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module3/exo3/_minted-exercice_R_en/00CED2E8E1398BB9B3D3E9837D2E642D90AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{extracted\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{l+m+mi}{1}\PYG{p}{:]} \PYG{o}{=} \PYG{p}{[}\PYG{n}{datetime}\PYG{o}{.}\PYG{n}{datetime}\PYG{o}{.}\PYG{n}{strptime}\PYG{p}{(}\PYG{n}{date}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}\PYGZpc{}m/}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+s2}{/\PYGZpc{}y\PYGZdq{}}\PYG{p}{)} \PYG{k}{for} \PYG{n}{date} \PYG{o+ow}{in} \PYG{n}{extracted\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{l+m+mi}{1}\PYG{p}{:]]}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/1973C94197001CA69F2F4EB5512E2A2DE36E7B2C8D886207B0A18BA1065D30A3.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{data}\PYG{o}{\PYGZdl{}}\PYG{n}{Date} \PYG{o}{\PYGZlt{}\PYGZhy{}} \PYG{n+nf}{as.Date}\PYG{p}{(}\PYG{n}{data}\PYG{o}{\PYGZdl{}}\PYG{n}{Date}\PYG{p}{)}
\PYG{n+nf}{summary}\PYG{p}{(}\PYG{n}{data}\PYG{p}{)}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/1E9B812903B722A26DC5A008EE67FDC290AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{k+kn}{import} \PYG{n+nn}{sys}
\PYG{k}{if} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{version\PYGZus{}info}\PYG{o}{.}\PYG{n}{major} \PYG{o}{\PYGZlt{}} \PYG{l+m+mi}{3} \PYG{o+ow}{or} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{version\PYGZus{}info}\PYG{o}{.}\PYG{n}{minor} \PYG{o}{\PYGZlt{}} \PYG{l+m+mi}{6}\PYG{p}{:}
\PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}Please use Python 3.6 (or higher)!\PYGZdq{}}\PYG{p}{)}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/61C9C811EFFF8966608130E9B3ECE76690AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{p}{[}\PYG{n}{flipped\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{],} \PYG{k+kc}{None}\PYG{p}{]} \PYG{o}{+} \PYG{n}{flipped\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{:]}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/97EB0B5EECE39484A8D3EDA779BF273C30332BB74E97A4D20FDB171C0EFB01F5.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{p}{(}\PYG{n+nb}{unless} \PYG{p}{(}\PYG{n+nb}{featurep} \PYG{l+s+ss}{\PYGZsq{}ob\PYGZhy{}python}\PYG{p}{)}
\PYG{p}{(}\PYG{n+nf}{print} \PYG{l+s}{\PYGZdq{}Please activate python in org\PYGZhy{}babel (org\PYGZhy{}babel\PYGZhy{}do\PYGZhy{}lnaguages)!\PYGZdq{}}\PYG{p}{))}
\PYG{p}{(}\PYG{n+nb}{unless} \PYG{p}{(}\PYG{n+nb}{featurep} \PYG{l+s+ss}{\PYGZsq{}ob\PYGZhy{}R}\PYG{p}{)}
\PYG{p}{(}\PYG{n+nf}{print} \PYG{l+s}{\PYGZdq{}Please activate R in org\PYGZhy{}babel (org\PYGZhy{}babel\PYGZhy{}do\PYGZhy{}lnaguages)!\PYGZdq{}}\PYG{p}{))}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/9909A0B413854E5E7EEA7260BBC6BB6B90AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{target\PYGZus{}countries} \PYG{o}{=} \PYG{p}{[}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Belgium\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{l+s+s2}{\PYGZdq{}Hong Kong\PYGZdq{}}\PYG{p}{,} \PYG{k+kc}{None}\PYG{p}{],}
\PYG{p}{[}\PYG{l+s+s2}{\PYGZdq{}Hong Kong\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}China\PYGZdq{}}\PYG{p}{],} \PYG{c+c1}{\PYGZsh{} China without Hong Kong}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}France\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Germany\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Iran\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Italy\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Japan\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}South Korea\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}Netherlands\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}United Kingdom\PYGZdq{}}\PYG{p}{],}
\PYG{p}{[}\PYG{k+kc}{None}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}US\PYGZdq{}}\PYG{p}{]}
\PYG{p}{]}
\PYG{k}{def} \PYG{n+nf}{is\PYGZus{}target\PYGZus{}country}\PYG{p}{(}\PYG{n}{province}\PYG{p}{,} \PYG{n}{country}\PYG{p}{):}
\PYG{n}{specific\PYGZus{}province} \PYG{o}{=} \PYG{k}{lambda} \PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{:} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{==} \PYG{n}{p} \PYG{o+ow}{and} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o+ow}{is} \PYG{k+kc}{None}
