R6 class for holding TOXSWA water concentration data and associated statistics
Source:R/TOXSWA_cwa.R
TOXSWA_cwa.Rd
An R6 class for holding TOXSWA water concentration (cwa) data
and some associated statistics. like maximum moving window average
concentrations, and dataframes holding the events exceeding specified
thresholds. Usually, an instance of this class will be generated
by read.TOXSWA_cwa
.
Public fields
filename
Length one character vector holding the filename.
basedir
Length one character vector holding the directory where the file came from.
zipfile
If not null, giving the path to the zip file from which the file was read.
segment
Length one integer, specifying for which segment the cwa data were read.
substance
The TOXSWA name of the substance.
cwas
Dataframe holding the concentrations.
events
List of dataframes holding the event statistics for each threshold.
windows
Matrix of maximum time weighted average concentrations (TWAC_max) and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.
Methods
Method new()
Create a TOXSWA_cwa object from a file
Usage
TOXSWA_cwa$new(
filename,
basedir,
zipfile = NULL,
segment = "last",
substance = "parent",
total = FALSE
)
Arguments
filename
The filename
basedir
The directory to look in
zipfile
Optional path to a zipfile holding the file
segment
Either "last" or the number of the segment for which to read the data
substance
The TOXSWA substance name (for TOXSWA 4 or higher)
total
Should total concentrations be read in? If FALSE, free concentrations are read
Method get_events()
Populate a datataframe with event information for the specified
threshold value. The resulting dataframe is stored in the events
field of the object.
Examples
H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa",
basedir = "SwashProjects/project_H_sw/TOXSWA",
zipfile = system.file("testdata/SwashProjects.zip",
package = "pfm"))
H_sw_R1_stream$get_events(c(2, 10))
H_sw_R1_stream$moving_windows(c(7, 21))
print(H_sw_R1_stream)
#> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20
#> datetime t t_firstjan t_rel_to_max cwa_mug_per_L
#> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
#> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
#> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
#> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
#> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
#> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
#> cwa_tot_mug_per_L
#> 20 0
#> 40 0
#> 60 0
#> 80 0
#> 100 0
#> 120 0
#> Moving window analysis
#> window max_TWAC max_AUC_h max_AUC_d
#> 1 7 days 2.3926551 401.9660 16.74859
#> 2 21 days 0.8369248 421.8101 17.57542
#> Event statistics for threshold 2
#> t_start cwa_max duration pre_interval AUC_h AUC_d
#> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501
#> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162
#> Event statistics for threshold 10
#> t_start cwa_max duration pre_interval AUC_h AUC_d
#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971