diff --git a/module3/exo1/analyse-syndrome-grippal.ipynb b/module3/exo1/analyse-syndrome-grippal.ipynb index 59d72b5b58a3ae26346460dd39e62a39c55243d7..856ed27e7957bd077319f9b514df4c6ab3cde7cc 100644 --- a/module3/exo1/analyse-syndrome-grippal.ipynb +++ b/module3/exo1/analyse-syndrome-grippal.ipynb @@ -9,14 +9,15 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", - "import isoweek" + "import isoweek\n", + "import os.path" ] }, { @@ -28,13 +29,11 @@ }, { "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, + "execution_count": 7, + "metadata": {}, "outputs": [], "source": [ - "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-3.csv\"" + "data_url = \"https://www.sentiweb.fr/datasets/incidence-PAY-3.csv\"" ] }, { @@ -61,11 +60,982 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
weekindicatorincinc_lowinc_upinc100inc100_lowinc100_upgeo_inseegeo_name
0202307311088298145.0123619.0167148.0186.0FRFrance
120230639807188232.0107910.0148133.0163.0FRFrance
220230539546986268.0104670.0144130.0158.0FRFrance
320230437490166916.082886.0113101.0125.0FRFrance
420230336957061893.077247.010593.0117.0FRFrance
520230237826070090.086430.0118106.0130.0FRFrance
62023013121773111024.0132522.0183167.0199.0FRFrance
72022523155383142015.0168751.0234214.0254.0FRFrance
82022513248311232120.0264502.0374350.0398.0FRFrance
92022503234279219533.0249025.0353331.0375.0FRFrance
102022493163421151727.0175115.0246228.0264.0FRFrance
112022483121884111932.0131836.0184169.0199.0FRFrance
1220224739644787259.0105635.0145131.0159.0FRFrance
1320224636773560075.075395.010290.0114.0FRFrance
1420224534530638909.051703.06858.078.0FRFrance
1520224433471328880.040546.05243.061.0FRFrance
1620224334476936884.052654.06856.080.0FRFrance
1720224234746240773.054151.07262.082.0FRFrance
1820224134858342388.054778.07364.082.0FRFrance
1920224034192736115.047739.06354.072.0FRFrance
2020223933990234168.045636.06051.069.0FRFrance
2120223832878123733.033829.04335.051.0FRFrance
2220223732139517076.025714.03225.039.0FRFrance
2320223631412010487.017753.02116.026.0FRFrance
24202235392836485.012081.01410.018.0FRFrance
25202234374984731.010265.0117.015.0FRFrance
26202233375864442.010730.0116.016.0FRFrance
272022323122227749.016695.01811.025.0FRFrance
282022313132578905.017609.02013.027.0FRFrance
2920223031500610738.019274.02317.029.0FRFrance
.................................
196919852132609619621.032571.04735.059.0FRFrance
197019852032789620885.034907.05138.064.0FRFrance
197119851934315432821.053487.07859.097.0FRFrance
197219851834055529935.051175.07455.093.0FRFrance
197319851733405324366.043740.06244.080.0FRFrance
197419851635036236451.064273.09166.0116.0FRFrance
197519851536388145538.082224.011683.0149.0FRFrance
19761985143134545114400.0154690.0244207.0281.0FRFrance
19771985133197206176080.0218332.0357319.0395.0FRFrance
19781985123245240223304.0267176.0445405.0485.0FRFrance
19791985113276205252399.0300011.0501458.0544.0FRFrance
19801985103353231326279.0380183.0640591.0689.0FRFrance
19811985093369895341109.0398681.0670618.0722.0FRFrance
19821985083389886359529.0420243.0707652.0762.0FRFrance
19831985073471852432599.0511105.0855784.0926.0FRFrance
19841985063565825518011.0613639.01026939.01113.0FRFrance
