diff --git a/DESCRIPTION b/DESCRIPTION index 54385c96..67cb619c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,10 +23,11 @@ Imports: EnvStats, ggplot2 License: MIT + file LICENSE +Encoding: UTF-8 LazyLoad: yes URL: http://kwb-r.github.io/kwb.qmra/ BugReports: https://github.com/KWB-R/kwb.qmra/issues -RoxygenNote: 6.0.1 +RoxygenNote: 6.1.0 Suggests: knitr, ggrepel, diff --git a/NEWS.md b/NEWS.md index 3a8a5e57..b14ee2e5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,8 @@ * current development version +* bugfix: distribution_repeater(), works now if number_of_events == 1 + # [kwb.qmra 0.1.1](https://github.com/KWB-R/kwb.qmra/releases/tag/v.0.1.1) * version developed within DEMOWARE project and also released on [Zenodo](https://zenodo.org/record/154111) diff --git a/R/random_distribution.R b/R/random_distribution.R index 467c99e5..04a6a1a9 100644 --- a/R/random_distribution.R +++ b/R/random_distribution.R @@ -16,18 +16,22 @@ distribution_repeater <- function(number_of_repeatings = 10, number_of_events = 365, func, ... ) { + + repl_tmp <- vapply(seq_len(number_of_repeatings), + function(x) {func(n = number_of_events, + ...)},FUN.VALUE = numeric(number_of_events)) + + if(number_of_events == 1) repl_tmp <- t(repl_tmp) - repl <- sapply(1:number_of_repeatings, - function(x) {func(n = number_of_events, - ...)}) %>% + repl <- repl_tmp %>% as.data.frame() %>% - cbind(eventID = 1:number_of_events ) - colnames(repl) <- c(1:number_of_repeatings, "eventID") + cbind(eventID = seq_len(number_of_events)) + colnames(repl) <- c(seq_len(number_of_repeatings), "eventID") repl_list <- tidyr::gather_(data = repl, key_col = "repeatID", value_col = "values", - gather_cols = as.character(1:number_of_repeatings)) + gather_cols = as.character(seq_len(number_of_repeatings))) repl_list$repeatID <- as.integer(repl_list$repeatID) diff --git a/docs/articles/doseresponse.html b/docs/articles/doseresponse.html index cc2eb3e2..96648b97 100644 --- a/docs/articles/doseresponse.html +++ b/docs/articles/doseresponse.html @@ -108,7 +108,7 @@

Dose-response modelling

Michael Rustler

-

2018-06-26

+

2018-10-15

@@ -120,7 +120,6 @@

2018-06-26

#1. Load the required R packages

library(kwb.qmra)
 library(dplyr)
-
## Warning: package 'dplyr' was built under R version 3.4.4
## 
 ## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
@@ -129,12 +128,13 @@ 
2018-06-26

 
## The following objects are masked from 'package:base':
 ## 
 ##     intersect, setdiff, setequal, union

-
+
+
## Warning: package 'ggplot2' was built under R version 3.5.1

+
 
#2. Dose-response database from QMRAwiki

 
2.1 Download

-
+
 
## Warning: Missing column names filled in: 'X1' [1]

 
## Parsed with column specification:
 ## cols(
@@ -160,21 +160,21 @@ 
2018-06-26

 ## )

 
##2.2 Visualise

 
Database:

-
-
## Warning: package 'bindrcpp' was built under R version 3.4.4

-
+
 
@@ -674,17 +674,17 @@ 
2018-06-26

 Table 1: Best-fit dose-response parameters (QMRAwiki, 2016)
 

 

 
 

-
+
 
Dose response for all microbial parameters:

-
+
 

 
Dose for all microbial parameters with 50% infection probability

 

diff --git a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-4-1.png
index e600a564..24acf6df 100644
Binary files a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png
index db955e8d..2762349f 100644
Binary files a/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/doseresponse_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/docs/articles/general.html b/docs/articles/general.html
index 2be5055e..deb55509 100644
--- a/docs/articles/general.html
+++ b/docs/articles/general.html
@@ -108,7 +108,7 @@
       
General workflow

                         
Michael Rustler

             
-            
26 June, 2018

+            
15 October, 2018

       
       
       
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de5b8d0b..1b8abd03 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -150,8 +150,6 @@ 
All vignettes

