2017-06-18 06:06:31 2017-06-18 06:06:31 R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" 2017-06-18 06:06:31 Copyright (C) 2017 The R Foundation for Statistical Computing 2017-06-18 06:06:31 Platform: x86_64-w64-mingw32/x64 (64-bit) 2017-06-18 06:06:31 2017-06-18 06:06:31 R is free software and comes with ABSOLUTELY NO WARRANTY. 2017-06-18 06:06:31 You are welcome to redistribute it under certain conditions. 2017-06-18 06:06:31 Type 'license()' or 'licence()' for distribution details. 2017-06-18 06:06:31 2017-06-18 06:06:31 Natural language support but running in an English locale 2017-06-18 06:06:31 2017-06-18 06:06:31 R is a collaborative project with many contributors. 2017-06-18 06:06:31 Type 'contributors()' for more information and 2017-06-18 06:06:31 'citation()' on how to cite R or R packages in publications. 2017-06-18 06:06:31 2017-06-18 06:06:31 Type 'demo()' for some demos, 'help()' for on-line help, or 2017-06-18 06:06:31 'help.start()' for an HTML browser interface to help. 2017-06-18 06:06:31 Type 'q()' to quit R. 2017-06-18 06:06:31 2017-06-18 06:06:31 > setwd( Sys.getenv( "RWD" ) ) 2017-06-18 06:06:31 > 2017-06-18 06:06:31 > machine_specific_replacements <- 2017-06-18 06:06:31 + list( 2017-06-18 06:06:31 + 2017-06-18 06:06:31 + # replace the folder path on macnix 2017-06-18 06:06:31 + c( 'path.expand( \"~\" ) , \"FAERS\"' , paste0( '"' , getwd() , '"' ) ) , 2017-06-18 06:06:31 + 2017-06-18 06:06:31 + # change other things in the script to be run 2017-06-18 06:06:31 + c( "hello" , "howdy" ) 2017-06-18 06:06:31 + 2017-06-18 06:06:31 + ) 2017-06-18 06:06:31 > 2017-06-18 06:06:31 > source( lodown::syntaxtractor( "faers" , replacements = machine_specific_replacements , setup_test = "setup" ) , echo = TRUE ) 2017-06-18 06:06:32 2017-06-18 06:06:32 > library(lodown) 2017-06-18 06:06:32 2017-06-18 06:06:32 > lodown("faers", output_dir = file.path("e:/eanthony/r-wd/faers-1497791167")) 2017-06-18 06:06:32 building catalog for faers 2017-06-18 06:06:32 2017-06-18 06:06:32 'https://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm082193.htm' 2017-06-18 06:06:32 cached in 2017-06-18 06:06:32 'E:/eanthony/r-tmp/faers/c1370db085b5c4206070f75f0bf33ed5.Rcache' 2017-06-18 06:06:32 copying to 2017-06-18 06:06:32 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file311864ed2c93' 2017-06-18 06:06:32 2017-06-18 06:06:33 'https://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm083765.htm' 2017-06-18 06:06:33 cached in 2017-06-18 06:06:33 'E:/eanthony/r-tmp/faers/0dc89eeff8211757af292df9c0be5dc6.Rcache' 2017-06-18 06:06:33 copying to 2017-06-18 06:06:33 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file311864ed2c93' 2017-06-18 06:06:33 2017-06-18 06:06:33 locally downloading faers 2017-06-18 06:06:33 2017-06-18 06:06:33 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM546946.zip' 2017-06-18 06:06:33 cached in 2017-06-18 06:06:33 'E:/eanthony/r-tmp/faers/177b9b3519c29c783a973693da34a624.Rcache' 2017-06-18 06:06:33 copying to 2017-06-18 06:06:33 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:06:33 2017-06-18 06:07:31 faers catalog entry 1 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2016 q4' 2017-06-18 06:07:31 2017-06-18 06:07:31 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM534900.zip' 2017-06-18 06:07:31 cached in 2017-06-18 06:07:31 'E:/eanthony/r-tmp/faers/5d3f31febb4eb6db8541375485d7247a.Rcache' 2017-06-18 06:07:31 copying to 2017-06-18 06:07:31 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:07:31 2017-06-18 06:09:14 faers catalog entry 2 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2016 q3' 2017-06-18 06:09:14 2017-06-18 06:09:14 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM521951.zip' 2017-06-18 06:09:14 cached in 2017-06-18 06:09:14 'E:/eanthony/r-tmp/faers/5b675773e15db6efee32e532894646c3.Rcache' 2017-06-18 06:09:14 copying to 2017-06-18 06:09:14 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:09:14 2017-06-18 06:11:29 faers catalog entry 3 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2016 q2' 2017-06-18 06:11:29 2017-06-18 06:11:29 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM509489.zip' 2017-06-18 06:11:29 cached in 2017-06-18 06:11:29 'E:/eanthony/r-tmp/faers/e817ef2bf96c53a47a80a64d0cf6a40a.Rcache' 2017-06-18 06:11:29 copying to 2017-06-18 06:11:29 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:11:29 2017-06-18 06:13:18 faers catalog