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

plot_mocis

R Documentation

plot_mocis

Description

Plots the data and the association between time and the contaminant

Usage

plot_mocis(mocis, var, loc, genus, nyears = 1, col.line = NULL,
  lty.line = c(1, 2), lwd.line = 2, col.sm = NULL, lty.sm = c(1,
  2), lwd.sm = 2, pval.line = c(0.05, 0.1), pval.line10 = c(0.05,
  0.1), pval.sm = c(0.05, 0.1), pch.point = 16, cex.point = 0.8,
  col.point = "black", col.lim = NULL, pch.data = 15,
  cex.data = 0.2, col.data = "black", nobs = 5, main = NULL,
  plot.changep = FALSE, xpos = 0.05, ypos = 0.95, cex.text = 0.8,
  cex.mtext = 0.8, mtext.at = NULL, bgcol = "white", ylim = NULL,
  fatadjust = FALSE, what = c("best", "line", "smooth", "last10",
  "all"), stats = stations(), specs = species(), trafo = NULL,
  outlier = "beta", col.rect = "grey90", force = FALSE,
  plotlabels = plotlabs(), statstext = TRUE, newlimit = NA, ...)

Arguments

`mocis`	Output from `mocis`.
`var`	A character. The contaminant of interest.
`loc`	A character. The locale of interest.
`genus`	A character. The species of interest.
`nyears`	An integer. The lowest number of years to plot. Defaults to 1.
`col.line`	A vector of two colors. Which color is used depends on the p-value for the linear model.
`lty.line`	A vector of length 2. The line types for the line. Which line type is used depends on the p-value for the linear model. Defaults to 'c(1, 2)'.
`lwd.line`	An integer. The line width for the regression line. Defaults to 2.
`col.sm`	A vector of two colors. Which color is used depends on the p-value for the smooth.
`lty.sm`	A vector of length 2. The line types for the smooth. Which line type is used depends on the p-value for the smooth. Defaults to `c(1, 2)`.
`lwd.sm`	An integer. The line width for the smooth. Defaults to 2.
`pval.line`	A vector of length 2. P-value cut-offs for when the line should be plotted. Defaults to 'c(0.05, 0.1)'. If the p-value from the linear model fit is lower than the first, the first color is used and if the p-value is between the first and second p-values the second color is used.
`pval.line10`	A vector of length 2. P-value cut-offs for when the line for the last 10 years should be plotted. Defaults to 'c(0.05, 0.1)'. If the p-value from the linear model fit is lower than the first, the first color is used and if the p-value is between the first and second p-values the second color is used.
`pval.sm`	A vector of length 2. P-value cut-offs for when the smooth should be plotted. Defaults to 'c(0.05, 0.1)'. If the p-value from the smooth is lower than the first, the first color is used and if the p-value is between the first and second p-values the second color is used.
`pch.point`	An integer. The point style for the yearly geometric mean values. Defaults to 16.
`cex.point`	Expansion factor for the points representing the mean values. Defaults to 0.8.
`col.point`	The color of the points.
`col.lim`	A vector of length 2. The colors of the polygon describing the limits. If `var` is not TCDDEQV the first color is used throughout.
`pch.data`	An integer. The point style for the raw data. Defaults to a dot (.)
`cex.data`	Expansion factor for the raw data points. Defaults to 0.8.
`col.data`	The color of the raw data points.
`nobs`	An integer. The number of observations that should be present in a year for confidence intervals to be plotted. Defaults to 5.
`main`	Not used.
`plot.changep`	A logical. Should the change point be plotted (if applicable)?
`xpos`	A value between 0 and 1. The position of the legend along the x-axis in Normalized Parent Coordinates. Defaults to 0.05.
`ypos`	A value between 0 and 1. The position of the legend along the y-axis in Normalized Parent Coordinates. Defaults to 0.95.
`cex.text`	Character expansion for the stats text. Defaults to 0.8.
`cex.mtext`	Character expansion for the margin text. Defaults to 0.8.
`mtext.at`	Position of the margin text. Defaults to par("usr")[1].
`bgcol`	Not used.
`ylim`	A vector of length 2. The y-axis limit.
`fatadjust`	Not used.
`what`	Determine what should be plotted provided the p-value(s) are in the specified range. Can be one or more of: `"best"` only plot the best fit, `"line"` only plot the line, `"smooth"` only plot the smooth, `"last10"` only plot the line for the last 10 years, `"all"` plot everything. Defaults to "best" and "line10".
`stats`	A list with station names. Defaults to `stations()`.
`specs`	A list with species names. Defaults to `species()`.
`trafo`	A function. Transformation for the y-axis. Experimental.
`outlier`	Set to NULL to suppress marking of suspected outliers.
`col.rect`	Color of the bar indicating that all measurements are below the LOD.
`force`	A logical. Force plotting even if the p-value(s) are not in the specified range? Defaults to FALSE.
`plotlabels`	A list with labels. Defaults to `plotlabs()`
`statstext`	A logical. Controls whether to print the statistics text or not. Defaults to TRUE.
`newlimit`	Set a new limit for the plot.
`...`	Other arguments to `plot()`.