docs: add initial user docs

.github/pull_request_template.md

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+
+### Checklist
+- [ ] Consider if documentation (like in `docs/`) needs to be updated
+- [ ] Consider if tests should be added

CONTRIBUTING.md

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+# Contributing to Chart Review
+
+First off, thank you!
+Read on below for tips on getting involved with the project.
+
+## Talk to Us
+
+If something annoys you, it probably annoys other folks too.
+Don't be afraid to suggest changes or improvements!
+
+Not every suggestion will align with project goals,
+but even if not, it can help to talk it out.
+
+Look at [open issues](https://github.com/smart-on-fhir/chart-review/issues),
+and if you don't see your concern,
+[file a new issue](https://github.com/smart-on-fhir/chart-review/issues/new)!
+
+## Set up your dev environment
+
+To use the same dev environment as us, you'll want to run these commands:
+```sh
+pip install .[dev]
+pre-commit install
+```
+
+This will install dependencies & build tools,
+as well as set up a `black` auto-formatter commit hook.
+
 ## Vocabulary
 
+Here is a quick introduction to some terminology you'll see in the source code.
+
 ### Labels
 - **Label**: a tag that can be applied to a word, like "Fever" or "Ideation".
   These are often applied by humans during a chart review in Label Studio,

README.md

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-# chart-review
-Measure agreement between two "_reviewers_" from the "_confusion matrix_"
+# Chart Review
+
+**Measure agreement between chart annotations.**
+
+Whether your chart annotations come from humans, machine-learning, or coded data like ICD-10,
+`chart-review` can compare them to reveal interesting statistics like:
 
 **Accuracy**
 * F1-score ([agreement](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1090460/))
 * [Sensitivity and Specificity](https://en.wikipedia.org/wiki/Sensitivity_and_specificity)
-* [Positive (PPV) or Negative Predictive Value (NPV)](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Relationship))
-* False Negative Rate (FNR) 
+* [Positive (PPV) or Negative Predictive Value (NPV)](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Relationship)
+* False Negative Rate (FNR)
 
-**Confusion Matrix** 
+**Confusion Matrix**
 * TP = True Positive (type I error)
 * TN = True Negative (type II error)
-* FP = False Positive 
-* FN = False Negative 
-
-**Power Calculations** for sample size estimation
-* Power = 1 - FNR 
-* FNR = FN / (FN + TP) 
+* FP = False Positive
+* FN = False Negative
 
+## Example
 
----
-**CHART-REVIEW** here is defined as "reading" and "annotating" (highlighting) medical notes to measure accuracy of a measurement.
-Measurements can establish the reliability of ICD10, or the reliable utility of NLP to automate labor intensive process. 
-
-Agreement among 2+ human subject matter expert reviewers is considered the defacto gold-standard for ground-truth labeling, but cannot be done manually at scale.  
-
-The most common chart-review measures agreement of the _**class_label**_ from a careful list of notes 
-* 1 human reviewer _vs_ ICD10 codes
-* 1 human reviewer _vs_ NLP results
-* 2 human reviewers _vs_ each other
+```shell
+$ ls
+config.yaml  labelstudio-export.json
+
+$ chart-review accuracy jane john
+accuracy-jane-john:
+F1     Sens  Spec  PPV  NPV  TP  FN  TN  FP  Label
+0.889  0.8   1.0   1.0  0.5  4   1   1   0   *
+1.0    1.0   1.0   1.0  1.0  1   0   1   0   Cough
+0      0     0     0    0    2   0   0   0   Fatigue
+0      0     0     0    0    1   1   0   0   Headache
+```
 
----
-### How to Install
+## Install
 1. Clone this repo.
 2. Install it locally like so: `pipx install .`
 
