📚 DOCS: Migrate Proposal to QMD

Merge pull request #5 from Thaza-Kun/proposal-md

.gitignore

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 .venv
 *.pyc
-*.csv
+*.csv
+
+# Quarto generated output
+*.quarto/
+*_book/
+*_site/

CHANGELOG.md

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+# Changelog
+
+## 0.1.1 2022-10-14
+
+### Added
+- Used [Quarto](https://quarto.org) for authoring
+  * Converted proposal written in docs to quarto markdown. [#2](https://github.com/Thaza-Kun/sarjana/issues/2)
+- Data fetching from [FRBSTATS](https://www.herta-experiment.org/frbstats/) in [`notebooks/01-get-data.ipynb`](notebooks/01-get-data.ipynb)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "sarjana-muda"
-version = "0.1.0"
+version = "0.1.1"
 description = ""
 authors = ["Thaza_Kun <[email protected]>"]
 

thesis/.gitignore

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+/.quarto/

thesis/_quarto.yml

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+project:
+  type: book
+  preview: 
+      port: 4000
+
+book:
+  title: "Characteristic Study Of Selected Fast Radio Bursts (FRB) Transients"
+  author: "Murthadza Aznam"
+  # TODO To be changed when published
+  date: '2022-07-14'
+  chapters:
+    - index.qmd
+    - literature.qmd
+    - methodology.qmd
+    - references.qmd
+
+bibliography: references.bib
+
+format:
+  html:
+    theme: cosmo
+  pdf:
+    documentclass: scrreprt

thesis/index.qmd

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+# Introduction
+
+Fast radio bursts (FRBs) are bright (50 mJy – 100 Jy), milliseconds long pulses of radio signal that is extra-terrestrial in nature.
+The frequency range of FRBs reported is between  400 MHz to 8 GHz [@petroff_fast_2019].
+The underlying process of its emission is still poorly understood.
+However, its detection has rapidly increased ever since its identification in Lorimer et al., (2007).
+By June 2022, @spanakis-misirlis_frbstats_2021 has reported 806 FRB events including 25 repeaters indexed from the Transient Name Server, the CHIME/FRB Collaboration and several other cited reports.
+
+## Instruments
+One reason for the abundance of the detection of FRBs is that many telescope dedicated to FRB has been built within the last decade.
+Listed here are several telescopes that have been known to provide open data for FRB transients:
+
+### CHIME/FRB
+The Canadian Hydrogen Intensity Mapping Experiment (CHIME) is a stationary radio telescope located in the southern parts of British Columbia, Canada (49^∘^ 19^'^ 14^''^.52 N,  119^∘^ 37^'^ 25^''^.25 W).
+Unlike conventional dish shaped radio telescope, CHIME consists of four 20m x 100m semi-cylindrical reflectors pointed skywards to achieve 8000m2¬ with a sensitivity between 400 to 800 MHz [@the_chimefrb_collaboration_chime_2018].
+This allows the telescope to map ≳200 square degrees of the sky continuously with three different output pipelines: CHIME/Cosmology, CHIME/FRB, and CHIME/Pulsar.
+The data relevant to this study is from the CHIME/FRB pipeline.
+
+### Parkes
+The Parkes radio telescope is a 64-meter steerable radio telescope located in the central-west region of New South Wales, Australia.
+It was the telescope used by Lorimer for the serendipitous discovery of the FRB in @lorimer_bright_2007.
+It has been given the name Murriyang in honour of Australian aboriginals in 2020.
+However, the name “Parkes radio telescope” or “Parkes” remains in use within the literature.
+
+## Problem Statement
+This proposal aims to answer questions such as:
+
+1. What relationship of its properties can be extracted from the population of known FRBs now that we have more than 800 observed transients?
+2. Which FRBs exhibit interesting properties compared to the rest of the population?
+3. What might be the reason behind the interesting properties of the FRBs in question (2)?
+
+## Objective
+Now that there is an abundant number of FRB detected, and many more are expected to be detected, this proposal aims to:
+
+1. Study the distribution of FRBs to understand the relationship between its properties.
+2. Study the properties of selected samples of FRB to gain insight on its source or emission mechanism.
+3. Implement programming methods for the distribution study of FRBs and for the feature study of selected FRBs.