entry 4 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2016 q1' 2017-06-18 06:13:18 2017-06-18 06:13:18 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM492340.zip' 2017-06-18 06:13:18 cached in 2017-06-18 06:13:18 'E:/eanthony/r-tmp/faers/aedd71a8182536e28c1c07948b868421.Rcache' 2017-06-18 06:13:18 copying to 2017-06-18 06:13:18 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:13:18 2017-06-18 06:14:55 faers catalog entry 5 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2015 q4' 2017-06-18 06:14:55 2017-06-18 06:14:55 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM477190.zip' 2017-06-18 06:14:55 cached in 2017-06-18 06:14:55 'E:/eanthony/r-tmp/faers/0f3402ee56a1686a80477ae0b737bdd9.Rcache' 2017-06-18 06:14:55 copying to 2017-06-18 06:14:55 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:14:55 2017-06-18 06:16:26 faers catalog entry 6 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2015 q3' 2017-06-18 06:16:26 2017-06-18 06:16:26 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM463272.zip' 2017-06-18 06:16:26 cached in 2017-06-18 06:16:26 'E:/eanthony/r-tmp/faers/1fe6736a41fcad83f58e0399a2f85b22.Rcache' 2017-06-18 06:16:26 copying to 2017-06-18 06:16:26 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:16:26 2017-06-18 06:18:01 faers catalog entry 7 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2015 q2' 2017-06-18 06:18:01 2017-06-18 06:18:01 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM458083.zip' 2017-06-18 06:18:01 cached in 2017-06-18 06:18:01 'E:/eanthony/r-tmp/faers/622bb7055a6850cb51552b924df0da60.Rcache' 2017-06-18 06:18:01 copying to 2017-06-18 06:18:01 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:18:01 2017-06-18 06:20:05 faers catalog entry 8 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2015 q1' 2017-06-18 06:20:05 2017-06-18 06:20:05 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM451489.zip' 2017-06-18 06:20:05 cached in 2017-06-18 06:20:05 'E:/eanthony/r-tmp/faers/f14a27257bc6ffab89725f3f158532af.Rcache' 2017-06-18 06:20:05 copying to 2017-06-18 06:20:05 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:20:05 2017-06-18 06:21:28 faers catalog entry 9 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2014 q4' 2017-06-18 06:21:28 2017-06-18 06:21:28 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM443579.zip' 2017-06-18 06:21:28 cached in 2017-06-18 06:21:28 'E:/eanthony/r-tmp/faers/28aa2c37bd80388517bb9e89629e7aa7.Rcache' 2017-06-18 06:21:28 copying to 2017-06-18 06:21:28 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:21:28 2017-06-18 06:23:17 faers catalog entry 10 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2014 q3' 2017-06-18 06:23:17 2017-06-18 06:23:17 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM429323.zip' 2017-06-18 06:23:17 cached in 2017-06-18 06:23:17 'E:/eanthony/r-tmp/faers/f44ef06a480055ec4576424b046ef7e5.Rcache' 2017-06-18 06:23:17 copying to 2017-06-18 06:23:17 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:23:17 2017-06-18 06:24:37 faers catalog entry 11 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2014 q2' 2017-06-18 06:24:37 2017-06-18 06:24:37 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM419914.zip' 2017-06-18 06:24:37 cached in 2017-06-18 06:24:37 'E:/eanthony/r-tmp/faers/1180179fdd4375299593495de6404499.Rcache' 2017-06-18 06:24:37 copying to 2017-06-18 06:24:37 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:24:37 2017-06-18 06:25:53 faers catalog entry 12 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2014 q1' 2017-06-18 06:25:53 2017-06-18 06:25:53 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM409890.zip' 2017-06-18 06:25:53 cached in 2017-06-18 06:25:53 'E:/eanthony/r-tmp/faers/079b7cb010688e587f456c887589d1c4.Rcache' 2017-06-18 06:25:53 copying to 2017-06-18 06:25:53 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:25:53 2017-06-18 06:27:00 faers catalog entry 13 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2013 q4' 2017-06-18 06:27:00 2017-06-18 06:27:00 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM399592.zip' 2017-06-18 06:27:00 cached in 2017-06-18 06:27:00 'E:/eanthony/r-tmp/faers/68337bc2d8de1830638118379dfeafa3.Rcache' 2017-06-18 06:27:00 copying to 2017-06-18 06:27:00 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:27:00 2017-06-18 06:28:36 faers catalog entry 14 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2013 