From 7c0e06c053303ea3f35fad3236ee5b3d930e7f08 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Wed, 22 Oct 2025 16:27:37 +0200 Subject: Improve test coverage and use testthat 3rd edition --- docs/coverage/coverage.html | 1251 +++++++++++++++++++++---------------------- 1 file changed, 622 insertions(+), 629 deletions(-) (limited to 'docs/coverage/coverage.html') diff --git a/docs/coverage/coverage.html b/docs/coverage/coverage.html index f881440..1e9d0ad 100644 --- a/docs/coverage/coverage.html +++ b/docs/coverage/coverage.html @@ -95,7 +95,7 @@ table.table-condensed { font-size: 11px; }
-

chents coverage - 32.25%

+

chents coverage - 34.64%

  • @@ -107,8 +107,8 @@ table.table-condensed {
-
- +
+
@@ -1218,14 +1218,14 @@ table.table-condensed { 158 - 
    try_pubchem = function(query, from = 'name') {
+ 
    try_pubchem = function(query = self$identifier, from = 'name') {
159 2x - 
      message("PubChem:")
+ 
      message("Querying PubChem for ", from , " ", query, " ...")
@@ -1260,7 +1260,7 @@ table.table-condensed { 164 ! - 
        message("Query ", query, " did not give results at PubChem")
+ 
        message("Querying for ", query, " as ", from, " did not give results at PubChem")
@@ -1729,7 +1729,7 @@ table.table-condensed { 231 2x - 
      message("Trying to get chemical information from RDKit using ",
+ 
      message("Get chemical information from RDKit using ",
@@ -1771,12 +1771,12 @@ table.table-condensed { 237 2x - 
      if (!is.na(self$mw)) {
+ 
      if (!is.null(self$mw) && !is.na(self$mw)) {
238 - 1x + 2x 
        if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {
@@ -1785,4134 +1785,4127 @@ table.table-condensed { 239 ! - 
          message("RDKit mw is ", self$rdkit$mw)
- - - - 240 - ! - - 
          message("mw is ", self$mw)
+ 
          warning("RDKit mw is ", self$rdkit$mw, " while mw is ", self$mw)
- 241 + 240 
        }
- 242 + 241 
      } else {
- - 243 - 1x + + 242 + ! 
        self$mw <- self$rdkit$mw
- - 244 - 1x + + 243 + ! 
        attr(self$mw, "source") <- "rdkit"
- 245 + 244 
      }
- 246 + 245 

                     
                   
                   
-                    247
+                    246
                     
                     
                       
      # Create an SVG representation

                     
                   
                   
-                    248
+                    247
                     2x
                     
                       
      rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol)

                     
                   
                   
-                    249
+                    248
                     2x
                     
                       
      if (!is.null(template)) {

                     
                   
                   
-                    250
+                    249
                     !
                     
                       
        rdkit_template <- rdkit_module$Chem$MolFromSmiles(template)

                     
                   
                   
-                    251
+                    250
                     !
                     
                       
        rdkit_module$Chem$rdDepictor$Compute2DCoords(template)

                     
                   
                   
-                    252
+                    251
                     !
                     
                       
        rdkit$Chem$AllChem$GenerateDepictionMatching2DStructure(self$mol, template)

                     
                   
                   
-                    253
+                    252
                     
                     
                       
      }

                     
                   
                   
-                    254
+                    253
                     2x
                     
                       
      d2d <- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L)

                     
                   
                   
-                    255
+                    254
                     2x
                     
                       
      d2d$DrawMolecule(self$mol)

                     
                   
                   
-                    256
+                    255
                     2x
                     
                       
      d2d$FinishDrawing()

                     
                   
                   
-                    257
+                    256
                     2x
                     
                       
      self$svg <- d2d$GetDrawingText()

                     
                   
                   
-                    258
+                    257
                     2x
                     
                       
      svgfile <- tempfile(fileext = ".svg")

                     
                   
                   
-                    259
+                    258
                     2x
                     
                       
      psfile <- tempfile(fileext = ".ps")

                     
                   
                   
-                    260
+                    259
                     2x
                     
                       
      writeLines(self$svg, svgfile)

                     
                   
                   
-                    261
+                    260
                     2x
                     
                       
      rsvg::rsvg_ps(svgfile, psfile)

                     
                   
                   
-                    262
+                    261
                     
                     
                       

                     
                   
                   
-                    263
+                    262
                     
                     
                       
      # Get size properties useful for plotting

                     
                   
                   
-                    264
+                    263
                     2x
                     
                       
      ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]

                     
                   
                   
-                    265
+                    264
                     2x
                     
                       
      ps_font_size <- gsub(" .*$", "", ps_font_line)

                     
                   
                   
-                    266
+                    265
                     2x
                     
                       
      self$Pict_font_size = as.numeric(ps_font_size)

                     
                   
                   
-                    267
+                    266
                     
                     
                       

                     
                   
                   
-                    268
+                    267
                     
                     
                       
      # Read in to create Picture

                     
                   
                   
-                    269
+                    268
                     2x
                     
                       
      xmlfile <- tempfile(fileext = ".xml")

                     
                   
                   
-                    270
+                    269
                     2x
                     
                       
      PostScriptTrace(psfile, outfilename = xmlfile)

                     
                   
                   
-                    271
+                    270
                     2x
                     
                       
      unlink(paste0("capture", basename(psfile)))

                     
                   
                   
-                    272
+                    271
                     2x
                     
                       
      self$Picture <- readPicture(xmlfile)

                     
                   
                   
-                    273
+                    272
                     2x
                     
                       
      unlink(c(xmlfile, psfile, svgfile))

                     
                   
                   
-                    274
+                    273
                     
                     
                       
    },

                     
                   
                   
-                    275
+                    274
                     
                     
                       

                     
                   
                   
-                    276
+                    275
                     
                     
                       
    #' @description

                     
                   
                   
-                    277
+                    276
                     
                     
                       
    #' Obtain information from a YAML file

                     
                   
                   
-                    278
+                    277
                     
                     
                       
    #' @param repo Should the file be looked for in the current working

                     
                   
                   
-                    279
+                    278
                     
                     
                       
    #' directory, a local git repository under `~/git/chyaml`, or from

                     
                   
                   
-                    280
+                    279
                     
                     
                       
    #' the web (not implemented).

