/
about.Rmd
139 lines (93 loc) · 5.1 KB
/
about.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
---
title: "About"
author: "Francisco Bischoff"
date: "on July 22, 2020"
bibliography: ../papers/references.bib
link-citations: true
csl: https://raw.githubusercontent.com/citation-style-language/styles/master/american-medical-association.csl
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(here)
knitr::opts_knit$set(root.dir = here("docs"), base.dir = here("docs"))
```
<!-- badges: start -->
 [](https://mybinder.org/v2/gh/franzbischoff/false.alarm/master?urlpath=rstudio)
[](https://franzbischoff.github.io/false.alarm/)
<!-- badges: end -->
# Abstract
Currently, Point-of-Care (POC) ECG monitoring works either as plot devices or alarms for abnormal cardiac rhythms using
predefined normal trigger ranges. On the other hand, full 12-derivation ECG machines are complex to use as simple
monitors and are used with strict techniques for formal diagnostics of hearth electric conduction pathologies, and the
automatic diagnostics are derived from a full analysis of the 12-dimension data after it is fully collected. Both
systems do not handle disconnected leads and patient's motions, being strictly necessary to have a good and stable
signal to allow proper diagnosis.
This research aims to identify abnormal hearth electric patterns using streaming data, specifically those who are
life-threatening, being a reliable signal for Intensive Care Units to respond quickly to those situations.
The study design is comparable to a Diagnostic study, where high accuracy is essential. It will use the Physionet
datasets[@Clifford2015], and the algorithm will try to minimize the false negatives and false positives.
The expected result is the concretization of a new method that, besides being accurate, accomplishes this task using
state of the art technology for time series analysis that allows minimum space and processor power to solve this
problem. Also, we expect that fading factors can contribute to the state of the art of this technology.
The research team is well experienced in time-series and has studied the Matrix Profile since its beginning, being
founders of the Matrix Profile Foundation whose goal is to have a concise and stable cross-language API for developing
with the Matrix Profile technology.[@RJ-2020-021; @VanBenschoten2020]
# About the ongoing project.
The document submitted for approval is
[here](https://github.com/franzbischoff/false.alarm/blob/master/protocol/Protocol.pdf).
To follow the thesis timeline you can access the full Gantt chart at Zenhub. Click
[here](https://app.zenhub.com/workspaces/phd-thesis-5eb2ce34f5f30b3aed0a35af/roadmap) (you need a github account, but
that's it).
# Reproducible Research[@krystalli_2019]
This thesis will follow the compendium principles:
## Following Standards
Aiming to create secure materials that are [FAIR](https://www.nature.com/articles/sdata201618) *findable, accessible,
interoperable, reusable*
### Research Data Management
- [**RDM
checklist**](http://www.dcc.ac.uk/sites/default/files/documents/resource/DMP/DMP_Checklist_2013.pdf)[@dcc_2013]
- Anticipate **data products** as part of your thesis **outputs**
- Think about what technologies to use
### Missing values are a fact of life
- Usually, best solution is to **leave blank**
- **`NA`** or **`NULL`** are also good options
- **NEVER use `0`**. Avoid numbers like **`-999`**
- Don't make up your own code for missing values
### Raw data are sacrosanct
- Don't, not even with a barge pole, not for one second, touch or otherwise edit the raw data files. Do an
manipulations in script
### Three principles for good (file) names
#### Machine readable
- Regular expression and globbing friendly
- Avoid spaces, punctuation, accented characters, case sensitivity
- Easy to compute on
- Deliberate use of delimiters
- Deliberate use of `"-"` and `"_"` allows recovery of metadata from the filenames:
- `"_"` underscore used to delimit units of metadata I want to access later
- `"-"` hyphen used to delimit words so our eyes don't bleed
#### Human readable
- Borrowing the concept from [slugs](https://en.wikipedia.org/wiki/Clean_URL#Slug) from semantic URLs
#### Play well with default ordering
- Put something numeric first
- Use the ISO 8601 standard for dates
- Left pad other numbers with zeros
# License
<center>
[](https://creativecommons.org/licenses/by-nc-sa/4.0/)
</center>
This work is licensed under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
License](https://creativecommons.org/licenses/by-nc-sa/4.0/).
# References