q3' 2017-06-18 06:28:36 2017-06-18 06:28:36 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM395994.zip' 2017-06-18 06:28:36 cached in 2017-06-18 06:28:36 'E:/eanthony/r-tmp/faers/819f57e914004235aa80a86de6144e1f.Rcache' 2017-06-18 06:28:36 copying to 2017-06-18 06:28:36 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:28:36 2017-06-18 06:29:16 faers catalog entry 15 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2013 q2' 2017-06-18 06:29:16 2017-06-18 06:29:16 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM387233.zip' 2017-06-18 06:29:16 cached in 2017-06-18 06:29:16 'E:/eanthony/r-tmp/faers/7eb919ebd996fef3db3ff9cd82fa5d5f.Rcache' 2017-06-18 06:29:16 copying to 2017-06-18 06:29:16 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:29:16 2017-06-18 06:31:07 faers catalog entry 16 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2013 q1' 2017-06-18 06:31:07 2017-06-18 06:31:07 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM364757.zip' 2017-06-18 06:31:07 cached in 2017-06-18 06:31:07 'E:/eanthony/r-tmp/faers/f81270550c56c68ac3e7f31e6a859372.Rcache' 2017-06-18 06:31:07 copying to 2017-06-18 06:31:07 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:31:07 2017-06-18 06:32:33 faers catalog entry 17 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2012 q4' 2017-06-18 06:32:33 2017-06-18 06:32:33 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM337616.zip' 2017-06-18 06:32:33 cached in 2017-06-18 06:32:33 'E:/eanthony/r-tmp/faers/76a02915972ca47ea2254722eb2cd424.Rcache' 2017-06-18 06:32:33 copying to 2017-06-18 06:32:33 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:32:33 2017-06-18 06:34:36 faers catalog entry 18 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2012 q3' 2017-06-18 06:34:36 2017-06-18 06:34:36 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/UCM319844.zip' 2017-06-18 06:34:36 cached in 2017-06-18 06:34:36 'E:/eanthony/r-tmp/faers/2c4b9ee9691a9acdae4d06a013600cfb.Rcache' 2017-06-18 06:34:36 copying to 2017-06-18 06:34:36 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:34:36 2017-06-18 06:44:35 faers catalog entry 19 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2012 q2' 2017-06-18 06:44:35 2017-06-18 06:44:35 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM307572.zip' 2017-06-18 06:44:35 cached in 2017-06-18 06:44:35 'E:/eanthony/r-tmp/faers/b325ed66aabcfb33bd9c3535ea783d70.Rcache' 2017-06-18 06:44:35 copying to 2017-06-18 06:44:35 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:44:35 2017-06-18 06:46:25 faers catalog entry 20 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2012 q1' 2017-06-18 06:46:25 2017-06-18 06:46:25 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM300452.zip' 2017-06-18 06:46:25 cached in 2017-06-18 06:46:25 'E:/eanthony/r-tmp/faers/9d254ada74b2dff6a4524b7a9cd72769.Rcache' 2017-06-18 06:46:25 copying to 2017-06-18 06:46:25 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:46:25 2017-06-18 06:51:12 faers catalog entry 21 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2011 q4' 2017-06-18 06:51:12 2017-06-18 06:51:12 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM287845.zip' 2017-06-18 06:51:12 cached in 2017-06-18 06:51:12 'E:/eanthony/r-tmp/faers/d0b2b6157deffdb5bb4a7b6cf636ccad.Rcache' 2017-06-18 06:51:12 copying to 2017-06-18 06:51:12 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:51:12 2017-06-18 06:56:52 faers catalog entry 22 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2011 q3' 2017-06-18 06:56:52 2017-06-18 06:56:52 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM278762.zip' 2017-06-18 06:56:52 cached in 2017-06-18 06:56:52 'E:/eanthony/r-tmp/faers/ea2abf8e8f231e55dfd0e11a28074941.Rcache' 2017-06-18 06:56:52 copying to 2017-06-18 06:56:52 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 06:56:52 2017-06-18 07:04:27 faers catalog entry 23 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2011 q2' 2017-06-18 07:04:27 2017-06-18 07:04:27 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM270803.zip' 2017-06-18 07:04:27 cached in 2017-06-18 07:04:27 'E:/eanthony/r-tmp/faers/648a921feb5ea13cdf6322a4fd85a574.Rcache' 2017-06-18 07:04:27 copying to 2017-06-18 07:04:27 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:04:27 2017-06-18 07:07:47 faers catalog entry 24 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2011 q1' 2017-06-18 07:07:47 