                     
                   
                   
-                    281
+                    280
                     
                     
                       
    #' @param chyaml The filename to be looked for

                     
                   
                   
-                    282
+                    281
                     
                     
                       
    get_chyaml = function(repo = c("wd", "local", "web"),

                     
                   
                   
-                    283
+                    282
                     
                     
                       
      chyaml = paste0(URLencode(self$identifier), ".yaml"))

                     
                   
                   
-                    284
+                    283
                     
                     
                       
    {

                     
                   
                   
-                    285
+                    284
                     !
                     
                       
      repo = match.arg(repo)

                     
                   
                   
-                    286
+                    285
                     !
                     
                       
      paths = c(

                     
                   
                   
-                    287
+                    286
                     !
                     
                       
        wd = ".",

                     
                   
                   
-                    288
+                    287
                     !
                     
                       
        local = file.path("~", "git/chyaml"))

                     
                   
                   
-                    289
+                    288
                     
                     
                       

                     
                   
                   
-                    290
+                    289
                     !
                     
                       
      chyaml_handlers = list(

                     
                   
                   
-                    291
+                    290
                     !
                     
                       
        expr = function(x) NULL, # To avoid security risks from reading chyaml files

                     
                   
                   
-                    292
+                    291
                     !
                     
                       
        dataframe = function(x)

                     
                   
                   
-                    293
+                    292
                     !
                     
                       
          eval(parse(text = paste0("data.frame(", x, ", stringsAsFactors = FALSE)"))))

                     
                   
                   
-                    294
+                    293
                     
                     
                       

                     
                   
                   
-                    295
+                    294
                     !
                     
                       
      if (repo %in% c("wd", "local")) {

                     
                   
                   
-                    296
+                    295
                     !
                     
                       
        path = paths[repo]

                     
                   
                   
-                    297
+                    296
                     !
                     
                       
        full = file.path(path, chyaml)

                     
                   
                   
-                    298
+                    297
                     !
                     
                       
        if (!file.exists(full)) {

                     
                   
                   
-                    299
+                    298
                     !
                     
                       
          message("Did not find chyaml file ", full)

                     
                   
                   
-                    300
+                    299
                     
                     
                       
        } else {

                     
                   
                   
-                    301
+                    300
                     !
                     
                       
          if (is(try(self$chyaml <- yaml.load_file(chyaml, handlers = chyaml_handlers)),

                     
                   
                   
-                    302
+                    301
                     !
                     
                       
                 "try-error")) {

                     
                   
                   
-                    303
+                    302
                     !
                     
                       
            message("Could not load ", full)

                     
                   
                   
-                    304
+                    303
                     
                     
                       
          } else {

                     
                   
                   
-                    305
+                    304
                     !
                     
                       
            message("Loaded ", full)

                     
                   
                   
-                    306
+                    305
                     
                     
                       
          }

                     
                   
                   
-                    307
+                    306
                     
                     
                       
        }

                     
                   
                   
-                    308
+                    307
                     
                     
                       
      } else {

                     
                   
                   
-                    309
+                    308
                     !
                     
                       
        message("web repositories not implemented")

                     
                   
                   
-                    310
+                    309
                     
                     
                       
      }

                     
                   
                   
-                    311
+                    310
                     
                     
                       
    },

                     
                   
                   
-                    312
+                    311
                     
                     
                       

                     
                   
                   
-                    313
+                    312
                     
                     
                       
    #' @description

                     
                   
                   
-                    314
+                    313
                     
                     
                       
    #' Add a vapour pressure

                     
                   
                   
-                    315
+                    314
                     
                     
                       
    #' @param p0 The vapour pressure in Pa

                     
                   
                   
-                    316
+                    315
                     
                     
                       
    add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {

                     
                   
                   
-                    317
+                    316
                     !
                     
                       
      self$p0 <- p0

                     
                   
                   
-                    318
+                    317
                     !
                     
                       
      attr(self$p0, "T") <- T

                     
                   
                   
-                    319
+                    318
                     !
                     
                       
      attr(self$p0, "source") <- source

                     
                   
                   
-                    320
+                    319
                     !
                     
                       
      attr(self$p0, "page") <- page

                     
                   
                   
-                    321
+                    320
                     !
                     
                       
      attr(self$p0, "remark") <- remark

                     
                   
                   
-                    322
+                    321
                     
                     
                       
    },

                     
                   
                   
-                    323
+                    322
                     
                     
                       

                     
                   
                   
-                    324
+                    323
                     
                     
                       
    #' @description

                     
                   
                   
-                    325
+                    324
                     
                     
                       
    #' Add a water solubility

                     
                   
                   
-                    326
+                    325
                     
                     
                       
    #' @param cwsat The water solubility in mg/L

                     
                   
                   
-                    327
+                    326
                     
                     
                       
    add_cwsat = function(cwsat, T = NA, pH = NA,

                     
                   
                   
-                    328
+                    327
                     
                     
                       
      source = NA, page = NA, remark = "")

                     
                   
                   
-                    329
+                    328
                     
                     
                       
    {

                     
                   
                   
-                    330
+                    329
                     !
                     
                       
      self$cwsat <- cwsat

                     
                   
                   
-                    331
+                    330
                     !
                     
                       
      attr(self$cwsat, "T") <- T

                     
                   
                   
-                    332
+                    331
                     !
                     
