## ----include = FALSE---------------------------------------------------------- Sys.setenv(R_USER_LIBS = tempdir()) #Just in case for CRAN library(biodosetools) knitr::opts_chunk$set( fig.dpi = 96, collapse = TRUE, comment = "#>" ) ## ----sc-dic-fit-01, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Data input options' and 'Fitting options' boxes in the dose-effect fitting module"---- knitr::include_graphics("figures/screenshot-dicentrics-fit-01.png") ## ----sc-dic-fit-03, echo=FALSE, out.width='75%', fig.align='center', fig.cap="'Data input' box in the dose-effect fitting module"---- knitr::include_graphics("figures/screenshot-dicentrics-fit-03.png") ## ----dic-count-data, tidy=TRUE, tidy.opts=list(width.cutoff=60)--------------- count_data <- system.file("extdata", "count-data-barquinero-1995.csv", package = "biodosetools") %>% utils::read.csv() %>% calculate_aberr_table(type = "count") ## ----------------------------------------------------------------------------- count_data ## ----sc-dic-fit-02, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Irradiation conditions' box in the dose-effect fitting module"---- knitr::include_graphics("figures/screenshot-dicentrics-fit-02.png") ## ----sc-dic-fit-04, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Results' tabbed box, 'Curve plot' and 'Export results' boxes in the dose-effect fitting module"---- knitr::include_graphics("figures/screenshot-dicentrics-fit-04.png") ## ----dic-fit-results---------------------------------------------------------- fit_results <- fit( count_data = count_data, model_formula = "lin-quad", model_family = "automatic", fit_link = "identity", aberr_module = "dicentrics" ) ## ----------------------------------------------------------------------------- names(fit_results) ## ----dic-fit-coeffs-r--------------------------------------------------------- fit_results$fit_coeffs ## ----dic-fit-dose-curve, fig.width=6, fig.height=3.5, fig.align='center', fig.cap="Plot of dose-effect curve generated by \\{biodosetools\\}. The grey shading indicates the uncertainties associated with the calibration curve."---- plot_fit_dose_curve( fit_results, aberr_name = "Dicentrics", place = "UI" )