mocis: mocis
In NRM-MOC/MoCiS: Monitoring of Contaminants in Sweden

mocis

R Documentation

mocis

Description

The main analysis function

Usage

mocis(file, vars = NULL, n0 = 4, outdir = NULL, add.vars = NULL,
  sheet = 1, nyears = 5, alpha = 0.05, crit = "gcv",
  fat_adj = fat_adjust(), generate_tables = TRUE, verbose = FALSE,
  agesel = age_select(), GRU = 1, roblm = FALSE, robsm = FALSE,
  lims = limits(), ord = statorder(), stationnames = stations(),
  specs = species(), yearvar = "YWD", subset_years = 10,
  b.pow = 0.1, power = 0.8, n.pow = 10)

Arguments

`file`	The Excel file which holds the data
`vars`	Variables that should be analyzed
`n0`	For use in `do_changep`, the minimum number of year on each side of the change point
`outdir`	Output directory. Defaults to the current working directory in left empty.
`add.vars`	Additional variables. The function tries to guess some sensible variables if left empty.
`sheet`	The sheet containing the data in the Excel file. Deafults to 1.
`nyears`	The minimum number of years that should be available for analysis. Defaults to 5.
`alpha`	The p-value threshold. Defaults to 0.05
`crit`	Criterion for automatic bandwidth selection. A character, "gcv" or "aic". Degaults to "gcv".
`fat_adj`	A list with rules for fat adjustment. Defaults to `fat_adjust()`.
`generate_tables`	Logical. Should tables be generated? Deafaults to TRUE.
`verbose`	Logical. If TRUE, prints the progress.
`agesel`	A list with rules for the age selection. Defaults to `age_select`.
`GRU`	For birds. Selection based on the GRU variable. Defaults to 1.
`roblm`	Logical. If TRUE, performs a robust linear model. Experimental.
`robsm`	Logical. If TRUE, performs a robust smooth. Experimental.
`lims`	Limits for the contaminants. Defaults to `limits()`.
`ord`	A list of `data.frames` giving the ordering in the tables. Defaults to `statorder()`.
`stationnames`	A list with station names. Defaults to `stations()`.
`yearvar`	The variable containing the years. Defaults to "YWD".
`subset_years`	Select a subset of years to run the analyses on. Defaults to 10.
`b.pow`	The slope, as a fraction e.g. 10 power calculations. Deafults to 0.1.
`power`	The desired power. Befaults to 0.8.
`n.pow`	The number of years for the power calculations. Defaults to 10.

Details

Main function to perform the analyses, i.e. linear model fit, smooth fit, outlier detection and creation of tables

Value

A list with elements:

data A data.frame containing the raw data.
aggdata A data.frame containing the aggregated data (yearly geometric mean values, yearly geometric standard deviations, number of measurements per year, if all values were below the LOD).
m Overall geometric mean value with 95
limit A list with elements tv the target value and fat the average fat percentage in the series.
linmod Output from do_reg.
linmod10 Output from do_reg applied to the last 10 years in the series if applicable.
smooth Output from do_smooth.
changepoint Output from do_changep.
fatadjust Either 1 or 0 dependeing on whether fat adjustment was done or not.
stattype A character vector of length 2 denoting which type of file was analyzed.