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# Prepare wide data for 3D printing
# Expects to be passed 3 columns: x,y,z
# x and y will be binned
# a function of z will be used to prepare the z coordinate

library(data.table)
library(ggplot2)
library(r2stl)
library(Hmisc)
library(assertthat)

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let blacklists = ["*://example.com/stuff/*", "*://mail.google.com/*", "http://localhost:*/notebooks/*"]

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class MixinOne(object):
    def print_name(self):
        print("{} is using MixinOne.".format(self.name))


class MixinTwo(object):
    def print_name(self):
        print("{} is using MixinTwo.".format(self.name))

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# Specify antibiotic characteristics
# Sepsis3 valid
# dosing interval (period) - assume less than 24 hourly unless otherwise specified
# rank as per Braykov NP, Morgan DJ, Schweizer ML, Uslan DZ, Kelesidis T, Weisenberg SA, et al. Assessment of empirical antibiotic therapy optimisation in six hospitals: an observational cohort study. Lancet Infect Dis. 2014;14: 1220–1227. doi:10.1016/S1473-3099(14)70952-1
NIHR_HIC_ICU_0414:
  Classification3: Aminoglycosides
  dataItem: Amikacin
  sepsis3_abx: TRUE
  rank_abx: 4
  period_abx: ~

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#  ==================================
#  = Define generic study variables =
#  ==================================
find_NHIC("shortName", "dead")

# Mortality
gen_mortality(wdt, "mort.icu", "NIHR_HIC_ICU_0097")
table(unique(wdt[,.(id,mort.icu)])$mort.icu)

gen_mortality(wdt, "mort.hosp", "NIHR_HIC_ICU_0095")

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# # apply response after field specification allows two possibilities
# # apply: drop_entry - just replace field with NA
# # apply: drop_episode - drop entire episode
# # range checks for continuous data *must* use traffic light terms
# # - red
# # - amber
# # - green
# # also concept of nodata check which will drop episode if data is missing
# # e.g. for something crucial like date of birth (age)
# # nodata:

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-
  fname: icnarc_score
  sqltype: tinyint
  varlab: ICNARC acute physiology score
  derived: True
  derived_missing_ok: True
  primaryfields:
    - hrate
    - bpsys
    - temperature

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OS X Preferences

---

most of these require logout/restart to take effect

# Enable character repeat on keydown
defaults write -g ApplePressAndHoldEnabled -bool false

# Set a shorter Delay until key repeat

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# coding: utf-8

# Load up the citation text file as per this link
#
# http://onlinelibrary.wiley.com/cochranelibrary/search/advanced?hiddenFields.strategySortBy=last-modified-date;desc&hiddenFields.showStrategies=true&hiddenFields.containerId=12670271652807976185&hiddenFields.originalContainerId=15960432450033216107&hiddenFields.etag=8064622093550521747
#
# And saved here as `citation-export.txt`

# Test example
testData = """