. 
*<code><nowiki>{{msgnw:Name}}</nowiki></code> when the page containing it is fetched, includes the template in a form that displays it as raw wiki syntax, like <code><nowiki>&lt;nowiki&gt;</nowiki></code> does

===Semantic Internal Objects===
Some of the templates in the wiki have embedded within them [http://www.mediawiki.org/wiki/Extension:Semantic_Internal_Objects semantic internal objects]. At the end of such templates, you will see additional code starting with <nowiki>{{Set Internal ... }}</nowiki>.  This allows the wiki assign [http://semantic-mediawiki.org/wiki/Help:Properties_and_types semantic properties] to the template variables.  Please do not change the names of template variables or edit the semantic internal object portion of the template.
  
===Control template inclusion===
You can control template inclusion by the use of <code><nowiki><noinclude></nowiki></code> and
<code><nowiki><includeonly></nowiki></code> tags.

Anything between <code><nowiki><noinclude></nowiki></code> and <code><nowiki></noinclude></nowiki></code> will be processed and
displayed only when the page is being viewed directly, not included.

Possible applications are:
* Categorising templates
* Interlanguage links to similar templates in other languages
* Explanatory text about how to use the template

The converse is <code><nowiki><includeonly></nowiki></code>. Text between <code><nowiki><includeonly></nowiki></code> and
<code><nowiki></includeonly></nowiki></code> will be processed and displayed only when the page is
being included. The obvious application is to add all pages containing a given template to a category.

Note that the usual update problems apply -- if you change the
categories inside a template, the categories of the referring pages
won't be updated until those pages are edited.

===Transcluding a page that isn't a template===
You can also transclude a non-template page by putting using <nowiki>{{Namespace:Page title}}</nowiki>.  The main namespace is the default, so using :Page title will include a regular article.  This kind of transclusion is used to make the "On one page" tabs on our gene pages.

===Watchlist===
Using Watchlist, the user can keep track of a list of pages that may have been altered. A summary of changes made to each of the pages being watched may be found by clicking on [[Special:Watchlist|"my watchlist"]]. This prevents the user from having to click through all of the pages one at a time.

===Getting email notification of changes===
In your preferences, you can set QMRAwiki to email you when a page on your watchlist has been edited.   It only emails you once until you view the page again while logged in, so you won't be inundated with emails if someone is making a bunch of changes.

===Adding to your watchlist===
When you are logged in, a "watch" tab appears at the top of every page you are viewing.  Clicking it places that page on your watchlist, sends you to a message telling you that you've added a page to your watchlist, and changes the tab to "unwatch"  the next time you view that page.

===See also===
[[wikipedia:Help:Watching_pages]] for how watchlists work on wikipedia.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Displaying computer code or wikitext</font></div>
  <div class="NavContent" style="text-align:left">
If you want to call attention to a piece of computer code, such as HMTL or wikitext, that you don't want QMRAwiki to interpret, you can place that code between the 'nowiki' tags.[[https://en.wikipedia.org/wiki/Help:Wiki_markup#Nowiki]] That will make a text block that stands out, like this:

 <nowiki>resultsbp <- mle(dev.bp,start=list(logalpha=-0.2, logN50=10),
        method='BFGS',fixed=list(obspos=positive,obsneg=negative,dose=dose))</nowiki>
        
Wikis are meant to allow anyone to easily add their thoughts & content, so just jump in and do it. Once you log in, you can edit any page by clicking the 'edit' tab at the top. The links below provide practical details about editing. If you want to experiment before altering an actual page, you can do it in the [[sandbox]] (you can go there anytime via the sidebar also). QMRAwiki is an implementation of the popular [http://mediawiki.org MediaWiki] program.

General info on editing wiki pages: [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page Editing Wiki]

Quick wikitext [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet 'wiki markup'] reference
**Get more in depth information here: [http://en.wikipedia.org/wiki/Help:Wiki_markup Detailed wiki markup reference]

[http://www.mediawiki.org/wiki/Images Adding images] can be tricky. The easiest way is to: 1) create the tag for the image file in the page you're editing, 2) save your edits, and then 3) click on the filename (which will be displayed in red inside a box); this will allow you to upload the file to the wiki.

Copying Tables
* If you want to transport information from QMRAwiki to Excel: 1) Highlight every cell in the table; 2) Right mouse click and click copy; 3) Open Excel; 4) In the Home tab of Excel click the down arrow below the paste icon; 5) click Paste Special...; 6) Click either Unicode Text or Text and click OK. All the data from the QMRAwiki table is now in Excel.
* To transfer from QMRAwiki into LibreOffice or OpenOffice: 1) Highlight every cell in the table; 2) Right mouse click and click copy; 3) Open your spreadsheet (Calc); 4) Click Edit > Paste Special...; 5) Choose 'HTML Format' and click OK. All the data from the QMRAwiki table is now in LibreOffice Calc.