\PYG{n}{without\PYGZus{}specific\PYGZus{}province} \PYG{o}{=} \PYG{k}{lambda} \PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{:} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o+ow}{is} \PYG{o+ow}{not} \PYG{k+kc}{None} \PYG{o+ow}{and} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{!=} \PYG{n}{p} \PYG{o+ow}{and} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{==} \PYG{n}{c}
\PYG{n}{without\PYGZus{}provinces} \PYG{o}{=} \PYG{k}{lambda} \PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{:} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o+ow}{is} \PYG{k+kc}{None} \PYG{o+ow}{and} \PYG{n}{p} \PYG{o}{==} \PYG{l+s+s2}{\PYGZdq{}\PYGZdq{}} \PYG{o+ow}{and} \PYG{n}{t}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{==} \PYG{n}{c}
\PYG{n}{check} \PYG{o}{=} \PYG{k}{lambda} \PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{:} \PYG{n}{specific\PYGZus{}province}\PYG{p}{(}\PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{)} \PYG{o+ow}{or} \PYG{n}{without\PYGZus{}specific\PYGZus{}province}\PYG{p}{(}\PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{)} \PYG{o+ow}{or} \PYG{n}{without\PYGZus{}provinces}\PYG{p}{(}\PYG{n}{t}\PYG{p}{,} \PYG{n}{p}\PYG{p}{,} \PYG{n}{c}\PYG{p}{)}
\PYG{n}{res} \PYG{o}{=} \PYG{p}{[}\PYG{n}{check}\PYG{p}{(}\PYG{n}{target}\PYG{p}{,} \PYG{n}{province}\PYG{p}{,} \PYG{n}{country}\PYG{p}{)} \PYG{k}{for} \PYG{n}{target} \PYG{o+ow}{in} \PYG{n}{target\PYGZus{}countries}\PYG{p}{]}
\PYG{k}{return} \PYG{n+nb}{any}\PYG{p}{(}\PYG{n}{res}\PYG{p}{)}
\PYG{n}{extracted\PYGZus{}data} \PYG{o}{=} \PYG{p}{[]}
\PYG{n}{extracted\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{([}\PYG{n}{data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{l+m+mi}{1}\PYG{p}{]]} \PYG{o}{+} \PYG{n}{data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{l+m+mi}{4}\PYG{p}{:])}
\PYG{k}{for} \PYG{n}{row} \PYG{o+ow}{in} \PYG{n}{valid\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{:]:}
\PYG{k}{if} \PYG{l+s+s2}{\PYGZdq{}Korea\PYGZdq{}} \PYG{o+ow}{in} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]:}
\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{])}
\PYG{k}{if} \PYG{n}{is\PYGZus{}target\PYGZus{}country}\PYG{p}{(}\PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{],} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]):}
\PYG{c+c1}{\PYGZsh{} print(row[0])}
\PYG{k}{if} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{==} \PYG{l+s+s2}{\PYGZdq{}Hong Kong\PYGZdq{}}\PYG{p}{:}
\PYG{n}{extracted\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{([}\PYG{l+s+s2}{\PYGZdq{}Hong Kong\PYGZdq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{4}\PYG{p}{:])}
\PYG{k}{elif} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{==} \PYG{l+s+s2}{\PYGZdq{}China\PYGZdq{}}\PYG{p}{:}
\PYG{k}{try}\PYG{p}{:}
\PYG{n}{idx} \PYG{o}{=} \PYG{p}{[}\PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{k}{for} \PYG{n}{row} \PYG{o+ow}{in} \PYG{n}{extracted\PYGZus{}data}\PYG{p}{]}\PYG{o}{.}\PYG{n}{index}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}China\PYGZdq{}}\PYG{p}{)}
\PYG{n}{extracted\PYGZus{}data}\PYG{p}{[}\PYG{n}{idx}\PYG{p}{][}\PYG{l+m+mi}{1}\PYG{p}{:]} \PYG{o}{=} \PYG{p}{[}\PYG{n+nb}{int}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{o}{+} \PYG{n+nb}{int}\PYG{p}{(}\PYG{n}{b}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a}\PYG{p}{,} \PYG{n}{b} \PYG{o+ow}{in} \PYG{n+nb}{zip}\PYG{p}{(}\PYG{n}{extracted\PYGZus{}data}\PYG{p}{[}\PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}\PYG{p}{][}\PYG{l+m+mi}{1}\PYG{p}{:],} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{4}\PYG{p}{:])]}
\PYG{k}{except} \PYG{n+ne}{ValueError}\PYG{p}{:}
\PYG{n}{extracted\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{([}\PYG{l+s+s2}{\PYGZdq{}China\PYGZdq{}}\PYG{p}{]} \PYG{o}{+} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{4}\PYG{p}{:])}
\PYG{k}{else}\PYG{p}{:}
\PYG{n}{extracted\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{([}\PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]]} \PYG{o}{+} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{4}\PYG{p}{:])}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/A3AE5B661045164799DE417D5E4BBA44E36E7B2C8D886207B0A18BA1065D30A3.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n+nf}{library}\PYG{p}{(}\PYG{n}{tidyverse}\PYG{p}{)}
