stats - confidence intervals

how_it_works/10-StatsRefresher.md

@@ -56,5 +56,14 @@ A relative uncertainty an absolute uncertainty (a standard deviation or a standa
 
 # Confidence Intervals
 
-You can calculate a mean, standard deviation, and standard error for any dataset with more than one measurement.  These three statistics are just the numbers calculated by the above formulas.  However, we usually want to make some more quantitative estimates about our data.  For instance, a 95% <wiki:confidence_interval> for the mean would be expected to contain the true value of the mean about 95% of the time.  This idea helps you make the leap from an uncertainty (just a number) to a mental picture of what values the .  
+You can calculate a mean, standard deviation, and standard error for any dataset with more than one measurement.  These three statistics are just the numbers calculated by the above formulas.  However, we usually want to make some more quantitative estimates about our data.  For instance, a 95% <wiki:confidence_interval> for the mean would be expected to contain the true value of the mean about 95% of the time.  This idea helps you make the leap from an uncertainty (just a number) to a mental picture of what range of values might reasonably be attributed to the parameter (e.g., isotope ratio) you're measuring.
+
+Isotope ratio data is often presented as a mean value and a ±2σ confidence interval, interpreted as a 95% confidence interval.  To construct a 95% confidence interval in this way, the $\sigma$ that you want is the {term}`standard error`, since it tells you about the uncertainty in the mean value.  For instance, if you measure 100 isotope ratios with a mean of 1.234 and a standard deviation of 0.0120, then the standard error of the ratios is 
+$$ \sigma_{\bar{x}} \  = \  \dfrac{\sigma}{\sqrt{n}} \  = \  \dfrac{0.0120}{\sqrt{100}} \  = \  0.0012, $$ 
+and a 95% confidence interval for the mean ratio would be 
+$$ \bar{x} \pm 2\sigma_{\bar{x}} \  = \  1.234 \pm 0.0024. $$
+
+To make a 95% confidence interval in this way, though, requires that you make a number of assumptions that are not always met by mass spectrometer data.
+
+## Assumptions
 

myst.yml

@@ -11,8 +11,8 @@ site:
   template: book-theme
   title: Tripoli Docs
   options:
-    logo: graphics/TripoliLogoLarge.png
-    favicon: graphics/favicon.ico
+    logo: ./graphics/TripoliLogoLarge.png
+    favicon: ./graphics/TripoliLogoLarge.png
   nav: []
   actions:
     - title: Report an Issue

setup/01-Installation.md

@@ -22,9 +22,6 @@ exports:
   - format: pdf
     id: paper
     template: lapreprint-typst
-downloads:
-  - id: paper
-    title: Download Java Instructions
 numbering:
   code: false
   headings: true

setup/03-QuickStart.md

@@ -99,19 +99,19 @@ An interactive panel at the bottom of the window contains checkboxes for showing
 
 You can load more than one mass spectrometer file into Tripoli at a time.  Close the plot window if it's open, and then drag another mass spectrometer data file onto the main Tripoli window.  The new file and plots should open immediately.
 
-To see both anayses in your new session, go to the menu at the top of the Tripoli window and choose Session -> Manage Session.  
+To see both analyses in your new session, go to the menu at the top of the Tripoli window and choose Session → Manage Session.  
 
 ```{image} ../graphics/TripoliManageSessionMenuSelection.png
 :alt: Tripoli Session Manager
 :width:
 :align: center
 ```
 
-You can name your session, see a list of the analyses included in this session, and add notes.  To save the entire session, including the data, data rejection, and data visualization choices for all analyses, go to Session -> Save Session as... The resulting session file will have the .tripoli extension.  
+You can name your session, see a list of the analyses included in this session, and add notes.  To save the entire session, including the data, data rejection, and data visualization choices for all analyses, go to Session → Save Session as... The resulting session file will have the .tripoli extension.  
 
 # Recap
 
-Now you're ready to load more mass spectrometry data files, examine the results, and export your data interpretations.  Tripoli is still under active development.  If you findn issues or bugs, go to the main Tripoli menu and find Help -> Contribute an Issue on GitHub.  If you have a question or want to start a discussion about new features to add, go to the main Tripoli menu and find Help -> Visit Tripoli Discussions on GitHub.  Note that both require a GitHub username and password (these are very handy!).
+Now you're ready to load more mass spectrometry data files, examine the results, and export your data interpretations.  Tripoli is still under active development.  If you find issues or bugs, go to the main Tripoli menu and find Help → Contribute an Issue on GitHub.  If you have a question or want to start a discussion about new features to add, go to the main Tripoli menu and find Help → Visit Tripoli Discussions on GitHub.  Note that both require a GitHub username and password (these are very handy!).
 
 For more detailed information on starting Tripoli, loading data, and making plots, please see the next section of the manual, Using Tripoli.
 
@@ -121,7 +121,7 @@ For more detailed information on starting Tripoli, loading data, and making plot
 
 :::{card}
 :header: [Starting Tripoli](../using_Tripoli/05-StartingTripoli.md "Starting Tripoli")
-Get Tripoli started using Java, from your file broswer or the command line.
+Get Tripoli started using Java, from your file browser or the command line.
 :::
 
 :::{card}