From f0bf040afbadf07c21dc65495e344c0d2a25f9c3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 24 Jun 2025 21:50:52 +0200 Subject: Redact README and rebuild static docs --- docs/reference/EFSA_GW_interception_2014.html | 4 +- docs/reference/EFSA_washoff_2017.html | 4 +- docs/reference/FOCUS_GW_scenarios_2012.html | 4 +- docs/reference/FOCUS_Step_12_scenarios.html | 4 +- docs/reference/FOMC_actual_twa.html | 4 +- docs/reference/GUS.html | 4 +- docs/reference/PEC_FOMC_accu_rel.html | 59 ++++++++--------- docs/reference/PEC_soil.html | 2 +- docs/reference/PEC_soil_mets.html | 59 ++++++++--------- docs/reference/PEC_sw_drainage_UK.html | 2 +- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_drainage.html | 2 +- docs/reference/PEC_sw_exposit_runoff.html | 6 +- docs/reference/PEC_sw_focus.html | 4 +- docs/reference/PEC_sw_sed.html | 4 +- docs/reference/Rplot001.png | Bin 8788 -> 1011 bytes docs/reference/Rplot002.png | Bin 9702 -> 13411 bytes docs/reference/Rplot003.png | Bin 9594 -> 13016 bytes docs/reference/SFO_actual_twa.html | 4 +- docs/reference/SSLRC_mobility_classification.html | 4 +- docs/reference/TOXSWA_cwa.html | 4 +- docs/reference/TSCF-1.png | Bin 39919 -> 40587 bytes docs/reference/TSCF.html | 4 +- docs/reference/chent_focus_sw.html | 73 ++++++++++------------ docs/reference/drift_data_JKI.html | 4 +- docs/reference/drift_parameters_focus.html | 4 +- docs/reference/drift_percentages_rautmann-1.png | Bin 41810 -> 42251 bytes docs/reference/drift_percentages_rautmann.html | 4 +- docs/reference/endpoint.html | 4 +- docs/reference/geomean.html | 61 ++++++++---------- docs/reference/get_vertex.html | 57 ++++++++--------- docs/reference/index.html | 2 +- docs/reference/max_twa.html | 4 +- docs/reference/one_box-1.png | Bin 24719 -> 25088 bytes docs/reference/one_box-2.png | Bin 21981 -> 22307 bytes docs/reference/one_box-3.png | Bin 34076 -> 34421 bytes docs/reference/one_box.html | 71 +++++++++------------ docs/reference/perc_runoff_exposit.html | 4 +- docs/reference/perc_runoff_reduction_exposit.html | 4 +- docs/reference/pfm_degradation.html | 61 ++++++++---------- docs/reference/plot.TOXSWA_cwa-1.png | Bin 34458 -> 34847 bytes docs/reference/plot.TOXSWA_cwa-2.png | Bin 33311 -> 33612 bytes docs/reference/plot.TOXSWA_cwa-3.png | Bin 35208 -> 35634 bytes docs/reference/plot.TOXSWA_cwa-4.png | Bin 35650 -> 36081 bytes docs/reference/plot.TOXSWA_cwa-5.png | Bin 23109 -> 23459 bytes docs/reference/plot.TOXSWA_cwa.html | 73 ++++++++++------------ docs/reference/plot.one_box.html | 6 +- docs/reference/read.TOXSWA_cwa.html | 73 ++++++++++------------ docs/reference/reexports.html | 49 ++++++--------- docs/reference/sawtooth-1.png | Bin 24497 -> 24812 bytes docs/reference/sawtooth-2.png | Bin 41819 -> 36815 bytes docs/reference/sawtooth-3.png | Bin 0 -> 35949 bytes docs/reference/sawtooth.html | 62 +++++++++--------- docs/reference/soil_scenario_data_EFSA_2015.html | 4 +- docs/reference/soil_scenario_data_EFSA_2017.html | 4 +- docs/reference/twa.html | 59 ++++++++--------- 56 files changed, 384 insertions(+), 479 deletions(-) create mode 100644 docs/reference/sawtooth-3.png (limited to 'docs/reference') diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index cf97c02..97d9e3a 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,5 +1,5 @@ -Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • pfm +Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • pfm Skip to contents @@ -7,7 +7,7 @@ pfm - 0.6.3 + 0.6.4 - +
-

Get the relative accumulation of an FOMC model over multiples of an interval

+ +

Get the relative accumulation of an FOMC model over multiples of an interval

Source: R/PEC_soil.R
PEC_FOMC_accu_rel.Rd
@@ -53,42 +44,42 @@

Arguments

-
n
+ + +
n

number of applications

-
interval
+
interval

Time between applications

-
FOMC
+
FOMC

Named numeric vector containing the FOMC parameters alpha and beta

Value

- - -

A numeric vector containing all n accumulation factors for the n applications

+

A numeric vector containing all n accumulation factors for the n applications

-
-

Developed by Johannes Ranke.