\PYG{n+nf}{library}\PYG{p}{(}\PYG{n}{ggrepel}\PYG{p}{)}
\PYG{n+nf}{library}\PYG{p}{(}\PYG{n}{scales}\PYG{p}{)}
\PYG{n}{last\PYGZus{}date} \PYG{o}{\PYGZlt{}\PYGZhy{}} \PYG{n}{data} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{gather}\PYG{p}{(}\PYG{n}{Country}\PYG{p}{,} \PYG{n}{Cases}\PYG{p}{,} \PYG{n}{Belgium}\PYG{o}{:}\PYG{n}{UnitedKingdom}\PYG{p}{)} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n}{dplyr}\PYG{o}{::}\PYG{n+nf}{filter}\PYG{p}{(}\PYG{n}{Date} \PYG{o}{==} \PYG{n+nf}{tail}\PYG{p}{(}\PYG{n}{data}\PYG{o}{\PYGZdl{}}\PYG{n}{Date}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{),} \PYG{n}{Country} \PYG{o}{\PYGZpc{}in\PYGZpc{}} \PYG{n+nf}{c}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}US\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}France\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}Germany\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}China\PYGZdq{}}\PYG{p}{))}
\PYG{c+c1}{\PYGZsh{} Color\PYGZhy{}blind friendly palette taken from}
\PYG{c+c1}{\PYGZsh{} https://bconnelly.net/posts/creating\PYGZus{}colorblind\PYGZhy{}friendly\PYGZus{}figures/}
\PYG{c+c1}{\PYGZsh{} with added grayscale values}
\PYG{n}{palette} \PYG{o}{\PYGZlt{}\PYGZhy{}} \PYG{n+nf}{c}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}\PYGZsh{}000000\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}E69F00\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}56B4E9\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}009E73\PYGZdq{}}\PYG{p}{,}
\PYG{l+s}{\PYGZdq{}\PYGZsh{}292929\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}555555\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}999999\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}BBBBBB\PYGZdq{}}\PYG{p}{,}
\PYG{l+s}{\PYGZdq{}\PYGZsh{}F0E442\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}0072B2\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}D55E00\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}\PYGZsh{}CC79A7\PYGZdq{}}\PYG{p}{)}
\PYG{n}{data} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{gather}\PYG{p}{(}\PYG{n}{Country}\PYG{p}{,} \PYG{n}{Cases}\PYG{p}{,} \PYG{n}{Belgium}\PYG{o}{:}\PYG{n}{UnitedKingdom}\PYG{p}{)} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{ggplot}\PYG{p}{(}\PYG{n+nf}{aes}\PYG{p}{(}\PYG{n}{x}\PYG{o}{=}\PYG{n}{Date}\PYG{p}{,} \PYG{n}{y}\PYG{o}{=}\PYG{n}{Cases}\PYG{p}{,} \PYG{n}{colour}\PYG{o}{=}\PYG{n}{Country}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{geom\PYGZus{}line}\PYG{p}{()} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}x\PYGZus{}date}\PYG{p}{(}\PYG{n}{breaks} \PYG{o}{=} \PYG{n+nf}{pretty\PYGZus{}breaks}\PYG{p}{(}\PYG{l+m}{8}\PYG{p}{),} \PYG{n}{labels} \PYG{o}{=} \PYG{n+nf}{date\PYGZus{}format}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}\PYGZpc{}b \PYGZpc{}Y\PYGZdq{}}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}color\PYGZus{}manual}\PYG{p}{(}\PYG{n}{values}\PYG{o}{=}\PYG{n}{palette}\PYG{p}{)} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}y\PYGZus{}continuous}\PYG{p}{(}\PYG{n}{labels} \PYG{o}{=} \PYG{n+nf}{comma\PYGZus{}format}\PYG{p}{(),} \PYG{n}{breaks} \PYG{o}{=} \PYG{n+nf}{pretty\PYGZus{}breaks}\PYG{p}{(}\PYG{l+m}{8}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{geom\PYGZus{}text\PYGZus{}repel}\PYG{p}{(}\PYG{n}{data}\PYG{o}{=}\PYG{n}{last\PYGZus{}date}\PYG{p}{,} \PYG{n+nf}{aes}\PYG{p}{(}\PYG{n}{label} \PYG{o}{=} \PYG{n}{Country}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{ggtitle}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}Cumulative confirmed cases of Covid\PYGZhy{}19\PYGZdq{}}\PYG{p}{,} \PYG{n}{subtitle}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}In selected countries since the beginning of 2020\PYGZdq{}}\PYG{p}{)} \PYG{o}{+}
