Man pages for sbpiper
Data Analysis Functions for 'SBpipe' Package

basic_themeA generic basic theme for time courses. It extends ggplot2...
check_exp_datasetCheck that the experimental data set exists.
combine_param_best_fits_statsCombine the parameter best fits statistics.
combine_param_ple_statsCombine the parameter PLE statistics.
compute_aicCompute the Akaike Information Criterion. Assuming additive...
compute_aiccCompute the corrected Akaike Information Criterion. Assuming...
compute_bicCompute the Bayesian Information Criterion. Assuming additive...
compute_cl_objvalCompute the confidence level based on the minimum objective...
compute_fratio_thresholdCompute the fratio threshold for the confidence level.
compute_sampled_ple_statsCompute the table for the sampled PLE statistics.
gen_stats_tableGenerate a table of statistics for each model readout.
get_param_namesGet parameter names
get_sorted_level_indexesReturn the indexes of the files as sorted by levels.
histogramplotPlot a generic histogram
insulin_receptor_1A stochastic model simulation
insulin_receptor_2A stochastic model simulation
insulin_receptor_3A stochastic model simulation
insulin_receptor_all_fitsA parameter estimation data set including all the evaluated...
insulin_receptor_best_fitsA parameter estimation data set including only the best...
insulin_receptor_exp_datasetExperimental data set for the insulin receptor beta...
insulin_receptor_IR_beta_pY1146A stochastic simulation data set for the insulin receptor...
insulin_receptor_ps1_l0A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l1A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l11A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l13A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l14A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l16A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l3A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l4A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l6A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l8A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps1_l9A deterministic simulation of the insulin receptor model upon...
insulin_receptor_ps2_tp2A deterministic simulation of the insulin receptor model upon...
kurtosisCalculate the kurtosis of a numeric vector
leftCIReturn the left value of the parameter confidence interval....
load_exp_datasetLoad the experimental data set.
normalise_vecNormalise a vector within 0 and 1
objval.colThe name of the Objective Value column
objval_vs_iters_analysisAnalysis of the Objective values vs Iterations.
parameter_density_analysisParameter density analysis.
parameter_pca_analysisPCA for the parameters. These plots rely on factoextra fviz...
pca_themeA generic basic theme for pca. It extends ggplot2...
pe_ds_preprocParameter estimation pre-processing. It renames the data set...
plot_combined_tcPlot repeated time courses in the same plot with mean, 1...
plot_comb_simsPlot the simulation time courses using a heatmap...
plot_double_param_scan_dataPlot model double parameter scan time courses.
plot_fitsPlot the number of iterations vs objective values in log10...
plot_heatmap_tcPlot time courses organised as data frame columns with a...
plot_objval_vs_itersPlot the Objective values vs Iterations
plot_parameter_densityPlot parameter density.
plot_raw_datasetAdd experimental data points to a plot. The length of the...
plot_repeated_tcPlot repeated time courses in the same plot separately. First...
plot_sampled_2d_plePlot 2D profile likelihood estimations.
plot_sampled_plePlot the sampled profile likelihood estimations (PLE). The...
plot_sep_simsPlot the simulations time course separately.
plot_single_param_scan_dataPlot model single parameter scan time courses
plot_single_param_scan_data_homogenPlot model single parameter scan time courses using...
replace_colnamesRename data frame columns. 'ObjectiveValue' is renamed as...
rightCIReturn the right value of the parameter confidence interval....
sampled_2d_ple_analysis2D profile likelihood estimation analysis.
sampled_ple_analysisRun the profile likelihood estimation analysis.
sbpiper-packagesbpiper: Data Analysis Functions for 'SBpipe' Package
sbpiper_peMain R function for SBpipe pipeline: parameter_estimation().
sbpiper_ps1Main R function for SBpipe pipeline: parameter_scan1().
sbpiper_ps2Main R function for SBpipe pipeline: parameter_scan2().
sbpiper_simMain R function for SBpipe pipeline: simulate().
scatterplotPlot a generic scatter plot
scatterplot_log10Plot a generic scatter plot in log10 scale
scatterplot_plePlot a profile likelihood estimation (PLE) scatter plot
scatterplot_w_colourPlot a scatter plot using a coloured palette
skewnessCalculate the skewness of a numeric vector
summarise_dataSummarise the model simulation repeats in a single file.
tc_themeA theme for time courses. It extends ggplot2 theme_classic().
sbpiper documentation built on June 26, 2018, 5:03 p.m.