         
  • Dose-response modelling
    • 
         
  • General workflow
    • 
         
  • Installation
    • 
-        
  • WWTP Old Ford: public irrigation scenario
    • 
-        
  • WWTP Old Ford: public irrigation scenario
    • 
         
  • Usage
    • 
         
  • Web-app development with OpenCpu
    • 
       
diff --git a/docs/articles/installation.html b/docs/articles/installation.html
index 36507fec..70eae4dd 100644
--- a/docs/articles/installation.html
+++ b/docs/articles/installation.html
@@ -108,7 +108,7 @@
       
    Installation
    
                         
    Michael Rustler
    
             
-            
    26 June, 2018
    
+            
    15 October, 2018
    
       
       
       
diff --git a/docs/articles/usage.html b/docs/articles/usage.html
index 8b4c7e56..882ae9b1 100644
--- a/docs/articles/usage.html
+++ b/docs/articles/usage.html
@@ -108,7 +108,7 @@
       
    Usage
    
                         
    Michael Rustler
    
             
-            
    26 June, 2018
    
+            
    15 October, 2018
    
       
       
       
@@ -126,8 +126,8 @@ 
    26 June, 2018
    
 
-
    ## [1] "C:/Users/mrustl.KWB/Documents/R/win-library/3.4/kwb.qmra/extdata/configs/dummy"
    
-
    The following screenshot shows the required configuration files located in confDir (here: C:/Users/mrustl.KWB/Documents/R/win-library/3.4/kwb.qmra/extdata/configs/dummy):
    
+
    ## [1] "C:/Users/mrustl.KWB/Documents/R/win-library/3.5/kwb.qmra/extdata/configs/dummy"
    
+
    The following screenshot shows the required configuration files located in confDir (here: C:/Users/mrustl.KWB/Documents/R/win-library/3.5/kwb.qmra/extdata/configs/dummy):
    
 
    
 Screenshot of required configuration files
    Screenshot of required configuration files
    
 
    
@@ -559,17 +559,16 @@ 
    26 June, 2018
    
 ## Simulated exposure: volume per event
 ## Create 10 random distribution(s): triangle (with parameters n: 365, min: 0.500000, max: 3.000000, mode = 1.500000)
    ## Joining, by = c("PathogenGroup", "eventID", "repeatID")
    -
    ## Warning: package 'bindrcpp' was built under R version 3.4.4
    ## Joining, by = c("eventID", "repeatID")
    ## 
 ## ### STEP 4: DOSE RESPONSE #################################################
 ## 
 ## # A tibble: 3 x 13
-##   PathogenID PathogenName    PathogenGroup `Best fit model~       k  alpha
-##        <int> <chr>           <chr>         <chr>              <dbl>  <dbl>
-## 1          3 Campylobacter ~ Bacteria      beta-Poisson     NA       0.144
-## 2         32 Rotavirus       Viruses       beta-Poisson     NA       0.253
-## 3         36 Giardia duoden~ Protozoa      exponential       0.0199 NA    
+##   PathogenID PathogenName PathogenGroup `Best fit model~       k  alpha
+##        <int> <chr>        <chr>         <chr>              <dbl>  <dbl>
+## 1          3 Campylobact~ Bacteria      beta-Poisson     NA       0.144
+## 2         32 Rotavirus    Viruses       beta-Poisson     NA       0.253
+## 3         36 Giardia duo~ Protozoa      exponential       0.0199 NA    
 ## # ... with 7 more variables: N50 <dbl>, `Host type` <chr>, `Dose
 ## #   units` <chr>, Route <chr>, Response <chr>, Reference <chr>, Link <chr>
 ## 
@@ -584,13 +583,13 @@ 
    26 June, 2018
    
 
    ## Joining, by = c("PathogenID", "PathogenName")
    
 
    All (input & output) data will be saved in the resulting R object risk which an be easily inspected by the user, e.g.:
    
 
    Input data
    
-
+
 
    ## List of 5
 ##  $ inflow      :List of 2
 ##   ..$ events:'data.frame':   10950 obs. of  6 variables:
 ##   .. ..$ repeatID     : int [1:10950] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID      : int [1:10950] 1 2 3 4 5 6 7 8 9 10 ...
-##   .. ..$ inflow       : num [1:10950] 2216 6146 3016 9300 9451 ...
+##   .. ..$ inflow       : num [1:10950] 2329 1767 5782 3421 4596 ...
 ##   .. ..$ PathogenID   : int [1:10950] 3 3 3 3 3 3 3 3 3 3 ...
 ##   .. ..$ PathogenName : chr [1:10950] "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" ...
 ##   .. ..$ PathogenGroup: chr [1:10950] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
@@ -607,7 +606,7 @@ 
    26 June, 2018
    
