From aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Wed, 31 Jan 2024 13:16:17 +0100 Subject: Reorganise data generation - Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory --- docs/reference/TOXSWA_cwa.html | 412 ++++++++++++++++++++--------------------- 1 file changed, 200 insertions(+), 212 deletions(-) (limited to 'docs/reference/TOXSWA_cwa.html') diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 16dc5db..a64ad40 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,71 +1,16 @@ - - - - - - - -R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - - - - - - - - - - - - - + + -
-
- -
- -
+

R6 class for holding TOXSWA water concentration data and associated statistics

@@ -117,179 +48,236 @@ by read.TOXSWA_cwa." /> 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.

+by read.TOXSWA_cwa.

+
+

Format

+

An R6Class generator object.

+
+
+

Public fields

+

filename
+

Length one character vector holding the filename.

-

Format

-

An R6Class generator object.

-

Public fields

+
basedir
+

Length one character vector holding the directory where the file came from.

+ -

-
filename

Length one character vector holding the filename.

+
zipfile
+

If not null, giving the path to the zip file from which the file was read.

-
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.

-
segment

Length one integer, specifying for which segment the cwa data were read.

-
substance

The TOXSWA name of the substance.

+
substance
+

The TOXSWA name of the substance.

-
cwas

Dataframe holding the concentrations.

-
events

List of dataframes holding the event statistics for each threshold.

+
cwas
+

Dataframe holding the concentrations.

-
windows

Matrix of maximum time weighted average concentrations (TWAC_max) + +

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

+

+
+
+

Methods

-

Public 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 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 +

+

Public 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 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.

-

-

-

Method get_events()

+ +

+
+ +

+

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.

Usage

-

TOXSWA_cwa$get_events(thresholds, total = FALSE)

+field of the object.

+

Usage

+

TOXSWA_cwa$get_events(thresholds, total = FALSE)

+
+ +
+

Arguments

+

thresholds
+

Threshold values in µg/L.

-

Arguments

-

-
thresholds

Threshold values in µg/L.

-
total

If TRUE, the total concentration including the amount adsorbed to +

total
+

If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.

-

-

-

Method print()

-

Print a `TOXSWA_cwa` object

Usage

-

TOXSWA_cwa$print()

- -

-

Method 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

- 
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
+ +

+
+ +

+

Method print()

+

Print a `TOXSWA_cwa` object

+

Usage

+

TOXSWA_cwa$print()

+
+ + +

+

Method 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

+ 
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
+
+
+
- - - + + -- cgit v1.2.1