read_data: Reads and formats cell abundance database

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

Description

Loads the data & applies some basic corrections. If reload.from.xlsx is TRUE, will read data from an appropriately-formatted xlsx file, which is time-consuming. Otherwise, will reload data from an R file, which may be the original, package-supplied database, or a user-modifed database (much faster). We recommend that users who wish to extend the database save the database as .RData files, rather than repeatedly reloading it from Excel files.

Usage

  read_data(reload.from.xlsx = FALSE, seds_fn,
    seds_sheet_name, sw_fn, sw_sheet_name,
    save_seds_ref_table = TRUE, seds_paper_table_fn = NA,
    all_data_fn = "data/all_data.RData",
    corrected_seds_fn = "data/corrected_seds.RData",
    corrected_sw_fn = "data/corrected_sw.RData")

Arguments

reload.from.xlsx	If TRUE, reload & reprocess the data from the .csv files. Otherwise, rely on .Rdata file
seds_fn	Filename for sediments data, as .xlsx. SHOULD INCLUDE .xlsx extension
seds_sheet_name	Name of worksheet for data in sediments file
sw_fn	Filename for seawater data, as .xlsx SHOULD INCLUDE .xlsx extension
sw_sheet_name	Name of worksheet for data in seawater file
save_data	Whether to save the compiled data for future use (as *both* .RData and .csv files)
all_data_fn	Filename for saved data - SHOULD HAVE NO EXTENSION as two files will be saved (one .Rdata file, one .csv file)

Details

In order to reproduce the analysis from our original database, simply use ‘invisible(read_data())' - you don’t have to assign the results to a variable, because 'read_data()' creates global variables for the

Examples

data_list <- read_data()
corrected_seds <- data_list$corrected_seds

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