 ##   ..$ events_long        :'data.frame':  54750 obs. of  8 variables:
 ##   .. ..$ repeatID           : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ eventID            : int [1:54750] 1 2 3 4 5 6 7 8 9 10 ...
-##   .. ..$ logreduction       : num [1:54750] 0.852 0.97 1.632 0.472 0.607 ...
+##   .. ..$ logreduction       : num [1:54750] 0.933 0.77 0.757 1.266 0.527 ...
 ##   .. ..$ TreatmentID        : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. ..$ PathogenGroup      : chr [1:54750] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   .. ..$ TreatmentSchemeID  : int [1:54750] 2 2 2 2 2 2 2 2 2 2 ...
@@ -620,10 +619,10 @@ 
    26 June, 2018
    
 ##   .. ..$ TreatmentSchemeID  : int [1:54750] 1 1 2 2 2 1 1 2 2 2 ...
 ##   .. ..$ TreatmentSchemeName: chr [1:54750] "Berlin (BF + Slow sand)" "Berlin (BF + Slow sand)" "Depth & surface filtration" "Depth & surface filtration" ...
 ##   .. ..$ TreatmentName      : chr [1:54750] "Bank filtration" "Slow sand filtration" "Conventional clarification" "Granular high-rate filtration" ...
-##   .. ..$ 1                  : num [1:54750] NA NA 0.852 NA NA ...
-##   .. ..$ 5                  : num [1:54750] NA NA NA 0.266 NA ...
-##   .. ..$ 8                  : num [1:54750] NA 3.46 NA NA NA ...
-##   .. ..$ 9                  : num [1:54750] 3.52 NA NA NA NA ...
+##   .. ..$ 1                  : num [1:54750] NA NA 0.933 NA NA ...
+##   .. ..$ 5                  : num [1:54750] NA NA NA 3.04 NA ...
+##   .. ..$ 8                  : num [1:54750] NA 5.04 NA NA NA ...
+##   .. ..$ 9                  : num [1:54750] 3.98 NA NA NA NA ...
 ##   .. ..$ 15                 : num [1:54750] NA NA NA NA 4 NA NA NA NA 4 ...
 ##   ..$ schemes_events_wide:'data.frame':  54750 obs. of  4 variables:
 ##   .. ..$ eventID      : int [1:54750] 1 1 1 1 1 1 1 1 1 1 ...
@@ -663,7 +662,7 @@ 
    26 June, 2018
    
 ##   .. ..$ events:'data.frame':    3650 obs. of  3 variables:
 ##   .. .. ..$ repeatID       : int [1:3650] 1 1 1 1 1 1 1 1 1 1 ...
 ##   .. .. ..$ eventID        : int [1:3650] 1 2 3 4 5 6 7 8 9 10 ...
-##   .. .. ..$ volume_perEvent: num [1:3650] 1.03 1.27 1.06 2.49 1.9 ...
+##   .. .. ..$ volume_perEvent: num [1:3650] 1.77 2.09 1.98 1.25 1.97 ...
 ##   .. ..$ paras :'data.frame':    1 obs. of  6 variables:
 ##   .. .. ..$ type      : Factor w/ 1 level "triangle": 1
 ##   .. .. ..$ repeatings: int 10
@@ -702,7 +701,7 @@ 
    26 June, 2018
    
 ##   ..$ infection_to_illness: num [1:3] 0.7 0.03 0.3
 ##   ..$ dalys_per_case      : num [1:3] 0.0046 0.014 0.0015
    
 
    Output data
    
-
+
 
    ## List of 2
 ##  $ events:Classes 'grouped_df', 'tbl_df', 'tbl' and 'data.frame':    21900 obs. of  18 variables:
 ##   ..$ TreatmentSchemeID      : int [1:21900] 1 2 1 2 1 2 1 2 1 2 ...
@@ -710,13 +709,13 @@ 
    26 June, 2018
    
