"use strict"; const {Fragment: _Fragment, jsx: _jsx, jsxs: _jsxs} = arguments[0]; const {useMDXComponents: _provideComponents} = arguments[0]; function _createMdxContent(props) { const _components = { a: "a", code: "code", img: "img", li: "li", ol: "ol", p: "p", pre: "pre", span: "span", strong: "strong", ul: "ul", ..._provideComponents(), ...props.components }; return _jsxs(_Fragment, { children: [_jsx(_components.p, { children: "Write a code :" }), "\n", _jsxs(_components.ul, { children: ["\n", _jsxs(_components.li, { children: ["load ", _jsx(_components.a, { href: "https://github.com/chrit88/Bioinformatics_data/tree/master/Workshop%203", target: "_blank", rel: "noopener noreferrer", children: "data" }), " on Github: ", _jsx(_components.code, { className: "language-auto", children: "to_sort_pop_1.csv" }), " and ", _jsx(_components.code, { className: "language-auto", children: "to_sort_pop_1.csv" }), ". These data are population counts for endangered species."] }), "\n", _jsxs(_components.li, { children: ["using both of these data together into a single tibble (", _jsx(_components.code, { className: "language-auto", children: "join" }), ")"] }), "\n", _jsx(_components.li, { children: "reshape them from wide to long format" }), "\n", _jsx(_components.li, { children: "make sure when you do this that you end up with" }), "\n"] }), "\n", _jsxs(_components.ol, { children: ["\n", _jsx(_components.li, { children: "a column specifying which population the data are from (i.e. population 1 or 2)," }), "\n", _jsx(_components.li, { children: "a column specifying the date the data were collected," }), "\n", _jsx(_components.li, { children: "a column with the population abundance estimates in it, and" }), "\n", _jsx(_components.li, { children: "that any missing values are dropped from the data. I.e. your data.frame should look like the figure below." }), "\n"] }), "\n", _jsxs(_components.ul, { children: ["\n", _jsxs(_components.li, { children: ["do the above with the ", _jsx(_components.strong, { children: "minimum" }), " amount of code (hint - ", _jsx(_components.code, { className: "language-auto", children: "%>%" }), ")"] }), "\n"] }), "\n", _jsxs(_components.p, { children: ["final format will like:\n", _jsx(_components.img, { src: "https://dg-of-obsidain-cafwell.flowershow.me/Pasted%20image%2020221105202913.png", alt: "Pasted image 20221105202913", className: "internal new" })] }), "\n", _jsx(_components.pre, { className: "language-r", children: _jsxs(_components.code, { className: "language-R code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Use vroom package input data from github" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["pop1 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " vroom", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"https://raw.githubusercontent.com/ExperimentalConservation/Bioinformatics_data/master/Workshop%203/to_sort_pop_1.csv\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["pop2 ", _jsx(_components.span, { className: "token operator", children: "<-" }), " vroom", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"https://raw.githubusercontent.com/ExperimentalConservation/Bioinformatics_data/master/Workshop%203/to_sort_pop_2.csv\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["pop_tidy ", _jsx(_components.span, { className: "token operator", children: "<-" }), " pop1 ", _jsx(_components.span, { className: "token percent-operator operator", children: "%>%" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# use pipeline and connect pop1 and pop2 via full_join()" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" full_join", _jsx(_components.span, { className: "token punctuation", children: "(" }), "pop2", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token percent-operator operator", children: "%>%" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# want to aggregate all columns starting with 'pop_1' and 'pop_2'" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" pivot_longer", _jsx(_components.span, { className: "token punctuation", children: "(" }), "cols ", _jsx(_components.span, { className: "token operator", children: "=" }), " starts_with", _jsx(_components.span, { className: "token punctuation", children: "(" }), "c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"pop_1\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"pop_2\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# there are multiple variables(population and date) in the column name" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" names_to ", _jsx(_components.span, { className: "token operator", children: "=" }), " c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"population\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token string", children: "\"date\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# use Regular expression to search and divide them" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" names_pattern ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"pop_(.)_(.*)\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# name value as 'abundance' " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" values_to ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token string", children: "\"abudance\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# delete Na from values" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" values_drop_na ", _jsx(_components.span, { className: "token operator", children: "=" }), " T", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# show result" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "pop_tidy\n" })] }) }), "\n", _jsx(_components.p, { children: "Result:" }), "\n", _jsx(_components.pre, { className: "language-r", children: _jsxs(_components.code, { className: "language-R code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## # A tibble: 696 × 7" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## species primary_th…¹ secon…² terti…³ popul…⁴ date abuda…⁵" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 1 Schistidium helveticum Habitat des… 1 2013… 353" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 2 Schistidium helveticum Habitat des… 1 2014… 419" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 3 Schistidium helveticum Habitat des… 1 2015… 359" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 4 Schistidium helveticum Habitat des… 1 2016… 363" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 5 Schistidium helveticum Habitat des… 1 2017… 321" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 6 Schistidium helveticum Habitat des… 1 2018… 280" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 7 Schistidium helveticum Habitat des… 1 2019… 379" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 8 Paraleucobryum longifolium Exploitation Habita… 1 2005… 24" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 9 Paraleucobryum longifolium Exploitation Habita… 1 2006… 12" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## 10 Paraleucobryum longifolium Exploitation Habita… 1 2007… 18" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## # … with 686 more rows, and abbreviated variable names ¹primary_threat," }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "## # ²secondary_threat, ³tertiary_threat, ⁴population, ⁵abudance" }), "\n"] })] }) })] }); } function MDXContent(props = {}) { const {wrapper: MDXLayout} = { ..._provideComponents(), ...props.components }; return MDXLayout ? _jsx(MDXLayout, { ...props, children: _jsx(_createMdxContent, { ...props }) }) : _createMdxContent(props); } return { default: MDXContent };