2017-06-18 07:07:47 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM251745.zip' 2017-06-18 07:07:47 cached in 2017-06-18 07:07:47 'E:/eanthony/r-tmp/faers/e383d74e4761cc845c1951d1aea52ad4.Rcache' 2017-06-18 07:07:47 copying to 2017-06-18 07:07:47 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:07:47 2017-06-18 07:09:44 faers catalog entry 25 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2010 q4' 2017-06-18 07:09:44 2017-06-18 07:09:44 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM244691.zip' 2017-06-18 07:09:44 cached in 2017-06-18 07:09:44 'E:/eanthony/r-tmp/faers/7cbe652ef9ab8316a9d3d2c5a5c867fc.Rcache' 2017-06-18 07:09:44 copying to 2017-06-18 07:09:44 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:09:44 2017-06-18 07:12:43 faers catalog entry 26 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2010 q3' 2017-06-18 07:12:43 2017-06-18 07:12:43 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM232595.zip' 2017-06-18 07:12:43 cached in 2017-06-18 07:12:43 'E:/eanthony/r-tmp/faers/bad66bad0adc70b09cba6a71af1ac07a.Rcache' 2017-06-18 07:12:43 copying to 2017-06-18 07:12:43 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:12:43 2017-06-18 07:15:17 faers catalog entry 27 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2010 q2' 2017-06-18 07:15:17 2017-06-18 07:15:17 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM220802.zip' 2017-06-18 07:15:17 cached in 2017-06-18 07:15:17 'E:/eanthony/r-tmp/faers/c0ca3bd5a16b08a5fd6c2e7d0c1f4760.Rcache' 2017-06-18 07:15:17 copying to 2017-06-18 07:15:17 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:15:17 2017-06-18 07:17:12 faers catalog entry 28 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2010 q1' 2017-06-18 07:17:12 2017-06-18 07:17:12 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM213485.zip' 2017-06-18 07:17:12 cached in 2017-06-18 07:17:12 'E:/eanthony/r-tmp/faers/19900ff46ff3a2a5e56989192579bbf6.Rcache' 2017-06-18 07:17:12 copying to 2017-06-18 07:17:12 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:17:12 2017-06-18 07:19:05 faers catalog entry 29 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2009 q4' 2017-06-18 07:19:05 2017-06-18 07:19:05 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM197917.zip' 2017-06-18 07:19:05 cached in 2017-06-18 07:19:05 'E:/eanthony/r-tmp/faers/18cdcfdab8c99234a023979fa0c68a4c.Rcache' 2017-06-18 07:19:05 copying to 2017-06-18 07:19:05 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:19:05 2017-06-18 07:20:40 faers catalog entry 30 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2009 q3' 2017-06-18 07:20:40 2017-06-18 07:20:40 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM186488.zip' 2017-06-18 07:20:40 cached in 2017-06-18 07:20:40 'E:/eanthony/r-tmp/faers/6c4f32520585f8463b20e97f5e51d42b.Rcache' 2017-06-18 07:20:40 copying to 2017-06-18 07:20:40 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:20:40 2017-06-18 07:22:55 faers catalog entry 31 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2009 q2' 2017-06-18 07:22:55 2017-06-18 07:22:55 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM173888.zip' 2017-06-18 07:22:55 cached in 2017-06-18 07:22:55 'E:/eanthony/r-tmp/faers/6dbc2876d9ddd958fd65d3dc30b14596.Rcache' 2017-06-18 07:22:55 copying to 2017-06-18 07:22:55 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:22:55 2017-06-18 07:24:13 faers catalog entry 32 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2009 q1' 2017-06-18 07:24:13 2017-06-18 07:24:13 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM150381.zip' 2017-06-18 07:24:13 cached in 2017-06-18 07:24:13 'E:/eanthony/r-tmp/faers/a2b02f2b497dc7f6218ae558256a142d.Rcache' 2017-06-18 07:24:13 copying to 2017-06-18 07:24:13 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:24:13 2017-06-18 07:26:25 faers catalog entry 33 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2008 q4' 2017-06-18 07:26:25 2017-06-18 07:26:25 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm085780.zip' 2017-06-18 07:26:25 cached in 2017-06-18 07:26:25 'E:/eanthony/r-tmp/faers/fb518c97c98278b9d6a2d1c7a14e8d80.Rcache' 2017-06-18 07:26:25 copying to 2017-06-18 07:26:25 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:26:25 2017-06-18 07:28:26 faers catalog entry 34 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2008 q3' 2017-06-18 07:28:26 2017-06-18 07:28:26 