From a2a8651319dec1dc8084948cd0e434687eff53bc Mon Sep 17 00:00:00 2001 From: Tom Pollard Date: Wed, 12 Oct 2016 10:30:25 -0400 Subject: [PATCH] fix travis build --- .travis.yml | 15 +- notebooks/first_labs.ipynb | 1998 +++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 2002 insertions(+), 11 deletions(-) diff --git a/.travis.yml b/.travis.yml index c98e08d..502aac4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,9 +10,9 @@ branches: # See https://docs.travis-ci.com/user/database-setup/ addons: postgresql: - - "9.4" - - "9.5" - - "9.6" + - "9.4" + - "9.5" + - "9.6" services: - postgresql @@ -21,9 +21,10 @@ services: # Set the language language: python python: - - "2.7" + - "2.7" before_script: + - sudo apt-get install python-dev # - psql -c 'create database mimic_test;' -U postgres # - psql -c 'create schema mimiciii;' -d mimic_test -U postgres # - psql target-db -U -p -h -c "\copy source-table from 'source-table.csv' with DELIMITER ','" @@ -31,9 +32,9 @@ before_script: # command to install dependencies install: - - pip install psycopg2 --quiet - - pip install pandas --quiet - - pip install MySQL-python --quiet + - pip install psycopg2 --quiet + - pip install pandas --quiet + - pip install MySQL-python --quiet # - pip install . # - pip install -r requirements.txt diff --git a/notebooks/first_labs.ipynb b/notebooks/first_labs.ipynb index 0c1a9dd..dadbb7b 100644 --- a/notebooks/first_labs.ipynb +++ b/notebooks/first_labs.ipynb @@ -585,13 +585,2003 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 30, "metadata": { - "collapsed": true + "collapsed": false }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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subject_idhadm_idicustay_idmort_icumort_hospaniongap_1stalbumin_1stbicarbonate_1stbilirubin_1stcreatinine_1st...magnesium_1stphosphate_1stplatelet_1stpotassium_1stptt_1stinr_1stpt_1stsodium_1stbun_1stwbc_1st
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..................................................................
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\n", + "

161 rows × 25 columns

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" + ], + "text/plain": [ + " subject_id hadm_id icustay_id mort_icu mort_hosp aniongap_1st \\\n", + "686 523 196271 227379 0 0 11 \n", + "962 757 149766 208658 0 0 20 \n", + "1094 852 162589 287998 0 0 7 \n", + "1402 1084 152984 212600 0 0 9 \n", + "1845 1446 150030 243265 0 0 22 \n", + "1993 1574 118935 232260 0 1 24 \n", + "2835 2246 182109 206293 0 0 31 \n", + "4329 3433 191469 213490 1 1 34 \n", + "4753 3786 123439 296542 0 0 11 \n", + "5030 3969 135568 277183 0 0 50 \n", + "5302 4171 122269 268233 0 0 25 \n", + "5911 4673 142612 281304 0 0 14 \n", + "6204 4905 108634 260148 0 0 23 \n", + "6205 4905 127949 287506 0 0 23 \n", + "6233 4926 146966 271339 0 0 21 \n", + "6818 5370 145390 201641 0 0 14 \n", + "6819 5370 151490 276687 1 1 13 \n", + "6857 5397 112979 272079 0 0 40 \n", + "6858 5397 138051 262012 0 0 53 \n", + "6862 5397 166056 286315 0 0 54 \n", + "6863 5397 190850 215172 0 0 35 \n", + "8132 6392 182162 234103 0 0 45 \n", + "8362 6579 115553 246944 0 0 16 \n", + "8384 6601 150624 289311 0 0 17 \n", + "8584 6759 121212 264628 1 1 11 \n", + "8735 6884 128932 211119 1 1 12 \n", + "8827 6953 108956 237382 0 0 22 \n", + "9051 7118 199855 202600 0 0 28 \n", + "9887 7755 121412 248095 0 0 6 \n", + "9949 7804 139468 245686 0 0 16 \n", + "... ... ... ... ... ... ... \n", + "53004 74545 127841 268706 0 0 12 \n", + "53362 75567 106747 271493 0 0 16 \n", + "53566 76151 183875 250028 0 0 14 \n", + "54550 79002 174343 299476 0 0 7 \n", + "54588 79118 110586 264337 0 0 11 \n", + "54807 79900 120644 221354 0 0 19 \n", + "54872 80106 104466 296360 0 0 10 \n", + "55279 81254 196317 206861 0 0 20 \n", + "55496 81810 147734 278458 0 0 9 \n", + "55882 82950 154983 238297 0 0 32 \n", + "55890 82982 126445 252090 0 0 18 \n", + "56250 84033 167689 275799 1 1 19 \n", + "56690 85490 177636 214898 0 0 8 \n", + "56706 85531 110644 245790 0 0 16 \n", + "56815 85853 137702 287229 0 0 17 \n", + "56888 86089 109354 245823 0 0 15 \n", + "56957 86306 158732 295079 0 0 19 \n", + "57819 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2.0 0.6 ... \n", + "6205 4.4 20 1.5 0.6 ... \n", + "6233 NaN 21 NaN 4.3 ... \n", + "6818 3.5 31 0.7 2.8 ... \n", + "6819 3.5 40 1.3 1.0 ... \n", + "6857 NaN 8 0.4 2.2 ... \n", + "6858 3.4 5 NaN 2.4 ... \n", + "6862 NaN 7 0.8 2.1 ... \n", + "6863 3.3 15 0.6 1.9 ... \n", + "8132 3.5 18 0.3 15.3 ... \n", + "8362 2.8 41 1.6 3.1 ... \n", + "8384 3.8 38 0.9 0.8 ... \n", + "8584 3.9 33 1.2 0.4 ... \n", + "8735 NaN 37 25.7 0.4 ... \n", + "8827 4.2 26 1.4 2.4 ... \n", + "9051 4.4 25 1.8 3.6 ... \n", + "9887 2.7 45 0.3 0.6 ... \n", + "9949 3.8 37 NaN 2.8 ... \n", + "... ... ... ... ... ... \n", + "53004 NaN 27 NaN 0.6 ... \n", + "53362 3.2 36 0.7 2.0 ... \n", + "53566 2.8 29 NaN 0.4 ... \n", + "54550 3.1 34 1.1 0.3 ... \n", + "54588 3.6 38 0.7 1.1 ... \n", + "54807 NaN 25 NaN 5.4 ... \n", + "54872 NaN 31 NaN 0.7 ... \n", + "55279 NaN 29 NaN 2.0 ... \n", + "55496 3.9 35 0.7 0.9 ... \n", + "55882 4.8 20 2.5 6.6 ... \n", + "55890 NaN 38 0.9 1.5 ... \n", + "56250 3.9 36 1.4 2.1 ... \n", + "56690 