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slide-script.html
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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>slide-script.knit</title>
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<textarea id="source">
background-image: url(images/logo.png), url(images/R_logo.png)
background-position: 0% 100%, 100% 0%
background-size: 20%, 10%
class: title-page, center, middle
## Easy webscraping with ralger package
<div>
<style type="text/css">.xaringan-extra-logo {
width: 110px;
height: 128px;
z-index: 0;
background-image: url(images/);
background-size: contain;
background-repeat: no-repeat;
position: absolute;
top:1em;right:1em;
}
</style>
<script>(function () {
let tries = 0
function addLogo () {
if (typeof slideshow === 'undefined') {
tries += 1
if (tries < 10) {
setTimeout(addLogo, 100)
}
} else {
document.querySelectorAll('.remark-slide-content:not(.title-page):not(.inverse):not(.hide_logo)')
.forEach(function (slide) {
const logo = document.createElement('a')
logo.classList = 'xaringan-extra-logo'
logo.href = 'https://bit.ly/gbganalyst'
slide.appendChild(logo)
})
}
}
document.addEventListener('DOMContentLoaded', addLogo)
})()</script>
</div>
---
class: about-me-slide, inverse, middle, center
## About Me
<img style="border-radius: 80%;" src="images/passport_new.jpg" width="180px"/>
### Ezekiel Adebayo Ogundepo
#### Data Specialist
.fade[54gene<br>Lagos, Nigeria]
[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg> https://bit.ly/gbganalyst](https://bit.ly/gbganalyst)
[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @gbganalyst](https://twitter.com/gbganalyst)
[<svg viewBox="0 0 496 512" style="position:relative;display:inline-block;top:.1em;height:1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> @gbganalyst](https://github.com/gbganalyst)
---
class: middle
.w-100.lh-copy[
Goal:
> The goal of ralger package is to make abundant of data on the web available to the researchers in real time.
]
---
class: inverse, middle
name: toc
# Major functions in ralger package
.w-100.lh-copy[
- [`scrap()`](#stp1)
- [`table_scrap()`](#stp2)
- [`tidy_scrap()`](#stp3)
- [`weblink_scrap()`](#stp4)
]
---
class: middle
name: stp1
## Released projects and packages
<https://www.repidemicsconsortium.org/projects>
<img src="images/example1.png" width="82%" height="30%" />
---
# `scap()`
```r
library(ralger)
link <- "https://www.repidemicsconsortium.org/projects/"
node <- ".item-name"
pkg_name <- scrap(link = link, node = node)
head(pkg_name)
```
```
[1] "distcrete" "EpiEstim" "earlyR" "epicontacts" "epitrix"
[6] "incidence"
```
```r
length(pkg_name)
```
```
[1] 39
```
---
name:stp2
## `table_scrap()`
This function is used to scrape an html table from a website.
.panelset[
.panel[.panel-name[COVID-19 Gambia]
```r
link <- "https://tradingeconomics.com/gambia/coronavirus-deaths"
data <- table_scrap(link = link)
data
```
```
# A tibble: 3 × 5
Related Last Previous Unit Reference
<chr> <dbl> <dbl> <chr> <chr>
1 Coronavirus Cases 12002 11999 Persons Jun 2022
2 Coronavirus Deaths 365 364 Persons Jun 2022
3 Coronavirus Recovered 5855 5844 Persons Dec 2021
```
]
.panel[.panel-name[COVID-19 Nigeria]
```r
link <- "https://covid19.ncdc.gov.ng/"
data <- table_scrap(link = link, choose = 1)
data
```
```
# A tibble: 37 × 5
states lab_confirmed no_of_cases_on_admission no_discharged no_of_deaths
<chr> <chr> <int> <chr> <int>
1 Lagos 99,688 857 98,062 769
2 FCT 28,699 27 28,423 249
3 Rivers 16,701 28 16,519 154
4 Kaduna 11,307 3 11,215 89
5 Plateau 10,256 1 10,180 75
6 Oyo 10,231 1 10,028 202
7 Edo 7,694 0 7,373 321
8 Ogun 5,810 11 5,717 82
9 Delta 5,403 122 5,170 111
10 Ondo 5,173 315 4,749 109
# … with 27 more rows
```
]
]
---
name:stp3
## `tidy_scrap()`
What of if the table is not an HTML table? `tidy_scrap()` is used to do just that.