 ##   ..$ PathogenGroup          : chr [1:21900] "Bacteria" "Bacteria" "Bacteria" "Bacteria" ...
 ##   ..$ eventID                : int [1:21900] 1 1 2 2 3 3 4 4 5 5 ...
 ##   ..$ repeatID               : int [1:21900] 1 1 1 1 1 1 1 1 1 1 ...
-##   ..$ logreduction           : num [1:21900] 6.98 5.12 8.91 7.07 9.19 ...
-##   ..$ inflow                 : num [1:21900] 2216 2216 6146 6146 3016 ...
+##   ..$ logreduction           : num [1:21900] 9.03 7.97 6.27 8.51 9.86 ...
+##   ..$ inflow                 : num [1:21900] 2329 2329 1767 1767 5782 ...
 ##   ..$ PathogenID             : int [1:21900] 3 3 3 3 3 3 3 3 3 3 ...
 ##   ..$ PathogenName           : chr [1:21900] "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" "Campylobacter jejuni and Campylobacter coli" ...
-##   ..$ effluent               : num [1:21900] 2.31e-04 1.69e-02 7.50e-06 5.21e-04 1.93e-06 ...
-##   ..$ volume_perEvent        : num [1:21900] 1.03 1.03 1.27 1.27 1.06 ...
-##   ..$ exposure_perEvent      : num [1:21900] 2.38e-04 1.74e-02 9.52e-06 6.62e-04 2.04e-06 ...
+##   ..$ effluent               : num [1:21900] 2.19e-06 2.49e-05 9.52e-04 5.45e-06 7.90e-07 ...
+##   ..$ volume_perEvent        : num [1:21900] 1.77 1.77 2.09 2.09 1.98 ...
+##   ..$ exposure_perEvent      : num [1:21900] 3.89e-06 4.42e-05 1.99e-03 1.14e-05 1.56e-06 ...
 ##   ..$ dose_perEvent          : int [1:21900] 0 0 0 0 0 0 0 0 0 0 ...
 ##   ..$ infectionProb_per_event: num [1:21900] 0 0 0 0 0 0 0 0 0 0 ...
 ##   ..$ infection_to_illness   : num [1:21900] 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 ...
@@ -843,48 +842,48 @@ 
    26 June, 2018
    
 ##   ..$ PathogenName       : chr [1:60] "Campylobacter jejuni and Campylobacter coli" "Rotavirus" "Giardia duodenalis" "Campylobacter jejuni and Campylobacter coli" ...
 ##   ..$ PathogenGroup      : chr [1:60] "Bacteria" "Viruses" "Protozoa" "Bacteria" ...
 ##   ..$ events             : int [1:60] 365 365 365 365 365 365 365 365 365 365 ...
-##   ..$ inflow_median      : num [1:60] 4533 4768 5409 4533 4768 ...
-##   ..$ logreduction_median: num [1:60] 8.04 7.54 4.09 7.38 7.32 ...
-##   ..$ volume_sum         : num [1:60] 618 618 618 618 618 ...
-##   ..$ exposure_sum       : num [1:60] 3.42 88.95 4990.57 2.81 4.95 ...
-##   ..$ dose_sum           : int [1:60] 5 90 4902 4 5 1 2 93 4413 3 ...
-##   ..$ infectionProb_sum  : num [1:60] 0.0865 1 1 0.0714 0.7831 ...
-##   ..$ illnessProb_sum    : num [1:60] 0.0612 0.2189 1 0.0504 0.0389 ...
-##   ..$ dalys_sum          : num [1:60] 0.000288 0.003436 0.02144 0.000236 0.000553 ...
+##   ..$ inflow_median      : num [1:60] 4625 4499 4900 4625 4499 ...
+##   ..$ logreduction_median: num [1:60] 8.13 7.41 4.1 7.32 7.5 ...
+##   ..$ volume_sum         : num [1:60] 595 595 595 595 595 ...
+##   ..$ exposure_sum       : num [1:60] 3.84 139.82 5157.58 3.3 3.64 ...
+##   ..$ dose_sum           : int [1:60] 8 145 5231 3 5 0 6 49 6215 5 ...
+##   ..$ infectionProb_sum  : num [1:60] 0.1275 1 1 0.0541 0.7831 ...
+##   ..$ illnessProb_sum    : num [1:60] 0.0905 0.3056 1 0.038 0.0389 ...
+##   ..$ dalys_sum          : num [1:60] 0.00043 0.005071 0.022738 0.000177 0.000553 ...
 ##   ..- attr(*, "vars")= chr [1:5] "repeatID" "TreatmentSchemeID" "TreatmentSchemeName" "PathogenID" ...
 ##   ..- attr(*, "drop")= logi TRUE
    