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm085785.zip' 2017-06-18 07:28:26 cached in 2017-06-18 07:28:26 'E:/eanthony/r-tmp/faers/9dbce0090c25b74a756890169cb43ad7.Rcache' 2017-06-18 07:28:26 copying to 2017-06-18 07:28:26 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:28:26 2017-06-18 07:29:45 faers catalog entry 35 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2008 q2' 2017-06-18 07:29:45 2017-06-18 07:29:45 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm085793.zip' 2017-06-18 07:29:45 cached in 2017-06-18 07:29:45 'E:/eanthony/r-tmp/faers/1c59642db85c0045973eb5ee266a1662.Rcache' 2017-06-18 07:29:45 copying to 2017-06-18 07:29:45 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:29:45 2017-06-18 07:30:30 faers catalog entry 36 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2008 q1' 2017-06-18 07:30:30 2017-06-18 07:30:30 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm085809.zip' 2017-06-18 07:30:30 cached in 2017-06-18 07:30:30 'E:/eanthony/r-tmp/faers/2a31fb54ef2de80e7b4795c8c8318b77.Rcache' 2017-06-18 07:30:30 copying to 2017-06-18 07:30:30 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:30:30 2017-06-18 07:31:28 faers catalog entry 37 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2007 q4' 2017-06-18 07:31:28 2017-06-18 07:31:28 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm083816.zip' 2017-06-18 07:31:28 cached in 2017-06-18 07:31:28 'E:/eanthony/r-tmp/faers/e101be389e4511d335051d94922f7a90.Rcache' 2017-06-18 07:31:28 copying to 2017-06-18 07:31:28 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:31:28 2017-06-18 07:32:44 faers catalog entry 38 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2007 q3' 2017-06-18 07:32:44 2017-06-18 07:32:44 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm083983.zip' 2017-06-18 07:32:44 cached in 2017-06-18 07:32:44 'E:/eanthony/r-tmp/faers/1918addf41e9d51f7b439ae2b13a689b.Rcache' 2017-06-18 07:32:44 copying to 2017-06-18 07:32:44 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:32:44 2017-06-18 07:33:30 faers catalog entry 39 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2007 q2' 2017-06-18 07:33:30 2017-06-18 07:33:30 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084042.zip' 2017-06-18 07:33:30 cached in 2017-06-18 07:33:30 'E:/eanthony/r-tmp/faers/9312651d508e07e3df11e3ba75a67020.Rcache' 2017-06-18 07:33:30 copying to 2017-06-18 07:33:30 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:33:30 2017-06-18 07:34:14 faers catalog entry 40 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2007 q1' 2017-06-18 07:34:14 2017-06-18 07:34:14 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084161.zip' 2017-06-18 07:34:14 cached in 2017-06-18 07:34:14 'E:/eanthony/r-tmp/faers/ac6127b9d8bf28f041a8d69c5aca3bd5.Rcache' 2017-06-18 07:34:14 copying to 2017-06-18 07:34:14 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:34:14 2017-06-18 07:34:42 faers catalog entry 41 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2006 q4' 2017-06-18 07:34:42 2017-06-18 07:34:42 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084206.zip' 2017-06-18 07:34:42 cached in 2017-06-18 07:34:42 'E:/eanthony/r-tmp/faers/0addaabff3430a23b421db7265780d57.Rcache' 2017-06-18 07:34:42 copying to 2017-06-18 07:34:42 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:34:42 2017-06-18 07:35:07 faers catalog entry 42 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2006 q3' 2017-06-18 07:35:07 2017-06-18 07:35:07 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084217.zip' 2017-06-18 07:35:07 cached in 2017-06-18 07:35:07 'E:/eanthony/r-tmp/faers/26c41b1b1800bc5dc0aa5b9786e168bb.Rcache' 2017-06-18 07:35:07 copying to 2017-06-18 07:35:07 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:35:07 2017-06-18 07:35:32 faers catalog entry 43 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2006 q2' 2017-06-18 07:35:32 2017-06-18 07:35:32 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084242.zip' 2017-06-18 07:35:32 cached in 2017-06-18 07:35:32 'E:/eanthony/r-tmp/faers/7b9b05e77d2b16464208e5db6607599a.Rcache' 2017-06-18 07:35:32 copying to 2017-06-18 07:35:32 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:35:32 2017-06-18 07:36:01 faers catalog entry 44 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2006 q1' 2017-06-18 07:36:01 2017-06-18 07:36:01 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084259.zip' 2017-06-18 