                       
      attr(self$cwsat, "pH") <- pH

                     
                   
                   
-                    333
+                    332
                     !
                     
                       
      attr(self$cwsat, "source") <- source

                     
                   
                   
-                    334
+                    333
                     !
                     
                       
      attr(self$cwsat, "page") <- page

                     
                   
                   
-                    335
+                    334
                     !
                     
                       
      attr(self$cwsat, "remark") <- remark

                     
                   
                   
-                    336
+                    335
                     
                     
                       
    },

                     
                   
                   
-                    337
+                    336
                     
                     
                       

                     
                   
                   
-                    338
+                    337
                     
                     
                       
    #' @description

                     
                   
                   
-                    339
+                    338
                     
                     
                       
    #' Add a plant uptake factor

                     
                   
                   
-                    340
+                    339
                     
                     
                       
    #' @param PUF The plant uptake factor, a number between 0 and 1

                     
                   
                   
-                    341
+                    340
                     
                     
                       
    add_PUF = function(PUF = 0,

                     
                   
                   
-                    342
+                    341
                     
                     
                       
      source = "focus_generic_gw_2014", page = 41,

                     
                   
                   
-                    343
+                    342
                     
                     
                       
      remark = "Conservative default value")

                     
                   
                   
-                    344
+                    343
                     
                     
                       
    {

                     
                   
                   
-                    345
+                    344
                     !
                     
                       
      self$PUF <- PUF

                     
                   
                   
-                    346
+                    345
                     !
                     
                       
      attr(self$PUF, "source") <- source

                     
                   
                   
-                    347
+                    346
                     !
                     
                       
      attr(self$PUF, "page") <- page

                     
                   
                   
-                    348
+                    347
                     !
                     
                       
      attr(self$PUF, "remark") <- remark

                     
                   
                   
-                    349
+                    348
                     
                     
                       
    },

                     
                   
                   
-                    350
+                    349
                     
                     
                       

                     
                   
                   
-                    351
+                    350
                     
                     
                       
    #' @field TPs List of transformation products as chent objects

                     
                   
                   
-                    352
+                    351
                     
                     
                       
    TPs = list(),

                     
                   
                   
-                    353
+                    352
                     
                     
                       

                     
                   
                   
-                    354
+                    353
                     
                     
                       
    #' @description

                     
                   
                   
-                    355
+                    354
                     
                     
                       
    #' Add a transformation product to the internal list

                     
                   
                   
-                    356
+                    355
                     
                     
                       
    #' @param x A [chent] object, or an identifier to generate a [chent] object

                     
                   
                   
-                    357
+                    356
                     
                     
                       
    #' @param pubchem Should chemical information be obtained from PubChem?

                     
                   
                   
-                    358
+                    357
                     
                     
                       
    add_TP = function(x, smiles = NULL, pubchem = FALSE) {

                     
                   
                   
-                    359
+                    358
                     !
                     
                       
      if (inherits(x, "chent")) {

                     
                   
                   
-                    360
+                    359
                     !
                     
                       
        id <- names(x$identifier)

                     
                   
                   
-                    361
+                    360
                     !
                     
                       
        chent <- x

                     
                   
                   
-                    362
+                    361
                     
                     
                       
      } else {

                     
                   
                   
-                    363
+                    362
                     !
                     
                       
        id <- make.names(x)

                     
                   
                   
-                    364
+                    363
                     !
                     
                       
        chent <- chent$new(x, smiles = smiles, pubchem = pubchem)

                     
                   
                   
-                    365
+                    364
                     
                     
                       
      }

                     
                   
                   
-                    366
+                    365
                     !
                     
                       
      self$TPs[[id]] <- chent

                     
                   
                   
-                    367
+                    366
                     
                     
                       
    },

                     
                   
                   
-                    368
+                    367
                     
                     
                       

                     
                   
                   
-                    369
+                    368
                     
                     
                       
    #' @field transformations Data frame of observed transformations

                     
                   
                   
-                    370
+                    369
                     
                     
                       
    transformations = data.frame(study_type = character(0),

                     
                   
                   
-                    371
+                    370
                     
                     
                       
      TP_identifier = character(0),

                     
                   
                   
-                    372
+                    371
                     
                     
                       
      max_occurrence = numeric(0),

                     
                   
                   
-                    373
+                    372
                     
                     
                       
      source = character(0),

                     
                   
                   
-                    374
+                    373
                     
                     
                       
      page = character(0),

                     
                   
                   
-                    375
+                    374
                     
                     
                       
      stringsAsFactors = FALSE),

                     
                   
                   
-                    376
+                    375
                     
                     
                       

                     
                   
                   
-                    377
+                    376
                     
                     
                       
    #' @description

                     
                   
                   
-                    378
+                    377
                     
                     
                       
    #' Add a line in the internal dataframe holding observed transformations

                     
                   
                   
-                    379
+                    378
                     
                     
                       
    #' @param study_type A characterisation of the study type

                     
                   
                   
-                    380
+                    379
                     
                     
                       
    #' @param TP_identifier An identifier of one of the transformation products

                     
                   
                   
-                    381
+                    380
                     
                     
                       
    #' in `self$TPs`

                     
                   
                   
-                    382
+                    381
                     
                     
                       
    #' @param max_occurrence The maximum observed occurrence of the

                     
                   
                   
-                    383
+                    382
                     
                     
                       
    #' transformation product, expressed as a fraction of the amount that would

                     
                   
                   
-                    384
+                    383
                     
                     
                       
    #' result from stochiometric transformation

                     
                   
                   
-                    385
+                    384
                     
                     
                       
    add_transformation = function(study_type, TP_identifier, max_occurrence,

                     
                   
                   
-                    386
+                    385
                     
                     
                       
      remark = "", source = NA, pages = NA)

                     
                   
                   
-                    387
+                    386
                     
                     
                       
    {

                     
                   
                   
-                    388
+                    387
                     !
                     