 
    Thus the user has access to all
    
 
    #5 Visualise results
    
 
    Finally the results of the QMRA can be visualised for each system component as shown below:
    
 
    ##5.1 Inflow
    
-
+
 
    
 Simulated inflow concentrations
    
 Simulated inflow concentrations
 
    
 
    
 
    ##5.2 Treatment
    
-
+
 
    
 Simulated reductions in the treatment plant
    
 Simulated reductions in the treatment plant
 
    
 
    
 
    ##5.3 Effluent
    
-
+
 
    
 Simulated effluent concentrations
    
 Simulated effluent concentrations
 
    
 
    
 
    ##5.4 Exposure
    
-
+
 
    
 Simulated dose per event
    
 Simulated dose per event
 
    
 
    
-
+
 
    
 Simulated ingested volume per event
    
 Simulated ingested volume per event
@@ -892,38 +891,38 @@ 
    26 June, 2018
    
 
    
 
    ##5.5 Health results
    
 
    ###5.5.1 Per event
    
-
+
 
    
 Simulated infection probability per event
    
 Simulated infection probability per event
 
    
 
    
-
+
 
    
 Simulated illness probability per event
    
 Simulated illness probability per event
 
    
 
    
-
+
 
    
 Simulated DALYs per event
    
 Simulated DALYs per event
 
    
 
    
 
    ###5.5.2 Total
    
-
+
 
    
 Simulated total infection probability (for all events)
    
 Simulated total infection probability (for all events)
 
    
 
    
-
+
 
    
 Simulated total illness probability (for all events
    
 Simulated total illness probability (for all events
 
    
 
    
-
+
 
    
 Simulated total DALYs (for all events)
    
 Simulated total DALYs (for all events)
@@ -958,14 +957,14 @@ 
    26 June, 2018
    
 Campylobacter jejuni and Campylobacter coli
 Bacteria
 365
-4532.811
-8.035069
-617.9005
-3.4190219
-5
-0.0865228
-0.0611605
-0.0002878
+4625.433
+8.131748
+594.7
+3.8379799
+8
+0.1274745
+0.0905006
+0.0004302
 
 
 1
@@ -975,14 +974,14 @@ 
    26 June, 2018
    
 Rotavirus
 Viruses
 365
-4767.988
-7.535198
-617.9005
-88.9485377
-90
-0.9999794
-0.2188515
-0.0034358
+4498.722
+7.408125
+594.7
+139.8199025
+145
+0.9999999
+0.3055813
+0.0050712
 
 
 1
@@ -992,14 +991,14 @@ 
    26 June, 2018
    
 Giardia duodenalis
 Protozoa
 365
-5408.589
-4.090440
-617.9005
-4990.5679959
-4902
+4899.646
+4.100530
+594.7
+5157.5783862
+5231
 1.0000000
 0.9999999
-0.0214401
+0.0227377
 
 
 1
@@ -1009,14 +1008,14 @@ 
    26 June, 2018
    
 Campylobacter jejuni and Campylobacter coli
 Bacteria
 365
-4532.811
-7.382850
-617.9005
-2.8097071
-4
-0.0714101
-0.0504026
-0.0002364
+4625.433
+7.324325
+594.7
+3.3005636
+3
+0.0540504
+0.0380453
+0.0001773
 
 
 1
@@ -1026,10 +1025,10 @@ 
    26 June, 2018
    
 Rotavirus
 Viruses
 365
-4767.988
-7.320194
-617.9005
-4.9468689
+4498.722
+7.504914
+594.7
+3.6441597
 5
 0.7830950
 0.0388850
@@ -1043,21 +1042,21 @@ 
    26 June, 2018
    
 Giardia duodenalis
 Protozoa
 365
-5408.589
-7.322425
-617.9005
-0.7126479
-1
-0.0197033
-0.0059110
-0.0000089
+4899.646
+7.404464
+594.7
+0.6926095
+0
+0.0000000
+0.0000000
+0.0000000
 
