| add_y_scale | Specifies the 'y' scale of a 'ggplot' object. |
| apply_named_args | a version of apply. if MARGIN = 1, the values in each column... |
| arrange_grid | arrange a list of ggplot objects into a grid in a single... |
| calc_LL_log10normal_threshold | Calculate the log likehood of data given true model outputs... |
| calc_moment_from_pmf | calculate the nth moment from a probability mass function |
| calc_r_camostat_stages | calculates r for the TEIV model with Erlang-distributed... |
| calc_r_camostat_stages_different_eclipse | calculates r for the TEIV model with Erlang-distributed... |
| calc_sol_add_stages | for a set of parameters without stages, add stages and... |
| calc_sol_chain | calculate solution to ODEs for each pathway, and extract... |
| calc_sol_chain_camostat_amphoB | calculate solution to ODEs for each pathway, and extract... |
| compile_model | compile an odin model |
| cont_MCMC | continue running MCMC |
| CREATE_POSTERIOR_FUNC_fn_camostat | creates a closure to calculate the likelihood and model... |
| CREATE_POSTERIOR_FUNC_fn_camostat_amphoB | creates a closure to calculate the likelihood and model... |
| darken | darken a vector of hex codes for colours |
| dl10norm | Analogue for dlnorm but in base 10 |
| extract_max_LL_iters | given an RData file, load the associated MCMC chains and find... |
| find_func_file | find the file containing a function |
| find_sign_change_ind | find the indices at which a vector changes sign |
| gen_default_mcmcPars | generate default MCMC parameters |
| generate_random_start | Generate random starting values from a parameter table |
| gen_mcmcPars | generate default MCMC parameter values |
| gen_mcmcPars_long | generate default MCMC parameter values |
| gen_mcmcPars_short | generate default MCMC parameter values for a short chain |
| gen_mcmcPars_timing | generate default MCMC parameter values for a very short chain... |
| gen_nice_breaks | format a numeric vector of breaks nicely for printing |
| gen_prediction_ci | produce confidence intervals for model predictions |
| gen_summary_statistics_fn_camostat | create closure to calculate summary statistics and provide... |
| gen_time_list | Generate vector of times at which to solve ODE for fitting |
| get_and_save_max_LL_params | given an RData file, load the associated MCMC chains, find... |
| get_func_names | return names of all functions in a .R file |
| get_max_LL_params | given an RData file, load the associated MCMC chains and find... |
| get_MCMC_chain | extract chain from MCMC output |
| get_package_dir | get name of directory which package is in |
| get_strain_names | determine strain names from parameter names |
| get_vars_from_list_with_check | extract variables from list, throwing an error if they are... |
| gg_color_hue | Emulates the ggplot colour palette. |
| ggsave_wch | version of ggsave which suppresses warnings that rows are... |
| ggsave_wrapper | wrapper function to feed arguments to ggsave |
| gm_mean | calculate geometric mean of a vector |
| interpolate_vector | interpolate ordered numeric vector into n_div intervals... |
| is_integer_like | check if x is within 'tol' of 'x' |
| lapply_w_name | a version of lapply() that supplies FUN with both the name... |
| lighten | lighten a vector of hex codes for colours |
| list2here | dump variables from a list to the parent frame |
| list_vars_from_environment | gather variables with given names from an environment into a... |
| load_into_list | load contents of RData file into a list |
| load_packages | loads a character vector of packages |
| make_factor | make factor out of a numeric vector |
| make_filename | construct plot filename |
| make_filename_from_number | make string from number in format acceptable for filename |
| make_p_value_str | format a p-value for plotting |
| make_seed | make a default list of random number generator seeds for MCMC |
| make_solving_time | make a vector of solving times from a vector of times |
| Map_vapply | a version of Map() where we specify the format of the output |
| mkdir_from_filename | makes a directory from a filename |
| normalise | normalises a vector so that it sums to 1 |
| no_warn | a version of a function that suppresses warnings |
| pairwise_stats_tests | test whether the ratio of a summary statistic between two... |
| pl10norm | Analogue for plnorm but in base 10 |
| plot_bivariate_scatter | make scatter plot of samples from joint posterior... |
| plot_bivariate_scatter_all | plot bivariate scatter plots of all fitted variables |
| plot_diagnostics | plot the potential scale reduction factor vs the number of... |
| plot_dynamics_camostat | plot viral dynamics |
| plot_dynamics_inner | plot virus dynamics |
| plot_histogram_general | plot a nicer-looking histogram |
| plot_LL | plot trace of log likelihood for each chain |
| plot_marginal_by_chain | plot marginal histogram, either coloured or faceted by chain |
| plot_marginal_histogram | plot the marginal histogram of a single fitted variable |
| plot_marginal_histogram_all | plotting the marginal histogram of all fitted variables |
| plot_trace | make a trace plot of a single fitted variable |
| plot_trace_all | plot the trace of all fitted variables |
| postprocess_chain | more postprocessing of MCMC output |
| postprocess_for_plotting | postprocessing of MCMC output |
| print_prctiles | calculate percentiles for fitted parameters |
| read_Calu3_data | read Calu 3 data with different drugs |
| read_camostat_data | read data with and without camostat |
| read_csv_or_rds | checks if file exists in rds or csv format, and reads rds... |
| read_PCR | read qPCR data |
| read_plaque | read plaque assay data |
| read_plaque_peacock | read plaque assay data from Peacock et al. (2021) Nat... |
| read_prism_file | construct a data frame from a prism file |
| read_summary_stats | reads summary stats from a tex file generated by running MCMC |
| rl10norm | Analogue for rlnorm but in base 10 |
| run_all | wrapper for running and postprocessing MCMC chain |
| run_exp_camostat | estimate parameters for the different models in the study |
| run_exp_camostat_amphoB | estimate parameters for the different models in the study |
| run_exp_camostat_fit_subset_pars | estimate prob_infect_tmprss2 and prob_infect_camostat, fix... |
| run_exp_camostat_shared_pars | mutlstrain fit with some shared parameters |
| sample_from_prior | samples from joint prior distribution |
| save_all | saves all variables in parent environment |
| set_default_seeds | set default random number generator seed for each |
| setup_and_run_MCMC | setup and run MCMC |
| solve_from_posterior_preincub | solve preincubation viral dynamics for one iteration of chain |
| solve_ODE_error_handling | solve an ODE with error handling |
| source_files | sources a character vector of files |
| specify_camostat_parameters_fn | make parameter table |
| specify_camostat_parameters_fn_fit_subset_pars | make parameter table where only some parameters are fitted... |
| sum_stages | sum time series of odin solution across compartments defined... |
| thin_chain | select evenly spaced iterations from MCMC chain |
| thin_csv_or_rds | thins a csv or rds file, saves it with new name, optionally... |
| transform_pars_wrapper_camostat | create a closure which transforms an unnamed numeric vector... |
| transform_pars_wrapper_tmprss2_only | create a closure which transforms an unnamed numeric vector... |
| try_fread | data.table::fread with tryCatch |
| try_read | reads rds or csv with tryCatch |
| vcapply | short for 'vapply(X, FUN, character(1), ...)' |
| viapply | short for 'vapply(X, FUN, integer(1), ...)' |
| vlapply | short for 'vapply(X, FUN, logical(1), ...)' |
| vnapply | short for 'vapply(X, FUN, numeric(1), ...)' |
