klsea / time_prefs_meta Goto Github PK

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\f0\fs24 \cf0 README for time_prefs_meta GitHub repository\
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Below is a description of each R script in the main directory of this repository:\
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\f1\b 00_clean_covidence_file.R 
\f0\b0 - Cleans the file containing data extracted from the systematic review on Covidence.\
- Input file = data/review_47118_extracted_data_csv_20200617040346.csv. \
- Output file = output/cleaned.csv. 
\f1\b *This input file is shared on OSF*
\f0\b0 \
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\f1\b 01_correct_omissions_errors.R
\f0\b0  - This script corrects errors and omissions in the systematic review file. \
- Input file = output/cleaned.csv. \
- Output file = output/corrected.csv\
\

\f1\b 02_missing_values_covidence.R 
\f0\b0 - Adds data from studies that were missing in the systematic review file (mostly data extracted by plot digitizer). \
- Input file = output/corrected.csv. \
- Output file = output/cleaned.csv\
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\f1\b 03_add_raw_data.R 
\f0\b0 -  Adds summary from raw data files. \
- Input file = output/cleaned.csv. \
- Output file = output/complete.csv 
\f1\b *This output file is shared on OSF*\
\
04_calculate_effect_size_continuous.R - 
\f0\b0 Calculates the effect sizes for all continuous designs. \
- Input file = output/complete.csv. \
- Output file = output/continuous_table.csv\
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\f1\b 05_calculate_effect_size_group.R 
\f0\b0 - Calculates the effect sizes for all group designs with means/SD/SE reported. \
- Input file = output/complete.csv. \
- Output file = output/extreme_group_table.csv\
\

\f1\b 06_calculate_effect_size_stat.R
\f0\b0  - Calculates the effect sizes for all group designs with t values reported. \
- Input file = output/complete.csv. \
- Output file = output/extreme_group_stat_table.csv\
\

\f1\b 07_make_es_tables.R
\f0\b0  - Creates publication-ready tables of effect sizes and merges together effect size tables for data analysis. \
- Input files =  output/continuous_table.csv, output/extreme_group_table.csv, output/extreme_group_stat_table.csv \
- Output files = figs/continuous_table.html, figs/extreme_group_table.html, output/effect_sizes.csv\
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\f1\b 08_meta_analysis.R 
\f0\b0 - Conducts basic meta-analysis and forest plot. \
- Input file = output/effect_sizes.csv. \
- Output files = figs/forestplot.png, output/cor_model.RDS, output/dl_model.RDS\
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\f1\b 09_heterogeneity_explorations.R
\f0\b0  - Runs outlier and influence analyses. \
- Input file = output/cor_model.RDS\
- no output files\
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\f1\b 10_funnel_plot_p_curve.R
\f0\b0  - Creates funnel plot, runs egger tests, and p-curve analysis. \
- Input file = output/cor_model.RDS. \
- Output files = figs/funnelplot.png, figs/funnelplot2.png, figs/funnelplot3.png, figs/pcurve.png\
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11_meta_regression.R - Runs 4 meta-regressions described in text.\
- Input file = output/effect_sizes.csv\
- no output files\
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12_nonlinear_analysis.RMD - Markdown file with nonlinear analyses.\
- Input file = data/overview.xlsx\
- Output file = 12_nonlinear_analysis.html\
\
Below is a description of each directory inside this repository:\
\

\f1\b /data 
\f0\b0 - not shared on GitHub; contains raw data shared with authors by other researchers. Some files \
relevant files shared on OSF: {\field{\*\fldinst{HYPERLINK "https://osf.io/ch9eg/"}}{\fldrslt 
\f2 \cf2 \expnd0\expndtw0\kerning0
\ul \ulc2 https://osf.io/ch9eg/}}
\f2 \cf2 \expnd0\expndtw0\kerning0
\ul \ulc2 .\
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\f0 \cf0 \kerning1\expnd0\expndtw0 \ulnone \

\f1\b /figs 
\f0\b0 - contains figures and tables for manuscript. All contents of this directory can be deleted and regenerated from scripts.\
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\f1\b /notes 
\f0\b0 - contains notes for researchers\
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\f1\b /output 
\f0\b0 - contains interim data sets and other script output. All contents of this directory can be deleted and regenerated from scripts. \
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\f1\b /scr 
\f0\b0 - Contains functions and other helper scripts.
\f2 \cf2 \expnd0\expndtw0\kerning0
\ul \
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