NaN 40 0.3 0.6 ... \n", + "56706 NaN 31 0.3 0.5 ... \n", + "56815 3.6 23 0.8 0.6 ... \n", + "56888 4.1 34 NaN 0.9 ... \n", + "56957 NaN 20 NaN 0.8 ... \n", + "57819 4.0 22 1.4 0.4 ... \n", + "58110 3.3 21 NaN 0.6 ... \n", + "58212 NaN 25 0.3 15.5 ... \n", + "58783 4.4 7 0.3 2.8 ... \n", + "59025 4.8 22 1.4 0.7 ... \n", + "59238 NaN 26 NaN 0.5 ... \n", + "59373 4.0 26 0.5 0.5 ... \n", + "60191 2.2 18 0.4 2.8 ... \n", + "60272 4.2 6 0.2 27.4 ... \n", + "60321 3.6 24 0.7 0.9 ... \n", + "60369 4.2 18 0.7 1.2 ... \n", + "60614 3.6 28 0.9 2.7 ... \n", + "61326 2.7 16 19.6 1.4 ... \n", + "\n", + " magnesium_1st phosphate_1st platelet_1st potassium_1st ptt_1st \\\n", + "686 1.4 4.6 491 2.6 NaN \n", + "962 1.1 2.5 321 4.4 19.1 \n", + "1094 1.3 1.3 255 3.7 37.0 \n", + "1402 1.2 2.2 172 3.4 22.7 \n", + "1845 1.9 3.5 439 3.3 27.9 \n", + "1993 3.1 6.5 416 6.5 34.2 \n", + "2835 2.8 2.5 305 5.3 20.0 \n", + "4329 1.4 8.4 NaN 4.3 26.0 \n", + "4753 2.5 10.5 509 3.1 21.7 \n", + "5030 3.9 7.7 159 9.3 17.9 \n", + "5302 1.9 3.9 240 2.6 29.7 \n", + "5911 2.2 3.5 155 1.7 35.0 \n", + "6204 1.3 1.9 584 3.0 29.5 \n", + "6205 1.4 2.0 322 2.6 NaN \n", + "6233 2.7 5.4 149 4.1 NaN \n", + "6818 2.2 7.1 255 5.4 28.6 \n", + "6819 1.7 2.9 541 5.0 43.3 \n", + "6857 1.7 1.9 268 5.7 26.7 \n", + "6858 1.9 4.5 282 5.1 NaN \n", + "6862 1.7 8.9 281 5.1 24.4 \n", + "6863 2.1 1.2 290 4.5 23.2 \n", + "8132 2.2 10.0 274 8.6 30.0 \n", + "8362 3.3 5.3 193 2.6 22.2 \n", + "8384 1.6 3.9 268 2.9 26.4 \n", + "8584 1.4 3.7 217 5.5 44.1 \n", + "8735 1.6 4.2 428 4.3 31.9 \n", + "8827 1.7 2.4 140 2.8 27.1 \n", + "9051 2.1 5.2 345 6.2 36.8 \n", + "9887 1.8 2.6 107 2.6 28.8 \n", + "9949 2.2 4.1 206 3.9 26.8 \n", + "... ... ... ... ... ... \n", + "53004 1.8 2.4 438 5.4 32.5 \n", + "53362 2.6 4.4 228 7.5 34.3 \n", + "53566 1.7 3.0 649 4.6 35.1 \n", + "54550 1.6 1.7 49 2.1 49.3 \n", + "54588 2.2 3.8 142 2.3 22.6 \n", + "54807 2.0 6.7 94 3.3 34.9 \n", + "54872 1.6 3.0 186 4.3 42.2 \n", + "55279 2.9 3.8 464 6.7 NaN \n", + "55496 1.6 2.3 168 2.7 33.8 \n", + "55882 2.2 5.2 687 6.2 30.5 \n", + "55890 2.2 2.4 29 3.2 25.8 \n", + "56250 2.6 4.5 107 3.7 38.9 \n", + "56690 2.0 0.9 146 5.0 27.5 \n", + "56706 1.9 3.2 353 4.9 25.1 \n", + "56815 1.5 2.2 854 5.1 33.4 \n", + "56888 2.1 1.8 310 2.9 35.4 \n", + "56957 1.8 3.2 147 4.8 33.3 \n", + "57819 1.3 1.8 83 2.9 48.9 \n", + "58110 1.4 3.1 344 4.8 NaN \n", + "58212 2.5 11.7 180 3.8 24.1 \n", + "58783 3.2 12.1 266 8.2 NaN \n", + "59025 1.7 2.6 317 4.1 32.5 \n", + "59238 1.7 1.6 392 2.6 27.8 \n", + "59373 1.4 2.5 203 4.2 21.9 \n", + "60191 2.4 3.1 280 4.1 22.4 \n", + "60272 