07:36:01 cached in 2017-06-18 07:36:01 'E:/eanthony/r-tmp/faers/5809e6271982495a761d0a6301f5f63e.Rcache' 2017-06-18 07:36:01 copying to 2017-06-18 07:36:01 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:36:01 2017-06-18 07:36:43 faers catalog entry 45 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2005 q4' 2017-06-18 07:36:43 2017-06-18 07:36:43 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084277.zip' 2017-06-18 07:36:43 cached in 2017-06-18 07:36:43 'E:/eanthony/r-tmp/faers/24ff2db582ceb8dd7b20aa0ba25cd44c.Rcache' 2017-06-18 07:36:43 copying to 2017-06-18 07:36:43 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:36:43 2017-06-18 07:37:18 faers catalog entry 46 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2005 q3' 2017-06-18 07:37:18 2017-06-18 07:37:18 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084916.zip' 2017-06-18 07:37:18 cached in 2017-06-18 07:37:18 'E:/eanthony/r-tmp/faers/c705d59380e4a59013bf3386eeb0250d.Rcache' 2017-06-18 07:37:18 copying to 2017-06-18 07:37:18 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:37:18 2017-06-18 07:37:57 faers catalog entry 47 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2005 q2' 2017-06-18 07:37:57 2017-06-18 07:37:57 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084918.zip' 2017-06-18 07:37:57 cached in 2017-06-18 07:37:57 'E:/eanthony/r-tmp/faers/be6d12263e52805b7486d89ff55e28e5.Rcache' 2017-06-18 07:37:57 copying to 2017-06-18 07:37:57 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:37:57 2017-06-18 07:38:37 faers catalog entry 48 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2005 q1' 2017-06-18 07:38:37 2017-06-18 07:38:37 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084920.zip' 2017-06-18 07:38:37 cached in 2017-06-18 07:38:37 'E:/eanthony/r-tmp/faers/af695a37dd49d78898928ccd7e3144a4.Rcache' 2017-06-18 07:38:37 copying to 2017-06-18 07:38:37 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:38:37 2017-06-18 07:39:19 faers catalog entry 49 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2004 q4' 2017-06-18 07:39:19 2017-06-18 07:39:19 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084922.zip' 2017-06-18 07:39:19 cached in 2017-06-18 07:39:19 'E:/eanthony/r-tmp/faers/7f8483fe62f05bc3ae136111d9a05ae2.Rcache' 2017-06-18 07:39:19 copying to 2017-06-18 07:39:19 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:39:19 2017-06-18 07:40:05 faers catalog entry 50 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2004 q3' 2017-06-18 07:40:05 2017-06-18 07:40:05 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084924.zip' 2017-06-18 07:40:05 cached in 2017-06-18 07:40:05 'E:/eanthony/r-tmp/faers/690ceb89de5ab8ced1685da4520e14ed.Rcache' 2017-06-18 07:40:05 copying to 2017-06-18 07:40:05 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:40:05 2017-06-18 07:40:57 faers catalog entry 51 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2004 q2' 2017-06-18 07:40:57 2017-06-18 07:40:57 'https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/ucm084927.zip' 2017-06-18 07:40:57 cached in 2017-06-18 07:40:57 'E:/eanthony/r-tmp/faers/41ac35a4dd8428afc7bf050de8795444.Rcache' 2017-06-18 07:40:57 copying to 2017-06-18 07:40:57 'E:\eanthony\r-tmp\faers\RtmpEZuyRF\file31186be24718' 2017-06-18 07:40:57 2017-06-18 07:41:28 faers catalog entry 52 of 52 stored in 'e:/eanthony/r-wd/faers-1497791167/2004 q1' 2017-06-18 07:41:28 2017-06-18 07:41:28 faers local download completed 2017-06-18 07:41:28 2017-06-18 07:41:28 > 2017-06-18 07:41:28 2017-06-18 07:41:28 R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" 2017-06-18 07:41:28 Copyright (C) 2017 The R Foundation for Statistical Computing 2017-06-18 07:41:28 Platform: x86_64-w64-mingw32/x64 (64-bit) 2017-06-18 07:41:28 2017-06-18 07:41:28 R is free software and comes with ABSOLUTELY NO WARRANTY. 2017-06-18 07:41:28 You are welcome to redistribute it under certain conditions. 2017-06-18 07:41:28 Type 'license()' or 'licence()' for distribution details. 2017-06-18 07:41:28 2017-06-18 07:41:28 Natural language support but running in an English locale 2017-06-18 07:41:28 2017-06-18 07:41:28 R is a collaborative project with many contributors. 2017-06-18 07:41:28 Type 'contributors()' for more information and 2017-06-18 07:41:28 'citation()' on how to cite R or R packages in publications. 