Page not found (404)

@@ -126,7 +125,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

sorption_aggregator = geomean, ...) # S3 method for GUS_result -print(x, ..., digits = 1) +print(x, ..., digits = 1)

Arguments

@@ -228,19 +227,23 @@ toxicology and chemistry8(4) 339–57.

+ + + diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html index be189bd..68436fb 100644 --- a/docs/reference/PEC_FOMC_accu_rel.html +++ b/docs/reference/PEC_FOMC_accu_rel.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -71,7 +74,7 @@ @@ -94,13 +92,14 @@ +

@@ -146,19 +145,23 @@

+ + + diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index b1cc84c..96e2db6 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -51,6 +53,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> + @@ -75,7 +78,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> @@ -98,13 +96,14 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> +

@@ -124,7 +123,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).

leaching_depth = tillage_depth, crop = "annual", cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, - scenarios = c("default", "EFSA_2017", "EFSA_2015"), + scenarios = c("default", "EFSA_2017", "EFSA_2015"), leaching = scenarios == "EFSA_2017", porewater = FALSE)

Arguments

@@ -303,21 +302,21 @@ from 2017 (p. 92).

# This is example 1 starting at p. 92 of the EFSA guidance (2017) # Note that TWA concentrations differ from the ones given in the guidance # for an unknown reason (the values from EFSA (2015) can be reproduced). -PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), +PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), Kom = 1000, scenarios = "EFSA_2017")

#> scenario #> t_avg CTN CTC CTS #> 0 19.76834 13.8619 10.53795 -#> 21 19.59345 13.7169 10.39882

PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), +#> 21 19.59345 13.7169 10.39882

PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE)

#> scenario #> t_avg CLN CLC CLS #> 0 0.5541984 0.6779249 0.9816693 #> 21 0.5484576 0.6693125 0.9609119

# This is example 1 starting at p. 79 of the EFSA guidance (2015) -PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), +PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = "EFSA_2015")

#> scenario #> t_avg CTN CTC CTS #> 0 21.96827 11.53750 9.145259 -#> 21 21.78517 11.40701 9.017370

PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), +#> 21 21.78517 11.40701 9.017370

PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)

#> scenario #> t_avg CLN CLC CLS #> 0 0.7589401 0.6674322 0.9147861 @@ -326,9 +325,9 @@ from 2017 (p. 92).

# Metabolite M2 # Calculate total and porewater soil concentrations for tier 1 scenarios # Relative molar mass is 100/300, formation fraction is 0.7 * 1 -results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), +results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = "EFSA_2015") -results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), +results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)

+ + + diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index fe59070..ce7c6b0 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -71,7 +74,7 @@ @@ -94,13 +92,14 @@ +

@@ -150,19 +149,23 @@ maximum occurrence in soil and their soil DT50

+ + + diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 5e96f42..8c55eed 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ published on the CRC website" /> + @@ -72,7 +75,7 @@ published on the CRC website" /> @@ -95,13 +93,14 @@ published on the CRC website" /> +

@@ -173,19 +172,23 @@ published on the CRC website

+ + + diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 3ce87e4..c1551e2 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ with input via spray drift." /> + @@ -73,7 +76,7 @@ with input via spray drift." /> @@ -96,13 +94,14 @@ with input via spray drift." /> +

@@ -116,7 +115,7 @@ with input via spray drift.

PEC_sw_drift(rate, applications = 1, water_depth = 30,
   drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
-  distances = c(1, 5, 10, 20), rate_units = "g/ha",
+  distances = c(1, 5, 10, 20), rate_units = "g/ha",
   PEC_units = "µg/L")

Arguments

@@ -185,19 +184,23 @@ with input via spray drift.

+ + + diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 1187559..641ee7d 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -53,6 +55,7 @@ details, see the discussion of the function arguments below." /> + @@ -77,7 +80,7 @@ details, see the discussion of the function arguments below." /> @@ -100,13 +98,14 @@ details, see the discussion of the function arguments below." /> +

@@ -123,8 +122,8 @@ details, see the discussion of the function arguments below.

