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diff --git a/docs/reference/TOXSWA_cwa.md b/docs/reference/TOXSWA_cwa.md new file mode 100644 index 0000000..3a362d8 --- /dev/null +++ b/docs/reference/TOXSWA_cwa.md @@ -0,0 +1,217 @@ +# R6 class for holding TOXSWA water concentration data and associated statistics + +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](https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.md). + +## Format + +An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator +object. + +## 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 + +### Public methods + +- [`TOXSWA_cwa$new()`](#method-TOXSWA_cwa-initialize) + +- [`TOXSWA_cwa$moving_windows()`](#method-TOXSWA_cwa-moving_windows) + +- [`TOXSWA_cwa$get_events()`](#method-TOXSWA_cwa-get_events) + +- [`TOXSWA_cwa$print()`](#method-TOXSWA_cwa-print) + +- [`TOXSWA_cwa$clone()`](#method-TOXSWA_cwa-clone) + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$new()` + +Create a TOXSWA_cwa object from a file + +#### Usage + + TOXSWA_cwa$new( + filename, + basedir, + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE + ) + +#### Arguments + +- `filename`: + + The filename + +- `basedir`: + + The directory to look in + +- `zipfile`: + + Optional path to a zipfile holding the file + +- `segment`: + + Either "last" or the number of the segment for which to read the data + +- `substance`: + + The TOXSWA substance name (for TOXSWA 4 or higher) + +- `total`: + + Should total concentrations be read in? If FALSE, free concentrations + are read + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$moving_windows()` + +Add to the `windows` field described above. + +#### Usage + + TOXSWA_cwa$moving_windows(windows, total = FALSE) + +#### Arguments + +- `windows`: + + Window sizes in days + +- `total`: + + If TRUE, the total concentration including the amount adsorbed to + suspended matter will be used. + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$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. + +#### Usage + + TOXSWA_cwa$get_events(thresholds, total = FALSE) + +#### Arguments + +- `thresholds`: + + Threshold values in µg/L. + +- `total`: + + If TRUE, the total concentration including the amount adsorbed to + suspended matter will be used. + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$print()` + +Print a `TOXSWA_cwa` object + +#### Usage + + TOXSWA_cwa$print() + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$clone()` + +The objects of this class are cloneable with this method. + +#### Usage + + TOXSWA_cwa$clone(deep = FALSE) + +#### Arguments + +- `deep`: + + Whether to make a deep clone. + +## Examples + +``` r +H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +H_sw_R1_stream$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 +``` |