Add PEC soil for product with serveral ais

2 files changed, 6 insertions, 271 deletions

diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R
index 73c7e42..3c3ae15 100644
--- a/pkg/R/PEC_soil.R
+++ b/pkg/R/PEC_soil.R
@@ -67,18 +67,19 @@ PEC_soil_product <- function(product, rate, rate_units = "L/ha", interception =
                         plateau_max = numeric(0), plateau_min = numeric(0), 
                         long_term_max = numeric(0),
                         stringsAsFactors = FALSE)
+
   for (ai_name in names(product$ais)) {
     ai <- product$ais[[ai_name]]
     ai_rate <- rate * product$concentrations[ai_name] 
     ini <- PEC_soil(ai_rate,
                     interception = interception, mixing_depth = mixing_depth,
                     bulk_density = bulk_density)
-    results[ai_name, "compound"] <- ai$acronym
+    results[ai_name, "compound"] <- ai$identifier
     results[ai_name, "initial"] <- ini
 
     ini_tillage <- ini * mixing_depth / tillage_depth
     DT50 <- subset(ai$soil_degradation_endpoints, destination == "PECsoil")$DT50
-    if (length(DT50) > 1) stop("More than one PECsoil DT50 for", ai$acronym)
+    if (length(DT50) > 1) stop("More than one PECsoil DT50 for", ai_name)
     if (length(DT50) > 0) {
       if (!is.na(DT50)) {
         k <- log(2) / DT50
@@ -94,16 +95,16 @@ PEC_soil_product <- function(product, rate, rate_units = "L/ha", interception =
       TP <- ai$TPs[[TP_name]]
       max_occurrence = max(subset(ai$transformations, 
                                   grepl("soil", study_type) & 
-                                  acronym == TP$acronym, max_occurrence))
+                                  TP_identifier == TP$identifier, max_occurrence))
       TP_rate <- ai_rate * TP$mw / ai$mw * max_occurrence
       ini <- PEC_soil(TP_rate, interception = interception, mixing_depth = mixing_depth,
                       bulk_density = bulk_density)
-      results[TP_name, "compound"] <- TP$acronym
+      results[TP_name, "compound"] <- TP$identifier
       results[TP_name, "initial"] <- ini
 
       ini_tillage <- ini * mixing_depth / tillage_depth
       DT50 <- subset(TP$soil_degradation_endpoints, destination == "PECsoil")$DT50
-      if (length(DT50) > 1) stop("More than one PECsoil DT50 for", TP$acronym)
+      if (length(DT50) > 1) stop("More than one PECsoil DT50 for", TP_name)
       if (length(DT50) > 0) {
         if (!is.na(DT50)) {
           k <- log(2) / DT50
diff --git a/pkg/R/pfm_chent.R b/pkg/R/pfm_chent.R
deleted file mode 100644
index 67037cb..0000000
--- a/pkg/R/pfm_chent.R
+++ /dev/null
@@ -1,266 +0,0 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program is free software: you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
-#' R6 class for holding a chemical entity
-#'
-#' An R6 class for holding information about a chemical entity that is useful
-#' for fate modelling
-#'
-#' @docType class
-#' @importFrom R6 R6Class
-#' @export
-#' @format An \code{\link{R6Class}} generator object
-#' @field acronym Acronym for local use
-#' @field smiles SMILES code
-#' @field mw Molecular weight
-#' @field main_source Main source of information
-#' @field transformations
-#' @field sorption_endpoints
-#' @examples
-#' atrazine  <- pfm_chent("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68)
-#' print(atrazine)
-#' @keywords data
-
-pfm_chent <- R6Class("pfm_chent",
-  public <- list(
-    acronym = NULL,
-    smiles = NULL,
-    mw = NULL,
-    main_source = NULL,
-    initialize = function(acronym, smiles = NULL, mw = NULL, main_source = NULL) {
-      self$acronym <- acronym
-      self$smiles <- smiles
-      self$mw <- mw
-      self$main_source <- main_source
-    },
-    p0 = data.frame(p0 = numeric(0), T = numeric(0),
-                    comment = character(0), 
-                    source = character(0), pages = character(0),
-                    stringsAsFactors = FALSE),
-    add_p0 = function(p0, T = 25, comment = "", source, pages = NA) {
-      i <- nrow(self$p0) + 1
-      self$p0[i, c("p0", "T")] <- c(p0, T)
-      self$p0[i, c("comment", "pages")] <- c(comment, pages)
-      if (!missing(source)) self$p0[i, "source"] <- source
-    },
-    cwsat = data.frame(cwsat = numeric(0), T = numeric(0),
-                       pH = numeric(0), comment = character(0),
-                       source = character(0), pages = character(0),
-                       stringsAsFactors = FALSE),
-    add_cwsat = function(cwsat, T = NA, pH = NA, comment = "", source, pages = NA) {
-      i <- nrow(self$cwsat) + 1
-      self$cwsat[i, c("cwsat", "T", "pH")] <- c(cwsat, T, pH)
