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authorJohannes Ranke <jranke@uni-bremen.de>2024-12-02 09:20:54 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2024-12-02 09:20:54 +0100
commitd97e57a36e6b76def7a980fa6a06b2827df39c3e (patch)
tree3c862e2034c46d47146fbb971f141eaafb04947c /R
parent1023deba646ca200fb5fbd992d6de73770d2034e (diff)
Add @description tags to R6 methodsHEADmain
Otherwise, the descriptions of the methods get mixed up
Diffstat (limited to 'R')
-rw-r--r--R/chent.R19
1 files changed, 16 insertions, 3 deletions
diff --git a/R/chent.R b/R/chent.R
index 7b3ba3f..aef0d68 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -102,7 +102,6 @@ chent <- R6Class("chent",
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
- #'
initialize = function(identifier, smiles = NULL, inchikey = NULL,
pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'),
rdkit = TRUE, template = NULL,
@@ -166,6 +165,7 @@ chent <- R6Class("chent",
invisible(self)
},
+ #' @description
#' Try to get chemical information from PubChem
#' @param query Query string to be passed to [get_cid][webchem::get_cid]
#' @param from Passed to [get_cid][webchem::get_cid]
@@ -181,6 +181,7 @@ chent <- R6Class("chent",
}
},
+ #' @description
#' Get chemical information from PubChem for a known PubChem CID
#' @param pubchem_cid CID
get_pubchem = function(pubchem_cid) {
@@ -274,6 +275,7 @@ chent <- R6Class("chent",
unlink(c(xmlfile, psfile, svgfile))
},
+ #' @description
#' Obtain information from a YAML file
#' @param repo Should the file be looked for in the current working
#' directory, a local git repository under `~/git/chyaml`, or from
@@ -310,6 +312,7 @@ chent <- R6Class("chent",
}
},
+ #' @description
#' Add a vapour pressure
#' @param p0 The vapour pressure in Pa
add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {
@@ -320,6 +323,7 @@ chent <- R6Class("chent",
attr(self$p0, "remark") <- remark
},
+ #' @description
#' Add a water solubility
#' @param cwsat The water solubility in mg/L
add_cwsat = function(cwsat, T = NA, pH = NA,
@@ -333,6 +337,7 @@ chent <- R6Class("chent",
attr(self$cwsat, "remark") <- remark
},
+ #' @description
#' Add a plant uptake factor
#' @param PUF The plant uptake factor, a number between 0 and 1
add_PUF = function(PUF = 0,
@@ -348,6 +353,7 @@ chent <- R6Class("chent",
#' @field TPs List of transformation products as chent objects
TPs = list(),
+ #' @description
#' Add a transformation product to the internal list
#' @param x A [chent] object, or an identifier to generate a [chent] object
#' @param pubchem Should chemical information be obtained from PubChem?
@@ -370,6 +376,7 @@ chent <- R6Class("chent",
page = character(0),
stringsAsFactors = FALSE),
+ #' @description
#' 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
@@ -400,6 +407,7 @@ chent <- R6Class("chent",
#' @field soil_degradation Dataframe of modelling DT50 values
soil_degradation = NULL,
+ #' @description
#' Add a line in the internal dataframe holding modelling DT50 values
#' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide
#' fate modelling
@@ -452,7 +460,8 @@ chent <- R6Class("chent",
#' @field soil_ff Dataframe of formation fractions
soil_ff = NULL,
- # Add one or more formation fractions for degradation in soil
+ #' @description
+ #' 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)
@@ -478,6 +487,7 @@ chent <- R6Class("chent",
#' @field soil_sorption Dataframe of soil sorption data
soil_sorption = NULL,
+ #' @description
#' Add soil sorption data
#' @param Kf The sorption constant in L/kg, either linear (then `N` is 1)
#' or according to Freundlich
@@ -535,6 +545,7 @@ chent <- R6Class("chent",
self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line))
},
+ #' @description
#' Write a PNG image of the structure
#' @param antialias Passed to [png][grDevices::png]
png = function(file = paste0(self$identifier, ".png"),
@@ -666,9 +677,10 @@ pai <- R6Class("pai",
#' at <pesticidecompendium.bcpc.org>
bcpc = NULL,
+ #' @description
+ #' Create a new pai object
#' @param iso The ISO common name to be used in the query of the
#' BCPC compendium
- #'
#' @param identifier Alternative identifier used for querying pubchem
#' @param smiles Optional user provided SMILES code
#' @param inchikey Optional user provided InChI Key
@@ -786,6 +798,7 @@ ppp <- R6Class("ppp",
#' @field density_units Defaults to g/L
density_units = "g/L",
+ #' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#' @param name The name of the product
#' @param ... Identifiers of the active ingredients

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