diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/chent.R | 204 |
1 files changed, 154 insertions, 50 deletions
@@ -23,6 +23,7 @@ #' if (!is.null(caffeine$Picture)) { #' plot(caffeine) #' } + chent <- R6Class("chent", public = list( #' @field identifier (`character(1)`)\cr @@ -241,6 +242,7 @@ chent <- R6Class("chent", #' @param repo Should the file be looked for in the current working #' directory, a local git repository under `~/git/chyaml`, or from #' the web (not implemented). + #' @param chyaml The filename to be looked for get_chyaml = function(repo = c("wd", "local", "web"), chyaml = paste0(URLencode(self$identifier), ".yaml")) { @@ -287,8 +289,15 @@ chent <- R6Class("chent", }, #' Add a water solubility - #' @param p0 The water solubility in mg/L - add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") { + #' @param cwsat The water solubility in mg/L + #' @param T Temperature + #' @param pH The pH value + #' @param source An acronym specifying the source of the information + #' @param page The page from which the information was taken + #' @param remark A remark + add_cwsat = function(cwsat, T = NA, pH = NA, + source = NA, page = NA, remark = "") + { self$cwsat <- cwsat attr(self$cwsat, "T") <- T attr(self$cwsat, "pH") <- pH @@ -299,7 +308,13 @@ chent <- R6Class("chent", #' Add a plant uptake factor #' @param PUF The plant uptake factor, a number between 0 and 1 - add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") { + #' @param source An acronym specifying the source of the information + #' @param page The page from which the information was taken + #' @param remark A remark + add_PUF = function(PUF = 0, + source = "focus_generic_gw_2014", page = 41, + remark = "Conservative default value") + { self$PUF <- PUF attr(self$PUF, "source") <- source attr(self$PUF, "page") <- page @@ -326,13 +341,22 @@ chent <- R6Class("chent", #' @field transformations Data frame of observed transformations transformations = data.frame(study_type = character(0), - TP_identifier = character(0), - max_occurrence = numeric(0), - source = character(0), - pages = character(0), - stringsAsFactors = FALSE), + TP_identifier = character(0), + max_occurrence = numeric(0), + source = character(0), + page = character(0), + stringsAsFactors = FALSE), #' Add a line in the internal dataframe holding observed transformations + #' @param study_type A characterisation of the study type + #' @param TP_identifier An identifier of one of the transformation products + #' in `self$TPs` + #' @param max_occurrence The maximum observed occurrence of the + #' transformation product, expressed as a fraction of the amount that would + #' result from stochiometric transformation + #' @param source An acronym specifying the source of the information + #' @param pages The page from which the information was taken + #' @param remark A remark add_transformation = function(study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA) { @@ -344,19 +368,40 @@ chent <- R6Class("chent", if (is.numeric(pages)) pages <- paste(pages, collapse = ", ") cn <- colnames(self$transformations) self$transformations <- rbind(self$transformations, - data.frame(study_type = study_type, - TP_identifier = TP_identifier, - max_occurrence = max_occurrence, - remark = remark, - source = source, - pages = pages, - stringsAsFactors = FALSE)) + data.frame(study_type = study_type, + TP_identifier = TP_identifier, + max_occurrence = max_occurrence, + remark = remark, + source = source, + page = page, + stringsAsFactors = FALSE)) }, #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, #' Add a line in the internal dataframe holding modelling DT50 values + #' @param soils Names of the soils + #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide + #' fate modelling + #' @param DT50_mod_ref The normalised modelling DT50 in the sense of + #' regulatory pesticide fate modelling + #' @param type The soil type + #' @param country The country (mainly for field studies) + #' @param pH_orig The pH stated in the study + #' @param pH_medium The medium in which this pH was measured + #' @param pH_H2O The pH extrapolated to pure water + #' @param perc_OC The percentage of organic carbon in the soil + #' @param temperature The temperature during the study in degrees Celsius + #' @param moisture The moisture during the study + #' @param category Is it a laboratory ('lab') or field study ('field') + #' @param formulation Name of the formulation applied, if it was not + #' the technical active ingredient + #' @param model The degradation model used for deriving `DT50_mod` + #' @param chi2 The relative error as defined in FOCUS kinetics + #' @param source An acronym specifying the source of the information + #' @param page The page from which the information was taken + #' @param remark A remark add_soil_degradation = function(soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, @@ -396,7 +441,13 @@ chent <- R6Class("chent", #' @field soil_ff Dataframe of formation fractions soil_ff = NULL, - add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) { + # Add one or more formation fractions for degradation in soil + #' @param target The identifier(s) of the transformation product + #' @param soils The soil name(s) in which the transformation was observed + #' @param ff The formation fraction(s) + add_soil_ff = function(target, soils, ff = 1, + remark = "", source, page = NA) + { new_soil_ff = data.frame( target = target, target = target, @@ -416,12 +467,19 @@ chent <- R6Class("chent", #' @field soil_sorption Dataframe of soil sorption data soil_sorption = NULL, + #' Add soil sorption data + #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) + #' or according to Freundlich + #' @param Kfoc The constant from above, normalised to soil organic carbon + #' @param N The Freundlich exponent + #' @param perc_clay The percentage of clay in the soil + #' @param CEC The cation exchange capacity add_soil_sorption = function(soils, Kf, Kfoc, N, - type = NA, - pH_orig = NA, pH_medium = NA, - pH_H2O = NA, - perc_OC = NA, perc_clay = NA, CEC = NA, - remark = "", source, page = NA) { + type = NA, pH_orig = NA, pH_medium = NA, + pH_H2O = NA, + perc_OC = NA, perc_clay = NA, CEC = NA, + remark = "", source, page = NA) + { new_soil_sorption = data.frame( soils = soils, Kf = Kf, Kfoc = Kfoc, N = N, @@ -441,6 +499,10 @@ chent <- R6Class("chent", } }, + #' Write a PDF image of the structure + #' @param file The file to write to + #' @param dir The directory to write the file to + #' @param template A template expressed as SMILES to use in RDKit pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL) { if (!dir.exists(dir)) { @@ -462,8 +524,12 @@ chent <- R6Class("chent", m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE)) self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) }, - png = function(file = paste0(self$identifier, ".png"), dir = "structures/png", - antialias = 'gray') { + + #' Write a PNG image of the structure + #' @param antialias Passed to [png][grDevices::png] + png = function(file = paste0(self$identifier, ".png"), + dir = "structures/png", antialias = 'gray') + { if (!dir.exists(dir)) { message("Directory '", dir, "' does not exist") message("Trying to create directory '", dir, "'") @@ -475,7 +541,12 @@ chent <- R6Class("chent", plot(self) dev.off() }, - emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") { + + #' Write an EMF image of the structure using [emf][devEMF::emf] + #' @param file The file to write to + emf = function(file = paste0(self$identifier, ".emf"), + dir = "structures/emf") + { if (!requireNamespace("devEMF")) { stop("You need to have the devEMF package installed for this function") } @@ -521,8 +592,8 @@ print.chent = function(x, ...) { #' @param subdir The path to which the file should be written #' @export draw_svg.chent = function(x, width = 300, height = 150, - filename = paste0(names(x$identifier), ".svg"), - subdir = "svg") { + filename = paste0(names(x$identifier), ".svg"), + subdir = "svg") { if (!rdkit_available) { stop("RDkit is not available via reticulate") } else { @@ -560,8 +631,6 @@ plot.chent = function(x, ...) { #' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object -#' @field iso ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org -#' @field bcpc List of information retrieved from pesticidecompendium.bcpc.org #' @examples #' # On Travis, we get a certificate validation error, #' # likely because the system (xenial) is so old, @@ -575,18 +644,35 @@ plot.chent = function(x, ...) { #' } #' #' } + pai <- R6Class("pai", inherit = chent, - public <- list( + public = list( + + #' @field iso ISO common name of the active ingredient according to ISO 1750 iso = NULL, + + #' @field bcpc Information retrieved from the BCPC compendium available online + #' at <pesticidecompendium.bcpc.org> bcpc = NULL, + + #' Creates a new instance of this [R6][R6::R6Class] class. + #' + #' @description This class is derived from [chent]. It makes it easy + #' to create a [chent] from the ISO common name of a pesticide active + #' ingredient, and additionally stores the ISO name as well as + #' the complete result of querying the BCPC compendium using + #' [bcpc_query][webchem::bcpc_query]. + #' + #' @param iso The ISO common name to be used in the query of the + #' BCPC compendium + #' + #' @param identifier Alternative identifier used for querying pubchem initialize = function(iso, identifier = iso, - smiles = NULL, - inchikey = NULL, - bcpc = TRUE, - pubchem = TRUE, pubchem_from = 'auto', - rdkit = TRUE, template = NULL, - chyaml = TRUE) + smiles = NULL, inchikey = NULL, bcpc = TRUE, + pubchem = TRUE, pubchem_from = 'auto', + rdkit = TRUE, template = NULL, + chyaml = TRUE) { if (!is.null(inchikey)) { @@ -631,10 +717,9 @@ pai <- R6Class("pai", } super$initialize(identifier = identifier, - smiles = smiles, - inchikey = self$inchikey, - pubchem = pubchem, pubchem_from = pubchem_from, - rdkit = rdkit, template = template, chyaml = chyaml) + smiles = smiles, inchikey = self$inchikey, + pubchem = pubchem, pubchem_from = pubchem_from, + rdkit = rdkit, template = template, chyaml = chyaml) invisible(self) } @@ -659,30 +744,47 @@ print.pai = function(x, ...) { } } -#' R6 class for holding a product with at least one active ingredient +#' @title R6 class for a plant protection product with at least one active ingredient #' -#' An R6 class for holding information about a product with at least one active ingredient +#' @description Contains basic information about the active ingredients in the +#' product #' #' @docType class #' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object. -#' @field name The name of the product -#' @field ais A list of active ingredients -#' @field concentrations The concentration of the ais -#' @field concentration_units Defaults to g/L -#' @keywords data - -pp <- R6Class("pp", - public <- list( + +ppp <- R6Class("ppp", + public = list( + + #' @field name The name of the product name = NULL, + + #' @field ais A list of active ingredients ais = list(), + + #' @field concentrations The concentration of the ais concentrations = NULL, + + #' @field concentration_units Defaults to g/L concentration_units = NULL, + + #' @field density The density of the product density = NULL, + + #' @field density_units Defaults to g/L density_units = "g/L", + + #' Creates a new instance of this [R6][R6::R6Class] class. + #' + #' @field ... Identifiers of the active ingredients + #' @field concentrations Concentrations of the active ingredients + #' @field concentration_units Defaults to g/L + #' @field density The density + #' @field density_units Defaults to g/L initialize = function(name, ..., concentrations, concentration_units = "g/L", - density = 1000, density_units = "g/L") { + density = 1000, density_units = "g/L") + { self$name <- name self$ais <- list(...) self$concentrations <- concentrations @@ -691,6 +793,8 @@ pp <- R6Class("pp", names(self$concentrations) <- names(self$ais) self$concentration_units <- concentration_units }, + + #' Printing method print = function() { cat("<pp> named", self$name, "\n") } |