 `chart-review` is not yet released on PyPI.
-
----
-### How to Run
-
-#### Set Up Project Folder
-
-Chart Review operates on a project folder that holds your config & data.
-1. Make a new folder.
-2. Export your Label Studio annotations and put that in the folder as `labelstudio-export.json`.
-3. Add a `config.yaml` file (or `config.json`) that looks something like this (read more on this format below):
-
-```yaml
-labels:
-  - cough
-  - fever
-
-annotators:
-  jane: 2
-  john: 6
-  jack: 8
-
-ranges:
-  jane: 242-250  # inclusive
-  john: [260-271, 277]
-  jack: [jane, john]
-```
-
-#### Run
-
-Call `chart-review` with the sub-command you want and its arguments:
-
-For Jane as truth for Jack's annotations:
-```shell
-chart-review accuracy jane jack
-```
-
-For Jack as truth for John's annotations:
-```shell
-chart-review accuracy jack john
-```
-
-Pass `--help` to see more options.
-
----
-### Config File Format 
-
-`config.yaml` defines study specific variables. 
-
-  * Class labels: `labels: ['cough', 'fever']`
-  * Annotators: `annotators: {'jane': 3, 'john': 8}`
-  * Note ranges: `ranges: {'jane': 40-50, 'john': [2, 3, 4, 5]}`
-
-`annotators` maps a name to a Label Studio User ID
-* human subject matter expert _like_ `jane`
-* computer method _like_ `nlp` 
-* coded data sources _like_ `icd10`
-
-`ranges` maps a selection of Note IDs from the corpus 
-* `corpus: start:end`
-* `annotator1_vs_2: [list, of, notes]`
-* `annotator2_vs_3: corpus`
-
-#### External Annotations
-
-You may have annotations from NLP or coded FHIR data that you want to compare against.
-Easy!
-
-Set up your config to point at a CSV file in your project folder that holds two columns:
-- DocRef ID (real or anonymous)
-- Label
-
-```yaml
-annotators:
-  human: 1
-  external_nlp:
-    filename: my_nlp.csv
-```
-
-When `chart-review` runs, it will inject the external annotations and match up the DocRef IDs
-to Label Studio notes based on metadata in your Label Studio export.
-
----
-**BASE COHORT METHODS**
-
-`cohort.py`
-* from chart_review import _labelstudio_, _mentions_, _agree_
-
-class **Cohort** defines the base class to analyze study cohorts.
-  * init(`config.py`)
-
-`simplify.py`
-* **rollup**(...) : return _LabelStudioExport_ with 1 "rollup" annotation replacing individual mentions
-
-`term_freq.py` (methods are rarely used currently)
-* overlaps(...) : test if two mentions overlap (True/False)
-* calc_term_freq(...) : term frequency of highlighted mention text
-* calc_term_label_confusion : report of exact mentions with 2+ class_labels
-
-`agree.py` get confusion matrix comparing annotators {truth, annotator}
-* **confusion_matrix** (truth, annotator, ...) returns List[TruePos, TrueNeg, FalsePos, FalseNeg]
-* **score_matrix** (matrix) returns dict with keys {F1, Sens, Spec, PPV, NPV, TP,FP,TN,FN}
-
-`labelstudio.py` handles LabelStudio JSON
-
-Class **LabelStudioExport**
-* init(`labelstudio-export.json`)
-
-Class **LabelStudioNote**
-* init(...)
-
-`publish.py` tables and figures for PubMed manuscripts 
-* table_csv(...)
-* table_json(...)
-
----
-**NICE TO HAVES LATER**
-
-* **_confusion matrix_** type support using Pandas
-* **score_matrix** would be nicer to use a Pandas strongly typed class
-
----
-### Set up your dev environment
-
-To use the same dev environment as us, you'll want to run these commands:
-```sh
-pip install .[dev]
-pre-commit install
-```

docs/README.md

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+# Chart Review Documentation
+
+These documents are meant to be built as one part of the larger body of
+[Cumulus documentation](https://docs.smarthealthit.org/cumulus).
+
+To test changes here locally, read more at the [Cumulus docs repo](https://github.com/smart-on-fhir/cumulus).

docs/accuracy.md

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+---
+title: Accuracy Command
+parent: Chart Review
+nav_order: 5
+# audience: lightly technical folks
+# type: how-to
+---
+
+# The Accuracy Command
+
+The `accuracy` command will print agreement statistics like F1 scores and confusion matrices
+for every label in your project, between two annotators.
+
+Provide two annotator names (the first name will be considered the ground truth) and
+your accuracy scores will be printed to the console.
+
+## Example
+
+```shell
+$ chart-review accuracy jane john
+accuracy-jane-john:
+F1     Sens   Spec   PPV    NPV    TP  FN  TN  FP  Label           
+0.929  0.958  0.908  0.901  0.961  91  4   99  10  *               
+0.895  0.895  0.938  0.895  0.938  17  2   30  2   cough     
+0.815  0.917  0.897  0.733  0.972  11  1   35  4   fever  
+0.959  1.0    0.812  0.921  1.0    35  0   13  3   headache   
+0.966  0.966  0.955  0.966  0.955  28  1   21  1   stuffy-nose
+```
+
+## Options
+
+### `--config=PATH`
+
+Use this to point to a secondary (non-default) config file.
+Useful if you have multiple label setups (e.g. one grouped into a binary label and one not).
+
+### `--project-dir=DIR`
+
+Use this to run `chart-review` outside of your project dir.
+Config files, external annotations, etc will be looked for in that directory. 
+
+### `--save`
+
+Use this to write a JSON and CSV file to the project directory,
+rather than printing to the console.
+Useful for passing results around in a machine-parsable format.