                       
      TP_name = make.names(TP_identifier)

                     
                   
                   
-                    389
+                    388
                     !
                     
                       
      if (!inherits(self$TPs[[TP_name]], "chent")) {

                     
                   
                   
-                    390
+                    389
                     !
                     
                       
        stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()"))

                     
                   
                   
-                    391
+                    390
                     
                     
                       
      }

                     
                   
                   
-                    392
+                    391
                     !
                     
                       
      TP_chent <- self$TPs[TP_name]

                     
                   
                   
-                    393
+                    392
                     !
                     
                       
      if (is.numeric(pages)) pages <- paste(pages, collapse = ", ")

                     
                   
                   
-                    394
+                    393
                     !
                     
                       
      cn <- colnames(self$transformations)

                     
                   
                   
-                    395
+                    394
                     !
                     
                       
      self$transformations <- rbind(self$transformations,

                     
                   
                   
-                    396
+                    395
                     !
                     
                       
        data.frame(study_type = study_type,

                     
                   
                   
-                    397
+                    396
                     !
                     
                       
          TP_identifier = TP_identifier,

                     
                   
                   
-                    398
+                    397
                     !
                     
                       
          max_occurrence = max_occurrence,

                     
                   
                   
-                    399
+                    398
                     !
                     
                       
          remark = remark,

                     
                   
                   
-                    400
+                    399
                     !
                     
                       
          source = source,

                     
                   
                   
-                    401
+                    400
                     !
                     
                       
          page = page,

                     
                   
                   
-                    402
+                    401
                     !
                     
                       
          stringsAsFactors = FALSE))

                     
                   
                   
-                    403
+                    402
                     
                     
                       
    },

                     
                   
                   
-                    404
+                    403
                     
                     
                       

                     
                   
                   
-                    405
+                    404
                     
                     
                       
    #' @field soil_degradation Dataframe of modelling DT50 values

                     
                   
                   
-                    406
+                    405
                     
                     
                       
    soil_degradation = NULL,

                     
                   
                   
-                    407
+                    406
                     
                     
                       

                     
                   
                   
-                    408
+                    407
                     
                     
                       
    #' @description

                     
                   
                   
-                    409
+                    408
                     
                     
                       
    #' Add a line in the internal dataframe holding modelling DT50 values

                     
                   
                   
-                    410
+                    409
                     
                     
                       
    #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide

                     
                   
                   
-                    411
+                    410
                     
                     
                       
    #' fate modelling

                     
                   
                   
-                    412
+                    411
                     
                     
                       
    #' @param DT50_mod_ref The normalised modelling DT50 in the sense of

                     
                   
                   
-                    413
+                    412
                     
                     
                       
    #' regulatory pesticide fate modelling

                     
                   
                   
-                    414
+                    413
                     
                     
                       
    #' @param country The country (mainly for field studies)

                     
                   
                   
-                    415
+                    414
                     
                     
                       
    #' @param temperature The temperature during the study in degrees Celsius

                     
                   
                   
-                    416
+                    415
                     
                     
                       
    #' @param moisture The moisture during the study

                     
                   
                   
-                    417
+                    416
                     
                     
                       
    #' @param category Is it a laboratory ('lab') or field study ('field')

                     
                   
                   
-                    418
+                    417
                     
                     
                       
    #' @param formulation Name of the formulation applied, if it was not

                     
                   
                   
-                    419
+                    418
                     
                     
                       
    #' the technical active ingredient

                     
                   
                   
-                    420
+                    419
                     
                     
                       
    #' @param model The degradation model used for deriving `DT50_mod`

                     
                   
                   
-                    421
+                    420
                     
                     
                       
    #' @param chi2 The relative error as defined in FOCUS kinetics

                     
                   
                   
-                    422
+                    421
                     
                     
                       
    add_soil_degradation = function(soils, DT50_mod, DT50_mod_ref,

                     
                   
                   
-                    423
+                    422
                     
                     
                       
      type = NA, country = NA,

                     
                   
                   
-                    424
+                    423
                     
                     
                       
      pH_orig = NA, pH_medium = NA, pH_H2O = NA,

                     
                   
                   
-                    425
+                    424
                     
                     
                       
      perc_OC = NA,

                     
                   
                   
-                    426
+                    425
                     
                     
                       
      temperature = NA, moisture = NA,

                     
                   
                   
-                    427
+                    426
                     
                     
                       
      category = "lab", formulation = NA,

                     
                   
                   
-                    428
+                    427
                     
                     
                       
      model = NA, chi2 = NA,

                     
                   
                   
-                    429
+                    428
                     
                     
                       
      remark = "", source, page = NA)

                     
                   
                   
-                    430
+                    429
                     
                     
                       
    {

                     
                   
                   
-                    431
+                    430
                     !
                     
                       
      new_soil_degradation = data.frame(

                     
                   
                   
-                    432
+                    431
                     !
                     
                       
        soil = soils,

                     
                   
                   
-                    433
+                    432
                     !
                     
                       
        DT50_mod = DT50_mod,

                     
                   
                   
-                    434
+                    433
                     !
                     
                       
        DT50_mod_ref = DT50_mod_ref,

                     
                   
                   
-                    435
+                    434
                     !
                     
                       
        type = type,

                     
                   
                   
-                    436
+                    435
                     !
                     
                       
        country = country,

                     
                   
                   
-                    437
+                    436
                     !
                     
                       
        pH_orig = pH_orig,

                     
                   
                   
-                    438
+                    437
                     !
                     
                       
        pH_medium = pH_medium,

                     
                   
                   
-                    439
+                    438
                     !
                     
                       
        pH_H2O = pH_H2O,

                     
                   
                   
-                    440
+                    439
                     !
                     
                       
        perc_OC = perc_OC,

                     
                   
                   
-                    441
+                    440
                     !
                     