19851985053637302592795.0681809.011551074.01236.0FRFrance
19861985043424937390794.0459080.0770708.0832.0FRFrance
19871985033213901174689.0253113.0388317.0459.0FRFrance
198819850239758680949.0114223.0177147.0207.0FRFrance
198919850138548965918.0105060.0155120.0190.0FRFrance
199019845238483060602.0109058.0154110.0198.0FRFrance
1991198451310172680242.0123210.0185146.0224.0FRFrance
19921984503123680101401.0145959.0225184.0266.0FRFrance
1993198449310107381684.0120462.0184149.0219.0FRFrance
199419844837862060634.096606.0143110.0176.0FRFrance
199519844737202954274.089784.013199.0163.0FRFrance
199619844638733067686.0106974.0159123.0195.0FRFrance
19971984453135223101414.0169032.0246184.0308.0FRFrance
199819844436842220056.0116788.012537.0213.0FRFrance
\n", + "

1999 rows × 10 columns

\n", + "
" + ], + "text/plain": [ + " week indicator inc inc_low inc_up inc100 inc100_low \\\n", + "0 202307 3 110882 98145.0 123619.0 167 148.0 \n", + "1 202306 3 98071 88232.0 107910.0 148 133.0 \n", + "2 202305 3 95469 86268.0 104670.0 144 130.0 \n", + "3 202304 3 74901 66916.0 82886.0 113 101.0 \n", + "4 202303 3 69570 61893.0 77247.0 105 93.0 \n", + "5 202302 3 78260 70090.0 86430.0 118 106.0 \n", + "6 202301 3 121773 111024.0 132522.0 183 167.0 \n", + "7 202252 3 155383 142015.0 168751.0 234 214.0 \n", + "8 202251 3 248311 232120.0 264502.0 374 350.0 \n", + "9 202250 3 234279 219533.0 249025.0 353 331.0 \n", + "10 202249 3 163421 151727.0 175115.0 246 228.0 \n", + "11 202248 3 121884 111932.0 131836.0 184 169.0 \n", + "12 202247 3 96447 87259.0 105635.0 145 131.0 \n", + "13 202246 3 67735 60075.0 75395.0 102 90.0 \n", + "14 202245 3 45306 38909.0 51703.0 68 58.0 \n", + "15 202244 3 34713 28880.0 40546.0 52 43.0 \n", + "16 202243 3 44769 36884.0 52654.0 68 56.0 \n", + "17 202242 3 47462 40773.0 54151.0 72 62.0 \n", + "18 202241 3 48583 42388.0 54778.0 73 64.0 \n", + "19 202240 3 41927 36115.0 47739.0 63 54.0 \n", + "20 202239 3 39902 34168.0 45636.0 60 51.0 \n", + "21 202238 3 28781 23733.0 33829.0 43 35.0 \n", + "22 202237 3 21395 17076.0 25714.0 32 25.0 \n", + "23 202236 3 14120 10487.0 17753.0 21 16.0 \n", + "24 202235 3 9283 6485.0 12081.0 14 10.0 \n", + "25 202234 3 7498 4731.0 10265.0 11 7.0 \n", + "26 202233 3 7586 4442.0 10730.0 11 6.0 \n", + "27 202232 3 12222 7749.0 16695.0 18 11.0 \n", + "28 202231 3 13257 8905.0 17609.0 20 13.0 \n", + "29 202230 3 15006 10738.0 19274.0 23 17.0 \n", + "... ... ... ... ... ... ... ... \n", + "1969 198521 3 26096 19621.0 32571.0 47 35.0 \n", + "1970 198520 3 27896 20885.0 34907.0 51 38.0 \n", + "1971 198519 3 43154 32821.0 53487.0 78 59.0 \n", + "1972 198518 3 40555 29935.0 51175.0 74 55.0 \n", + "1973 198517 3 34053 24366.0 43740.0 62 44.0 \n", + "1974 198516 3 50362 36451.0 64273.0 91 66.0 \n", + "1975 198515 3 63881 45538.0 82224.0 116 83.0 \n", + "1976 198514 3 134545 114400.0 154690.0 244 207.0 \n", + "1977 198513 3 197206 176080.0 218332.0 357 319.0 \n", + "1978 198512 3 245240 223304.0 267176.0 445 405.0 \n", + "1979 198511 3 276205 252399.0 300011.0 501 458.0 \n", + "1980 198510 3 353231 326279.0 380183.0 640 591.0 \n", + "1981 198509 3 369895 341109.0 398681.0 670 618.0 \n", + "1982 