# 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
```