Do not execute package creation script

.Rbuildignore

@@ -1,4 +1,4 @@
-^BerlinWaterModel\.Rproj$
+^kwb\.BerlinWaterModel\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^_pkgdown\.yml$
@@ -8,3 +8,4 @@
 ^codecov\.yml$
 ^index\.md$
 ^README\.md$
+^data-raw$

.github/workflows/R-CMD-check.yaml

@@ -22,11 +22,11 @@ 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: windows-latest, r: 'oldrel'}
-          - {os: windows-latest, r: 'release'}
+          - { os: macOS-latest, r: 'release' }
+          - { os: ubuntu-24.04, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest" }
+          - { os: windows-latest, r: 'devel' }
+          - { os: windows-latest, r: 'oldrel' }
+          - { os: windows-latest, r: 'release' }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -51,20 +51,16 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
 
-      - name: Install system dependencies
+      - name: Install linux system dependencies
         if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+        run: sudo apt-get install -y libglpk-dev
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
@@ -81,3 +77,4 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+

.github/workflows/pkgdown.yaml

@@ -30,7 +30,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/test-coverage.yaml

@@ -30,7 +30,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

DESCRIPTION

@@ -2,6 +2,8 @@ Package: kwb.BerlinWaterModel
 Title: R Package of Berlin Water Model
 Version: 0.0.0.9000
 Authors@R: c(
+    person("Daniel", "Wicke", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-5722-5433")),
     person("Michael", "Rustler", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0647-7726")),
     person("IMPETUS", role = "fnd"),
@@ -11,11 +13,25 @@ Description: R Package of Berlin Water Model.
 License: MIT + file LICENSE
 URL: https://github.com/KWB-R/kwb.BerlinWaterModel
 BugReports: https://github.com/KWB-R/kwb.BerlinWaterModel/issues
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+Depends: 
+    R (>= 2.10)
+Imports: 
+    dplyr,
+    igraph,
+    magrittr,
+    readr,
+    rlang,
+    stringr,
+    tibble,
+    tidyr,
+    tidyselect
 Suggests: 
     covr,
     knitr,
     rmarkdown
-VignetteBuilder: knitr
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,2 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+export(calculate_flowpath)
+export(config_read)
+export(fill_timeseries)
+export(find_node_orders)
+importFrom(dplyr,arrange)
+importFrom(dplyr,arrange_at)
+importFrom(dplyr,desc)
+importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
+importFrom(dplyr,mutate)
+importFrom(igraph,V)
+importFrom(igraph,distances)
+importFrom(igraph,reverse_edges)
+importFrom(igraph,vcount)
+importFrom(magrittr,"%>%")
+importFrom(readr,locale)
+importFrom(readr,read_csv2)
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(stats,setNames)
+importFrom(stringr,str_remove)
+importFrom(tibble,tibble)
+importFrom(tidyr,fill)
+importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
+importFrom(tidyselect,matches)