                       
        temperature = temperature,

                     
                   
                   
-                    442
+                    441
                     !
                     
                       
        moisture = moisture,

                     
                   
                   
-                    443
+                    442
                     !
                     
                       
        category = category,

                     
                   
                   
-                    444
+                    443
                     !
                     
                       
        formulation = formulation,

                     
                   
                   
-                    445
+                    444
                     !
                     
                       
        model = model,

                     
                   
                   
-                    446
+                    445
                     !
                     
                       
        chi2 = chi2,

                     
                   
                   
-                    447
+                    446
                     !
                     
                       
        remark = remark,

                     
                   
                   
-                    448
+                    447
                     !
                     
                       
        source = source,

                     
                   
                   
-                    449
+                    448
                     !
                     
                       
        page = page,

                     
                   
                   
-                    450
+                    449
                     !
                     
                       
        stringsAsFactors = FALSE)

                     
                   
                   
-                    451
+                    450
                     !
                     
                       
      if (is.null(self$soil_degradation)) {

                     
                   
                   
-                    452
+                    451
                     !
                     
                       
        self$soil_degradation <- new_soil_degradation

                     
                   
                   
-                    453
+                    452
                     
                     
                       
      } else {

                     
                   
                   
-                    454
+                    453
                     !
                     
                       
        self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation)

                     
                   
                   
-                    455
+                    454
                     
                     
                       
      }

                     
                   
                   
-                    456
+                    455
                     
                     
                       
    },

                     
                   
                   
-                    457
+                    456
                     
                     
                       

                     
                   
                   
-                    458
+                    457
                     
                     
                       
    #' @field soil_ff Dataframe of formation fractions

                     
                   
                   
-                    459
+                    458
                     
                     
                       
    soil_ff = NULL,

                     
                   
                   
-                    460
+                    459
                     
                     
                       

                     
                   
                   
-                    461
+                    460
                     
                     
                       
    #' @description

                     
                   
                   
-                    462
+                    461
                     
                     
                       
    #' Add one or more formation fractions for degradation in soil

                     
                   
                   
-                    463
+                    462
                     
                     
                       
    #' @param target The identifier(s) of the transformation product

                     
                   
                   
-                    464
+                    463
                     
                     
                       
    #' @param soils The soil name(s) in which the transformation was observed

                     
                   
                   
-                    465
+                    464
                     
                     
                       
    #' @param ff The formation fraction(s)

                     
                   
                   
-                    466
+                    465
                     
                     
                       
    add_soil_ff = function(target, soils, ff = 1,

                     
                   
                   
-                    467
+                    466
                     
                     
                       
      remark = "", source, page = NA)

                     
                   
                   
-                    468
+                    467
                     
                     
                       
    {

                     
                   
                   
-                    469
+                    468
                     !
                     
                       
      new_soil_ff = data.frame(

                     
                   
                   
-                    470
+                    469
                     !
                     
                       
        target = target,

                     
                   
                   
-                    471
+                    470
                     !
                     
                       
        target = target,

                     
                   
                   
-                    472
+                    471
                     !
                     
                       
        soil = soils,

                     
                   
                   
-                    473
+                    472
                     !
                     
                       
        ff = ff,

                     
                   
                   
-                    474
+                    473
                     !
                     
                       
        remark = remark,

                     
                   
                   
-                    475
+                    474
                     !
                     
                       
        source = source,

                     
                   
                   
-                    476
+                    475
                     !
                     
                       
        page = page,

                     
                   
                   
-                    477
+                    476
                     !
                     
                       
        stringsAsFactors = FALSE)

                     
                   
                   
-                    478
+                    477
                     !
                     
                       
      if (is.null(self$soil_ff)) {

                     
                   
                   
-                    479
+                    478
                     !
                     
                       
        self$soil_ff <- new_soil_ff

                     
                   
                   
-                    480
+                    479
                     
                     
                       
      } else {

                     
                   
                   
-                    481
+                    480
                     !
                     
                       
        self$soil_ff <- rbind(self$soil_ff, new_soil_ff)

                     
                   
                   
-                    482
+                    481
                     
                     
                       
      }

                     
                   
                   
-                    483
+                    482
                     
                     
                       
    },

                     
                   
                   
-                    484
+                    483
                     
                     
                       

                     
                   
                   
-                    485
+                    484
                     
                     
                       
    #' @field soil_sorption Dataframe of soil sorption data

                     
                   
                   
-                    486
+                    485
                     
                     
                       
    soil_sorption = NULL,

                     
                   
                   
-                    487
+                    486
                     
                     
                       

                     
                   
                   
-                    488
+                    487
                     
                     
                       
    #' @description

                     
                   
                   
-                    489
+                    488
                     
                     
                       
    #' Add soil sorption data

                     
                   
                   
-                    490
+                    489
                     
                     
                       
    #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1)

                     
                   
                   
-                    491
+                    490
                     
                     
                       
    #' or according to Freundlich

                     
                   
                   
-                    492
+                    491
                     
                     
                       
    #' @param Kfoc The constant from above, normalised to soil organic carbon

                     
                   
                   
-                    493
+                    492
                     
                     
                       
    #' @param N The Freundlich exponent

                     
                   
                   
-                    494
+                    493
                     
                     
                       
    #' @param perc_clay The percentage of clay in the soil

                     
                   
                   
-                    495
+                    494
                     
                     
                       
    #' @param CEC The cation exchange capacity

                     
                   
                   
-                    496
+                    495
                     
                     
                       
    add_soil_sorption = function(soils, 

                     
                   
                   
-                    497
+                    496
                     
                     
                       
      Kf, Kfoc, N,

                     
                   
                   
-                    498
+                    497
                     
                     
                       
      type = NA, pH_orig = NA, pH_medium = NA,

                     
                   
                   
-                    499
+                    498
                     
                     
                       
      pH_H2O = NA,

                     
                   
                   
-                    500
+                    499
                     
                     
                       
      perc_OC = NA, perc_clay = NA, CEC = NA,

                     
                   
                   
-                    501
+                    500
                     
                     
                       
      remark = "", source, page = NA)

                     
                   
                   
-                    502
+                    501
                     
                     
                       
    {

                     
                   
                   
-                    503
+                    502
                     !
                     
