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dataAndInfo.R
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dataAndInfo.R
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# Copyright: (C) 2017-2018 Sachs Undergraduate Research Apprentice Program
# This program and its accompanying materials are distributed
# under the terms of the GNU General Public License v3.
# Filename: dataAndInfo.R
# Purpose: Concerns radiogenic mouse Harderian gland tumorigenesis. Loads
# ion and tumor prevalence data from CSV files. It is part of the
# source code for the NASAmouseHG project.
# Contact: Rainer K. Sachs
# Website: https://github.com/sachsURAP/NASAmouseHG
# Mod history: 18 Jun 2018
# Attribution: This R script and the scripts that depend on it (notably
# synergyTheory.R, monteCarlo.R and plots.R) were developed at
# UC Berkeley 2017-18. An early version was written by
# Dae Woong Ham Summer 2017. Additions, corrections, changes,
# quality control, and major reorganization by Edward G. Huang,
# Yimin Lin, Mark Ebert, Yunzhi Zhang and Ray Sachs,
# UCB Fall 2017 - Summer 2018.
# Relevant references and abbreviations:
# ".93Alp" = Alpen et al. "Tumorigenic potential of high-Z, high-LET charged-
# particle radiations." Rad Res 136:382-391 (1993).
# ".94Alp" = Alpen et al. "Fluence-based relative biological effectiveness for
# charged particle carcinogenesis in mouse Harderian
# gland." Adv Space Res 14(10): 573-581. (1994).
# "16Chang" = Chang et al. "Harderian Gland Tumorigenesis: Low-Dose and LET
# Response." Radiat Res 185(5): 449-460. (2016).
# "16Srn" = Siranart et al. "Mixed Beam Murine Harderian Gland Tumorigenesis:
# Predicted Dose-Effect Relationships if neither
# Synergism nor Antagonism Occurs."
# Radiat Res 186(6): 577-591 (2016).
# "17Cuc" = Cucinotta & Cacao. "Non-Targeted Effects Models Predict
# Significantly Higher Mars Mission Cancer Risk
# than Targeted Effects Models."
# Sci Rep 7(1): 1832. (2017). PMC5431989
# "HZE" = High atomic number and energy
# "LET" = Linear energy transfer
# "NTE" = Non-targeted effects
# "TE" = Targeted effects
# "DER" = Dose-effect relation(ship)"
# "SEA" = Simple Effect Additivity
# "IEA" = Incremental Effect Additivity
# "cGy" = Centigray
# Data used in 16Chang; includes data analyzed in .93Alp and .94Alp. Does not
# include gamma-ray data. Includes LET = 100 keV / micron for Ti, an ad-hoc
# compromise between lower value at beam entry and higher value at mouse cage.
# These two lines of script plus the .csv file (which will need work as
# additions and perhaps corrections come up) should be all we need.
ion_data <- data.frame(read.csv("data/raw_data_ordered.csv"))
# Older versions show how to compute ion speed and the Katz track structure
# parameter.