hpiwowar

#!/usr/bin/env python
# Initially written by Heather Piwowar, June 2011
# Public domain: have at it!
# For annotating bibtex files, pulling in article info from customized spreadsheets

import csv
import re
import codecs
from pybtex.database.input import bibtex as bibtex_in
from pybtex.database.output import bibtex as bibtex_out

hpiwowar

#!/usr/bin/env python
# Initially written by Heather Piwowar, June 2011
# Public domain: have at it!
# For converting ISI Web of Science tab-delimited exports into bibtex format

import csv
import glob
import random
from collections import defaultdict
import codecs

hpiwowar

### Heather Piwowar
### MIT open license. 
### blog post about interm results:  

library(rms)

# if true, draw figures on screen instead of in a file
SCREEN=TRUE

# set to ".eps" or ".png"

hpiwowar

### Heather Piwowar
# Modifications to add confidence intervals added by Heather Piwowar

# Based on dotchart2{Hmisc}
dotchart2.CIs = 
function (data, labels, groups = NULL, gdata = NA, horizontal = TRUE, 
    pch = 16, xlab = "", ylab = "", auxdata, auxgdata = NULL, 
    auxtitle, lty = if (.R.) 1 else 2, lines = TRUE, dotsize = 0.8, 
    cex = par("cex"), cex.labels = cex, cex.group.labels = cex.labels * 
        1.25, sort. = TRUE, add = FALSE, dotfont = par("font"), 

hpiwowar

dotchart2.CIs = 
function (data, labels, groups = NULL, gdata = NA, horizontal = TRUE, 
    pch = 16, xlab = "", ylab = "", auxdata, auxgdata = NULL, 
    auxtitle, lty = if (.R.) 1 else 2, lines = TRUE, dotsize = 0.8, 
    cex = par("cex"), cex.labels = cex, cex.group.labels = cex.labels * 
        1.25, sort. = TRUE, add = FALSE, dotfont = par("font"), 
    groupfont = 2, reset.par = add, xaxis = TRUE, width.factor = 1.1, 
    lcolor = if (.R.) "gray" else par("col"), ...) 
{
    if (.R. && !add) {

hpiwowar

library(Hmisc)

journdat = read.csv("~/Downloads/JournalData.csv", as.is=TRUE, na.strings="N/A")

journdat$is.Environmental.Sciences = 0
journdat$is.Environmental.Sciences[grep("*Environmental Sciences*", journdat$ISI.Category)] = 1


summary(Policy.request...require.code ~ Impact.Factor + Policy.has.instructions.for.how.to.cite.data. + Subscription.Model + is.Environmental.Sciences, journdat)
response = summary(Policy.request...require.code ~ Impact.Factor + Policy.has.instructions.for.how.to.cite.data. + Subscription.Model + is.Environmental.Sciences, journdat)

hpiwowar

import os
import time
import re
import nose
from nose.tools import assert_equals
from collections import defaultdict
import EUtils
from EUtils import HistoryClient, ThinClient
import dataset
import datasources

hpiwowar

humans[mesh] AND "magnetic resonance imaging"[mesh] 
NOT "magnetic resonance imaging/ethics"[mesh] 
AND "mental disorders"[mesh] 
AND (fmri[Title/Abstract] OR "Functional MRI"[Title/Abstract] 
OR "Functional magnetic resonance imaging"[Title/Abstract] 
OR "Functional MR Imaging"[Title/Abstract]) 
AND Journal Article[ptyp] AND English[lang]
NOT (Editorial[ptyp] OR Letter[ptyp] OR Meta-Analysis[ptyp] 
OR Practice Guideline[ptyp] OR Review[ptyp] OR Case Reports[ptyp] 
OR Comment[ptyp] OR Corrected and Republished Article[ptyp]) 

hpiwowar

humans[mesh] AND "magnetic resonance imaging"[mesh] 
NOT "magnetic resonance imaging/ethics"[mesh]
NOT "mental disorders"[mesh] 
AND (fmri[Title/Abstract] OR "Functional MRI"[Title/Abstract] 
OR "Functional magnetic resonance imaging"[Title/Abstract] 
OR "Functional MR Imaging"[Title/Abstract]) 
AND Journal Article[ptyp] AND English[lang]
NOT (Editorial[ptyp] OR Letter[ptyp] OR Meta-Analysis[ptyp] 
OR Practice Guideline[ptyp] OR Review[ptyp] OR Case Reports[ptyp] 
OR Comment[ptyp] OR Corrected and Republished Article[ptyp]) 

hpiwowar

import nose
from nose.tools import assert_equals
from tests import slow, online, notimplemented, acceptance

import urllib2
import random
import datasources
from datasources import pubmed
from datasources import urlopener