PEC_sw_exposit_drainage(rate, interception = 0, Koc = NA,
-  mobility = c(NA, "low", "high"), DT50 = Inf, t_drainage = 3,
-  V_ditch = 30, V_drainage = c(spring = 10, autumn = 100),
+  mobility = c(NA, "low", "high"), DT50 = Inf, t_drainage = 3,
+  V_ditch = 30, V_drainage = c(spring = 10, autumn = 100),
   dilution = 2)

Arguments

@@ -182,7 +181,8 @@ autumn/winter/early spring.

runoff

A matrix containing dissolved and bound input for the different distances

PEC_sw_runoff

A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.

- + +

Arguments

@@ -173,7 +172,8 @@ and the bound fraction.

runoff

A matrix containing dissolved and bound input for the different distances

PEC_sw_runoff

A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.

- + +

Arguments

@@ -178,19 +177,23 @@ g/cm3)

+ + + diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index c290ade..1f3a140 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -71,7 +74,7 @@ @@ -94,13 +92,14 @@ +

@@ -110,7 +109,7 @@

SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42,
+    SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42,
   50, 100))
     
     Arguments
@@ -162,19 +161,23 @@

+ + + diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 9cfa9c8..ddb21de 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ checked against the spreadsheet published on the CRC website" /> + @@ -72,7 +75,7 @@ checked against the spreadsheet published on the CRC website" /> @@ -95,13 +93,14 @@ checked against the spreadsheet published on the CRC website" /> +

@@ -152,19 +151,23 @@ checked against the spreadsheet published on the CRC website

+ + + diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index d840e52..ab741ae 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> + @@ -72,7 +75,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> @@ -95,13 +93,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> +

@@ -121,21 +120,29 @@ Usually, an instance of this class will be generated by


+
+
 filename
Length one character vector.
-    basedir
Length one character vector.
-    segment
Length one integer, specifying for which segment the cwa data were read.
-    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)
+
+
basedir
Length one character vector.
+
+segment
Length one integer, specifying for which segment the cwa data were read.
+
+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
 
     
-    
+
+
   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
@@ -143,17 +150,19 @@ for the requested moving window sizes in days.
   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.
+
 
+
     
 
     Examples
     H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                 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 
+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
@@ -196,19 +205,23 @@ for the requested moving window sizes in days.


 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+


 
   
 
+
   
 
 
+
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 2579c47..922c405 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Create a chemical compound object for FOCUS Step 1 calculations
-    Source: R/PEC_sw_focus.R
+    
     chent_focus_sw.Rd
     
 
@@ -178,19 +177,23 @@ systems
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index 9c14f54..665cb83 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -17,13 +17,15 @@ published by the JKI — drift_data_JKI • pfm
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -50,6 +52,7 @@ published by the German Julius-Kühn Institute (JKI)." />
 
 
 
+
   
 
   
@@ -74,7 +77,7 @@ published by the German Julius-Kühn Institute (JKI)." />
       
         
   
-    
+    
      
   
 
@@ -84,12 +87,7 @@ published by the German Julius-Kühn Institute (JKI)." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -97,6 +95,7 @@ published by the German Julius-Kühn Institute (JKI)." />
 
 
       
+
       
 
 
@@ -104,7 +103,7 @@ published by the German Julius-Kühn Institute (JKI)." />
     
     Deposition from spray drift expressed as percent of the applied dose as
 published by the JKI
-    Source: R/drift_data_JKI.R
+    
     drift_data_JKI.Rd
     
 
@@ -151,50 +150,51 @@ included.
 
     Examples
     
-
# NOT RUN {
+if (FALSE) {
   # This is the code that was used to extract the data
-  library(readxl)
+  library(readxl)
   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
-  JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet",
+  JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet",
     "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen")
-  names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late",
+  names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late",
     "Vines early", "Vines late", "Hops", "Areic cultures > 900 L/ha", "Railroad tracks")
-  drift_data_JKI <- list()
+  drift_data_JKI <- list()
 
   for (n in 1:8) {
     drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
-    drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops))
-    dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9],
+    drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops))
+    dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9],
                                             crop = JKI_crops)
     if (n == 1) { # Values for railroad tracks only present for one application
-      drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ])
+      drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ])
     } else {
-      drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ])
+      drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ])
     }
     drift_data_JKI[[n]] <- drift_data
   }
 