\PYG{n+nf}{theme\PYGZus{}bw}\PYG{p}{()}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/B99FD72F34E3FE085DF64C34D79C004A90AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{flipped\PYGZus{}data} \PYG{o}{=} \PYG{p}{[[}\PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{row}\PYG{p}{[}\PYG{n}{i}\PYG{p}{])} \PYG{k}{for} \PYG{n}{row} \PYG{o+ow}{in} \PYG{n}{extracted\PYGZus{}data}\PYG{p}{]} \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{,} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{extracted\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]))]}
\PYG{n}{flipped\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{=} \PYG{l+s+s2}{\PYGZdq{}Date\PYGZdq{}}
\PYG{n}{flipped\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{=} \PYG{p}{[}\PYG{n}{s}\PYG{o}{.}\PYG{n}{replace}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{} \PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}\PYGZdq{}}\PYG{p}{)} \PYG{k}{for} \PYG{n}{s} \PYG{o+ow}{in} \PYG{n}{flipped\PYGZus{}data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]]}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/BA7101633D4DEEC096F5E438CBE00111E36E7B2C8D886207B0A18BA1065D30A3.pygtex 0 → 100644
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\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n+nf}{plot}\PYG{p}{(}\PYG{n}{data}\PYG{p}{[,}\PYG{l+s}{\PYGZsq{}Date\PYGZsq{}}\PYG{p}{],} \PYG{n}{data}\PYG{p}{[,}\PYG{l+s}{\PYGZsq{}France\PYGZsq{}}\PYG{p}{],} \PYG{n}{xlab}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}Date\PYGZdq{}}\PYG{p}{,}
\PYG{n}{ylab}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}Confirmed cases in Metropolitan France, cumulative\PYGZdq{}}\PYG{p}{)}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/C53AECC732D77D7C3BBE75E369D44F2090AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
View file @ 97687917
\begin{Verbatim}[commandchars=\\\{\}]
\PYG{k+kn}{from} \PYG{n+nn}{urllib.request} \PYG{k+kn}{import} \PYG{n}{urlopen}
\PYG{k+kn}{import} \PYG{n+nn}{datetime}
\PYG{n}{temp\PYGZus{}file\PYGZus{}name} \PYG{o}{=} \PYG{l+s+s1}{\PYGZsq{}data.csv\PYGZsq{}}
\PYG{c+c1}{\PYGZsh{} Downloads the data from GitHub}
\PYG{k}{def} \PYG{n+nf}{download\PYGZus{}data}\PYG{p}{():}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{urlopen}\PYG{p}{(}\PYG{n}{data\PYGZus{}url}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{()}
\PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{temp\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}wb\PYGZsq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{f}\PYG{p}{:}
\PYG{n}{f}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{data}\PYG{p}{)}
\PYG{c+c1}{\PYGZsh{} Tries to read data from the local file and returns the content}
\PYG{c+c1}{\PYGZsh{} parsed as a series of lines}
\PYG{k}{def} \PYG{n+nf}{read\PYGZus{}data}\PYG{p}{():}
\PYG{k}{try}\PYG{p}{:}
\PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{temp\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}r\PYGZsq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{f}\PYG{p}{:}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{f}\PYG{o}{.}\PYG{n}{read}\PYG{p}{()}
\PYG{n}{lines} \PYG{o}{=} \PYG{n}{data}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)}
\PYG{n}{table} \PYG{o}{=} \PYG{p}{[}\PYG{n}{line}\PYG{o}{.}\PYG{n}{replace}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s+s2}{Korea, South}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}South Korea\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{l+s+s1}{\PYGZsq{},\PYGZsq{}}\PYG{p}{)} \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n}{lines}\PYG{p}{]}
\PYG{k}{return} \PYG{n}{table}\PYG{p}{[:}\PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{2}\PYG{p}{]} \PYG{c+c1}{\PYGZsh{} Removing the empty last line}
\PYG{k}{except} \PYG{n+ne}{IOError} \PYG{k}{as} \PYG{n}{e}\PYG{p}{:}
\PYG{k}{raise} \PYG{n}{e}
\PYG{c+c1}{\PYGZsh{} Decides whether or not to download the file from GitHub based on the}
\PYG{c+c1}{\PYGZsh{} presence of a local file and the last recorded date in the local}
\PYG{c+c1}{\PYGZsh{} file}
\PYG{k}{def} \PYG{n+nf}{try\PYGZus{}download\PYGZus{}data}\PYG{p}{():}
\PYG{n}{data} \PYG{o}{=} \PYG{k+kc}{None}
\PYG{k}{try}\PYG{p}{:}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{read\PYGZus{}data}\PYG{p}{()}