thesis/literature.qmd

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+# Literature Review
+## Observed Properties
+### Dispersion Measure
+As radio signals propagate through space, it interacts with mediums it encounters and thus is dispersed.
+As a consequence, its arrival time is directly dependent on its frequency with lower frequencies arriving later [@day_pinpointing_2022; @kulkarni_dispersion_2020].
+The measure of this dispersion – its dispersion measure (DM) – is a key observable quantity in studies of FRBs [@keane_fast_2016].
+It is generally accepted that the DM of a FRB transient is due to free electrons encountered, $n_e$, along the path, dl, with the relation,
+$$
+\text{DM} = \int_0^d n_e \text{d}l.
+$$ {#eq-DM}
+
+However, it is worth noting that ionized particles, plasma temperature, magnetic fields and its relative motion contribute to this measure even though these other contributions are very small and can be neglected [@kulkarni_dispersion_2020].
+The DM of a given transient is calculated using two observables: its arrival time, $t$, and its frequency, $\nu$; where the DM is related by the slope relation
+$$
+\Delta t = a\frac{\text{DM}}{\Delta\nu^2},
+$$ {#eq-DM-slope-a}
+or more directly
+$$
+\text{DM} = K\Delta\nu^2\Delta t,
+$$ {#eq-DM-slope-k}
+where $a=K^{-1}$ and $\Delta\nu^2$ is the difference of the highest and lowest frequency.
+Users of calculation software should be made aware which conventions are used.
+For the sake of precision, both values with its uncertainty are provided here [@kulkarni_dispersion_2020]:
+
+<!-- TODO Align Eq -->
+$a=4.148 806 4239(11) \text{GH}^2\text{pc}^{-1}\text{cm}^3\text{ms}$
+
+$K=241.033 1786(66)  \text{GH}^{-2}\text{pc}\text{cm}^{-3}\text{s}$
+
+###	Fluence And Peak Flux Density
+The fluence, $\mathcal{F}$, of a transient is the total energy received by the antenna throughout the duration of the signal typically measured in Jansky seconds, $\text{J}\cdot\text{s}$.
+It then is characterized by the expression [@petroff_fast_2019]
+$$
+\mathcal{F} = \int_\text{pulse} S(t) \text{d}t,
+$$ {#eq-fluence-by-integral}
+where $S(t)$ is the flux density of the signal. We can then characterize the peak flux density, $S_\text{peak}$ and its pulse width, $W_\text{pulse}$ like so
+$$
+\mathcal{F} = S_\text{peak} W_\text{peak}.
+$$ {#eq-fluence-by-peaks}
+
+###	Rotation Measure
+Analogous to dispersion measure, where the frequency is dispersed by the interacting medium, the radio wave may also be rotated as electrons interact with its magnetic field component.
+This rotation is measurable via its polarization, $\Theta$, which is proportional to its wavelength squared, $\lambda^2$,
+$$
+\Theta = \text{RM} \lambda^2,
+$$ {#eq-RM}
+where RM is the Faraday rotation measure.
+This quantity, RM, is analogous to @eq-DM for DM as it is the total interaction along the line of sight [@brentjens_faraday_2005; @feng_frequency-dependent_2022],
+$$
+\text{RM} = -0.81\int_0^d B(l)_\parallel n_e(l) \text{d}l.
+$$ {#eq-RM-intergral}
+
+## Derived Properties
+
+### Distance Constraints
+The DM of the FRBs can be used to infer the distance of the source by estimating contributions along the line of sight.
+FRBs typically have DM more than the contributions from Milky Way, $\text{DM}_\text{MW}$, suggesting it is an extragalactic phenomenon.
+The Milky Way contribution can be calculated using an electron density model associated with @eq-DM.
+The YMW16 model in @yao_new_2017 uses known distances of pulsars using independent methods and matching it with their respective DMs.
+Its value highly depends on its galactic latitude as there is little material higher up in the latitude so its DM is expected to be small [@thornton_population_2013].
+Non-Milky Way contributions to the observed DM (dubbed dispersion measure excess, $\text{DM}_\text{E}$) come from the intergalactic medium (IGM) and the host galaxy [@deng_cosmological_2014; @petroff_fast_2019],
+$$
+\text{DM}_\text{E} = \text{DM} =\text{DM}_\text{MW} + \left(\frac{\text{DM}_\text{Host}}{1+z}\right),
+$$ {#eq-DM-excess}
+where $z$ is the redshift associated with the host galaxy.
+The $\text{DM}_\text{Host}$ of the transient depends its distance from the host galactic core and viewing angle [@thornton_population_2013] because those factor determines how much material interacts with the signal throughout its propagation.