   # Manual data entry from the Rautmann paper
   drift_data_JKI[[1]]["3", "Ackerbau"] <- 0.95
-  drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03)
+  drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03)
   drift_data_JKI[[2]]["3", "Ackerbau"] <- 0.79
-  drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02)
+  drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02)
   drift_data_JKI[[3]]["3", "Ackerbau"] <- 0.68
-  drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02)
+  drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02)
   drift_data_JKI[[4]]["3", "Ackerbau"] <- 0.62
-  drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02)
+  drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02)
   drift_data_JKI[[5]]["3", "Ackerbau"] <- 0.59
-  drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02)
+  drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02)
   drift_data_JKI[[6]]["3", "Ackerbau"] <- 0.56
-  drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02)
+  drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02)
   drift_data_JKI[[7]]["3", "Ackerbau"] <- 0.55
-  drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02)
+  drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02)
   drift_data_JKI[[8]]["3", "Ackerbau"] <- 0.52
-  drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02)
+  drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02)
 
   # Save the data
-  save(drift_data_JKI, file = "data/drift_data_JKI.RData")
-# }
+  save(drift_data_JKI, file = "data/drift_data_JKI.RData")
+}
+
 # And this is the resulting data
 drift_data_JKI
#> [[1]]
 #>         crop
@@ -405,19 +405,23 @@ included.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index f5520f6..2875b7a 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -50,6 +52,7 @@ this function." />
 
 
 
+
   
 
   
@@ -74,7 +77,7 @@ this function." />
       
         
   
-    
+    
      
   
 
@@ -84,12 +87,7 @@ this function." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -97,13 +95,14 @@ this function." />
 
 
       
+
       
 
 
   
     
     Retrieve endpoint information from the chyaml field of a chent object
-    Source: R/endpoint.R
+    
     endpoint.Rd
     
 
@@ -116,9 +115,9 @@ this function.
     
     
 
-    endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
-  lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
-  "anaerobic"), value = c("DT50ref", "Kfoc", "N"),
+    endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
+  lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
+  "anaerobic"), value = c("DT50ref", "Kfoc", "N"),
   aggregator = geomean, raw = FALSE, signif = 3)
 
 soil_DT50(chent, aggregator = geomean, signif = 3,
@@ -130,8 +129,8 @@ this function.
 
 soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
 
-soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
-  geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
+soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
+  geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
   raw = FALSE)
     
     Arguments
@@ -217,19 +216,23 @@ exponent is often called 1/n.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index c52e3e8..5775b27 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -50,6 +52,7 @@ returns 0 if at least one element of the vector is 0." />
 
 
 
+
   
 
   
@@ -74,7 +77,7 @@ returns 0 if at least one element of the vector is 0." />
       
         
   
-    
+    
      
   
 
@@ -84,12 +87,7 @@ returns 0 if at least one element of the vector is 0." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -97,13 +95,14 @@ returns 0 if at least one element of the vector is 0." />
 
 
       
+
       
 
 
   
     
     Calculate the geometric mean
-    Source: R/geomean.R
+    
     geomean.Rd
     
 
@@ -137,9 +136,7 @@ returns 0 if at least one element of the vector is 0.
     
 
     Examples
-    geomean(c(1, 3, 9))
#> [1] 3
geomean(c(1, 3, NA, 9))
#> [1] 3
# NOT RUN {
-geomean(c(1, -3, 9)) # returns an error
-# }
+    geomean(c(1, 3, 9))
#> [1] 3
geomean(c(1, 3, NA, 9))
#> [1] 3
if (FALSE) geomean(c(1, -3, 9)) # returns an error
   
   
     Contents
@@ -156,19 +153,23 @@ returns 0 if at least one element of the vector is 0.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html
index 73c0b22..5c2205a 100644
--- a/docs/reference/get_vertex.html
+++ b/docs/reference/get_vertex.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@ https://stackoverflow.com/a/717791" />
 
 
 
+
   
 
   
@@ -72,7 +75,7 @@ https://stackoverflow.com/a/717791" />
       
         
   
-    
+    
      
   
 
@@ -82,12 +85,7 @@ https://stackoverflow.com/a/717791" />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -95,13 +93,14 @@ https://stackoverflow.com/a/717791" />
 