R/calculate_flowpath.R

@@ -0,0 +1,83 @@
+#' Helper function: find node order
+#'
+#' @param links links
+#' @param nodes nodes
+#' @param start_node start node
+#' @param reverse should network direction be reversed? (default: FALSE)
+#' @param mode 	Character constant, gives whether the shortest paths to or from
+#' the given vertices should be calculated for directed graphs. If out then the
+#' shortest paths from the vertex, if ⁠in⁠ then to it will be considered. If all,
+#' the default, then the graph is treated as undirected, i.e. edge directions
+#' are not taken into account. This argument is ignored for undirected graphs
+#' (default: "out")
+#'
+#' @return data frame with additional column "order"
+#' @export
+#' @importFrom igraph distances reverse_edges V vcount
+#' @importFrom dplyr mutate
+#' @importFrom rlang .data
+find_node_orders <- function(links, nodes, start_node, reverse = FALSE, mode = "out") {
+
+
+    # Erstellen eines gerichteten Graphen aus den Links
+  graph <- igraph::graph_from_data_frame(d = links,
+                                         vertices = nodes,
+                                         directed = TRUE)
+
+
+  if(reverse) {
+    graph <- igraph::reverse_edges(graph)
+  }
+
+  # Berechnen der Kürzesten Wege vom Startknoten
+  distances <- igraph::distances(graph, v = start_node, mode = mode)
+
+  # Initialisieren der Ordnungen
+  orders <- rep(NA, igraph::vcount(graph))
+  names(orders) <- igraph::V(graph)$name
+
+  # Zuweisen der Knoten zu ihren jeweiligen Ordnungen
+  for (i in 1:igraph::vcount(graph)) {
+    node_name <- igraph::V(graph)[i]$name
+    if (!is.infinite(distances[start_node, node_name])) {
+      orders[node_name] <- distances[start_node, node_name]
+    } else {
+      orders[node_name] <- NA  # Knoten, die vom Startknoten aus nicht erreichbar sind
+    }
+  }
+
+  # Hinzufügen der Ordnungen zu den Knoten
+  nodes <- nodes %>%
+    dplyr::mutate(order = orders[.data$name])
+
+  return(nodes)
+}
+
+
+#' Calculate Flowpath
+#'
+#' @param flow_name flow name (as named in nodes) where calculation should start
+#' @param links links
+#' @param nodes nodes
+#' @param backward should flowpath be calculated backwards? (default: FALSE)
+#'
+#' @return data frame with column "order" indicating the flow path order
+#' @export
+#' @importFrom dplyr arrange desc filter
+calculate_flowpath <- function(flow_name,
+                               links,
+                               nodes,
+                               backward = FALSE) {
+
+  stopifnot(flow_name %in% nodes$name)
+  stopifnot(any(nodes$group == "Fliessabschnitt"))
+
+  find_node_orders(links = links,
+                   nodes = nodes,
+                   start_node = flow_name,
+                   reverse = backward,
+                   mode = "out") %>%
+    dplyr::arrange(dplyr::desc(.data$order)) %>%
+    dplyr::filter(.data$group == "Fliessabschnitt",
+                  !is.na(.data$order))
+}

R/config_read.R

@@ -0,0 +1,31 @@
+#' Configuration: Read
+#'
+#' @param config_dir directory with configuration files (default:
+#' system.file("extdata/config", package = "kwb.BerlinWaterModel")). It is mandatory
+#' that there are three files within this folder: "flows_in_out.csv", "outflows_multiple.csv"
+#' and "sections.csv"
+#' @param file_encoding encoding for reading the files (default: "UTF-8")
+#'
+#' @return list with three sublists "flows_in_out", "outflows_multiple" and
+#' "sections
+#' @export
+#'
+#' @examples
+#' config <- kwb.BerlinWaterModel::config_read()
+#' config
+#' @importFrom stats setNames
+#' @importFrom readr read_csv2 locale
+#' @importFrom stringr str_remove
+config_read <- function(config_dir = "inst/extdata/config", file_encoding = "UTF-8") {
+
+  files <- list.files(config_dir, full.names = TRUE)
+
+  filenames_without_extension <- basename(files) %>% stringr::str_remove("\\..*")
+
+  stopifnot(all(filenames_without_extension %in% c("flows_in_out", "outflows_multiple", "sections")))
+
+  stats::setNames(lapply(files, function(file) {
+
+    readr::read_csv2(file, locale = readr::locale(encoding = file_encoding))
+  }), nm =   filenames_without_extension)
+}

R/dataset_inflows.R

@@ -0,0 +1,11 @@
+#' Dataset: Inflows
+#'
+#' Dataset with inflows
+#'
+#' @format A tibble with 398,840 rows and three columns
+#' \describe{
+#'   \item{date}{date}
+#'   \item{id}{id of inflow station}
+#'   \item{cbm_per_second}{measured flow in cubicmeter per second}
+#' }
+"inflows"

R/dataset_ww.R

@@ -0,0 +1,13 @@
+#' Dataset: Waterworks (WW) Abstractions per Gallery
+#'
+#' Dataset with waterworks abstractions per gallery
+#'
+#' @format A tibble with 17,141 rows and three columns
+#' \describe{
+#'   \item{date}{date}
+#'   \item{id}{id of WW gallery}
+#'   \item{cbm_per_second}{measured flow in cubicmeter per second, backcalculated
+#'   from monthly abstraction sums by dividing through number of days in month}
+#' }
+"ww"
+

