Iain Marshall ijmarshall

## Regression analyses SOTE in R with lme4.ipynb

      
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                ijmarshall
                / Regression analyses SOTE in R with lme4.ipynb
            
            
              Created
              September 22, 2020 16:18
            
              
                Regression analyses for the State of the Evidence paper
              
          
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## Regression analyses SOTE in R with lme4.ipynb

      
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                ijmarshall
                / Regression analyses SOTE in R with lme4.ipynb
            
            
              Created
              September 22, 2020 16:16
            
              
                Regression analyses for State of the Evidence manuscript
              
          
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## Dockerfile
# GPU development environment for RobotReviewer

FROM nvidia/cuda:8.0-devel-ubuntu16.04
RUN apt-get update && apt-get install -y --no-install-recommends \
        curl && \
    rm -rf /var/lib/apt/lists/*

ENV CUDNN_VERSION 5.1.10
LABEL com.nvidia.cudnn.version="${CUDNN_VERSION}"

## Dockerfile
# GPU development environment for RobotReviewer

FROM nvidia/cuda:8.0-devel-ubuntu16.04
RUN apt-get update && apt-get install -y --no-install-recommends \
        curl && \
    rm -rf /var/lib/apt/lists/*

ENV CUDNN_VERSION 5.1.10
LABEL com.nvidia.cudnn.version="${CUDNN_VERSION}"

## Dockerfile
# GPU development environment for RobotReviewer

FROM nvidia/cuda:8.0-devel-ubuntu16.04
RUN apt-get update && apt-get install -y --no-install-recommends \
        curl && \
    rm -rf /var/lib/apt/lists/*

ENV CUDNN_VERSION 5.1.10
LABEL com.nvidia.cudnn.version="${CUDNN_VERSION}"

## Dockerfile
# GPU development environment for RobotReviewer

FROM nvidia/cuda:8.0-devel-ubuntu16.04
RUN apt-get update && apt-get install -y --no-install-recommends \
        curl && \
    rm -rf /var/lib/apt/lists/*

ENV CUDNN_VERSION 5.1.10
LABEL com.nvidia.cudnn.version="${CUDNN_VERSION}"

## .zshrc
# If you come from bash you might have to change your $PATH.
# export PATH=$HOME/bin:/usr/local/bin:$PATH

# Path to your oh-my-zsh installation.
export ZSH=$HOME/.oh-my-zsh

# Set name of the theme to load. Optionally, if you set this to "random"
# it'll load a random theme each time that oh-my-zsh is loaded.
# See https://github.com/robbyrussell/oh-my-zsh/wiki/Themes
ZSH_THEME="pure"

## lookup_pubmed_ids.py
#
#	cdsr2pubmed_linker.py
#

""" Tries multiple searches using different parts of the reference
each time Then iterates through all possible combinations of result
sets, intersections are likely matches Choose the id with the most
hits (which appears most frequently as a single intersection). Saves
all in the RobotReviewer sqlite database

## abbreviations.py
'''Link abbreviations to their full names

Based on

A Simple Algorithm for Identifying Abbreviations Definitions in Biomedical Text
A. Schwartz and M. Hearst
Biocomputing, 2003, pp 451-462.


# License: GNU General Public License, see http://www.clips.ua.ac.be/~vincent/scripts/LICENSE.txt

## get_pubmed.py
#
#   get all pubmed abstracts
#

from cochranenlp.readers import pmlib, pubmed
import yaml
import os
from glob import glob
import xml.etree.cElementTree as ET
	# GPU development environment for RobotReviewer

	FROM nvidia/cuda:8.0-devel-ubuntu16.04
	RUN apt-get update && apt-get install -y --no-install-recommends \
	curl && \
	rm -rf /var/lib/apt/lists/*

	ENV CUDNN_VERSION 5.1.10
	LABEL com.nvidia.cudnn.version="${CUDNN_VERSION}"
	# If you come from bash you might have to change your $PATH.
	# export PATH=$HOME/bin:/usr/local/bin:$PATH

	# Path to your oh-my-zsh installation.
	export ZSH=$HOME/.oh-my-zsh

	# Set name of the theme to load. Optionally, if you set this to "random"
	# it'll load a random theme each time that oh-my-zsh is loaded.
	# See https://github.com/robbyrussell/oh-my-zsh/wiki/Themes
	ZSH_THEME="pure"
	#
	# cdsr2pubmed_linker.py
	#

	""" Tries multiple searches using different parts of the reference
	each time Then iterates through all possible combinations of result
	sets, intersections are likely matches Choose the id with the most
	hits (which appears most frequently as a single intersection). Saves
	all in the RobotReviewer sqlite database
	'''Link abbreviations to their full names

	Based on

	A Simple Algorithm for Identifying Abbreviations Definitions in Biomedical Text
	A. Schwartz and M. Hearst
	Biocomputing, 2003, pp 451-462.


	# License: GNU General Public License, see http://www.clips.ua.ac.be/~vincent/scripts/LICENSE.txt
	#
	# get all pubmed abstracts
	#

	from cochranenlp.readers import pmlib, pubmed
	import yaml
	import os
	from glob import glob
	import xml.etree.cElementTree as ET