2017-06-18 07:41:28 2017-06-18 07:41:28 Type 'demo()' for some demos, 'help()' for on-line help, or 2017-06-18 07:41:28 'help.start()' for an HTML browser interface to help. 2017-06-18 07:41:28 Type 'q()' to quit R. 2017-06-18 07:41:28 2017-06-18 07:41:29 > setwd( Sys.getenv( "RWD" ) ) 2017-06-18 07:41:29 > 2017-06-18 07:41:29 > machine_specific_replacements <- 2017-06-18 07:41:29 + list( 2017-06-18 07:41:29 + 2017-06-18 07:41:29 + # replace the folder path on macnix 2017-06-18 07:41:29 + c( 'path.expand( \"~\" ) , \"FAERS\"' , paste0( '"' , getwd() , '"' ) ) , 2017-06-18 07:41:29 + 2017-06-18 07:41:29 + # change other things in the script to be run 2017-06-18 07:41:29 + c( "hello" , "howdy" ) 2017-06-18 07:41:29 + 2017-06-18 07:41:29 + ) 2017-06-18 07:41:29 > 2017-06-18 07:41:29 > source( lodown::syntaxtractor( "faers" , replacements = machine_specific_replacements , setup_test = "test" ) , echo = TRUE ) 2017-06-18 07:41:30 2017-06-18 07:41:30 > faers_drug_df <- readRDS(file.path("e:/eanthony/r-wd/faers-1497791167", 2017-06-18 07:41:30 + "2016 q4/drug16q4.rds")) 2017-06-18 07:41:31 2017-06-18 07:41:31 > faers_outcome_df <- readRDS(file.path("e:/eanthony/r-wd/faers-1497791167", 2017-06-18 07:41:31 + "2016 q4/outc16q4.rds")) 2017-06-18 07:41:31 2017-06-18 07:41:31 > faers_demo_df <- readRDS(file.path("e:/eanthony/r-wd/faers-1497791167", 2017-06-18 07:41:31 + "2016 q4/demo16q4.rds")) 2017-06-18 07:41:32 2017-06-18 07:41:32 > faers_df <- merge(faers_drug_df, faers_outcome_df) 2017-06-18 07:41:43 2017-06-18 07:41:43 > faers_df <- merge(faers_df, faers_demo_df, all.x = TRUE) 2017-06-18 07:41:53 2017-06-18 07:41:53 > faers_df <- transform(faers_df, physician_reported = as.numeric(occp_cod == 2017-06-18 07:41:53 + "MD"), init_fda_year = as.numeric(substr(init_fda_dt, 1, 2017-06-18 07:41:53 + 4 .... [TRUNCATED] 2017-06-18 07:41:54 2017-06-18 07:41:54 > nrow(faers_df) 2017-06-18 07:41:54 [1] 1039275 2017-06-18 07:41:54 2017-06-18 07:41:54 > table(faers_df[, "outc_code"], useNA = "always") 2017-06-18 07:41:54 2017-06-18 07:41:54 CA DE DS HO LT OT RI 2017-06-18 07:41:54 2806 102441 27201 380922 44556 480813 536 0 2017-06-18 07:41:54 2017-06-18 07:41:54 > mean(faers_df[, "init_fda_year"], na.rm = TRUE) 2017-06-18 07:41:54 [1] 2015.782 2017-06-18 07:41:54 2017-06-18 07:41:54 > tapply(faers_df[, "init_fda_year"], faers_df[, "outc_code"], 2017-06-18 07:41:54 + mean, na.rm = TRUE) 2017-06-18 07:41:54 CA DE DS HO LT OT RI 2017-06-18 07:41:54 2015.823 2015.845 2015.729 2015.777 2015.763 2015.777 2016.000 2017-06-18 07:41:54 2017-06-18 07:41:54 > prop.table(table(faers_df[, "sex"])) 2017-06-18 07:41:54 2017-06-18 07:41:54 F M UNK 2017-06-18 07:41:54 0.0722080296 0.5127959395 0.4147612518 0.0002347791 2017-06-18 07:41:54 2017-06-18 07:41:54 > prop.table(table(faers_df[, c("sex", "outc_code")]), 2017-06-18 07:41:54 + margin = 2) 2017-06-18 07:41:54 outc_code 2017-06-18 07:41:54 sex CA DE DS HO LT 2017-06-18 07:41:54 0.4358517463 0.1080719634 0.0537847873 0.0486582555 0.0483661011 2017-06-18 07:41:54 F 0.2940128297 0.4006403686 0.5402742546 0.5112568977 0.4756710656 2017-06-18 07:41:54 M 0.2690662865 0.4905848244 0.4057571413 0.4399299594 0.4756710656 2017-06-18 07:41:54 UNK 0.0010691376 0.0007028436 0.0001838168 0.0001548874 0.0002917677 2017-06-18 07:41:54 outc_code 2017-06-18 07:41:54 sex OT RI 2017-06-18 07:41:54 0.0844236741 0.0093283582 2017-06-18 07:41:54 F 0.5411542533 0.4402985075 2017-06-18 07:41:54 M 0.3742307300 0.5503731343 2017-06-18 07:41:54 UNK 0.0001913426 0.0000000000 2017-06-18 07:41:54 2017-06-18 07:41:54 > sum(faers_df[, "init_fda_year"], na.rm = TRUE) 2017-06-18 07:41:54 [1] 2094952079 2017-06-18 07:41:54 2017-06-18 07:41:54 > tapply(faers_df[, "init_fda_year"], faers_df[, "outc_code"], 2017-06-18 07:41:54 + sum, na.rm = TRUE) 2017-06-18 07:41:54 CA DE DS HO LT OT RI 2017-06-18 07:41:54 5656400 206505128 54829836 767853807 89814345 969211987 1080576 2017-06-18 07:41:54 2017-06-18 07:41:54 > quantile(faers_df[, "init_fda_year"], 0.5, na.rm = TRUE) 2017-06-18 07:41:54 50% 2017-06-18 07:41:54 2016 2017-06-18 07:41:54 2017-06-18 07:41:54 > tapply(faers_df[, "init_fda_year"], faers_df[, "outc_code"], 2017-06-18 07:41:54 + quantile, 0.5, na.rm = TRUE) 2017-06-18 07:41:54 CA DE DS HO LT OT RI 2017-06-18 07:41:54 2016 2016 2016 2016 2016 2016 2016 2017-06-18 07:41:54 2017-06-18 07:41:54 > sub_faers_df <- subset(faers_df, age_grp == "E") 2017-06-18 07:41:54 2017-06-18 07:41:54 > mean(sub_faers_df[, "init_fda_year"], na.rm = TRUE) 