 
 
 
    ##6 Export results
    
-
    E.g. Write reports for all configurations in package subfolder extdata/configs/ (here: C:/Users/mrustl.KWB/Documents/R/win-library/3.4/kwb.qmra/extdata/configs):
    
-
+
    E.g. Write reports for all configurations in package subfolder extdata/configs/ (here: C:/Users/mrustl.KWB/Documents/R/win-library/3.5/kwb.qmra/extdata/configs):
    
+
   
    
 
   
     
    
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 2c29975a..4eaaa281 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,8 +5,6 @@ articles:
   doseresponse: doseresponse.html
   general: general.html
   installation: installation.html
-  OldFord_PotableReuse: OldFord_PotableReuse.html
-  OldFord_PublicIrrigation: OldFord_PublicIrrigation.html
   usage: usage.html
   web_app: web_app.html
 urls:
diff --git a/docs/reference/backcalcHelper_infectionRisk_perDay.html b/docs/reference/backcalcHelper_infectionRisk_perDay.html
index e2e64a4e..2574d82d 100644
--- a/docs/reference/backcalcHelper_infectionRisk_perDay.html
+++ b/docs/reference/backcalcHelper_infectionRisk_perDay.html
@@ -153,8 +153,8 @@ 
    Backcalculate risk: infection (helper function)
    
     
     
    
 
-    
    backcalcHelper_infectionRisk_perDay(infectionRisk_perDay, exposure_daysPerYear,
-  target_infectionRisk_perYear = 1/10000)
    
+    
    backcalcHelper_infectionRisk_perDay(infectionRisk_perDay,
+  exposure_daysPerYear, target_infectionRisk_perYear = 1/10000)
    
     
     
    Arguments
    
     
diff --git a/docs/reference/calc_infection_risk.html b/docs/reference/calc_infection_risk.html
index 0e7ec1b6..c7fc4dab 100644
--- a/docs/reference/calc_infection_risk.html
+++ b/docs/reference/calc_infection_risk.html
@@ -153,10 +153,10 @@ 
    Risk calculation: infection
    
 
-    
    calc_infection_risk(inflow_orgPerLitre = 10, treatment_logRemoval = 5.8,
-  exposure_daysPerYear = 365, doseresponse_modelType = "dr.expo",
-  waterConsumption_LitrePerDay = 1, target_infectionRisk_perYear = 1/10000,
-  ...)
    
+    
    calc_infection_risk(inflow_orgPerLitre = 10,
+  treatment_logRemoval = 5.8, exposure_daysPerYear = 365,
+  doseresponse_modelType = "dr.expo", waterConsumption_LitrePerDay = 1,
+  target_infectionRisk_perYear = 1/10000, ...)
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/config_write_dummy.html b/docs/reference/config_write_dummy.html
index f84cd593..716e7f58 100644
--- a/docs/reference/config_write_dummy.html
+++ b/docs/reference/config_write_dummy.html
@@ -153,8 +153,8 @@ 
    Config: create dummy configuration
    
 
-    
    config_write_dummy(confDir = system.file("extdata/configs/dummy", package =
-  "kwb.qmra"))
    
+    
    config_write_dummy(confDir = system.file("extdata/configs/dummy", package
+  = "kwb.qmra"))
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/distribution_repeater.html b/docs/reference/distribution_repeater.html
index 7d6d0e76..cf13fa03 100644
--- a/docs/reference/distribution_repeater.html
+++ b/docs/reference/distribution_repeater.html
@@ -153,8 +153,8 @@ 
    Helper function: distributon repeater
    
 
-    
    distribution_repeater(number_of_repeatings = 10, number_of_events = 365,
-  func, ...)
    
