KWB-R · mrustl · Aug 30, 2021 · Sep 9, 2021 · Sep 9, 2021 · Sep 10, 2021
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,13 +22,14 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'release'}      
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}      
-          - {os: windows-latest, r: 'devel'}          
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'devel'}
           - {os: windows-latest, r: 'oldrel'}
           - {os: windows-latest, r: 'release'}
 
     env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
 

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -21,7 +21,7 @@ jobs:
         run: Rscript -e 'roxygen2::roxygenise()'
       - name: commit
         run: |
-          git add man/\* NAMESPACE
+          git add man/\* NAMESPACE DESCRIPTION
           git commit -m 'Document'
       - uses: r-lib/actions/pr-push@master
         with:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,35 +1,19 @@
 Package: kwb.qmra
 Title: QMRA (quantitative microbial risk assessment)
-Version: 0.3.0
-Authors@R: 
-    c(person(given = "Michael",
-             family = "Rustler",
-             role = c("aut", "cre"),
-             email = "michael.rustler@kompetenz-wasser.de",
-             comment = c(ORCID = "0000-0003-0647-7726")),
-      person(given = "Hauke",
-             family = "Sonnenberg",
-             role = "aut",
-             email = "hauke.sonnenberg@kompetenz-wasser.de",
-             comment = c(ORCID = "0000-0001-9134-2871")),
-      person(given = "Wolfgang",
-             family = "Seis",
-             role = c("ctb", "rev"),
-             email = "wolfgang.seis@kompetenz-wasser.de",
-             comment = c(ORCID = "0000-0002-7436-8575")),
-      person(given = "Ralf",
-             family = "Junghanns",
-             role = c("ctb"),
-             email = "ralf.junghanns@gmail.com",
-             comment = c(ORCID = "")),
-      person(given = "Kompetenzzentrum Wasser Berlin gGmbH",
-             role = "cph"),
-      person(given = "AquaNES",
-             role = "fnd"),
-      person(given = "DEMOWARE",
-             role = "fnd"),
-      person(given = "Smart-Control",
-             role = "fnd"))
+Version: 0.3.0.9000
+Authors@R: c(
+    person("Michael", "Rustler", , "michael.rustler@kompetenz-wasser.de", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-0647-7726")),
+    person("Hauke", "Sonnenberg", , "hauke.sonnenberg@kompetenz-wasser.de", role = "aut",
+           comment = c(ORCID = "0000-0001-9134-2871")),
+    person("Wolfgang", "Seis", , "wolfgang.seis@kompetenz-wasser.de", role = c("ctb", "rev"),
+           comment = c(ORCID = "0000-0002-7436-8575")),
+    person("Ralf", "Junghanns", , "ralf.junghanns@gmail.com", role = "ctb"),
+    person("Kompetenzzentrum Wasser Berlin gGmbH (KWB)", role = "cph"),
+    person("AquaNES", role = "fnd"),
+    person("DEMOWARE", role = "fnd"),
+    person("Smart-Control", role = "fnd")
+  )
 Description: QMRA for water supply systems.
 License: MIT + file LICENSE
 URL: http://github.com/KWB-R/kwb.qmra/
@@ -66,9 +50,9 @@ Suggests:
 VignetteBuilder: 
     knitr
 Remotes: 
-    github::kwb-r/kwb.utils@v0.7.0,
-    github::kwb-r/qmra.db@v0.10.0
+    github::kwb-r/kwb.utils,
+    github::kwb-r/qmra.db
+Config/testthat/edition: 3
 Encoding: UTF-8
 LazyLoad: yes
 RoxygenNote: 7.1.1
-Config/testthat/edition: 3
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2016 - 2020 Kompetenzzentrum Wasser Berlin gGmbH (KWB)
+Copyright (c) 2016 - 2022 Kompetenzzentrum Wasser Berlin gGmbH (KWB)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2016 - 2020 Kompetenzzentrum Wasser Berlin gGmbH (KWB)
+Copyright (c) 2016 - 20220 Kompetenzzentrum Wasser Berlin gGmbH (KWB)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# [kwb.qmra 0.3.1](https://github.com/KWB-R/kwb.qmra/releases/tag/v0.3.1) <small>2022-06-08</small>
+
+* Harmonise with kwb.pkgbuild
+
 # [kwb.qmra 0.3.0](https://github.com/KWB-R/kwb.qmra/releases/tag/v0.3.0) <small>2021-02-23</small>
 