-      self$cwsat[i, c("comment", "pages")] <- c(comment, pages)
-      if (!missing(source)) self$cwsat[i, "source"] <- source
-    },
-    TPs = list(),
-    add_TP = function(x, smiles = NULL, mw = NULL, main_source = NULL) {
-      if (inherits(x, "pfm_chent")) {
-        chent_name <- deparse(substitute(x))
-        chent <- x
-      } else {
-        chent_name <- make.names(x)
-        chent <- pfm_chent$new(x, smiles, mw, main_source) 
-      }
-      self$TPs[[chent_name]] <- chent
-    },
-    transformations = data.frame(study_type = character(0),
-                                 acronym = character(0), 
-                                 max_occurrence = numeric(0), 
-                                 source = character(0), 
-                                 pages = character(0),
-                                 stringsAsFactors = FALSE),
-    add_transformations = function(study_type, TPs, max_occurrence, 
-                                   comment = "", source, pages = NA) {
-      TP_names = make.names(TPs)
-      TP_is_chent = sapply(self$TPs[TP_names], function(x) inherits(x, "pfm_chent"))
-      if (!all(TP_is_chent)) {
-        stop(paste("Please add all TPs using pfm_chent$add_TP()", print(TP_is_chent)))
-      } 
-      chents <- self$TPs[TP_names]
-      if (missing(source)) source <- self$main_source
-      if (is.numeric(pages)) pages <- paste(pages, collapse = ", ")
-      transformations <- data.frame(study_type = study_type, 
-                                    acronym = sapply(chents, function(x) x$acronym),
-                                    max_occurrence = max_occurrence, 
-                                    comment = comment,
-                                    source = source, 
-                                    pages = pages,
-                                    row.names = NULL,
-                                    stringsAsFactors = FALSE)
-      self$transformations <- rbind(self$transformations, transformations)
-    },
-    soil_degradation_endpoints = data.frame(destination = character(0), 
-                                            DT50 = numeric(0),
-                                            comment = character(0),
-                                            pages = character(0),
-                                            stringsAsFactors = FALSE),
-    add_soil_degradation_endpoints = function(destination, DT50 = NA,
-                                              comment = "", pages = NA) {
-      i <- nrow(self$soil_degradation_endpoints) + 1
-      self$soil_degradation_endpoints[i, c("destination", "comment", "pages")] <- 
-        c(destination, comment, pages)
-      self$soil_degradation_endpoints[i, "DT50"] <- DT50
-    },
-    ws_degradation_endpoints = data.frame(destination = character(0), 
-                                          DT50 = numeric(0),
-                                          comment = character(0),
-                                          tier = character(0),
-                                          pages = character(0),
-                                          stringsAsFactors = FALSE),
-    add_ws_degradation_endpoints = function(destination, DT50 = NA, tier = NA,
-                                            comment = "", pages = NA) {
-      i <- nrow(self$ws_degradation_endpoints) + 1
-      self$ws_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- 
-        c(destination, tier, comment, pages)
-      self$ws_degradation_endpoints[i, "DT50"] <- DT50
-    },
-    water_degradation_endpoints = data.frame(destination = character(0), 
-                                             DT50 = numeric(0),
-                                             tier = character(0),
-                                             comment = character(0),
-                                             pages = character(0),
-                                             stringsAsFactors = FALSE),
-    add_water_degradation_endpoints = function(destination, DT50 = NA, tier = NA,
-                                               comment = "", pages = NA) {
-      i <- nrow(self$water_degradation_endpoints) + 1
-      self$water_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- 
-        c(destination, tier, comment, pages)
-      self$water_degradation_endpoints[i, "DT50"] <- DT50
-    },
-    sediment_degradation_endpoints = data.frame(destination = character(0), 
-                                                DT50 = numeric(0),
-                                                tier = character(0),
-                                                comment = character(0),
