From 90fa42c86596c85168931148bf8d5fa014fa7794 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 23 Jul 2020 10:51:39 +0200 Subject: Update docs, use R6 support of roxygen --- docs/pkgdown.yml | 2 +- docs/reference/TOXSWA_cwa.html | 82 +++++++++++++++++++++++------------- docs/reference/index.html | 19 +++++++++ docs/reference/pfm_degradation.html | 52 +++++++++++------------ docs/reference/sawtooth-2.png | Bin 37285 -> 42340 bytes docs/reference/sawtooth.html | 46 ++++++++++---------- 6 files changed, 121 insertions(+), 80 deletions(-) (limited to 'docs') diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 077f218..8b86fe9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.2.1 pkgdown: 1.5.1 pkgdown_sha: ~ articles: [] -last_built: 2020-06-17T11:36Z +last_built: 2020-07-22T15:06Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 9f9e3c3..16dc5db 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -40,8 +40,11 @@ - + @@ -110,8 +113,11 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
-

An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. -Usually, an instance of this class will be generated by read.TOXSWA_cwa.

+

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.

@@ -119,30 +125,19 @@ Usually, an instance of this class will be generated by -
get_events(threshold, total = FALSE)

Populate a datataframe with event information for the specified threshold value - in µg/L. If total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - events field of the object.

-
moving_windows(windows, total = FALSE)

Add to the windows field described above. - Again, if total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used.

- - -

Public fields

-
filename

Length one character vector.

+
filename

Length one character vector holding the filename.

-
basedir

Length one character vector.

+
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.

@@ -166,8 +161,7 @@ for the requested moving window sizes in days.

Method new()

- -

Usage

+

Create a TOXSWA_cwa object from a file

Usage

TOXSWA_cwa$new(
   filename,
   basedir,
@@ -177,22 +171,52 @@ for the requested moving window sizes in days.

   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()

- -

Usage

+

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()

- -

Usage

+

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.

+ +

Method print()

- -

Usage

+

Print a `TOXSWA_cwa` object

Usage

TOXSWA_cwa$print()

diff --git a/docs/reference/index.html b/docs/reference/index.html index 944f1f2..186390e 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -390,6 +390,25 @@ water concentrations

Groundwater ubiquity score based on Gustafson (1989)

+ + + +

Work with chent objects containing relevant information

+

+ + + + + + + + + + +

endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption()

+ +

Retrieve endpoint information from the chyaml field of a chent object

+ diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index d2e62f6..8d06107 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
- @@ -178,7 +176,7 @@ is calculated (SFO model).

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png index ad93165..87da954 100644 Binary files a/docs/reference/sawtooth-2.png and b/docs/reference/sawtooth-2.png differ diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 7720afc..fea24d4 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -36,9 +40,8 @@ - - @@ -56,7 +59,7 @@ n and i are disregarded." /> - +
-

If the application pattern is specified in applications, +

If the application pattern is specified in applications, n and i are disregarded.

@@ -145,10 +148,10 @@ the corresponding amounts applied in the second column.

Examples

applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3))
 pred <- one_box(10)
-plot(sawtooth(pred, applications = applications))

-m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
pred_2 <- one_box(fit_2, ini = 1)
+plot(sawtooth(pred, applications = applications))

+m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Warning: Shapiro-Wilk test for standardized residuals: p =  0.0165
pred_2 <- one_box(fit_2, ini = 1)
 pred_2_saw <- sawtooth(pred_2, 2, 7)
-plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")

+plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")

 max_twa(pred_2_saw)
#> $max
 #>    parent        m1 
 #> 0.7834480 0.8617048 
@@ -162,13 +165,10 @@ the corresponding amounts applied in the second column.

 #>  21.00  47.85 
 #>
- @@ -179,7 +179,7 @@ the corresponding amounts applied in the second column.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

-- cgit v1.2.1