\PYG{n}{last\PYGZus{}date} \PYG{o}{=} \PYG{n}{datetime}\PYG{o}{.}\PYG{n}{datetime}\PYG{o}{.}\PYG{n}{strptime}\PYG{p}{(}\PYG{n}{data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{][}\PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}\PYG{p}{],} \PYG{l+s+s2}{\PYGZdq{}\PYGZpc{}m/}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+s2}{/\PYGZpc{}y\PYGZdq{}}\PYG{p}{)}
\PYG{n}{today} \PYG{o}{=} \PYG{n}{datetime}\PYG{o}{.}\PYG{n}{datetime}\PYG{o}{.}\PYG{n}{today}\PYG{p}{()}
\PYG{k}{if} \PYG{n}{today} \PYG{o}{\PYGZhy{}} \PYG{n}{last\PYGZus{}date} \PYG{o}{\PYGZgt{}} \PYG{n}{datetime}\PYG{o}{.}\PYG{n}{timedelta}\PYG{p}{(}\PYG{n}{day}\PYG{o}{=}\PYG{l+m+mi}{1}\PYG{p}{):}
\PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}Data obsolete, downloading new data...\PYGZdq{}}\PYG{p}{)}
\PYG{n}{download\PYGZus{}data}\PYG{p}{()}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{read\PYGZus{}data}\PYG{p}{()}
\PYG{k}{except} \PYG{n+ne}{IOError}\PYG{p}{:}
\PYG{n}{download\PYGZus{}data}\PYG{p}{()}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{read\PYGZus{}data}\PYG{p}{()}
\PYG{k}{finally}\PYG{p}{:}
\PYG{k}{return} \PYG{n}{data}
\PYG{n}{data} \PYG{o}{=} \PYG{n}{try\PYGZus{}download\PYGZus{}data}\PYG{p}{()}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/E0F7E9C109B345B97FA041B7428DBE27E36E7B2C8D886207B0A18BA1065D30A3.pygtex 0 → 100644
View file @ 97687917
\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{last\PYGZus{}date} \PYG{o}{\PYGZlt{}\PYGZhy{}} \PYG{n}{data} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{gather}\PYG{p}{(}\PYG{n}{Country}\PYG{p}{,} \PYG{n}{Cases}\PYG{p}{,} \PYG{n}{Belgium}\PYG{o}{:}\PYG{n}{UnitedKingdom}\PYG{p}{)} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n}{dplyr}\PYG{o}{::}\PYG{n+nf}{filter}\PYG{p}{(}\PYG{n}{Date} \PYG{o}{==} \PYG{n+nf}{tail}\PYG{p}{(}\PYG{n}{data}\PYG{o}{\PYGZdl{}}\PYG{n}{Date}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{))}
\PYG{n}{data} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{gather}\PYG{p}{(}\PYG{n}{Country}\PYG{p}{,} \PYG{n}{Cases}\PYG{p}{,} \PYG{n}{Belgium}\PYG{o}{:}\PYG{n}{UnitedKingdom}\PYG{p}{)} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
\PYG{n+nf}{ggplot}\PYG{p}{(}\PYG{n+nf}{aes}\PYG{p}{(}\PYG{n}{x}\PYG{o}{=}\PYG{n}{Date}\PYG{p}{,} \PYG{n}{y}\PYG{o}{=}\PYG{n}{Cases}\PYG{p}{,} \PYG{n}{colour}\PYG{o}{=}\PYG{n}{Country}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{geom\PYGZus{}line}\PYG{p}{()} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}x\PYGZus{}date}\PYG{p}{(}\PYG{n}{breaks} \PYG{o}{=} \PYG{n+nf}{pretty\PYGZus{}breaks}\PYG{p}{(}\PYG{l+m}{8}\PYG{p}{),} \PYG{n}{labels} \PYG{o}{=} \PYG{n+nf}{date\PYGZus{}format}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}\PYGZpc{}b \PYGZpc{}Y\PYGZdq{}}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}color\PYGZus{}manual}\PYG{p}{(}\PYG{n}{values}\PYG{o}{=}\PYG{n}{palette}\PYG{p}{)} \PYG{o}{+}
\PYG{n+nf}{scale\PYGZus{}y\PYGZus{}continuous}\PYG{p}{(}\PYG{n}{trans}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}log10\PYGZdq{}}\PYG{p}{,} \PYG{n}{labels} \PYG{o}{=} \PYG{n+nf}{comma\PYGZus{}format}\PYG{p}{())} \PYG{o}{+}
\PYG{n+nf}{geom\PYGZus{}text\PYGZus{}repel}\PYG{p}{(}\PYG{n}{data}\PYG{o}{=}\PYG{n}{last\PYGZus{}date}\PYG{p}{,} \PYG{n+nf}{aes}\PYG{p}{(}\PYG{n}{label} \PYG{o}{=} \PYG{n}{Country}\PYG{p}{))} \PYG{o}{+}
\PYG{n+nf}{ggtitle}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}Cumulative confirmed cases of Covid\PYGZhy{}19\PYGZdq{}}\PYG{p}{,} \PYG{n}{subtitle}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}In selected countries since the beginning of 2020, on a logarithmic scale\PYGZdq{}}\PYG{p}{)} \PYG{o}{+}
\PYG{n+nf}{theme\PYGZus{}bw}\PYG{p}{()}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/ECCAD93592B44EF37345D6E1CDCDC68690AFCAC6097827C17CEC8F1010D6D783.pygtex 0 → 100644
View file @ 97687917
\begin{Verbatim}[commandchars=\\\{\}]
\PYG{n}{valid\PYGZus{}data} \PYG{o}{=} \PYG{p}{[]}
\PYG{n}{valid\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{data}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{])}
\PYG{k}{for} \PYG{n}{row} \PYG{o+ow}{in} \PYG{n}{data}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{:]:}
\PYG{n}{missing} \PYG{o}{=} \PYG{n+nb}{any}\PYG{p}{([}\PYG{n}{value} \PYG{o}{==} \PYG{l+s+s1}{\PYGZsq{}\PYGZsq{}} \PYG{k}{for} \PYG{n}{value} \PYG{o+ow}{in} \PYG{n}{row}\PYG{p}{[}\PYG{l+m+mi}{4}\PYG{p}{:]])}