The list of [[Special:SpecialPages|special pages]] available in QMRAwiki will help you understand what  meta-information is available about the content of QMRAwiki. It is always available at the bottom of the sidebar.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Dose response summary tables</font></div>
  <div class="NavContent" style="text-align:left">
There is an example here [http://wiki.camra.msu.edu/index.php?title=Help%3ATemplates#Briefly_presenting_results_for_several_models_together_in_one_table] of how to format a table summarizing multiple dose response models. All cells in the table must be filled. If an abbreviation is necessary that is not in the [[glossary]], please add it to the [[glossary]]. Use a plural noun for 'Host type'. 
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Presenting data from feeding experiments</font></div>
  <div class="NavContent" style="text-align:left">
[[Template:DRExperimentDataTable3]] formats data from dose response experiments with 3 dose levels. It is actually a family of templates: there are similar templates for each possible number of dose levels ([[Template:DRExperimentDataTable4]], [[Template:DRExperimentDataTable5]], etc.). For example, this code:

<code><nowiki>{{DRExperimentDataTable3|title=''Ornythorchis sumiomis'' fed to gerbils|refer=Eco 1990|reference=Eco U, 1990. Death in gerbils, mediated by ''O. sumiomis''. ''Journal of Irreproducible Results'' '''24'''(3):123.|pos=death|neg=undeath|d1=10|p1=3|n1=0|t1=3|d2=5|p2=2|n2=1|t2=3|d3=1|p3=1|n3=2|t3=3}}

</nowiki></code>

yields this formatted output (the detailed formatting info is contained within [[Template:DRExperimentDataTable3]]):

{{DRExperimentDataTable3|title=''Ornythorchis sumiomis'' fed to gerbils|refer=Eco 1990|reference=Eco U, '''1990'''. Death in gerbils, mediated by ''O. sumiomis''. ''Journal of Irreproducible Results'' '''24'''(3):123.|pos=death|neg=undeath|d1=10|p1=3|n1=0|t1=3|d2=5|p2=2|n2=1|t2=3|d3=1|p3=1|n3=2|t3=3}}


Note that italics (for proper display of scientific names, etc.) must be added manually, like this: <code><nowiki>''Italicized text''</nowiki></code>

This family of templates incorporates citations. It can correctly handle repeated citations, i.e., when two different tables cite the same reference. To do this, the 'refer' field is the short reference name (e.g., Smith 2003), and the 'reference' field is the full reference that you want in the bibliography (e.g., Smith J, '''2003'''. Bacilli I have known, ''JAMA'', '''1023'''(4):2023.). See the Mediawiki Cite extension [http://www.mediawiki.org/wiki/Extension:Cite].

==References==
<references/>

</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Presenting results from fitting dose response models to data from feeding experiments</font></div>
  <div class="NavContent" style="text-align:left">
[[Template:DRFit]] presents results from fitting feeding experiment data to the exponential and beta-Poisson dose response models, including an assessment of which model is preferred for those data.

{{DRFit|title=Goodness of fit and model selection|devE=2.99|devB=0.0156|delta=2.98|DFE=2|DFB=1|X2bPbetter=3.84|pbPbetter=0.0845|X2GOFe=5.99|pGOFe=0.224|X2GOFb=3.84|pGOFb=0.901|interpretation=Exponential is preferred to beta-Poisson; cannot reject good fit for exponential.}}

===Presenting detailed results for a particular model===

[[Template:DRConfidenceExponential]] presents bootstrapped parameter estimates for the exponential dose response model.

{{DRConfidenceExponential|title=Optimized k parameter for the exponential model, from 500 bootstrap iterations|MLEk=1.22E-08|p5k=4.44E-14|p25k=2.19E-09|p50k=4.40E-09|p950k=1.17E-07|p975k=1.17E-07|p995k=4.03E-07|N50type=ID50/LD50/ETC|MLEN=5.7E+07|p5N=1.72E+06|p25N=5.92E+06|p50N=5.92E+06|p950N=1.58E+08|p975N=3.17E+08|p995N=2.82E+17}}

[[Template:DRConfidenceBetaPoisson]] is very similar; it presents bootstrapped parameter estimates for the beta-Poisson dose response model.

{{DRConfidenceBetaPoisson|title=Optimized parameters for the beta-Poisson model, from 500 bootstrap iterations|MLEa=2.13E-01|p5a=1.26E-03|p25a=3.22E-02|p50a=3.82E-02|p950a=3.62E+02|p975a=1.25E+03|p995a=1.25E+03|MLEN=3.41E+07|p5N= 2.78E+06|p25N= 3.47E+06|p50N= 5.92E+06|p950N= 1.17E+12|p975N= 1.01E+14|p995N=9.22E+140}}

===Briefly presenting results for several models together in one table===

There are a set of templates which are combined to format summary tables of dose response models. [[Template:DRSummaryTableStart]] provides the table headings. [[Template:DRSummaryTablePreferredModel]] should be called immediately afterwards, and provides the preferred model for a particular agent. It is followed by any number of calls to [[Template:DRSummaryTableNonpreferredModel]], describing other available dose response models for that agent. The table is completed by a call to [[Template:DRSummaryTableEnd]], which has no arguments and adds the final footnote row.