<https://www.repidemicsconsortium.org/projects>
```r
link <- "https://www.repidemicsconsortium.org/projects/"
node <- c(".item-name", ".item-desc")
pkg_details <- tidy_scrap(link = link, nodes = node, colnames = c("Packages", "Description"))
pkg_details
```
```
# A tibble: 39 × 2
Packages Description
<chr> <chr>
1 distcrete Discretized probability distributions.
2 EpiEstim Quantifying transmissibility throughout an epidemic from inciden…
3 earlyR Estimation of infectiousness in the early stage of an outbreak
4 epicontacts Handling, visualisation and analysis of epidemiological contacts.
5 epitrix Small helpers and tricks for epidemics analysis
6 incidence Computation, handling, visualisation and simple modelling of inc…
7 aweek Convert dates to arbitrary week definitions including epiweek, i…
8 outbreaker2 Modular framework for outbreak reconstruction.
9 outbreaks Collection of outbreak data.
10 projections Projections of future incidence
# … with 29 more rows
```
---
name:stp4
## `weblink_scrap()`
This function is used to scrape web links from a website.
<https://www.repidemicsconsortium.org/projects>
```r
link <- "https://www.repidemicsconsortium.org/projects/"
weblink_scrap(link = link, contain = "github.com")
```
```
[1] "https://github.com/reconhub/distcrete"
[2] "https://github.com/annecori/EpiEstim"
[3] "https://github.com/reconhub/earlyR"
[4] "https://github.com/reconhub/epicontacts"
[5] "https://github.com/reconhub/epitrix"
[6] "https://github.com/reconhub/incidence"
[7] "https://github.com/reconhub/aweek"
[8] "https://github.com/reconhub/outbreaker2"
[9] "https://github.com/reconhub/outbreaks"
[10] "https://github.com/reconhub/projections"
[11] "https://github.com/reconhub/learn"
[12] "https://github.com/reconhub/epiflows"
[13] "https://github.com/sbfnk/bpmodels"
[14] "https://github.com/reconhub/branchr"
[15] "https://github.com/Hackout3/cleanr"
[16] "https://github.com/reconhub/drat"
[17] "https://github.com/reconhub/deployer"
[18] "https://github.com/reconhub/dibbler"
[19] "https://github.com/reconhub/docker"
[20] "https://github.com/reconhub/epicontacts.ui"
[21] "https://github.com/reconhub/epimaps"
[22] "https://github.com/Hackout3/epimatch"
[23] "https://github.com/reconhub/gisfirstaid"
[24] "https://github.com/reconhub/incidence.ui"
[25] "https://github.com/reconhub/linelist"
[26] "https://github.com/reconhub/nomad"
[27] "https://github.com/reconhub/recontools"
[28] "https://github.com/reconhub/recon.ui"
[29] "https://github.com/reconhub/reportfactory"
[30] "https://github.com/thibautjombart/vimes"
[31] "https://github.com/thibautjombart/OutbreakTools"
[32] "https://github.com/Hackout2/EpiJSON"
[33] "https://github.com/Hackout2/repijson"
[34] "https://github.com/thibautjombart/outbreaker"
[35] "https://github.com/ahgroup/DSAIDE"
[36] "https://github.com/statnet/EpiModel"
[37] "https://github.com/emvolz/treedater"
[38] "https://github.com/mrc-ide/skygrowth"
[39] "https://github.com/reconhub/reconhub.github.io"
```
---
name:stp5
## `paragraphs_scrap()`
This function is used to scrape text paragraphs from a website.
<https://data.org/people/adam-kucharski>
```r
paragraphs_scrap("https://data.org/people/adam-kucharski", collapse = T)
```
```
Dr. Adam Kucharski is an Associate Professor and Sir Henry Dale Fellow in the
Department of Infectious Disease Epidemiology at the London School of Hygiene
& Tropical Medicine. Adam’s research uses mathematical and statistical models
to understand disease outbreaks and the effects of social behavior and immunity
on transmission and control.From 2013–17, Adam held a Medical Research Council
Career Development Award in Biostatistics. During 2014–15, Adam suspended my
fellowship to work on the analysis of the Ebola epidemic in West Africa, funded
by the R2HC programme.
