reproduce_research: Reproduces analysis from Lloyd et al (submitted)

In adsteen/Lloyd.et.al.Cell.abundance.metaanalysis: Package to reproduce analysis from Lloyd et al (2013), Applied and Environmental Microbiology

Description

Reproduces entire analysis from Lloyd et al, 2013, Applied and Environmental Microbiology.

Usage

  reproduce_research(print_plots = TRUE,
    save_plots = FALSE, reload_data = FALSE,
    fast_calc = TRUE, n_reps = 1000)

Arguments

print_plots	If true, print the plots to screen
save_plots	If true, save plots. There is currently no option to change the filenames of the saved plots.
reload_data	If true, reload the data from .xlsx files. Otherwise read data from .Rdata files. This is passed along to 'read_data'.
fast_calc	If true, skip the bootstrapped parts of the analysis, which take the lion's share of computational time.
n_reps	Number of reps for bootstrapped analyses.

Value

Returns the three central data frames used in the analysis: 'all_data', 'corrected_seds', and 'corrected_sw', as named elements in a list. Note that 'corrected_seds' and 'corrected_sw' are, collectively, redundant with 'all_data'

adsteen/Lloyd.et.al.Cell.abundance.metaanalysis documentation built on May 10, 2019, 7:26 a.m.