1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
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
```
|
