diff options
| -rw-r--r-- | ChangeLog | 8 | ||||
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | R/chent.R | 98 | ||||
| -rw-r--r-- | man/chent.Rd | 8 |
4 files changed, 91 insertions, 25 deletions
@@ -1,3 +1,11 @@ +commit 12e69e162df47660d139cb3c4a5c9bff0f6a1d85 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2018-05-16 17:13:05 +0200 + + Vapour pressure and water solubility, use remark + + instead of comment, as comment is a special attribute in R + commit 4bd4606c76dfc152547e0f5899a98494a4290d33 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2018-03-01 09:48:02 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index f2b4656..5d4d81c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: chents Type: Package Title: Chemical Entities as R Objects Version: 0.2-6 -Date: 2018-05-16 +Date: 2018-05-18 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de")) Description: Utilities for dealing with chemical entities and associated @@ -42,7 +42,10 @@ #' @field p0 Vapour pressure in Pa #' @field cwsat Water solubility in mg/L #' @field chyaml List of information obtained from a YAML file -#' @field degradation List of degradation endpoints +#' @field soil_degradation Dataframe of modelling DT50 values +#' @field soil_ff Dataframe of formation fractions +#' @field soil_sorption Dataframe of soil sorption data +#' @field PUF Plant uptake factor #' @example inst/examples/octanol.R #' @example inst/examples/caffeine.R #' @keywords data @@ -61,8 +64,8 @@ chent <- R6Class("chent", pdf_height = NULL, p0 = NULL, cwsat = NULL, + PUF = NULL, chyaml = NULL, - degradation = NULL, initialize = function(identifier, smiles = NULL, smiles_source = 'user', inchikey = NULL, inchikey_source = 'user', pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), @@ -260,6 +263,12 @@ chent <- R6Class("chent", attr(self$cwsat, "page") <- page attr(self$cwsat, "remark") <- remark }, + add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") { + self$PUF <- PUF + attr(self$PUF, "source") <- source + attr(self$PUF, "page") <- page + attr(self$PUF, "remark") <- remark + }, TPs = list(), add_TP = function(x, smiles = NULL) { if (inherits(x, "chent")) { @@ -295,29 +304,72 @@ chent <- R6Class("chent", pages = pages, stringsAsFactors = FALSE)) }, - soil_degradation_endpoints = data.frame(destination = character(0), - DT50 = numeric(0), - remark = character(0), - pages = character(0), - stringsAsFactors = FALSE), - add_soil_degradation_endpoints = function(destination, DT50 = NA, - remark = "", pages = NA) { - if (length(pages) > 1) pages = paste(pages, collapse = ", ") - i <- nrow(self$soil_degradation_endpoints) + 1 - self$soil_degradation_endpoints[i, c("destination", "remark", "pages")] <- - c(destination, remark, pages) - self$soil_degradation_endpoints[i, "DT50"] <- DT50 + soil_degradation = NULL, + add_soil_degradation = function(soils, DT50, + type = NA, + pH_orig = NA, pH_type = NA, pH_H2O = NA, + temperature = NA, moisture = NA, + category = "lab", formulation = NA, + remark = "", source, page = NA) { + new_soil_degradation = data.frame( + soil = soils, + DT50 = DT50, + type = type, + pH_orig = pH_orig, + pH_type = pH_type, + pH_H2O = pH_H2O, + temperature = temperature, + moisture = moisture, + category = category, + formulation = formulation, + remark = remark, + source = source, + page = page, + stringsAsFactors = FALSE) + if (is.null(self$soil_degradation)) { + self$soil_degradation <- new_soil_degradation + } else { + self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation) + } }, - ff = data.frame(from = character(0), to = character(0), ff = numeric(0), - remark = character(0), pages = character(0), - stringsAsFactors = FALSE), - add_ff = function(from = "parent", to, ff = 1, remark = "", pages = NA) { - i <- nrow(self$ff) + 1 - if (from != "parent") { - if (!exists(from, self$TPs)) stop(from, " was not found in TPs") + soil_ff = NULL, + add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) { + new_soil_ff = data.frame( + target = target, + soil = soils, + ff = ff, + remark = remark, + source = source, + page = page, + stringsAsFactors = FALSE) + if (is.null(self$soil_ff)) { + self$soil_ff <- new_soil_ff + } else { + self$soil_ff <- rbind(self$soil_ff, new_soil_ff) + } + }, + soil_sorption = NULL, + add_soil_sorption = function(type, Kf, Kfoc, N, + pH_orig = NA, pH_type = NA, + pH_H2O = NA, + perc_OC = NA, perc_clay = NA, CEC = NA, + remark = "", source, page = NA) { + new_soil_sorption = data.frame( + type = type, + Kf = Kf, Kfoc = Kfoc, N = N, + pH_orig = pH_orig, + pH_type = pH_type, + pH_H2O = pH_H2O, + perc_OC = perc_OC, perc_clay = perc_clay, CEC = CEC, + remark = remark, + source = source, + page = page, + stringsAsFactors = FALSE) + if (is.null(self$soil_sorption)) { + self$soil_sorption <- new_soil_sorption + } else { + self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption) } - if (!exists(to, self$TPs)) stop(to, " was not found in TPs") - self$ff[i, ] <- c(from, to, ff, remark, pages) }, pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL) { diff --git a/man/chent.Rd b/man/chent.Rd index f5ed2dc..8d85de1 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -43,7 +43,13 @@ configured for use with PythonInR} \item{\code{chyaml}}{List of information obtained from a YAML file} -\item{\code{degradation}}{List of degradation endpoints} +\item{\code{soil_degradation}}{Dataframe of modelling DT50 values} + +\item{\code{soil_ff}}{Dataframe of formation fractions} + +\item{\code{soil_sorption}}{Dataframe of soil sorption data} + +\item{\code{PUF}}{Plant uptake factor} }} \examples{ |