                       
      new_soil_sorption = data.frame(

                     
                   
                   
-                    504
+                    503
                     !
                     
                       
        soils = soils,

                     
                   
                   
-                    505
+                    504
                     !
                     
                       
        Kf = Kf, Kfoc = Kfoc, N = N,

                     
                   
                   
-                    506
+                    505
                     !
                     
                       
        type = type,

                     
                   
                   
-                    507
+                    506
                     !
                     
                       
        pH_orig = pH_orig,

                     
                   
                   
-                    508
+                    507
                     !
                     
                       
        pH_medium = pH_medium,

                     
                   
                   
-                    509
+                    508
                     !
                     
                       
        pH_H2O = pH_H2O,

                     
                   
                   
-                    510
+                    509
                     !
                     
                       
        perc_OC = perc_OC, perc_clay = perc_clay, CEC = CEC,

                     
                   
                   
-                    511
+                    510
                     !
                     
                       
        remark = remark,

                     
                   
                   
-                    512
+                    511
                     !
                     
                       
        source = source,

                     
                   
                   
-                    513
+                    512
                     !
                     
                       
        page = page,

                     
                   
                   
-                    514
+                    513
                     !
                     
                       
        stringsAsFactors = FALSE)

                     
                   
                   
-                    515
+                    514
                     !
                     
                       
      if (is.null(self$soil_sorption)) {

                     
                   
                   
-                    516
+                    515
                     !
                     
                       
        self$soil_sorption <- new_soil_sorption

                     
                   
                   
-                    517
+                    516
                     
                     
                       
      } else {

                     
                   
                   
-                    518
+                    517
                     !
                     
                       
        self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption)

                     
                   
                   
-                    519
+                    518
                     
                     
                       
      }

                     
                   
                   
-                    520
+                    519
                     
                     
                       
    },

                     
                   
                   
-                    521
+                    520
                     
                     
                       

                     
                   
                   
-                    522
+                    521
                     
                     
                       
    #' @description

                     
                   
                   
-                    523
+                    522
                     
                     
                       
    #' Write a PDF image of the structure

                     
                   
                   
-                    524
+                    523
                     
                     
                       
    pdf = function(file = paste0(self$identifier, ".pdf"),

                     
                   
                   
-                    525
+                    524
                     
                     
                       
        dir = "structures/pdf", template = NULL) {

                     
                   
                   
-                    526
+                    525
                     !
                     
                       
      if (!dir.exists(dir)) {

                     
                   
                   
-                    527
+                    526
                     !
                     
                       
        message("Directory '", dir, "' does not exist")

                     
                   
                   
-                    528
+                    527
                     !
                     
                       
        message("Trying to create directory '", dir, "'")

                     
                   
                   
-                    529
+                    528
                     !
                     
                       
        dir.create(dir, recursive = TRUE)

                     
                   
                   
-                    530
+                    529
                     
                     
                       
      }

                     
                   
                   
-                    531
+                    530
                     !
                     
                       
      path = file.path(dir, file)

                     
                   
                   
-                    532
+                    531
                     !
                     
                       
      message("Creating file '", path, "'")

                     
                   
                   
-                    533
+                    532
                     !
                     
                       
      pdf(path)

                     
                   
                   
-                    534
+                    533
                     !
                     
                       
      plot(self)

                     
                   
                   
-                    535
+                    534
                     !
                     
                       
      dev.off()

                     
                   
                   
-                    536
+                    535
                     !
                     
                       
      message("Cropping file '", path, "' using pdfcrop")

                     
                   
                   
-                    537
+                    536
                     !
                     
                       
      bash_path <- shQuote(path)

                     
                   
                   
-                    538
+                    537
                     !
                     
                       
      system(paste("pdfcrop --margin 10", bash_path, bash_path, "> /dev/null"))

                     
                   
                   
-                    539
+                    538
                     
                     
                       

                     
                   
                   
-                    540
+                    539
                     
                     
                       
      # Get the height of the MediaBox

                     
                   
                   
-                    541
+                    540
                     !
                     
                       
      head <- readLines(path, n = 20, skipNul = TRUE)

                     
                   
                   
-                    542
+                    541
                     !
                     
                       
      m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE))

                     
                   
                   
-                    543
+                    542
                     !
                     
                       
      self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line))

                     
                   
                   
-                    544
+                    543
                     
                     
                       
    },

                     
                   
                   
-                    545
+                    544
                     
                     
                       

                     
                   
                   
-                    546
+                    545
                     
                     
                       
    #' @description

                     
                   
                   
-                    547
+                    546
                     
                     
                       
    #' Write a PNG image of the structure

                     
                   
                   
-                    548
+                    547
                     
                     
                       
    #' @param antialias Passed to [png][grDevices::png]

                     
                   
                   
-                    549
+                    548
                     
                     
                       
    png = function(file = paste0(self$identifier, ".png"),

                     
                   
                   
-                    550
+                    549
                     
                     
                       
      dir = "structures/png", antialias = 'gray')

                     
                   
                   
-                    551
+                    550
                     
                     
                       
    {

                     
                   
                   
-                    552
+                    551
                     !
                     
                       
      if (!dir.exists(dir)) {

                     
                   
                   
-                    553
+                    552
                     !
                     
                       
        message("Directory '", dir, "' does not exist")

                     
                   
                   
-                    554
+                    553
                     !
                     
                       
        message("Trying to create directory '", dir, "'")

                     
                   
                   
-                    555
+                    554
                     !
                     
