snakemake.pe_analysis

Module Contents

snakemake.pe_analysis.pe_combine_param_best_fits_stats(plots_dir, fileout_param_estim_best_fits_details)

Combine the statistics for the parameter estimation details

Parameters:
  • plots_dir – the directory to save the generated plots
  • fileout_param_estim_best_fits_details – the name of the file containing the detailed statistics for the estimated parameters
snakemake.pe_analysis.pe_combine_param_ple_stats(plots_dir, fileout_param_estim_details)

Combine the statistics for the parameter estimation details

Parameters:
  • plots_dir – the directory to save the generated plots
  • fileout_param_estim_details – the name of the file containing the detailed statistics for the estimated parameters
snakemake.pe_analysis.pe_ds_preproc(filename, param_names, logspace=True, all_fits=False, data_point_num=0, fileout_param_estim_summary="param_estim_summary.csv")

Parameter estimation pre-processing. It renames the data set columns, and applies a log10 transformation if logspace is TRUE. If all.fits is true, it also computes the confidence levels.

Parameters:
  • filename – the dataset filename containing the fits sequence
  • param_names – the list of estimated parameter names
  • logspace – true if the data set shoud be log10-transformed.
  • all_fits – true if filename contains all fits, false otherwise
  • data_point_num – the number of data points used for parameterise the model. Ignored if all.fits is false
  • fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Ignored if all.fits is false
snakemake.pe_analysis.pe_objval_vs_iters_analysis(model_name, filename, plots_dir)

Analysis of the Objective values vs Iterations.

Parameters:
  • model_name – the model name without extension
  • filename – the filename containing the fits sequence
  • plots_dir – the directory for storing the plots
snakemake.pe_analysis.pe_parameter_density_analysis(model_name, filename, parameter, plots_dir, thres="BestFits", best_fits_percent=100, fileout_param_estim_summary="", logspace=True, scientific_notation=True)

Parameter density analysis.

Parameters:
  • model_name – the model name without extension
  • filename – the filename containing the fits sequence
  • parameter – the name of the parameter to plot the density
  • plots_dir – the directory for storing the plots
  • thres – the threshold used to filter the dataset. Values: “BestFits”, “CL66”, “CL95”, “CL99”, “All”.
  • best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
  • fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Only used if thres!=”BestFits”.
  • logspace – true if the parameters should be plotted in logspace
  • scientific_notation – true if the axis labels should be plotted in scientific notation
snakemake.pe_analysis.pe_parameter_pca_analysis(model_name, filename, plots_dir, best_fits_percent=100)

PCA for the best fits of the estimated parameters.

Parameters:
  • model_name – the model name without extension
  • filename – the filename containing the fits sequence
  • plots_dir – the directory for storing the plots
  • best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
snakemake.pe_analysis.pe_sampled_2d_ple_analysis(model_name, filename, parameter1, parameter2, plots_dir, thres="BestFits", best_fits_percent=100, fileout_param_estim_summary="", logspace=True, scientific_notation=True)

2D profile likelihood estimation analysis.

Parameters:
  • model_name – the model name without extension
  • filename – the filename containing the fits sequence
  • parameter1 – the name of the first parameter
  • parameter2 – the name of the second parameter
  • plots_dir – the directory for storing the plots
  • thres – the threshold used to filter the dataset. Values: “BestFits”, “CL66”, “CL95”, “CL99”, “All”.
  • best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
  • fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Only used if thres!=”BestFits”.
  • logspace – true if the parameters should be plotted in logspace
  • scientific_notation – true if the axis labels should be plotted in scientific notation
snakemake.pe_analysis.pe_sampled_ple_analysis(model_name, filename, parameter, plots_dir, fileout_param_estim_summary, logspace=True, scientific_notation=True)

Run the profile likelihood estimation analysis.

Parameters:
  • model_name – the model name without extension
  • filename – the filename containing the fits sequence
  • parameter – the parameter to compute the PLE analysis
  • plots_dir – the directory to save the generated plots
  • fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation
  • logspace – true if parameters should be plotted in logspace
  • scientific_notation – true if the axis labels should be plotted in scientific notation