 Adaptions for project [Smart-Control](https://www.kompetenz-wasser.de/en/project/smart-control/):

diff --git a/R/random_distribution.R b/R/random_distribution.R
@@ -89,52 +89,60 @@ get_percentile <- function(percent_within_minmax = 0.9)
 }
 
 #' Create random distribution
-#' @param type "uniform" calls runif(), "log10_uniform" calls 
-#' 10^runif(number_of_events, log10_min, log10_max), "triangle" calls 
-#' EnvStats::rtri(), "lognorm" calls rlnorm(), "norm" calls rnorm() and 
-#' "log10_norm" calls 10^rnorm(number_of_events, mean = log10_mean, 
+#' @param type "uniform" calls \code{\link[stats]{runif}}, "log10_uniform" calls 
+#' 10^\code{\link[stats]{runif}}(number_of_events, log10_min, log10_max), "triangle" 
+#' calls \code{\link[EnvStats]{rtri}}, "lognorm" calls \code{\link[stats]{rlnorm}}, 
+#' "norm" calls \code{\link[stats]{rnorm}} and "log10_norm" calls 
+#' 10^\code{\link[stats]{rnorm}}(number_of_events, mean = log10_mean, 
 #' sdev = log10_sdev), (default: "uniform") 
 #' @param number_of_repeatings how often should the random distribution with the
 #' same parameters be generated (default: 1)
 #' @param  number_of_events number of events
 #' @param value constant value (no random number), gets repeated number_of_events
 #' times (if 'type' = 'value')
-#' @param min minimum value (default: 10), only used if 'type' is "runif" or
+#' @param min minimum value (default: 10), only used if 'type' is "uniform" or
 #' "triangle"
-#' @param max maximum value (default: 1000), only used if 'type' is "runif" or
+#' @param max maximum value (default: 1000), only used if 'type' is "uniform" or
 #' "triangle"
 #' @param percent_within_minmax percent of data point within min/max (default: 
-#' 0.9 i.e. 90 percent
+#' 0.9 i.e. 90 percent,see also \code{\link{get_percentile}}
 #' @param min_zero  only used if 'type' is "log10_uniform" or 
 #' "log10_norm", "norm" or "lognorm" and "min" value equal zero. 
 #' In this case the zero is replaced by this value (default: 0.01), see also 
 #' \code{\link{default_min}}
-#' @param log10_min minimum value (default: default_min(min, max, 
+#' @param log10_min minimum value (default: \code{\link{default_min}}(min, max, 
 #' min_zero, f = log10)), only used if 'type' is "log10_uniform" or "log10_norm"
-#' @param log10_max maximum value (default: ifelse(max > 0, log10(max), 
-#' log10_zero_threshold), only used if 'type' is "log10_uniform" or "log10_norm"
+#' @param log10_max maximum value (default: \code{\link{default_max}}(max, 
+#' min_zero * 10, f = log10)), only used if 'type' is "log10_uniform" or "log10_norm"
 #' @param log10_mean mean value (default: (log10_min + log10_max)/2), only used 
 #' if 'type' is "log10_norm"
 #' @param log10_sdev standard deviation (default: abs((log10_max- log10_mean) / 
-#' get_percentile(0.95)), only used if 'type' is "log10_norm"
-#' @param mean mean value (default: (default_min(min, max, min_zero) / 
-#' default_max(max, 10*min_zero)) / 2), only used if 'type' is "norm"
-#' @param sdev standard deviation (default: abs((default_max(max, 10*min_zero) - 
-#' mean) / get_percentile(0.95))), only used if 'type' is "norm"
-#' @param meanlog log mean value (default: mean(log((min + max) / 2))), only
+#' \code{\link{get_percentile}}(percent_within_minmax))), only used if 'type' is 
+#' "log10_norm"
+#' @param mean mean value (default: (\code{\link{default_min}}(min, max, min_zero) / 
+#' \code{\link{default_max}}(max, 10*min_zero)) / 2), only used if 'type' is "norm"
+#' @param sdev standard deviation (default: abs((log10_max - log10_mean) / 
+#' \code{\link{get_percentile}}(percent_within_minmax))), only used if 'type' is 
+#' "norm"
+#' @param meanlog log mean value (default: 
+#' mean(log( \code{\link{default_min}}(min, max, min_zero) +  
+#' \code{\link{default_max}}(max, 10 * min_zero)) / 2)), only
 #' used if 'type' is "lognorm"
-#' @param sdlog standard deviation (default: abs(sd(c(default_min(min, max, 
-#' min_zero, f = log)))) ), only used if 'type' is "lognorm"
-#' @param mode (default: default_min(min, max, min_zero) + 
-#' default_max(max, 10 * min_zero) / 2), only used if 'type' is "triangle"
+#' @param sdlog standard deviation (default: abs(sd(c(
+#' \code{\link{default_min}}(min, max, min_zero, f = log), 
+#' \code{\link{default_max}}(max, 10 * min_zero, f = log)))), 
+#' only used if 'type' is "lognorm"
+#' @param mode (default: \code{\link{default_min}}(min, max, min_zero) + 
+#' \code{\link{default_max}}(max, 10 * min_zero) / 2), only used if 'type' is 
+#' "triangle"
 #' @param debug print debug information (default: TRUE)
 #' @return list with parameters of user defined random distribution and
 #' corresponding values
 #' @export
 #' @importFrom stats sd qnorm runif rnorm rlnorm
 #' @importFrom dplyr mutate
 #' @importFrom rlang .data
-#' @seealso for random triangle see \code{\link{rtri}}, for default 
+#' @seealso for random triangle see \code{\link[EnvStats]{rtri}}, for default 
 #' min/max see \code{\link{default_min}},  \code{\link{default_max}} and 
 #' \code{\link{get_percentile}} 
 #' 