                       
        dir.create(dir, recursive = TRUE)

                     
                   
                   
-                    556
+                    555
                     
                     
                       
      }

                     
                   
                   
-                    557
+                    556
                     !
                     
                       
      path = file.path(dir, file)

                     
                   
                   
-                    558
+                    557
                     !
                     
                       
      message("Creating file '", path, "'")

                     
                   
                   
-                    559
+                    558
                     !
                     
                       
      png(path, antialias = antialias)

                     
                   
                   
-                    560
+                    559
                     !
                     
                       
      plot(self)

                     
                   
                   
-                    561
+                    560
                     !
                     
                       
      dev.off()

                     
                   
                   
-                    562
+                    561
                     
                     
                       
    },

                     
                   
                   
-                    563
+                    562
                     
                     
                       

                     
                   
                   
-                    564
+                    563
                     
                     
                       
    #' @description

                     
                   
                   
-                    565
+                    564
                     
                     
                       
    #' Write an EMF image of the structure using [emf][devEMF::emf]

                     
                   
                   
-                    566
+                    565
                     
                     
                       
    emf = function(file = paste0(self$identifier, ".emf"),

                     
                   
                   
-                    567
+                    566
                     
                     
                       
      dir = "structures/emf")

                     
                   
                   
-                    568
+                    567
                     
                     
                       
    {

                     
                   
                   
-                    569
+                    568
                     !
                     
                       
      if (!requireNamespace("devEMF")) {

                     
                   
                   
-                    570
+                    569
                     !
                     
                       
        stop("You need to have the devEMF package installed for this function")

                     
                   
                   
-                    571
+                    570
                     
                     
                       
      }

                     
                   
                   
-                    572
+                    571
                     !
                     
                       
      if (!dir.exists(dir)) {

                     
                   
                   
-                    573
+                    572
                     !
                     
                       
        message("Directory '", dir, "' does not exist")

                     
                   
                   
-                    574
+                    573
                     !
                     
                       
        message("Trying to create directory '", dir, "'")

                     
                   
                   
-                    575
+                    574
                     !
                     
                       
        dir.create(dir, recursive = TRUE)

                     
                   
                   
-                    576
+                    575
                     
                     
                       
      }

                     
                   
                   
-                    577
+                    576
                     !
                     
                       
      path = file.path(dir, file)

                     
                   
                   
-                    578
+                    577
                     !
                     
                       
      message("Creating file '", path, "'")

                     
                   
                   
-                    579
+                    578
                     !
                     
                       
      devEMF::emf(path)

                     
                   
                   
-                    580
+                    579
                     !
                     
                       
      plot(self)

                     
                   
                   
-                    581
+                    580
                     !
                     
                       
      dev.off()

                     
                   
                   
-                    582
+                    581
                     
                     
                       
    }

                     
                   
                   
-                    583
+                    582
                     
                     
                       
  )

                     
                   
                   
-                    584
+                    583
                     
                     
                       
)

                     
                   
                   
-                    585
+                    584
                     
                     
                       

                     
                   
                   
-                    586
+                    585
                     
                     
                       
#' Printing method for chent objects

                     
                   
                   
-                    587
+                    586
                     
                     
                       
#'

                     
                   
                   
-                    588
+                    587
                     
                     
                       
#' @param x The chent object to be printed

                     
                   
                   
-                    589
+                    588
                     
                     
                       
#' @param ... Further arguments for compatibility with the S3 method

                     
                   
                   
-                    590
+                    589
                     
                     
                       
#' @importFrom utils head

                     
                   
                   
-                    591
+                    590
                     
                     
                       
#' @export

                     
                   
                   
-                    592
+                    591
                     
                     
                       
print.chent = function(x, ...) {

                     
                   
-                  
-                    593
-                    !
+                  
+                    592
+                    1x
                     
                       
  cat("<chent>\n")

                     
                   
-                  
-                    594
-                    !
+                  
+                    593
+                    1x
                     
                       
  cat("Identifier $identifier", x$identifier, "\n")

                     
                   
-                  
-                    595
-                    !
+                  
+                    594
+                    1x
                     
                       
  cat ("InChI Key $inchikey", x$inchikey, "\n")

                     
                   
-                  
-                    596
-                    !
+                  
+                    595
+                    1x
                     
                       
  cat ("SMILES string $smiles:\n")

                     
                   
-                  
-                    597
-                    !
+                  
+                    596
+                    1x
                     
                       
  print(x$smiles)

                     
                   
-                  
-                    598
-                    !
+                  
+                    597
+                    1x
                     
                       
  if (!is.null(x$mw)) cat ("Molecular weight $mw:", round(x$mw, 1), "\n")

                     
                   
-                  
-                    599
-                    !
+                  
+                    598
+                    1x
                     
                       
  if (!is.null(x$pubchem$synonyms)) {

                     
                   
-                  
-                    600
-                    !
+                  
+                    599
+                    1x
                     
                       
    cat ("PubChem synonyms (up to 10):\n")

                     
                   
-                  
-                    601
-                    !
+                  
+                    600
+                    1x
                     
                       
    print(head(x$pubchem$synonyms, n = 10L))

                     
                   
                   
-                    602
+                    601
                     
                     
                       
  }

                     
                   
                   
-                    603
+                    602
                     
                     
                       
}

                     
                   
                   
-                    604
+                    603
                     
                     
                       

                     
                   
                   
-                    605
+                    604
                     
                     
                       
#' Draw SVG graph from a chent object using RDKit

                     
                   
                   
-                    606
+                    605
                     
                     
                       
#'

                     
                   
                   
-                    607
+                    606
                     
                     
                       
#' @param x The chent object to be plotted

                     
                   
                   
-                    608
+                    607
                     
                     
                       
#' @param width The desired width in pixels

                     
                   
                   
-                    609
+                    608
                     
                     
                       
#' @param height The desired height in pixels

                     
                   
                   
-                    610
+                    609
                     
                     
                       
#' @param filename The filename

                     
                   
                   
-                    611
+                    610
                     
                     
                       
#' @param subdir The path to which the file should be written

                     
                   
                   
-                    612
+                    611
                     
                     
                       
#' @export

                     
                   
                   
-                    613
+                    612
                     
                     
                       
draw_svg.chent = function(x, width = 300, height = 150,

                     
                   
                   
-                    614
+                    613
                     
                     
                       
   filename = paste0(names(x$identifier), ".svg"),

                     
                   
                   
-                    615
+                    614
                     
                     
                       
   subdir = "svg") {

                     
                   
                   
-                    616
+                    615
                     !
                     