\PYG{k}{if} \PYG{n}{missing}\PYG{p}{:}
\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{row}\PYG{p}{)}
\PYG{k}{else}\PYG{p}{:}
\PYG{n}{valid\PYGZus{}data}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{row}\PYG{p}{)}
\end{Verbatim}
module3/exo3/_minted-exercice_R_en/default-pyg-prefix.pygstyle 0 → 100644
View file @ 97687917
\makeatletter
\def\PYG@reset{\let\PYG@it=\relax \let\PYG@bf=\relax%
\let\PYG@ul=\relax \let\PYG@tc=\relax%
\let\PYG@bc=\relax \let\PYG@ff=\relax}
\def\PYG@tok#1{\csname PYG@tok@#1\endcsname}
\def\PYG@toks#1+{\ifx\relax#1\empty\else%
\PYG@tok{#1}\expandafter\PYG@toks\fi}
\def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{%
\PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}}
\def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}}
\expandafter\def\csname PYG@tok@w\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
\expandafter\def\csname PYG@tok@c\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PYG@tok@cp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}}
\expandafter\def\csname PYG@tok@k\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PYG@tok@kp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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% for compatibility with earlier versions
\def\PYGdefaultZat{@}
\def\PYGdefaultZlb{[}
\def\PYGdefaultZrb{]}
\makeatother
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{
"cells": [],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
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"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
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"pygments_lexer": "ipython3",
"version": "3.6.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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#+TITLE: Votre titre
#+AUTHOR: Votre nom
#+DATE: La date du jour
#+LANGUAGE: fr
# #+PROPERTY: header-args :eval never-export
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
* Quelques explications
Ceci est un document org-mode avec quelques exemples de code
R. Une fois ouvert dans emacs, ce document peut aisément être
exporté au format HTML, PDF, et Office. Pour plus de détails sur
org-mode vous pouvez consulter https://orgmode.org/guide/.
Lorsque vous utiliserez le raccourci =C-c C-e h o=, ce document sera
compilé en html. Tout le code contenu sera ré-exécuté, les résultats
récupérés et inclus dans un document final. Si vous ne souhaitez pas
ré-exécuter tout le code à chaque fois, il vous suffit de supprimer
le # et l'espace qui sont devant le ~#+PROPERTY:~ au début de ce
document.
Comme nous vous l'avons montré dans la vidéo, on inclut du code
R de la façon suivante (et on l'exécute en faisant ~C-c C-c~):
#+begin_src R :results output :exports both
print("Hello world!")
#+end_src
#+RESULTS:
: [1] "Hello world!"
Voici la même chose, mais avec une session R (c'est le cas le
plus courant, R étant vraiment un langage interactif), donc une
persistance d'un bloc à l'autre (et on l'exécute toujours en faisant
~C-c C-c~).
#+begin_src R :results output :session *R* :exports both
summary(cars)
#+end_src
#+RESULTS:
: speed dist
: Min. : 4.0 Min. : 2.00
: 1st Qu.:12.0 1st Qu.: 26.00
: Median :15.0 Median : 36.00
: Mean :15.4 Mean : 42.98
: 3rd Qu.:19.0 3rd Qu.: 56.00
: Max. :25.0 Max. :120.00
Et enfin, voici un exemple de sortie graphique:
#+begin_src R :results output graphics :file "./cars.png" :exports results :width 600 :height 400 :session *R*
plot(cars)
#+end_src
#+RESULTS:
[[file:./cars.png]]
Vous remarquerez le paramètre ~:exports results~ qui indique que le code
ne doit pas apparaître dans la version finale du document. Nous vous
recommandons dans le cadre de ce MOOC de ne pas changer ce paramètre
(indiquer ~both~) car l'objectif est que vos analyses de données soient
parfaitement transparentes pour être reproductibles.
Attention, la figure ainsi générée n'est pas stockée dans le document
org. C'est un fichier ordinaire, ici nommé ~cars.png~. N'oubliez pas
de le committer si vous voulez que votre analyse soit lisible et
compréhensible sur GitLab.