diff --git a/README.md b/README.md
@@ -4,6 +4,8 @@
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![DOI](https://zenodo.org/badge/68301647.svg)](https://zenodo.org/badge/latestdoi/68301647)
 [![Binder](http://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/kwb-r/kwb.qmra/master?urlpath=rstudio)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/kwb.qmra)]()
+[![R-Universe_Status_Badge](https://kwb-r.r-universe.dev/badges/kwb.qmra)](https://kwb-r.r-universe.dev/)
 
 # kwb.qmra
 
@@ -13,6 +15,23 @@ Launch repository (from master) in cloud RStudio session:
 
 [![Binder](http://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/kwb-r/kwb.qmra/master?urlpath=rstudio)
 
+## Installation
+
+For installing the latest release of this R package run the following code below:
+
+```r
+# Enable repository from kwb-r
+options(repos = c(
+  kwbr = 'https://kwb-r.r-universe.dev',
+  CRAN = 'https://cloud.r-project.org'))
+
+# Download and install kwb.qmra in R
+install.packages('kwb.qmra')
+
+# Browse the kwb.qmra manual pages
+help(package = 'kwb.qmra')
+```
+
 ## Documentation
 
 Development version: [https://kwb-r.github.io/kwb.qmra/dev](https://kwb-r.github.io/kwb.qmra/dev)