thesis/methodology.qmd

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+# Methodology
+## Data Source
+<!-- TODO Beautify -->
+Listed below are open data on FRBs released by their respective telescopes that might be helpful for the research:
+Telescope	Server	Data
+
+- CHIME/FRB
+    * Server: CANFAR
+        - [doi:10.11570/19.0004](doi:10.11570/19.0004)
+        - [doi:10.11570/19.0005](doi:10.11570/19.0005)
+        - [doi:10.11570/20.0002](doi:10.11570/20.0002)
+        - [doi:10.11570/20.0006](doi:10.11570/20.0006)
+        - [doi:10.11570/20.0006](doi:10.11570/20.0006)
+        <!-- TODO Link to data paper -->
+- Parkes
+    * Sever: gDCMP	
+        - [https://data-portal.hpc.swin.edu.au/dataset/parkes-frbs-archival-data](https://data-portal.hpc.swin.edu.au/dataset/parkes-frbs-archival-data)
+        - [https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-high-time-resolution-universe-survey-high-latitude](https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-high-time-resolution-universe-survey-high-latitude)
+        - [https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-frb-140514](https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-frb-140514)
+        - [https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-frb-150215](https://data-portal.hpc.swin.edu.au/dataset/fast-radio-burst-data-frb-150215)
+        <!-- TODO Link to data paper -->
+- Lovell
+    * Server: Zenodo
+        - [https://zenodo.org/record/3974768#.YGWzqK8zap0](https://zenodo.org/record/3974768#.YGWzqK8zap0)
+        <!-- TODO Link to data paper -->
+- STARE2
+    * Server: CalTechDATA
+        - [https://data.caltech.edu/records/1647](https://data.caltech.edu/records/1647)
+        <!-- TODO Link to data paper -->
+
+
+Other than that, the FRBSTATS^[@spanakis-misirlis_frbstats_2021 [https://www.herta-experiment.org/frbstats/](https://www.herta-experiment.org/frbstats/)] website provides an open-source live update of known FRBs, its properties, and its references. This will be helpful for statistical analysis for the entire population. It can be accessed programmatically via an Application Programming Interface (API) or downloaded as a comma separated value (.csv) or excel (.xlsx) files.
+
+## Data Analysis
+The study will be using Python3.8 or higher to conduct the analysis of the data. It has good support for `.hd5`, `.msgpack`, `.fits` and other common file formats used in astronomy and statistics. In addition to that, the CHIME/FRB Open Data package that aims to assist the analysis of CHIME/FRB datasets, and the ‘astropy’ package (a reliable package for astronomy) is also written in Python.
+
+## Expected Outcome
+The study expects to output the distribution of selected properties mentioned throughout the proposal and pick out important characteristics from the distribution.
+
+## Timeline
+This study can be divided roughly into four phases and is expected to be 2 years long:
+
+1.	Distribution study. Phase 1 will consist of a statistical study to the whole population of known FRBs. This is done to get a big picture of the landscape of FRBs.
+2.	Selection of FRBs. Phase 2 is the selection phase where several FRBs with interesting properties will be chosen. The selection phase includes the gathering of observation data on the selected FRB.
+3.	Feature study. Phase 3 will study the chosen FRBs for features that contribute to the interesting properties mentioned in phase 2. This is expected to be longest of the four phases.
+4.	Thesis writing and defence.
+
+<!-- TODO Gantt Chart Here refer https://mermaid-js.github.io/mermaid/#/gantt -->
+<!-- ? DO we have to? -->