Enfin, pour les prochains exercices, nous ne vous fournirons pas
forcément de fichier de départ, ça sera à vous de le créer, par
exemple en repartant de ce document et de le commiter vers
gitlab. N'oubliez pas que nous vous fournissons dans les ressources de
ce MOOC une configuration avec un certain nombre de raccourcis
claviers permettant de créer rapidement les blocs de code R (en
faisant ~<r~ ou ~<R~ suivi de ~Tab~).
Maintenant, à vous de jouer! Vous pouvez effacer toutes ces
informations et les remplacer par votre document computationnel.
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---
title: "Your title"
author: "Your name"
date: "Today's date"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Some explanations
This is an R Markdown document that you can easily export to HTML, PDF, and MS Word formats. For more information on R Markdown, see <http://rmarkdown.rstudio.com>.
When you click on the button **Knit**, the document will be compiled in order to re-execute the R code and to include the results into the final document. As we have shown in the video, R code is inserted as follows:
```{r cars}
summary(cars)
```
It is also straightforward to include figures. For example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note the parameter `echo = FALSE` that indicates that the code will not appear in the final version of the document. We recommend not to use this parameter in the context of this MOOC, because we want your data analyses to be perfectly transparent and reproducible.
Since the results are not stored in Rmd files, you should generate an HTML or PDF version of your exercises and commit them. Otherwise reading and checking your analysis will be difficult for anyone else but you.
Now it's your turn! You can delete all this information and replace it by your computational document.
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{
"cells": [],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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---
title: "Votre titre"
author: "Votre nom"
date: "La date du jour"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Quelques explications
Ceci est un document R markdown que vous pouvez aisément exporter au format HTML, PDF, et MS Word. Pour plus de détails sur R Markdown consultez <http://rmarkdown.rstudio.com>.
Lorsque vous cliquerez sur le bouton **Knit** ce document sera compilé afin de ré-exécuter le code R et d'inclure les résultats dans un document final. Comme nous vous l'avons montré dans la vidéo, on inclue du code R de la façon suivante:
```{r cars}
summary(cars)
```
Et on peut aussi aisément inclure des figures. Par exemple:
```{r pressure, echo=FALSE}
plot(pressure)
```
Vous remarquerez le paramètre `echo = FALSE` qui indique que le code ne doit pas apparaître dans la version finale du document. Nous vous recommandons dans le cadre de ce MOOC de ne pas utiliser ce paramètre car l'objectif est que vos analyses de données soient parfaitement transparentes pour être reproductibles.
Comme les résultats ne sont pas stockés dans les fichiers Rmd, pour faciliter la relecture de vos analyses par d'autres personnes, vous aurez donc intérêt à générer un HTML ou un PDF et à le commiter.
Maintenant, à vous de jouer! Vous pouvez effacer toutes ces informations et les remplacer par votre document computationnel.
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{
"cells": [],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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#+TITLE: Your title
#+AUTHOR: Your name
#+DATE: Today's date
#+LANGUAGE: en
# #+PROPERTY: header-args :eval never-export
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
* Some explanations
This is an org-mode document with code examples in R. Once opened in
Emacs, this document can easily be exported to HTML, PDF, and Office
formats. For more information on org-mode, see
https://orgmode.org/guide/.
When you type the shortcut =C-c C-e h o=, this document will be
exported as HTML. All the code in it will be re-executed, and the
results will be retrieved and included into the exported document. If
you do not want to re-execute all code each time, you can delete the #
and the space before ~#+PROPERTY:~ in the header of this document.
Like we showed in the video, Python code is included as follows (and
is exxecuted by typing ~C-c C-c~):
#+begin_src python :results output :exports both
print("Hello world!")
#+end_src
#+RESULTS:
: Hello world!
And now the same but in an Python session. With a session, Python's
state, i.e. the values of all the variables, remains persistent from
one code block to the next. The code is still executed using ~C-c
C-c~.
#+begin_src python :results output :session :exports both
import numpy
x=numpy.linspace(-15,15)
print(x)
#+end_src
#+RESULTS:
#+begin_example
[-15. -14.3877551 -13.7755102 -13.16326531 -12.55102041
-11.93877551 -11.32653061 -10.71428571 -10.10204082 -9.48979592
-8.87755102 -8.26530612 -7.65306122 -7.04081633 -6.42857143
-5.81632653 -5.20408163 -4.59183673 -3.97959184 -3.36734694
-2.75510204 -2.14285714 -1.53061224 -0.91836735 -0.30612245
0.30612245 0.91836735 1.53061224 2.14285714 2.75510204
3.36734694 3.97959184 4.59183673 5.20408163 5.81632653
6.42857143 7.04081633 7.65306122 8.26530612 8.87755102
9.48979592 10.10204082 10.71428571 11.32653061 11.93877551
12.55102041 13.16326531 13.7755102 14.3877551 15. ]
#+end_example
Finally, an example for graphical output:
#+begin_src python :results output file :session :var matplot_lib_filename="./cosxsx.png" :exports results
import matplotlib.pyplot as plt
plt.figure(figsize=(10,5))
plt.plot(x,numpy.cos(x)/x)
plt.tight_layout()
plt.savefig(matplot_lib_filename)
print(matplot_lib_filename)
#+end_src
#+RESULTS:
[[file:./cosxsx.png]]
Note the parameter ~:exports results~, which indicates that the code
will not appear in the exported document. We recommend that in the
context of this MOOC, you always leave this parameter setting as
~:exports both~, because we want your analyses to be perfectly
transparent and reproducible.