+    
    distribution_repeater(number_of_repeatings = 10,
+  number_of_events = 365, func, ...)
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/dr.db_model.html b/docs/reference/dr.db_model.html
index a1776d8a..d6826c0f 100644
--- a/docs/reference/dr.db_model.html
+++ b/docs/reference/dr.db_model.html
@@ -153,8 +153,8 @@ 
    Generate table with different doses for dr.db_download()
    
 
-    
    dr.db_model(dr.db = dr.db_download(), dose = sfsmisc::lseq(from = 1, to =
-  10^10, length = 1000))
    
+    
    dr.db_model(dr.db = dr.db_download(), dose = sfsmisc::lseq(from = 1, to
+  = 10^10, length = 1000))
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/generate_random_values.html b/docs/reference/generate_random_values.html
index 7735b01f..034c7d1f 100644
--- a/docs/reference/generate_random_values.html
+++ b/docs/reference/generate_random_values.html
@@ -153,8 +153,8 @@ 
    Create random distribution based on configuration file
    
 
-    
    generate_random_values(config, number_of_repeatings = 1, number_of_events,
-  debug = TRUE)
    
+    
    generate_random_values(config, number_of_repeatings = 1,
+  number_of_events, debug = TRUE)
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/plot_total_dalys.html b/docs/reference/plot_total_dalys.html
index 0bc85fee..b07d9e32 100644
--- a/docs/reference/plot_total_dalys.html
+++ b/docs/reference/plot_total_dalys.html
@@ -153,7 +153,8 @@ 
    plot total DALYs
    
 
-    
    plot_total_dalys(risk, labelling = FALSE, title = "", tolerance = 1e-06)
    
+    
    plot_total_dalys(risk, labelling = FALSE, title = "",
+  tolerance = 1e-06)
    Arguments
    
     
     
     
     
     
    
diff --git a/docs/reference/report_workflow.html b/docs/reference/report_workflow.html
index efe0648d..08bf489b 100644
--- a/docs/reference/report_workflow.html
+++ b/docs/reference/report_workflow.html
@@ -154,8 +154,8 @@ 
    Create report (not working for "shiny" reports)
    report_workflow(confDirs = system.file("extdata/configs/", package =
-  "kwb.qmra"), report_template_dir = system.file("extdata/report", package =
-  "kwb.qmra"), report_template_name = "workflow.Rmd",
+  "kwb.qmra"), report_template_dir = system.file("extdata/report",
+  package = "kwb.qmra"), report_template_name = "workflow.Rmd",
   report_output_dir = NULL, openReport = TRUE)
    Arguments
    
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index dcef8517..d4224ea0 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -132,12 +132,6 @@
   
     https://kwb-r.github.io/kwb.qmra/articles/installation.html
   
-  
-    https://kwb-r.github.io/kwb.qmra/articles/OldFord_PotableReuse.html
-  
-  
-    https://kwb-r.github.io/kwb.qmra/articles/OldFord_PublicIrrigation.html
-  
     https://kwb-r.github.io/kwb.qmra/articles/usage.html
   