diff --git a/_pkgdown.yaml b/_pkgdown.yaml
@@ -2,31 +2,39 @@ authors:
   Michael Rustler:
     href: https://mrustl.de
   Hauke Sonnenberg:
-    href: https://github.com/hsonne
+    href: https://www.kompetenz-wasser.de/en/ueber-uns/team/hauke-sonnenberg
   Wolfgang Seis:
-    href: https://www.researchgate.net/profile/Wolfgang_Seis
-  Kompetenzzentrum Wasser Berlin gGmbH:
-    href: https://www.kompetenz-wasser.de
-    html: <img src="http://www.kompetenz-wasser.de/wp-content/uploads/2017/08/cropped-logo-kwb_klein-new.png" height="24" />
-  AquaNES: 
-    href: https://www.kompetenz-wasser.de/en/project/aquanes/
-    html: <img src="https://www.kompetenz-wasser.de/wp-content/uploads/2017/09/11-558x122.jpg" height="24" />
+    href: https://www.kompetenz-wasser.de/en/ueber-uns/team/wolfgang-seis
+  AquaNES:
+    href: https://www.kompetenz-wasser.de/en/forschung/projekte/aquanes
+    html: <img src='https://old.kompetenz-wasser.de/wp-content/uploads/2017/09/11-558x122.jpg' alt='Project AquaNES'
+      width='72' />
   DEMOWARE: 
-    href: https://www.kompetenz-wasser.de/en/project/demoware/
-    html: <img src="https://www.kompetenz-wasser.de/wp-content/uploads/2017/05/demoware-logo.png" height="24" />
+    href: https://www.kompetenz-wasser.de/en/forschung/projekte/demoware/
+    html: <img src='https://www.kompetenz-wasser.de/media/pages/forschung/projekte/demoware/46595105f4-1639132759/demoware-logo.png' alt='Project DEMOWARE'
+      width='72' />
   Smart-Control:
-    href: https://www.kompetenz-wasser.de/en/project/smart-control/
-    html: <img src='https://smart-control.inowas.com/wp-content/uploads/2020/06/cropped-SMART_logo_black.png'
-      height='24' />
+    href: https://www.kompetenz-wasser.de/en/forschung/projekte/smart-control/
+    html: <img src='https://smart-control.inowas.com/wp-content/uploads/2020/06/cropped-SMART_logo_black.png' alt='Project Smart-Control'
+      width='72' />
+  Kompetenzzentrum Wasser Berlin gGmbH (KWB):
+    href: https://www.kompetenz-wasser.de
+    html: <img src='https://publications.kompetenz-wasser.de/img/KWB-Logo.svg' alt='KWB'
+      width='72' />
 template:
-  params:
-    bootswatch: cerulean
-    docsearch:
-      api_key: ba545525664b60ab9e580ae0f7f4ac02
-      index_name: kwb_qmra
+  bootstrap: 5
+  bootswatch: cerulean
+  bslib:
+    bg: '#ffffff'
+    fg: '#000000'
+    primary: '#007aff'
+    border-radius: 0.5rem
+    btn-border-radius: 0.25rem
+development:
+  mode: auto
+
 navbar:
   title: ~
-  type: default
   left:
   - text: Background
     href: articles/general.html
@@ -89,6 +97,14 @@ reference:
       Functions for plotting QMRA results
     contents: 
       - starts_with("plot_")
+
+  - title: Datasets
+    desc: >
+      Datasets within R package
+    contents:       
+      - config_default_json
+      - config_dummy_json
+      - risk_dummy_json
 
   - title: Export data
     desc: >
@@ -100,16 +116,22 @@ reference:
   - title: Helper functions
     desc: >
       Helper functions for performing QMRA
-    contents: 
+    contents:
+      - backcalc_infectionRisk_perDay
+      - calc_health_risk
+      - calc_infection_risk
       - config_write_dummy
       - create_random_distribution
-      - start_with("default")
+      - default_max
+      - default_min
       - generate_random_values 
+      - get_percentile
       - distribution_repeater 
       - dr.betapoisson
       - dr.db_download 
       - dr.db_model 
       - dr.expo
       - poisson_dose
+      - run_app
       - who_getTreatment
 
diff --git a/index.md b/index.md
@@ -4,14 +4,25 @@
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![DOI](https://zenodo.org/badge/68301647.svg)](https://zenodo.org/badge/latestdoi/68301647)
 [![Binder](http://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/kwb-r/kwb.qmra/master?urlpath=rstudio)
-
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/kwb.qmra)]()
+[![R-Universe_Status_Badge](https://kwb-r.r-universe.dev/badges/kwb.qmra)](https://kwb-r.r-universe.dev/)
 
 An R package for QMRA (quantitative microbial risk assessment) of water supply systems
 
 
 ## Installation
 
+For installing the latest release of this R package run the following code below:
+
 ```r
-#install.packages("remotes", repos = "https://cloud.r-project.org")
-remotes::install_github("KWB-R/kwb.qmra")
+# Enable repository from kwb-r
+options(repos = c(
+  kwbr = 'https://kwb-r.r-universe.dev',
+  CRAN = 'https://cloud.r-project.org'))
+
+# Download and install kwb.qmra in R
+install.packages('kwb.qmra')
+
+# Browse the kwb.qmra manual pages
+help(package = 'kwb.qmra')
 ```