<code>
<nowiki>{{DRSummaryTableStart|agent=''Bacillus necromancicum''}}</nowiki><br />

<nowiki>{{DRSummaryTablePreferredModel|expID=99|refer=Torgerson 2011|reference=Torgerson JL, Hobart IV, (2011) Journal of Postmortem Studies, 34 (13) 1365-1367.|host=zombies, Lugubrious strain|agentStrain=Voldemort Q|route=injected|nDoses=4|doseUnits=CFU|response=reanimation|bestFitModel=exponential|parameters=k = 0.02|N50=37}}

{{DRSummaryTableNonpreferredModel|expID=101|refer=Umberto 2012|reference=Umberto UU, Oxnard QT, Rehoboth ILB (2012) Journal of Non-Mundane Behavior, 34 (13), 1365-1563.|host=zombies, strain I56/8|agentStrain=Voldemort A|route=injected|nDoses=6|doseUnits=CFU|response=reanimation|bestFitModel=beta-Poisson|parameters=α = 0.1, N<sub>50</sub> = 100|N50=100}}

{{DRSummaryTableEnd}}

</nowiki>
</code>

{{DRSummaryTableStart|agent=''Bacillus necromancicum''}}
{{DRSummaryTablePreferredModel|expID=99|refer=Torgerson 2011|reference=Torgerson JL, Hobart IV, (2011) Journal of Postmortem Studies, 34 (13) 1365-1367.|host=zombies, Lugubrious strain|agentStrain=Voldemort Q|route=injected|nDoses=4|doseUnits=CFU|response=reanimation|bestFitModel=exponential|parameters=k = 0.02|N50=37}}
{{DRSummaryTableNonpreferredModel|expID=101|refer=Umberto 2012|reference=Umberto UU, Oxnard QT, Rehoboth ILB (2012) Journal of Non-Mundane Behavior, 34 (13), 1365-1563.|host=zombies, strain I56/8|agentStrain=Voldemort A|route=injected|nDoses=6|doseUnits=CFU|response=reanimation|bestFitModel=beta-Poisson|parameters=α = 0.1, N<sub>50</sub> = 100|N50=100}}
{{DRSummaryTableEnd}}

<references/>

</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">Header tabs</font></div>
  <div class="NavContent" style="text-align:left">
Some pages have tabs along the top (for example, [[Social Science of Risk]]). This is accomplished using the 'Header tabs' extension[[http://www.mediawiki.org/wiki/Extension:Header_Tabs]], which essentially converts top-level headings to tabs. Even though a page using header tabs looks like several different pages (one per tab), it is actually a single page. To enable header tabs within a page, simply add the tag <nowiki><headertabs/></nowiki> at the bottom of the page.

Referencing is a bit tricky with header tabs. Since the placement of the <nowiki><references/></nowiki> tag governs where a reference list is placed, you can have a single reference list covering all header tabs if you place <nowiki><references/></nowiki> below <nowiki><headertabs/></nowiki>. Alternatively, you can have a reference list that is limited to the visible references on a particular tab if you place a <nowiki><references/></nowiki> tag at the end of that section.
</div>
</div>

<div class="NavFrame collapsed">
  <div class="NavHead" style="text-align:left; background-color:#99DDFF"><font size="3">General tips</font></div>
  <div class="NavContent" style="text-align:left">
There are several templates[https://secure.wikimedia.org/wikipedia/meta/wiki/Help:Template] on this wiki that are used to format content, particularly relating to dose response. We have code (written in R) for fitting dose response models; that code outputs appropriate template calls that can be pasted directly into QMRAwiki pages. If a template is changed, the R code must also be changed to avoid errors. All of these templates use named fields (rather than numbered fields). Text that is capitalized must be modified by a human when the template call is pasted into QMRAwiki; it represents necessary information that the R code cannot automatically add.

If you are editing templates, some templates have embedded Semantic Internal Objects, which occur at the end of the template. All text within {{#set_internal|...}} can (and should) be ignored when modifying the template. 

When adding a new dose response model page please also add a category tag for the Agent. Use a preexisting one from the [[:Category:Agent|subcategory tree]] if possible. If the agent you wish to add does not exist you may create a new category. Please also tag the page associated with the new category you just created with one of the higher level tags found [[:Category:Agent|here]].
</div>
</div>

<headertabs/>