198508 3 389886 359529.0 420243.0 707 652.0 \n", + "1983 198507 3 471852 432599.0 511105.0 855 784.0 \n", + "1984 198506 3 565825 518011.0 613639.0 1026 939.0 \n", + "1985 198505 3 637302 592795.0 681809.0 1155 1074.0 \n", + "1986 198504 3 424937 390794.0 459080.0 770 708.0 \n", + "1987 198503 3 213901 174689.0 253113.0 388 317.0 \n", + "1988 198502 3 97586 80949.0 114223.0 177 147.0 \n", + "1989 198501 3 85489 65918.0 105060.0 155 120.0 \n", + "1990 198452 3 84830 60602.0 109058.0 154 110.0 \n", + "1991 198451 3 101726 80242.0 123210.0 185 146.0 \n", + "1992 198450 3 123680 101401.0 145959.0 225 184.0 \n", + "1993 198449 3 101073 81684.0 120462.0 184 149.0 \n", + "1994 198448 3 78620 60634.0 96606.0 143 110.0 \n", + "1995 198447 3 72029 54274.0 89784.0 131 99.0 \n", + "1996 198446 3 87330 67686.0 106974.0 159 123.0 \n", + "1997 198445 3 135223 101414.0 169032.0 246 184.0 \n", + "1998 198444 3 68422 20056.0 116788.0 125 37.0 \n", + "\n", + " inc100_up geo_insee geo_name \n", + "0 186.0 FR France \n", + "1 163.0 FR France \n", + "2 158.0 FR France \n", + "3 125.0 FR France \n", + "4 117.0 FR France \n", + "5 130.0 FR France \n", + "6 199.0 FR France \n", + "7 254.0 FR France \n", + "8 398.0 FR France \n", + "9 375.0 FR France \n", + "10 264.0 FR France \n", + "11 199.0 FR France \n", + "12 159.0 FR France \n", + "13 114.0 FR France \n", + "14 78.0 FR France \n", + "15 61.0 FR France \n", + "16 80.0 FR France \n", + "17 82.0 FR France \n", + "18 82.0 FR France \n", + "19 72.0 FR France \n", + "20 69.0 FR France \n", + "21 51.0 FR France \n", + "22 39.0 FR France \n", + "23 26.0 FR France \n", + "24 18.0 FR France \n", + "25 15.0 FR France \n", + "26 16.0 FR France \n", + "27 25.0 FR France \n", + "28 27.0 FR France \n", + "29 29.0 FR France \n", + "... ... ... ... \n", + "1969 59.0 FR France \n", + "1970 64.0 FR France \n", + "1971 97.0 FR France \n", + "1972 93.0 FR France \n", + "1973 80.0 FR France \n", + "1974 116.0 FR France \n", + "1975 149.0 FR France \n", + "1976 281.0 FR France \n", + "1977 395.0 FR France \n", + "1978 485.0 FR France \n", + "1979 544.0 FR France \n", + "1980 689.0 FR France \n", + "1981 722.0 FR France \n", + "1982 762.0 FR France \n", + "1983 926.0 FR France \n", + "1984 1113.0 FR France \n", + "1985 1236.0 FR France \n", + "1986 832.0 FR France \n", + "1987 459.0 FR France \n", + "1988 207.0 FR France \n", + "1989 190.0 FR France \n", + "1990 198.0 FR France \n", + "1991 224.0 FR France \n", + "1992 266.0 FR France \n", + "1993 219.0 FR France \n", + "1994 176.0 FR France \n", + "1995 163.0 FR France \n", + "1996 195.0 FR France \n", + "1997 308.0 FR France \n", + "1998 213.0 FR France \n", + "\n", + "[1999 rows x 10 columns]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "raw_data = pd.read_csv(data_url, skiprows=1)\n", + "path='/home/mhashan/Documents/Formation/Recherche_reproductible/Module3/incidence-PAY-3.csv'\n", + "if os.path.exists(path)==False:\n", + " raw_data = pd.read_csv(data_url, skiprows=1)\n", + "else:\n", + " raw_data=pd.read_csv(path, skiprow=1)\n", "raw_data" ] }, @@ -364,7 +1334,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.1" + "version": "3.6.4" } }, "nbformat": 4,