diff --git a/man/backcalcHelper_infectionRisk_perDay.Rd b/man/backcalcHelper_infectionRisk_perDay.Rd
index 455af75d..cf320cdd 100644
--- a/man/backcalcHelper_infectionRisk_perDay.Rd
+++ b/man/backcalcHelper_infectionRisk_perDay.Rd
@@ -4,8 +4,8 @@
 \alias{backcalcHelper_infectionRisk_perDay}
 \title{Backcalculate risk: infection (helper function)}
 \usage{
-backcalcHelper_infectionRisk_perDay(infectionRisk_perDay, exposure_daysPerYear,
-  target_infectionRisk_perYear = 1/10000)
+backcalcHelper_infectionRisk_perDay(infectionRisk_perDay,
+  exposure_daysPerYear, target_infectionRisk_perYear = 1/10000)
 }
 \arguments{
 \item{infectionRisk_perDay}{no default. will be set by function backcalc_infectionRisk_perDay()}
diff --git a/man/calc_infection_risk.Rd b/man/calc_infection_risk.Rd
index 2293a3ea..ce786d6a 100644
--- a/man/calc_infection_risk.Rd
+++ b/man/calc_infection_risk.Rd
@@ -4,10 +4,10 @@
 \alias{calc_infection_risk}
 \title{Risk calculation: infection}
 \usage{
-calc_infection_risk(inflow_orgPerLitre = 10, treatment_logRemoval = 5.8,
-  exposure_daysPerYear = 365, doseresponse_modelType = "dr.expo",
-  waterConsumption_LitrePerDay = 1, target_infectionRisk_perYear = 1/10000,
-  ...)
+calc_infection_risk(inflow_orgPerLitre = 10,
+  treatment_logRemoval = 5.8, exposure_daysPerYear = 365,
+  doseresponse_modelType = "dr.expo", waterConsumption_LitrePerDay = 1,
+  target_infectionRisk_perYear = 1/10000, ...)
 }
 \arguments{
 \item{inflow_orgPerLitre}{concentration of microbiological parameter in inflow
diff --git a/man/config_write_dummy.Rd b/man/config_write_dummy.Rd
index 5cb15a77..b68f54f8 100644
--- a/man/config_write_dummy.Rd
+++ b/man/config_write_dummy.Rd
@@ -4,8 +4,8 @@
 \alias{config_write_dummy}
 \title{Config: create dummy configuration}
 \usage{
-config_write_dummy(confDir = system.file("extdata/configs/dummy", package =
-  "kwb.qmra"))
+config_write_dummy(confDir = system.file("extdata/configs/dummy", package
+  = "kwb.qmra"))
 }
 \arguments{
 \item{confDir}{directory to save the dummy configuration files (Default:
diff --git a/man/distribution_repeater.Rd b/man/distribution_repeater.Rd
index a74ba596..6e499052 100644
--- a/man/distribution_repeater.Rd
+++ b/man/distribution_repeater.Rd
@@ -4,8 +4,8 @@
 \alias{distribution_repeater}
 \title{Helper function: distributon repeater}
 \usage{
-distribution_repeater(number_of_repeatings = 10, number_of_events = 365,
-  func, ...)
+distribution_repeater(number_of_repeatings = 10,
+  number_of_events = 365, func, ...)
 }
 \arguments{
 \item{number_of_repeatings}{how often should the random distribution with the 
diff --git a/man/dr.db_model.Rd b/man/dr.db_model.Rd
index ee76b371..491fe5c5 100644
--- a/man/dr.db_model.Rd
+++ b/man/dr.db_model.Rd
@@ -4,8 +4,8 @@
 \alias{dr.db_model}
 \title{Generate table with different doses for dr.db_download()}
 \usage{
-dr.db_model(dr.db = dr.db_download(), dose = sfsmisc::lseq(from = 1, to =
-  10^10, length = 1000))
+dr.db_model(dr.db = dr.db_download(), dose = sfsmisc::lseq(from = 1, to
+  = 10^10, length = 1000))
 }
 \arguments{
 \item{dr.db}{as retrieved by dr.db_download(), default: dr.db_download()}
diff --git a/man/generate_random_values.Rd b/man/generate_random_values.Rd
index 43a1e1b3..472d19d6 100644
--- a/man/generate_random_values.Rd
+++ b/man/generate_random_values.Rd
@@ -4,8 +4,8 @@
 \alias{generate_random_values}
 \title{Create random distribution based on configuration file}
 \usage{
-generate_random_values(config, number_of_repeatings = 1, number_of_events,
-  debug = TRUE)
+generate_random_values(config, number_of_repeatings = 1,
+  number_of_events, debug = TRUE)
 }
 \arguments{
 \item{config}{as retrieved by config_read()}
diff --git a/man/plot_total_dalys.Rd b/man/plot_total_dalys.Rd
index 25722439..52c594e0 100644
--- a/man/plot_total_dalys.Rd
+++ b/man/plot_total_dalys.Rd
@@ -4,7 +4,8 @@
 \alias{plot_total_dalys}
 \title{plot total DALYs}
 \usage{
-plot_total_dalys(risk, labelling = FALSE, title = "", tolerance = 1e-06)
+plot_total_dalys(risk, labelling = FALSE, title = "",
+  tolerance = 1e-06)
 }
 \arguments{
 \item{risk}{list as retrieved by simulate_risk()}
diff --git a/man/report_workflow.Rd b/man/report_workflow.Rd
index 38b75df0..56258531 100644
--- a/man/report_workflow.Rd
+++ b/man/report_workflow.Rd
@@ -5,8 +5,8 @@
 \title{Create report (not working for "shiny" reports)}
 \usage{
 report_workflow(confDirs = system.file("extdata/configs/", package =
-  "kwb.qmra"), report_template_dir = system.file("extdata/report", package =
-  "kwb.qmra"), report_template_name = "workflow.Rmd",
+  "kwb.qmra"), report_template_dir = system.file("extdata/report",
+  package = "kwb.qmra"), report_template_name = "workflow.Rmd",
   report_output_dir = NULL, openReport = TRUE)
 }
 \arguments{