6.6 17.6 523 8.9 28.8 \n", + "60321 1.7 3.5 386 4.2 34.5 \n", + "60369 2.9 5.9 415 5.3 22.5 \n", + "60614 2.2 4.9 230 5.5 32.6 \n", + "61326 1.2 3.3 215 3.6 48.5 \n", + "\n", + " inr_1st pt_1st sodium_1st bun_1st wbc_1st \n", + "686 NaN NaN 86 8 13.1 \n", + "962 1.2 13.7 118 4 17.8 \n", + "1094 2.0 21.9 84 1 5.7 \n", + "1402 1.2 13.6 100 13 14.3 \n", + "1845 1.0 11.9 104 25 16.5 \n", + "1993 6.5 31.3 120 82 14.7 \n", + "2835 1.2 13.6 113 53 14.3 \n", + "4329 1.2 13.7 124 118 22.3 \n", + "4753 1.0 12.5 121 43 17.7 \n", + "5030 1.0 11.6 127 76 8.2 \n", + "5302 1.8 16.2 111 5 19.2 \n", + "5911 3.7 33.9 120 26 5.9 \n", + "6204 1.1 12.8 108 8 9.4 \n", + "6205 NaN NaN 104 5 6.5 \n", + "6233 NaN NaN 114 150 14.9 \n", + "6818 1.0 12.8 119 36 8.3 \n", + "6819 7.8 35.3 126 47 14.8 \n", + "6857 1.2 13.1 120 64 21.0 \n", + "6858 NaN NaN 120 63 17.6 \n", + "6862 1.1 12.9 129 47 20.6 \n", + "6863 1.0 11.7 124 59 12.9 \n", + "8132 1.3 13.6 134 99 13.9 \n", + "8362 1.2 13.5 126 149 14.7 \n", + "8384 1.0 12.8 130 12 9.1 \n", + "8584 3.9 35.6 112 18 15.9 \n", + "8735 1.2 14.3 123 16 18.1 \n", + "8827 0.9 11.9 115 12 8.0 \n", + "9051 2.8 21.1 122 68 18.1 \n", + "9887 1.1 12.6 120 16 4.2 \n", + "9949 2.1 22.1 125 70 14.4 \n", + "... ... ... ... ... ... \n", + "53004 1.0 12.1 112 12 10.3 \n", + "53362 1.3 15.0 125 101 7.5 \n", + "53566 1.5 15.7 116 14 22.8 \n", + "54550 1.0 12.1 115 14 15.8 \n", + "54588 1.0 10.6 126 29 14.0 \n", + "54807 2.4 25.3 119 108 5.3 \n", + "54872 1.7 18.8 107 8 4.4 \n", + "55279 NaN NaN 118 37 6.3 \n", + "55496 1.5 16.5 117 19 9.1 \n", + "55882 1.6 17.3 124 129 12.3 \n", + "55890 1.2 14.4 118 36 9.2 \n", + "56250 2.4 25.1 128 107 11.9 \n", + "56690 1.0 12.3 141 22 10.0 \n", + "56706 1.1 13.3 117 11 9.4 \n", + "56815 1.1 13.0 96 14 10.0 \n", + "56888 1.1 12.8 113 10 9.8 \n", + "56957 1.3 14.7 109 10 10.1 \n", + "57819 5.2 52.3 106 15 5.8 \n", + "58110 NaN NaN 110 8 6.4 \n", + "58212 1.1 13.2 133 97 12.8 \n", + "58783 NaN NaN 123 60 16.2 \n", + "59025 1.1 13.3 108 15 21.9 \n", + "59238 1.2 13.8 108 9 16.7 \n", + "59373 1.0 12.2 113 11 7.5 \n", + "60191 1.0 12.1 116 67 16.2 \n", + "60272 1.2 13.6 125 224 22.2 \n", + "60321 3.9 38.0 109 24 6.8 \n", + "60369 0.9 9.3 121 27 14.3 \n", + "60614 1.3 15.1 118 74 6.4 \n", + "61326 1.6 17.8 118 14 23.4 \n", + "\n", + "[161 rows x 25 columns]" + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "# Risk of patients with labs outside the normal range\n" + "for l in lab_ranges:\n", + " print l\n", + " \n", + "# data.loc[(data['mort_icu']==0) & ((data['mort_icu'])]\n", + "data.loc[data[l.lower()+'_1st'] < 80]" ] } ],