```
---
class: middle
## Other functions in ralger
- `titles_scrap()`
- `images_scrap()`
- `attribute_scrap()`
and many more.
---
class: middle
# ralger CRAN Page
<img src="images/example2.jpg" width="82%" height="30%" />
---
class: center, middle, inverse
# The end
--
**Thank you**
</textarea>
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(function(d) {
var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
if (!r) return;
s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
d.head.appendChild(s);
})(document);
(function(d) {
var el = d.getElementsByClassName("remark-slides-area");
if (!el) return;
var slide, slides = slideshow.getSlides(), els = el[0].children;
for (var i = 1; i < slides.length; i++) {
slide = slides[i];
if (slide.properties.continued === "true" || slide.properties.count === "false") {
els[i - 1].className += ' has-continuation';
}
}
var s = d.createElement("style");
s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
d.head.appendChild(s);
})(document);
// delete the temporary CSS (for displaying all slides initially) when the user
// starts to view slides
(function() {
var deleted = false;
slideshow.on('beforeShowSlide', function(slide) {
if (deleted) return;
var sheets = document.styleSheets, node;
for (var i = 0; i < sheets.length; i++) {
node = sheets[i].ownerNode;
if (node.dataset["target"] !== "print-only") continue;
node.parentNode.removeChild(node);
}
deleted = true;
});
})();
// add `data-at-shortcutkeys` attribute to <body> to resolve conflicts with JAWS
// screen reader (see PR #262)
(function(d) {
let res = {};
d.querySelectorAll('.remark-help-content table tr').forEach(tr => {
const t = tr.querySelector('td:nth-child(2)').innerText;
tr.querySelectorAll('td:first-child .key').forEach(key => {
const k = key.innerText;
if (/^[a-z]$/.test(k)) res[k] = t; // must be a single letter (key)
});
});
d.body.setAttribute('data-at-shortcutkeys', JSON.stringify(res));
})(document);
(function() {
"use strict"
// Replace <script> tags in slides area to make them executable
var scripts = document.querySelectorAll(
'.remark-slides-area .remark-slide-container script'
);
if (!scripts.length) return;
for (var i = 0; i < scripts.length; i++) {
var s = document.createElement('script');
var code = document.createTextNode(scripts[i].textContent);
s.appendChild(code);
var scriptAttrs = scripts[i].attributes;
for (var j = 0; j < scriptAttrs.length; j++) {
s.setAttribute(scriptAttrs[j].name, scriptAttrs[j].value);
}
scripts[i].parentElement.replaceChild(s, scripts[i]);
}
})();
(function() {
var links = document.getElementsByTagName('a');
for (var i = 0; i < links.length; i++) {
if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
links[i].target = '_blank';
}
}
})();
// adds .remark-code-has-line-highlighted class to <pre> parent elements
// of code chunks containing highlighted lines with class .remark-code-line-highlighted
(function(d) {
const hlines = d.querySelectorAll('.remark-code-line-highlighted');
const preParents = [];
const findPreParent = function(line, p = 0) {
if (p > 1) return null; // traverse up no further than grandparent
const el = line.parentElement;
return el.tagName === "PRE" ? el : findPreParent(el, ++p);
};
for (let line of hlines) {
let pre = findPreParent(line);
if (pre && !preParents.includes(pre)) preParents.push(pre);
}
preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
})(document);</script>
<script>
slideshow._releaseMath = function(el) {
var i, text, code, codes = el.getElementsByTagName('code');
for (i = 0; i < codes.length;) {
code = codes[i];
if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
text = code.textContent;
if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
/^\$\$(.|\s)+\$\$$/.test(text) ||
/^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
code.outerHTML = code.innerHTML; // remove <code></code>
continue;
}
}
i++;
}
};
slideshow._releaseMath(document);
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement('script');
script.type = 'text/javascript';
script.src = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
if (location.protocol !== 'file:' && /^https?:/.test(script.src))
script.src = script.src.replace(/^https?:/, '');
document.getElementsByTagName('head')[0].appendChild(script);
})();
</script>
</body>
</html>