 
       
+
       
 
 
   
     
     Fit a parabola through three points
-    Source: R/PEC_soil.R
+    
     get_vertex.Rd
     
 
@@ -138,19 +137,23 @@ https://stackoverflow.com/a/717791
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index c24f7cc..ca8cd18 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -44,6 +46,7 @@
 
 
 
+
   
 
   
@@ -68,7 +71,7 @@
       
         
   
-    
+    
      
   
 
@@ -78,12 +81,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -91,6 +89,7 @@
 
 
       
+
       
 
 
@@ -366,19 +365,23 @@ water concentrations
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index fee0ceb..1078f3e 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ max_twa." />
 
 
 
+
   
 
   
@@ -75,7 +78,7 @@ max_twa." />
       
         
   
-    
+    
      
   
 
@@ -85,12 +88,7 @@ max_twa." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -98,13 +96,14 @@ max_twa." />
 
 
       
+
       
 
 
   
     
     The maximum time weighted average concentration for a moving window
-    Source: R/twa.R
+    
     max_twa.Rd
     
 
@@ -154,7 +153,7 @@ SFO, FOMC and DFOP models and to the parent compound
 
     Examples
     pred <- sawtooth(one_box(10),
-  applications = data.frame(time = c(0, 7), amount = c(1, 1)))
+  applications = data.frame(time = c(0, 7), amount = c(1, 1)))
 max_twa(pred)
#> $max
 #>    parent 
 #> 0.9537545 
@@ -187,19 +186,23 @@ SFO, FOMC and DFOP models and to the parent compound
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index e7379e2..ebfb872 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Create a time series of decline data
-    Source: R/twa.R
+    
     one_box.Rd
     
 
@@ -130,7 +129,7 @@


@@ -162,22 +161,21 @@ all observed variables.
     
     Value
 
-    An object of class one_box, inheriting from ts.
+    An object of class one_box, inheriting from ts.
     
 
     Examples
     # Only use a half-life
 pred_0 <- one_box(10)
-plot(pred_0)

+plot(pred_0)

 # Use a fitted mkinfit model
-require(mkin)
-fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+require(mkin)
+fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 pred_1 <- one_box(fit)
-plot(pred_1)

+plot(pred_1)

 # Use a model with more than one observed variable
-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)
-pred_2 <- one_box(fit_2, ini = "model")
-plot(pred_2)

+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 = "model")
+plot(pred_2)

   
   
     Contents
@@ -192,19 +190,23 @@ all observed variables.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html
index 4473907..745d1f1 100644
--- a/docs/reference/perc_runoff_exposit.html
+++ b/docs/reference/perc_runoff_exposit.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Runoff loss percentages as used in Exposit 3
-    Source: R/PEC_sw_exposit_runoff.R
+    
     perc_runoff_exposit.Rd
     
 
@@ -120,7 +119,8 @@
       adjacent water body in the dissolved phase
     bound
The percentage of the applied substance transferred to an
       adjacent water body bound to eroding particles
-  
+  
+
     
     Source
 
@@ -129,7 +129,7 @@
     
 
     Examples
-    print(perc_runoff_exposit)
#>              Koc_lower_bound dissolved bound
+    print(perc_runoff_exposit)
#>              Koc_lower_bound dissolved bound
 #> 0-20                       0     0.110 0.000
 #> >20-50                    20     0.151 0.000
 #> >50-100                   50     0.197 0.000
@@ -157,19 +157,23 @@
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index ff71d24..8b1da13 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     

@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Runoff reduction percentages as used in Exposit
-    Source: R/PEC_sw_exposit_runoff.R
+    
     perc_runoff_reduction_exposit.Rd
     
 
@@ -120,7 +119,8 @@ vegetated buffer widths as row names. The names of the list items are the Exposi
 from which the values were taken.

     dissolved
The reduction percentage for the dissolved phase
     bound
The reduction percentage for the particulate phase
-  
+  
+
     
     Source
 
@@ -131,7 +131,7 @@ from which the values were taken.

     
 
     Examples
-    print(perc_runoff_reduction_exposit)
#> $`3.02`
+    print(perc_runoff_reduction_exposit)
#> $`3.02`
 #>           dissolved bound
 #> No buffer         0     0
 #> 5 m              40    40
@@ -172,19 +172,23 @@ from which the values were taken.

