From 4a2fe6637e41139ea43f536ab3fd749196488f10 Mon Sep 17 00:00:00 2001
From: Sahil Jhawar <sahil.jhawar448@gmail.com>
Date: Sat, 2 Nov 2024 17:39:19 +0100
Subject: [PATCH 1/2] systematics docs

---
 doc/index.rst      |  1 +
 doc/systematics.md | 78 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 doc/systematics.md

diff --git a/doc/index.rst b/doc/index.rst
index a8c4254b..464c6d51 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -485,6 +485,7 @@ User Guide
    models
    training
    data_inj_obs
+   systematics
    fitting
    lfi_analysis
    gw_inference
diff --git a/doc/systematics.md b/doc/systematics.md
new file mode 100644
index 00000000..53459a0f
--- /dev/null
+++ b/doc/systematics.md
@@ -0,0 +1,78 @@
+
+## Systematics Uncertainties
+
+NMMA currently uses `--error-budget` to specify the constant systematic uncertainties to be added to the likelihood quadrature.
+
+However, it is now possible to use systematic error ($\sigma_{sys}$) prior  in form of a freely sampled parameter, time dependent and/or filter dependent systematic error. This can done by specifying the file path using the `--systematics-file` in `lightcurve-analysis` command.
+
+For more information on systematics error, please refer to the [paper](https://arxiv.org/abs/2410.21978).
+
+The following are the examples of the systematics file:
+
+#### Example 1: Freely sampled (time independent) systematic error
+
+In this case the systematic error is freely sampled and is not dependent on time or filter.
+
+```yaml
+config:
+  withTime:
+    value: true
+    filters:
+      - null
+    time_nodes: 4
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+  withoutTime:
+    value: false
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+```
+
+#### Example 2: Time dependent systematic error
+
+In this configuration, a single systematic error is applied across all filters.
+
+```yaml
+config:
+  withTime:
+    value: true
+    filters:
+      - null
+    time_nodes: 4
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+  withoutTime:
+    value: true
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+```
+
+#### Example 3: Time and filter dependent systematic error
+
+In this configuration, the `sdssu` and ~ztfr~ filters are sampled together for systematic errors, while the `2massks` filter is sampled independently. All other filters are grouped and sampled together
+
+```yaml
+config:
+  withTime:
+    value: true
+    filters:
+      - [sdssu, ztfr]
+      - [2massks]
+      - null
+    time_nodes: 4
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+  withoutTime:
+    value: true
+    type: "Uniform"
+    minimum: 0
+    maximum: 2
+```
+
+### Distribution types
+Distribution can be of any of the `analytical` prior from [bilby](https://git.ligo.org/lscsoft/bilby). Please refer to bilby documentation for more information on the available distribution type and their usage. Only positional arguments are required for any of the distrbutions.

From 8613261ac3840a294a77e5c7af6ed6c64f43e34b Mon Sep 17 00:00:00 2001
From: Sahil Jhawar <sahil.jhawar448@gmail.com>
Date: Sat, 2 Nov 2024 18:05:48 +0100
Subject: [PATCH 2/2] bibtex in readme

---
 README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/README.md b/README.md
index 4cb496fc..c25f306d 100644
--- a/README.md
+++ b/README.md
@@ -54,6 +54,18 @@ When utilizing this code for a publication, kindly make a reference to the packa
       url={https://doi.org/10.1038/s41467-023-43932-6}
 }
 ```
+If you are using the systematics error, please also cite the paper [A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties](https://arxiv.org/abs/2410.21978). The BibTeX entry for the paper is:
+```bibtex
+@article{Jhawar:2024ezm,
+    author = "Jhawar, Sahil and Wouters, Thibeau and Pang, Peter T. H. and Bulla, Mattia and Coughlin, Michael W. and Dietrich, Tim",
+    title = "{A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties}",
+    eprint = "2410.21978",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    month = "10",
+    year = "2024"
+}
+```
 
 ### Acknowledgments
 If you benefited from participating in our community, we ask that you please acknowledge the Nuclear Multi-Messenger Astronomy collaboration, and particular individuals who helped you, in any publications.