2017-06-18 07:41:54 [1] 2015.843 2017-06-18 07:41:54 2017-06-18 07:41:54 > var(faers_df[, "init_fda_year"], na.rm = TRUE) 2017-06-18 07:41:54 [1] 0.5642665 2017-06-18 07:41:54 2017-06-18 07:41:54 > tapply(faers_df[, "init_fda_year"], faers_df[, "outc_code"], 2017-06-18 07:41:54 + var, na.rm = TRUE) 2017-06-18 07:41:55 CA DE DS HO LT OT RI 2017-06-18 07:41:55 0.4514528 0.4231105 0.7456510 0.5671948 0.6878350 0.5704722 0.0000000 2017-06-18 07:41:55 2017-06-18 07:41:55 > t.test(init_fda_year ~ physician_reported, faers_df) 2017-06-18 07:41:58 2017-06-18 07:41:58 Welch Two Sample t-test 2017-06-18 07:41:58 2017-06-18 07:41:58 data: init_fda_year by physician_reported 2017-06-18 07:41:58 t = 51.658, df = 636250, p-value < 2.2e-16 2017-06-18 07:41:58 alternative hypothesis: true difference in means is not equal to 0 2017-06-18 07:41:58 95 percent confidence interval: 2017-06-18 07:41:58 0.08070765 0.08707345 2017-06-18 07:41:58 sample estimates: 2017-06-18 07:41:58 mean in group 0 mean in group 1 2017-06-18 07:41:58 2015.811 2015.727 2017-06-18 07:41:58 2017-06-18 07:41:58 2017-06-18 07:41:58 > this_table <- table(faers_df[, c("physician_reported", 2017-06-18 07:41:58 + "sex")]) 2017-06-18 07:41:59 2017-06-18 07:41:59 > chisq.test(this_table) 2017-06-18 07:41:59 2017-06-18 07:41:59 Pearson's Chi-squared test 2017-06-18 07:41:59 2017-06-18 07:41:59 data: this_table 2017-06-18 07:41:59 X-squared = 2432.9, df = 3, p-value < 2.2e-16 2017-06-18 07:41:59 2017-06-18 07:41:59 2017-06-18 07:41:59 > glm_result <- glm(init_fda_year ~ physician_reported + 2017-06-18 07:41:59 + sex, data = faers_df) 2017-06-18 07:42:01 2017-06-18 07:42:01 > summary(glm_result) 2017-06-18 07:42:01 2017-06-18 07:42:01 Call: 2017-06-18 07:42:01 glm(formula = init_fda_year ~ physician_reported + sex, data = faers_df) 2017-06-18 07:42:01 2017-06-18 07:42:01 Deviance Residuals: 2017-06-18 07:42:01 Min 1Q Median 3Q Max 2017-06-18 07:42:01 -11.8353 0.1647 0.2284 0.2489 0.3125 2017-06-18 07:42:01 2017-06-18 07:42:01 Coefficients: 2017-06-18 07:42:01 Estimate Std. Error t value Pr(>|t|) 2017-06-18 07:42:01 (Intercept) 2.016e+03 2.771e-03 727567.376 <2e-16 *** 2017-06-18 07:42:01 physician_reported -8.415e-02 1.548e-03 -54.349 <2e-16 *** 2017-06-18 07:42:01 sexF -1.806e-01 2.919e-03 -61.870 <2e-16 *** 2017-06-18 07:42:01 sexM -1.169e-01 2.962e-03 -39.464 <2e-16 *** 2017-06-18 07:42:01 sexUNK 4.924e-02 4.800e-02 1.026 0.305 2017-06-18 07:42:01 --- 2017-06-18 07:42:01 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 2017-06-18 07:42:01 2017-06-18 07:42:01 (Dispersion parameter for gaussian family taken to be 0.5601948) 2017-06-18 07:42:01 2017-06-18 07:42:01 Null deviance: 586427 on 1039274 degrees of freedom 2017-06-18 07:42:01 Residual deviance: 582194 on 1039270 degrees of freedom 2017-06-18 07:42:01 AIC: 2347112 2017-06-18 07:42:01 2017-06-18 07:42:01 Number of Fisher Scoring iterations: 2 2017-06-18 07:42:01 2017-06-18 07:42:01 2017-06-18 07:42:01 > library(dplyr) 2017-06-18 07:42:02 2017-06-18 07:42:02 Attaching package: 'dplyr' 2017-06-18 07:42:02 2017-06-18 07:42:02 The following objects are masked from 'package:stats': 2017-06-18 07:42:02 2017-06-18 07:42:02 filter, lag 2017-06-18 07:42:02 2017-06-18 07:42:02 The following objects are masked from 'package:base': 2017-06-18 07:42:02 2017-06-18 07:42:02 intersect, setdiff, setequal, union 2017-06-18 07:42:02 2017-06-18 07:42:02 2017-06-18 07:42:02 > faers_tbl <- tbl_df(faers_df) 2017-06-18 07:42:02 2017-06-18 07:42:02 > faers_tbl %>% summarize(mean = mean(init_fda_year, 2017-06-18 07:42:02 + na.rm = TRUE)) 2017-06-18 07:42:02 # A tibble: 1 x 1 2017-06-18 07:42:02 mean 2017-06-18 07:42:02 2017-06-18 07:42:02 1 2015.782 2017-06-18 07:42:02 2017-06-18 07:42:02 > faers_tbl %>% group_by(outc_code) %>% summarize(mean = mean(init_fda_year, 2017-06-18 07:42:02 + na.rm = TRUE)) 2017-06-18 07:42:02 # A tibble: 7 x 2 2017-06-18 07:42:02 outc_code mean 2017-06-18 07:42:02 2017-06-18 07:42:02 1 CA 2015.823 2017-06-18 07:42:02 2 DE 2015.845 2017-06-18 07:42:02 3 DS 2015.729 2017-06-18 07:42:02 4 HO 2015.777 2017-06-18 07:42:02 5 LT 2015.763 2017-06-18 07:42:02 6 OT 2015.777 2017-06-18 07:42:02 7 RI 2016.000 2017-06-18 07:42:02 Warning message: 2017-06-18 07:42:02 Installed Rcpp (0.12.10) different from Rcpp used to build dplyr (0.12.11). 2017-06-18 07:42:02 Please reinstall dplyr to avoid random crashes or undefined behavior. 2017-06-18 07:42:02 >