   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index 79fbfe1..0154be0 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     

@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Calculate a time course of relative concentrations based on an mkinmod model
-    Source: R/pfm_degradation.R
+    
     pfm_degradation.Rd
     
 
@@ -110,8 +109,8 @@
     
     
 
-    pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
-  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365,
+    pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
+  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365,
   by = step_days))
     
     Arguments
@@ -147,7 +146,7 @@ is calculated (SFO model).
     
 
     Examples
-    head(pfm_degradation("SFO", DT50 = 10))
#>   time    parent
+    head(pfm_degradation("SFO", DT50 = 10))
#>   time    parent
 #> 1    0 1.0000000
 #> 2    1 0.9330330
 #> 3    2 0.8705506
@@ -168,19 +167,23 @@ is calculated (SFO model).
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index 78a29ae..0a69f2e 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@ segment of a TOXSWA surface water body." />
 
 
 
+
   
 
   
@@ -72,7 +75,7 @@ segment of a TOXSWA surface water body." />
       
         
   
-    
+    
      
   
 
@@ -82,12 +85,7 @@ segment of a TOXSWA surface water body." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -95,13 +93,14 @@ segment of a TOXSWA surface water body." />
 
 
       
+
       
 
 
   
     
     Plot TOXSWA surface water concentrations
-    Source: R/TOXSWA_cwa.R
+    
     plot.TOXSWA_cwa.Rd
     
 
@@ -113,7 +112,7 @@ segment of a TOXSWA surface water body.
     
 
     # S3 method for TOXSWA_cwa
-plot(x, time_column = c("datetime", "t",
+plot(x, time_column = c("datetime", "t",
   "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default",
   add = FALSE, threshold_factor = 1000, thin_low = 1,
   total = FALSE, LC_TIME = "C", ...)
@@ -168,12 +167,12 @@ to suspended matter?
     Examples
     H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
   basedir = "SwashProjects/project_H_sw/TOXSWA",
-  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
-plot(H_sw_D4_pond)
plot(H_sw_D4_pond, time_column = "t")
plot(H_sw_D4_pond, time_column = "t_firstjan")
plot(H_sw_D4_pond, time_column = "t_rel_to_max")

+  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
+plot(H_sw_D4_pond)
plot(H_sw_D4_pond, time_column = "t")
plot(H_sw_D4_pond, time_column = "t_firstjan")
plot(H_sw_D4_pond, time_column = "t_rel_to_max")

 H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
   basedir = "SwashProjects/project_H_sw/TOXSWA",
-  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
-plot(H_sw_R1_stream, time_column = "t_rel_to_max")

+  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
+plot(H_sw_R1_stream, time_column = "t_rel_to_max")

   
   
     Contents
@@ -188,19 +187,23 @@ to suspended matter?
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png
index ad93165..fc8116b 100644
Binary files a/docs/reference/plot.one_box-3.png and b/docs/reference/plot.one_box-3.png differ
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 6b8fdbb..89958c5 100644
--- a/docs/reference/plot.one_box.html
+++ b/docs/reference/plot.one_box.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -71,7 +74,7 @@
       
         
   
-    
+    
      
   
 
@@ -81,12 +84,7 @@
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -94,13 +92,14 @@
 
 
       
+
       
 
 
   
     
     Plot time series of decline data
-    Source: R/twa.R
+    
     plot.one_box.Rd
     
 
@@ -111,9 +110,9 @@
     
 
     # S3 method for one_box
-plot(x, xlim = range(time(x)), ylim = c(0, max(x)),
+plot(x, xlim = range(time(x)), ylim = c(0, max(x)),
   xlab = "Time", ylab = "Residue", max_twa = NULL,
-  max_twa_var = dimnames(x)[[2]][1], ...)
+  max_twa_var = dimnames(x)[[2]][1], ...)
     
     Arguments

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 paramters. +e.g. `FOMC`, `parms` must contain the corresponding parameters. If x is an `mkinfit` object, the decline is calculated from this object.


@@ -160,13 +159,12 @@ be shown if max_twa is not NULL.
     