R/dataset_wwtp.R

@@ -0,0 +1,13 @@
+#' Dataset: WWTP (Wastewater Treatment Plant) Flows
+#'
+#' Dataset with WWTP inflows
+#'
+#' @format A tibble with 1,152 rows and three columns
+#' \describe{
+#'   \item{date}{date}
+#'   \item{id}{id of WWTP}
+#'   \item{cbm_per_second}{measured flow in cubicmeter per second, backcalculated
+#'   from monthly effluent sums by dividing through number of days in month}
+#' }
+"wwtp"
+

R/fill_timeseries.R

@@ -0,0 +1,64 @@
+#' Fill Timeseries based on User Defined Intervall (days, hours, minutes or seconds)
+#'
+#' @param df data frame with data
+#' @param col_datetime column of date or datetime
+#' @param temporal_resolution select one of ("days", "hours", "minutes", "seconds"),
+#' (default: "days")
+#' @param direction in which direction should the parameter be filled ("up" or
+#' "down"), default: "up"
+#' @return tibble with filled dates. Note that if min(daste) == "xxxx-xx-end-of-month-day"
+#' the min(date) is set to "xxxx-xx-01", as monthly measured (originally summed)
+#' values were set to the last day of the month, but are valid for the whole month
+#' @export
+#'
+#' @importFrom tibble tibble
+#' @importFrom dplyr arrange_at full_join
+#' @importFrom tidyr fill pivot_wider separate
+#' @importFrom tidyselect matches
+#' @importFrom rlang :=
+fill_timeseries <- function(df, col_datetime = "date", temporal_resolution = "days", direction = "up")
+{
+  stopifnot(col_datetime %in% names(df))
+
+  temp_res <- c("seconds" = "sec", "minutes" = "min", "hours" = "hour", "days" = "days")
+  stopifnot(temporal_resolution %in% names(temp_res))
+
+  stopifnot(direction %in% c("up", "down"))
+
+  dates <- df[[col_datetime]]
+  date_min_monthly <- as.Date(paste0(stringr::str_sub(min(dates), 1, 8), "01"))
+
+  date_min <- if (min(dates) != date_min_monthly) {
+    date_min_monthly
+  } else {
+    min(dates)
+  }
+
+
+  date_sequence <- if(names(temp_res[temporal_resolution]) == "days") {
+    seq.Date(from = date_min, to = max(dates),
+             by = temp_res[temporal_resolution])
+  } else {
+    seq.POSIXt(from = as.POSIXct(date_min, tz = "UTC"),
+               to = as.POSIXct(max(dates), tz = "UTC"),
+               by = temp_res[temporal_resolution])
+  }
+
+  new_dates <-  tibble::tibble(!!(col_datetime) := date_sequence)
+
+
+  df_new <- df %>%
+    dplyr::full_join(new_dates,
+                     by = col_datetime) %>%
+    dplyr::arrange_at(col_datetime) %>%
+    tidyr::fill(!tidyselect::matches(col_datetime), .direction = direction)
+
+
+  if(temporal_resolution != "days") {
+    df_new <- df_new %>%
+      dplyr::rename(datetime = col_datetime)
+  }
+
+  df_new
+
+}

R/utils-pipe.R

@@ -0,0 +1,14 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+#' @param lhs A value or the magrittr placeholder.
+#' @param rhs A function call using the magrittr semantics.
+#' @return The result of calling `rhs(lhs)`.
+NULL

_pkgdown.yml

@@ -1,7 +1,9 @@
 url: https://kwb-r.github.io/kwb.BerlinWaterModel
 authors:
+  Daniel Wicke:
+    href: https://www.kompetenz-wasser.de/en/ueber-uns/team/daniel-wicke
   Michael Rustler:
-    href: https://mrustl.de
+    href: https://www.kompetenz-wasser.de/en/ueber-uns/team/michael-rustler
   IMPETUS:
     href: https://www.kompetenz-wasser.de/en/forschung/projekte/impetus
     html: <img src='https://climate-impetus.eu/wp-content/uploads/2021/12/horizontal.png'