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authorJohannes Ranke <jranke@uni-bremen.de>2018-05-18 17:32:47 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-05-18 17:32:47 +0200
commit7ac3347283fdcaa0a8c76af20b0a7cfa423368b9 (patch)
treee6612ff7d90861586550965b516343b99b2a7fa5
parent12e69e162df47660d139cb3c4a5c9bff0f6a1d85 (diff)
Revisited soil degradation and sorption
-rw-r--r--ChangeLog8
-rw-r--r--DESCRIPTION2
-rw-r--r--R/chent.R98
-rw-r--r--man/chent.Rd8
4 files changed, 91 insertions, 25 deletions
diff --git a/ChangeLog b/ChangeLog
index cfb6411..2e32bd3 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -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
diff --git a/R/chent.R b/R/chent.R
index ad3bc3c..3bf0afe 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -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{

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