 
     Examples
-    dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7))
-plot(dfop_pred)
plot(sawtooth(dfop_pred, 3, 7), max_twa = 21)

+    dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7))
+plot(dfop_pred)
plot(sawtooth(dfop_pred, 3, 7), max_twa = 21)

 # Use a fitted mkinfit model
-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)
-pred_2 <- one_box(fit_2, ini = 1)
+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)
 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")

   
   
     Contents
@@ -181,19 +179,23 @@ be shown if max_twa is not NULL.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index f081162..f1d4a47 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -52,6 +54,7 @@ renamed to ConLiqWatLay in the out file." />
 
 
 
+
   
 
   
@@ -76,7 +79,7 @@ renamed to ConLiqWatLay in the out file." />
       
         
   
-    
+    
      
   
 
@@ -86,12 +89,7 @@ renamed to ConLiqWatLay in the out file." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -99,13 +97,14 @@ renamed to ConLiqWatLay in the out file." />
 
 
       
+
       
 
 
   
     
     Read TOXSWA surface water concentrations
-    Source: R/TOXSWA_cwa.R
+    
     read.TOXSWA_cwa.Rd
     
 
@@ -178,7 +177,7 @@ generating event statistics.
     Examples
     H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
                                                        package = "pfm"))
   
   
@@ -196,19 +195,23 @@ generating event statistics.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png
index ad93165..fc8116b 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 a94833c..050e5eb 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@ n and i are disregarded." />
 
 
 
+
   
 
   
@@ -72,7 +75,7 @@ n and i are disregarded." />
       
         
   
-    
+    
      
   
 
@@ -82,12 +85,7 @@ n and i are disregarded." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -95,13 +93,14 @@ n and i are disregarded." />
 
 
       
+
       
 
 
   
     
     Create decline time series for multiple applications
-    Source: R/twa.R
+    
     sawtooth.Rd
     
 
@@ -112,7 +111,7 @@ n and i are disregarded." />
     
     
 
-    sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0,
+    sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0,
   (n - 1) * i, length.out = n), amount = 1))
     
     Arguments
@@ -140,13 +139,12 @@ the corresponding amounts applied in the second column.
     
 
     Examples
-    applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3))
+    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)
-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
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 
@@ -171,19 +169,23 @@ the corresponding amounts applied in the second column.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index cb2e1fa..5551d82 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -49,6 +51,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
 
 
 
+
   
 
   
@@ -73,7 +76,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
       
         
   
-    
+    
      
   
 
@@ -83,12 +86,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -96,13 +94,14 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
 
 
       
+
       
 
 
   
     
     Properties of the predefined scenarios from the EFSA guidance from 2015
-    Source: R/soil_scenario_data_EFSA_2015.R
+    
     soil_scenario_data_EFSA_2015.Rd
     
 
@@ -131,24 +130,25 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.
     
 
     Examples
-    # NOT RUN {
+    if (FALSE) {
   # This is the code that was used to define the data
-  soil_scenario_data_EFSA_2015 <- data.frame(
-    Zone = rep(c("North", "Central", "South"), 2),
-    Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
-    T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
-    T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
-    Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
-    f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
-    theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
-    rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
-    f_sce = c(3, 2, 2, 2, 1.5, 1.5),
-    f_mod = c(2, 2, 2, 4, 4, 4),
+  soil_scenario_data_EFSA_2015 <- data.frame(
+    Zone = rep(c("North", "Central", "South"), 2),
+    Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
+    T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
+    T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
+    Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
+    f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
+    theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
+    rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
+    f_sce = c(3, 2, 2, 2, 1.5, 1.5),
+    f_mod = c(2, 2, 2, 4, 4, 4),
     stringsAsFactors = FALSE,
-    row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
+    row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
   )
-  save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
-# }
+  save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
+}
+
 # And this is the resulting dataframe
 soil_scenario_data_EFSA_2015
#>        Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
 #> CTN   North        Estonia    4.7   7.0      Coarse 0.118    0.244 0.95   3.0
@@ -179,19 +179,23 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html
index 21f69a2..bb898b8 100644
--- a/docs/reference/soil_scenario_data_EFSA_2017.html
+++ b/docs/reference/soil_scenario_data_EFSA_2017.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -49,6 +51,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
 
 
 
