genwhisker: Box and whisker plot - overview of dataset

In genasis: Global ENvironmental ASsessment Information System (GENASIS) computational tools

Description

Function genwisker allows to draw several box & whisker plots of the dataset. Boxes and whiskers could be drawn for all the data on each pollutant or differentiated by colours over individual years.

Usage

genwhisker(x, y=NA, input="openair", method="mqm", pollutant=NA,
        distr="norm", by.years=FALSE, col="#A52375",
        legend=TRUE, xlab="", ylab="Concentration", main=NA)

Arguments

x	vector of concentration values or data frame of "genasis"/"openair" type. See 'Details' for more detailed description of both data types.
y	vector of measurement dates in the case of vector input only.
input	type of data.frame in the case of data.frame input. The allowed values are "openair" (default) and "genasis". In case of vector input, this argument is meaningless.
method	arrangement of boxes and whiskers. Default "mqm" means median-quartiles-min/max, alternative "mqq" (median-quartiles-5/95quantiles) and "tqm" (trimean-quartiles-min/max) are available.
pollutant	name of the pollutant(s), which will be included into the box & whisker plot. Not necessary if only data for one pollutant is available in x. If not specified, all pollutants are included into the box & whisker plot.
distr	if distr="norm" (default), the linear y-axis is used, if distr="lnorm", the logarithmic scale is used.
by.years	logical. If by.years=FALSE, all data for each pollutant are used together, if by.years=TRUE, individual years are distinguished by colors specified in argument col.
col	vector of colors of the boxes & whiskers. If a length of the vector in the color-by-years version is different from the number of years in the measurement period, implicit colors are used.
legend	logical. Should a legend be drawn in a multi-color mode?
xlab	a label for the x axis.
ylab	a label for the y axis.
main	a main title for the plot.

Details

The genwhisker function draws a box & whisker plot of selected compounds from the dataset. The function recognises three different input formats: Option input="openair" uses "openair" format of data frame with first column of name 'date' and class "Date", optional columns of names "date_end", "temp", "wind" and "note" and other columns of class "numeric" containing concentration values and named by names of the compounds. input="genasis" is used for the data frame with six columns "valu", "comp", "date_start", "date_end", "temp" and "wind" where the first, fifth and sixth are of class "numeric", second of class "character" and third and fourth columns could be both "character" or "Date" class. The names of columns in input="genasis" are not rigid, only their order is assumed. There is also a possibility to specify x and y as two vectors of equal lenght, first of class "numeric" containing concentration values, second of class "character" or "Date" containing measurement dates.

Central tendency of the dataset for selected pollutants from x is drawn as a bold horizontal line, 25th and 75th quantiles (e.g. 1st and 3rd quartiles) as a lighter box and extremes by a light horizontal lines (whiskers) at the ends of vertical line connecting all the values. There are three possibilities of boxes & whiskers arrangement. Option method="mqm" (default) means that central tendency lies in median, box margins in 1st and 3rd quartiles and whiskers in min/max. Alternative method="mqq" means that central tendency lies in median, box margins in 1st and 3rd quartiles and whiskers in 5th and 95th quantiles, finally method="tqm" means that central tendency lies in trimean, box margins in 1st and 3rd quartiles and whiskers in min/max.

There are two posibilities of drawing. The default option by.years=FALSE plots all the values for each pollutant in one box & whisker arrangement, while by.years=TRUE plots a number of color-distinguished overlapping boxes & whiskers. The colors could be defined by the argument col as a vector of the same length as the period of measurement. If the length of the vector and the period differ, default colors are used for plotting.

If by.years=TRUE and legend=TRUE, the legend is drawn upon the plot as a colored years according to the color(s) of box(es) & whisker(s).

Author(s)

Jiri Kalina
[e-mail]

See Also

genloq, genoutlier, genhistogram, genpastoact, genanaggr, genplot, genstatistic, gentransform

Examples

## Definition of simple data sources:
c1<-c(0.386,0.269,0.182,0.254,0.455,0.263,0.405,0.211)
c2<-"benzo(ghi)perylene"
c3<-c("2012-02-01","2012-05-03","2012-08-05","2012-11-07",
      "2013-02-15","2013-05-10","2013-08-02","2013-11-06")
c4<-c("2012-02-08","2012-05-10","2012-08-12","2012-11-14",
      "2013-02-22","2013-05-17","2013-08-09","2013-11-13")

sample_genasis<-data.frame(c1,c2,c3,c4)
sample_openair<-data.frame(c4,c1)
colnames(sample_openair)=c("date",c2)

## Examples of different usages:
genwhisker(sample_openair,distr="lnorm",col="black")
genwhisker(sample_genasis,input="genasis",distr="norm",by.years=TRUE,
           col=c("blue","red"),legend=TRUE,main="benzo(ghi)perylene")
genwhisker(c1,c3,main="benzo(ghi)perylene")

## Use of example data from the package:
data(kosetice.pas.openair)
genwhisker(kosetice.pas.openair[,1:8],
           col=c("gold","orange","red","black"),by.years=TRUE)
data(kosetice.pas.genasis)
genwhisker(kosetice.pas.genasis[1:208,],input="genasis",distr="lnorm",
           col="orange")

Example output

Loading required package: Kendall
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: npsurv
Loading required package: lsei

genasis documentation built on May 1, 2019, 10:16 p.m.