PR3: publish paper examples to docs/figures and refresh README

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.2.0
+message: "If you use nSTAT, please cite the toolbox paper below."
+title: "nSTAT: Neural Spike Train Analysis Toolbox for MATLAB"
+type: software
+license: GPL-2.0-only
+repository-code: "https://github.com/cajigaslab/nSTAT"
+authors:
+  - family-names: Cajigas
+    given-names: Iahn
+    email: icajigas@upenn.edu
+  - family-names: Malik
+    given-names: Wasim Q.
+  - family-names: Brown
+    given-names: Emery N.
+preferred-citation:
+  type: article
+  title: "nSTAT: Open-source neural spike train analysis toolbox for Matlab"
+  authors:
+    - family-names: Cajigas
+      given-names: I.
+    - family-names: Malik
+      given-names: W. Q.
+    - family-names: Brown
+      given-names: E. N.
+  journal: "Journal of Neuroscience Methods"
+  year: 2012
+  volume: 211
+  issue: 2
+  start: 245
+  end: 264
+  doi: "10.1016/j.jneumeth.2012.08.009"
+

README.md

@@ -37,6 +37,34 @@ nSTAT_Install('RebuildDocSearch', true, 'CleanUserPathPrefs', false)
 - `RebuildDocSearch` rebuilds the help search database in `helpfiles/`.
 - `CleanUserPathPrefs` removes stale user MATLAB path entries.
 
+Quickstart (MATLAB 2025b):
+
+```matlab
+cd('/path/to/nSTAT')
+nSTAT_Install('RebuildDocSearch',true,'CleanUserPathPrefs',true);
+addpath(fullfile(pwd,'tools'));
+run_all_checks('GenerateBaseline',false,'CheckParity',true,'RunTests',true,'PublishDocs',false,'Style','legacy');
+```
+
+Reproduce paper examples and export generated figures:
+
+```matlab
+addpath(fullfile(pwd,'tools'));
+
+% Default docs style (readability-focused)
+publish_examples('Style','modern');
+
+% Strict visual reproduction mode
+publish_examples('Style','legacy');
+```
+
+Outputs are generated under `docs/figures/` and are created from repository
+code only (no publication PDF image embedding).
+
+Example generated output (modern style):
+
+![nSTAT paper examples (modern)](docs/figures/paper_examples_modern/figure_001.png)
+
 Plot style policy:
 
 ```matlab
@@ -46,7 +74,6 @@ nstat.setPlotStyle('modern');
 % Legacy visual style for strict reproduction
 nstat.setPlotStyle('legacy');
 ```
-
 Rendered help documentation (GitHub Pages):
 - https://cajigaslab.github.io/nSTAT/
 
@@ -76,7 +103,7 @@ This page ties major toolbox components to the paper's workflow categories:
 If you use nSTAT in your work, please remember to cite the above paper in any publications.
 nSTAT is protected by the GPL v2 Open Source License.
 
-The code respository for nSTAT is hosted on GitHub at https://github.com/iahncajigas/nSTAT. 
+The code repository for nSTAT is hosted on GitHub at https://github.com/cajigaslab/nSTAT.
 You can download the example data file from the paper at: https://doi.org/10.6084/m9.figshare.4834640
 
 Python port

docs/figures/plot_structure_legacy.json

@@ -0,0 +1,162 @@
+{
+  "style": "legacy",
+  "figureCount": 1,
+  "figures": {
+    "index": 1,
+    "number": 1,
+    "name": "",
+    "axesCount": 7,
+    "lineCount": 422,
+    "scatterCount": 0,
+    "barCount": 0,
+    "imageCount": 0,
+    "legendEntries": [
+      "Actual",
+      "PPAF+Goal",
+      "PPAF"
+    ],
+    "axes": [
+      {
+        "title": "Estimated vs. Actual State",
+        "xlabel": "time [s]",
+        "ylabel": "state",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
+        ],
+        "ylim": [
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+          2.5
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 63,
+        "childrenCount": 63
+      },
+      {
+        "title": "Probability of State",
+        "xlabel": "time [s]",
+        "ylabel": "P(s(t)=M | data)",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
+        ],
+        "ylim": [
+          0,
+          1.1
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 42,
+        "childrenCount": 42
+      },
+      {
+        "title": "Estimated vs. Actual Reach Path",
+        "xlabel": "x [cm]",
+        "ylabel": "y [cm]",
+        "zlabel": "",
+        "xlim": [
+          -12,
+          2
+        ],
+        "ylim": [
+          -25,
+          5
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 65,
+        "childrenCount": 65
+      },
+      {
+        "title": "X Position",
+        "xlabel": "time [s]",
+        "ylabel": "x(t) [cm]",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
+        ],
+        "ylim": [
+          -11.040198295095344,
+          1.4776499210046437
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 63,
+        "childrenCount": 63
+      },
+      {
+        "title": "Y Position",
+        "xlabel": "time [s]",
+        "ylabel": "y(t) [cm]",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
+        ],
+        "ylim": [
+          -25,
+          5
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 63,
+        "childrenCount": 63
+      },
+      {
+        "title": "X Velocity",
+        "xlabel": "time [s]",
+        "ylabel": "v_{x}(t) [cm/s]",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
+        ],
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+          -40,
+          10
+        ],
+        "zlim": [
+          -1,
+          1
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+        "lineCount": 63,
+        "childrenCount": 63
+      },
+      {
+        "title": "Y Velocity",
+        "xlabel": "time [s]",
+        "ylabel": "v_{y}(t) [cm/s]",
+        "zlabel": "",
+        "xlim": [
+          0,
+          2
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+          20
+        ],
+        "zlim": [
+          -1,
+          1
+        ],
+        "lineCount": 63,
+        "childrenCount": 63
+      }
+    ],
+    "exportPath": "/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local/docs/figures/paper_examples_legacy/figure_001.png"
+  }
+}