+
   
 
   
@@ -73,7 +76,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
       
         
   
-    
+    
      
   
 
@@ -83,12 +86,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     

@@ -96,13 +94,14 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
 
 
       
+
       
 
 
   
     
     Properties of the predefined scenarios from the EFSA guidance from 2017
-    Source: R/soil_scenario_data_EFSA_2017.R
+    
     soil_scenario_data_EFSA_2017.Rd
     
 
@@ -160,19 +159,23 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
index 86c0f9b..016380a 100644
--- a/docs/reference/twa.html
+++ b/docs/reference/twa.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -49,6 +51,7 @@ is after one window has passed." />
 
 
 
+
   
 
   
@@ -73,7 +76,7 @@ is after one window has passed." />
       
         
   
-    
+    
      
   
 
@@ -83,12 +86,7 @@ is after one window has passed." />
       
       
       
-        
-  
-    
-     
-  
-
+        
       
       
     
@@ -96,13 +94,14 @@ is after one window has passed." />
 
 
       
+
       
 
 
   
     
     Calculate a time weighted average concentration
-    Source: R/twa.R
+    
     twa.Rd
     
 
@@ -139,7 +138,7 @@ is after one window has passed.
 
     Examples
     pred <- sawtooth(one_box(10),
-  applications = data.frame(time = c(0, 7), amount = c(1, 1)))
+  applications = data.frame(time = c(0, 7), amount = c(1, 1)))
 max_twa(pred)
#> $max
 #>    parent 
 #> 0.9537545 
@@ -166,19 +165,23 @@ is after one window has passed.
   
 
 
+
       
       
   Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 1.3.0.
+  Site built with pkgdown 1.4.1.
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
new file mode 100644
index 0000000..285ffb2
--- /dev/null
+++ b/docs/sitemap.xml
@@ -0,0 +1,105 @@
+
+
+  
+    https://pkgdown.jrwb.de/pfm/index.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/GUS.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/endpoint.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/geomean.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/get_vertex.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/max_twa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/one_box.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/sawtooth.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html
+  
+  
+    https://pkgdown.jrwb.de/pfm/reference/twa.html
+  
+
-- 
cgit v1.2.1

Installation

@@ -96,14 +91,7 @@

Links

License

Developers

A very small subset of the FOCUS Groundwater scenario definitions

Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

Examples

Actual and maximum moving window time average concentrations for FOMC kinetics

Arguments

Groundwater ubiquity score based on Gustafson (1989)

Arguments

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

Calculate predicted environmental concentrations in soil

Arguments

Calculate initial and accumulation PEC soil for a set of metabolites

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

Calculate predicted environmental concentrations in surface water due to drift

Arguments

Calculate PEC surface water due to drainage as in Exposit 3

Arguments

See also

Calculate PEC surface water due to runoff and erosion as in Exposit 3

Arguments

See also

Calculate PEC surface water at FOCUS Step 1

Calculate predicted environmental concentrations in sediment from surface water concentrations

Arguments

Actual and maximum moving window time average concentrations for SFO kinetics

Arguments

Determine the SSLRC mobility classification for a chemical substance from its Koc

R6 class for holding TOXSWA water concentration data and associated statistics

Methods

Examples

Create a chemical compound object for FOCUS Step 1 calculations

Deposition from spray drift expressed as percent of the applied dose as published by the JKI

Examples

Retrieve endpoint information from the chyaml field of a chent object

Arguments

Calculate the geometric mean

Examples

Contents

Fit a parabola through three points

The maximum time weighted average concentration for a moving window

Examples

Create a time series of decline data

Value

Examples

Contents

Runoff loss percentages as used in Exposit 3

Source

Examples

Runoff reduction percentages as used in Exposit

Source

Examples

Calculate a time course of relative concentrations based on an mkinmod model

Arguments

Examples

Plot TOXSWA surface water concentrations

Examples

Contents

Plot time series of decline data

Arguments

Examples

Contents

Read TOXSWA surface water concentrations

Examples

Create decline time series for multiple applications

Arguments

Examples

Properties of the predefined scenarios from the EFSA guidance from 2015

Examples

Properties of the predefined scenarios from the EFSA guidance from 2017

Calculate a time weighted average concentration

Examples