Watch out: the figure generated by the code block is /not/ stored in
the org document. It's a plain file, here named ~cosxsx.png~. You have
to commit it explicitly if you want your analysis to be legible and
understandable on GitLab.
Finally, don't forget that we provide in the resource section of this
MOOC a configuration with a few keyboard shortcuts that allow you to
quickly create code blocks in Python by typing ~<p~, ~<P~ or ~<PP~
followed by ~Tab~.
Now it's your turn! You can delete all this information and replace it
by your computational document.
module3/exo3/exercice_python_fr.org deleted 100644 → 0
View file @ 8c01d519
#+TITLE: Votre titre
#+AUTHOR: Votre nom
#+DATE: La date du jour
#+LANGUAGE: fr
# #+PROPERTY: header-args :eval never-export
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
* Quelques explications
Ceci est un document org-mode avec quelques exemples de code
python. Une fois ouvert dans emacs, ce document peut aisément être
exporté au format HTML, PDF, et Office. Pour plus de détails sur
org-mode vous pouvez consulter https://orgmode.org/guide/.
Lorsque vous utiliserez le raccourci =C-c C-e h o=, ce document sera
compilé en html. Tout le code contenu sera ré-exécuté, les résultats
récupérés et inclus dans un document final. Si vous ne souhaitez pas
ré-exécuter tout le code à chaque fois, il vous suffit de supprimer
le # et l'espace qui sont devant le ~#+PROPERTY:~ au début de ce
document.
Comme nous vous l'avons montré dans la vidéo, on inclue du code
python de la façon suivante (et on l'exécute en faisant ~C-c C-c~):
#+begin_src python :results output :exports both
print("Hello world!")
#+end_src
#+RESULTS:
: Hello world!
Voici la même chose, mais avec une session python, donc une
persistance d'un bloc à l'autre (et on l'exécute toujours en faisant
~C-c C-c~).
#+begin_src python :results output :session :exports both
import numpy
x=numpy.linspace(-15,15)
print(x)
#+end_src
#+RESULTS:
#+begin_example
[-15. -14.3877551 -13.7755102 -13.16326531 -12.55102041
-11.93877551 -11.32653061 -10.71428571 -10.10204082 -9.48979592
-8.87755102 -8.26530612 -7.65306122 -7.04081633 -6.42857143
-5.81632653 -5.20408163 -4.59183673 -3.97959184 -3.36734694
-2.75510204 -2.14285714 -1.53061224 -0.91836735 -0.30612245
0.30612245 0.91836735 1.53061224 2.14285714 2.75510204
3.36734694 3.97959184 4.59183673 5.20408163 5.81632653
6.42857143 7.04081633 7.65306122 8.26530612 8.87755102
9.48979592 10.10204082 10.71428571 11.32653061 11.93877551
12.55102041 13.16326531 13.7755102 14.3877551 15. ]
#+end_example
Et enfin, voici un exemple de sortie graphique:
#+begin_src python :results output file :session :var matplot_lib_filename="./cosxsx.png" :exports results
import matplotlib.pyplot as plt
plt.figure(figsize=(10,5))
plt.plot(x,numpy.cos(x)/x)
plt.tight_layout()
plt.savefig(matplot_lib_filename)
print(matplot_lib_filename)
#+end_src
#+RESULTS:
[[file:./cosxsx.png]]
Vous remarquerez le paramètre ~:exports results~ qui indique que le code
ne doit pas apparaître dans la version finale du document. Nous vous
recommandons dans le cadre de ce MOOC de ne pas changer ce paramètre
(indiquer ~both~) car l'objectif est que vos analyses de données soient
parfaitement transparentes pour être reproductibles.
Attention, la figure ainsi générée n'est pas stockée dans le document
org. C'est un fichier ordinaire, ici nommé ~cosxsx.png~. N'oubliez pas
de le committer si vous voulez que votre analyse soit lisible et
compréhensible sur GitLab.
Enfin, n'oubliez pas que nous vous fournissons dans les ressources de
ce MOOC une configuration avec un certain nombre de raccourcis
claviers permettant de créer rapidement les blocs de code python (en
faisant ~<p~, ~<P~ ou ~<PP~ suivi de ~Tab~).
Maintenant, à vous de jouer! Vous pouvez effacer toutes ces
informations et les remplacer par votre document computationnel.
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