+

Developed by Johannes Ranke.

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index e214173..e405bdf 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,5 +1,5 @@ -Calculate predicted environmental concentrations in soil — PEC_soil • pfmCalculate predicted environmental concentrations in soil — PEC_soil • pfmCalculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm +Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm Skip to contents - -
-

Create a chemical compound object for FOCUS Step 1 calculations

+ +

Create a chemical compound object for FOCUS Step 1 calculations

Source: R/PEC_sw_focus.R
chent_focus_sw.Rd
@@ -64,72 +55,72 @@

Arguments

-
name
+ + +
name

Length one character vector containing the name

-
Koc
+
Koc

Partition coefficient between organic carbon and water in L/kg.

-
DT50_ws
+
DT50_ws

Half-life in water/sediment systems in days

-
DT50_soil
+
DT50_soil

Half-life in soil in days

-
DT50_water
+
DT50_water

Half-life in water in days (Step 2)

-
DT50_sediment
+
DT50_sediment

Half-life in sediment in days (Step 2)

-
cwsat
+
cwsat

Water solubility in mg/L

-
mw
+
mw

Molar weight in g/mol.

-
max_soil
+
max_soil

Maximum observed fraction (dimensionless) in soil

-
max_ws
+
max_ws

Maximum observed fraction (dimensionless) in water/sediment systems

Value

- - -

A list with the substance specific properties

+

A list with the substance specific properties

-
-

Developed by Johannes Ranke.

+

Developed by Johannes Ranke.

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 064264f..c8a2d1d 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -1,5 +1,5 @@ -Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • pfmDeposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • pfm Skip to contents @@ -9,7 +9,7 @@ published by the German Julius-Kühn Institute (JKI)."> pfm - 0.6.3 + 0.6.4 - +
-

Calculate the geometric mean

+ +

Calculate the geometric mean

Source: R/geomean.R
geomean.Rd
@@ -65,19 +56,19 @@ If at least one element of the vector is 0, it returns 0.

Arguments

-
x
+ + +
x

Vector of numbers

-
na.rm
+
na.rm

Should NA values be omitted?

Value

- - -

The geometric mean

+

The geometric mean

Author

@@ -94,23 +85,23 @@ If at least one element of the vector is 0, it returns 0.

#> Error in geomean(c(1, -3, 9)): Only defined for positive numbers
-
- - + + diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index d0eff28..45a3408 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -1,45 +1,36 @@ -Fit a parabola through three points — get_vertex • pfm +Fit a parabola through three points — get_vertex • pfm Skip to contents - -
-

Create a time series of decline data

+ +

Create a time series of decline data

Source: R/twa.R
one_box.Rd
@@ -50,19 +41,21 @@

Usage

one_box(x, ini, ..., t_end = 100, res = 0.01)
 
-# S3 method for numeric
+# S3 method for class 'numeric'
 one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
 
-# S3 method for character
+# S3 method for class 'character'
 one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
 
-# S3 method for mkinfit
+# S3 method for class 'mkinfit'
 one_box(x, ini = "model", ..., t_end = 100, res = 0.01)

Arguments

-
x
+ + +
x

When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. FOMC, parms must contain the corresponding parameters. @@ -70,7 +63,7 @@ If x is an

-
ini
+
ini

The initial amount. If x is an mkinfit object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and @@ -78,27 +71,25 @@ initial values of metabolites are zero, otherwise, it must give values for all observed variables.

-
...
+
...

Further arguments passed to methods

-
t_end
+
t_end

End of the time series

-
res
+
res

Resolution of the time series

-
parms
+
parms

A named numeric vector containing the model parameters

Value

- - -

An object of class one_box, inheriting from ts.

+

An object of class one_box, inheriting from ts.

@@ -125,23 +116,23 @@ all observed variables.

-