all_output: Create a composite dataframe for a batch of simulations,...
In robjohnnoble/demonanalysis: Analysis and plotting of demon data

Description Usage Arguments Details Value Examples

Create a composite dataframe for a batch of simulations, derived from multiple data files per simulation.

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all_output(input_dir, include_diversities = TRUE, df_type = "output",
  max_generation = FALSE, vaf_cut_off = NA, generation = NA,
  numcells = NA, n_cores = NA, ExitCode4 = FALSE)

`input_dir`	base input directory name
`include_diversities`	boolean whether to include diversity metrics
`df_type`	which dataframes to combine
`max_generation`	If TRUE then results are returned only for the final generation
`vaf_cut_off`	exclude genotypes with vaf lower cut off from combined_df
`generation`	Generation at which to filter (default NA corresponds to no filtering)
`numcells`	Number of cells at which to filter (default NA corresponds to no filtering)
`n_cores`	Number of cores to use (default NA is not parallelized)
`ExitCode4`	: if TRUE, this means that we want to include in the analysis the simulations whose error message is Exit Code 4. This will call the function combine_dfs with argument ExitCode4=TRUE.

If both generation and numcells are provided then numcells takes precedent.

a combined dataframe

all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE))
all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "driver_genotype_properties")
all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "genotype_properties", vaf_cut_off = 0.002)
all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "allele_counts", generation = 10)