-                                                pages = character(0),
-                                                stringsAsFactors = FALSE),
-    add_sediment_degradation_endpoints = function(destination, DT50 = NA, tier = NA,
-                                                  comment = "", pages = NA) {
-      i <- nrow(self$sediment_degradation_endpoints) + 1
-      self$sediment_degradation_endpoints[i, c("destination", "tier", "comment", "pages")] <- 
-        c(destination, tier, comment, pages)
-      self$sediment_degradation_endpoints[i, "DT50"] <- DT50
-    },
-    sorption_endpoints = data.frame(Kfoc = numeric(0), f1.n = numeric(0),
-                                    type = character(0),
-                                    comment = character(0),
-                                    pages = character(0),
-                                    stringsAsFactors = FALSE),
-    add_sorption_endpoints = function(Kfoc, f1.n = 1, type = "arithmetic mean",
-                                      comment = "", pages = NA) {
-      i <- nrow(self$sorption_endpoints) + 1
-      self$sorption_endpoints[i, c("Kfoc", "f1.n")] <- c(Kfoc, f1.n)
-      self$sorption_endpoints[i, c("type", "comment", "pages")] <- c(type, comment, pages)
-    },
-    print = function(TPs = TRUE) {
-      cat("<pfm_chent> with acronym", self$acronym, "\n")
-      if (!is.null(self$smiles)) cat ("SMILES:", self$smiles, "\n")
-      if (!is.null(self$mw)) cat ("Molecular weight:", round(self$mw, 1), "\n")
-      if (!is.null(self$main_source)) cat ("Main source of information:", self$main_source, "\n")
-      if (TPs) {
-        if (length(self$TPs) > 0) {
-          cat("\nTransformation products:\n")
-          print(self$TPs)
-        }
-        if (nrow(self$transformations) > 0) {
-          cat("\nTransformations:\n")
-          print(self$transformations[order(self$transformations$study_type), ], row.names = FALSE)
-        }
-      }
-    }
-  )
-)
-
-#' R6 class for holding active ingredients
-#'
-#' An R6 class for holding information about active ingredients
-#'
-#' @docType class
-#' @importFrom R6 R6Class
-#' @export
-#' @format An \code{\link{R6Class}} generator object.
-#' @field iso ISO common name
-#' @examples
-#' atrazine  <- pfm_ai("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68)
-#' print(atrazine)
-#' @keywords data
-
-pfm_ai <- R6Class("pfm_ai",
-  inherit = pfm_chent,
-  public <- list(
-    iso = NULL,
-    initialize = function(iso, acronym = iso, smiles = NULL, mw = NULL, main_source = NULL) {
-      super$initialize(acronym = acronym, smiles = smiles, mw = mw, main_source = main_source)
-      self$iso <- iso
-    },
-    ff = data.frame(from = character(0), to = character(0), ff = numeric(0),
-                    comment = character(0), pages = character(0),
-                    stringsAsFactors = FALSE),
-    add_ff = function(from = "parent", to, ff = 1, comment = "", pages = NA) {
-      i <- nrow(self$ff) + 1
-      if (from != "parent") {
-        if (!exists(from, self$TPs)) stop(from, " was not found in TPs")
-      }
-      if (!exists(to, self$TPs)) stop(to, " was not found in TPs")
-      self$ff[i, ] <- c(from, to, ff, comment, pages)
-    },
-    print = function() {
-      if (is.null(self$iso)) cat("<pfm_ai> with acronym", self$acronym, "\n")
-      else cat("<pfm_ai> with ISO common name", self$iso, "\n")
-      super$print()
-    }
-  )
-)
-
-#' R6 class for holding a product with at least one active ingredient
-#'
-#' An R6 class for holding information about a product with at least one active ingredient
-#'
-#' @docType class
-#' @importFrom R6 R6Class
-#' @export
-#' @format An \code{\link{R6Class}} generator object.
-#' @field name The name of the product
-#' @field ais A list of active ingredients
-#' @field concentrations The concentration of the ais
-#' @field concentration_units Defaults to g/L
-#' @keywords data
-
-pfm_product <- R6Class("pfm_product",
-  public <- list(
-    name = NULL,
-    ais = list(),
-    concentrations = NULL,
-    concentration_units = NULL,
-    density = NULL,
-    density_units = "g/L",
-    initialize = function(name, ..., concentrations, concentration_units = "g/L",
-                          density = 1000, density_units = "g/L") {
-      self$name <- name
-      self$ais <- list(...)
-      self$concentrations <- concentrations
-      self$density <- density
-      self$density_units <- density_units
-      names(self$concentrations) <- names(self$ais)
-      self$concentration_units <- concentration_units
-    },
-    print = function() {
-      cat("<pfm_product> named", self$name, "\n")
-    }
-  )
-)
-