                       
  if (!rdkit_available) {

                     
                   
                   
-                    617
+                    616
                     !
                     
                       
    stop("RDkit is not available via reticulate")

                     
                   
                   
-                    618
+                    617
                     
                     
                       
  } else {

                     
                   
                   
-                    619
+                    618
                     !
                     
                       
    if (!dir.exists(subdir)) dir.create(subdir)

                     
                   
                   
-                    620
+                    619
                     !
                     
                       
    mol <- rdkit_module$Chem$MolFromSmiles(x$smiles)

                     
                   
                   
-                    621
+                    620
                     
                     
                       

                     
                   
                   
-                    622
+                    621
                     !
                     
                       
    rdkit_module$Chem$Draw$MolToFile(mol, file.path(subdir, filename),

                     
                   
                   
-                    623
+                    622
                     !
                     
                       
      size = c(as.integer(width), as.integer(height)))

                     
                   
                   
-                    624
+                    623
                     
                     
                       
  }

                     
                   
                   
-                    625
+                    624
                     
                     
                       
}

                     
                   
                   
-                    626
+                    625
                     
                     
                       

                     
                   
                   
-                    627
+                    626
                     
                     
                       
#' Plot method for chent objects

                     
                   
                   
-                    628
+                    627
                     
                     
                       
#'

                     
                   
                   
-                    629
+                    628
                     
                     
                       
#' @importFrom grImport grid.picture

                     
                   
                   
-                    630
+                    629
                     
                     
                       
#' @param x The chent object to be plotted

                     
                   
                   
-                    631
+                    630
                     
                     
                       
#' @param ... Further arguments passed to [grImport::grid.picture]

                     
                   
                   
-                    632
+                    631
                     
                     
                       
#' @export

                     
                   
                   
-                    633
+                    632
                     
                     
                       
#' @examples

                     
                   
                   
-                    634
+                    633
                     
                     
                       
#' caffeine <- chent$new("caffeine")

                     
                   
                   
-                    635
+                    634
                     
                     
                       
#' print(caffeine)

                     
                   
                   
-                    636
+                    635
                     
                     
                       
#' if (!is.null(caffeine$Picture)) {

                     
                   
                   
-                    637
+                    636
                     
                     
                       
#'   plot(caffeine)

                     
                   
                   
-                    638
+                    637
                     
                     
                       
#' }

                     
                   
                   
-                    639
+                    638
                     
                     
                       
plot.chent = function(x, ...) {

                     
                   
                   
-                    640
+                    639
                     !
                     
                       
  if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?")

                     
                   
                   
-                    641
+                    640
                     !
                     
                       
  grid.picture(x$Picture)

                     
                   
                   
-                    642
+                    641
                     
                     
                       
}

                     
                   
                   
-                    643
+                    642
                     
                     
                       

                     
                   
                   
-                    644
+                    643
                     
                     
                       
#' @title An R6 class for pesticidal active ingredients and associated data

                     
                   
                   
-                    645
+                    644
                     
                     
                       
#'

                     
                   
                   
-                    646
+                    645
                     
                     
                       
#' @description This class is derived from [chent]. It makes it easy

                     
                   
                   
-                    647
+                    646
                     
                     
                       
#' to create a [chent] from the ISO common name of a pesticide active

                     
                   
                   
-                    648
+                    647
                     
                     
                       
#' ingredient, and additionally stores the ISO name as well as

                     
                   
                   
-                    649
+                    648
                     
                     
                       
#' the complete result of querying the BCPC compendium using

                     
                   
                   
-                    650
+                    649
                     
                     
                       
#' [bcpc_query][webchem::bcpc_query].

                     
                   
                   
-                    651
+                    650
                     
                     
                       
#'

                     
                   
                   
-                    652
+                    651
                     
                     
                       
#' @export

                     
                   
                   
-                    653
+                    652
                     
                     
                       
#' @format An [R6::R6Class] generator object

                     
                   
                   
-                    654
+                    653
                     
                     
                       
#' @examples

                     
                   
                   
-                    655
+                    654
                     
                     
                       
#' # On Travis, we get a certificate validation error,

                     
                   
                   
-                    656
+                    655
                     
                     
                       
#' # likely because the system (xenial) is so old,

                     
                   
                   
-                    657
+                    656
                     
                     
                       
#' # therefore don't run this example on Travis

                     
                   
                   
-                    658
+                    657
                     
                     
                       
#' if (Sys.getenv("TRAVIS") == "") {

                     
                   
                   
-                    659
+                    658
                     
                     
                       
#'

                     
                   
                   
-                    660
+                    659
                     
                     
                       
#' atr <- pai$new("atrazine")

                     
                   
                   
-                    661
+                    660
                     
                     
                       
#' print(atr)

                     
                   
                   
-                    662
+                    661
                     
                     
                       
#' if (!is.null(atr$Picture)) {

                     
                   
                   
-                    663
+                    662
                     
                     
                       
#'   plot(atr)

                     
                   
                   
-                    664
+                    663
                     
                     
                       
#' }

                     
                   
                   
-                    665
+                    664
                     
                     
                       
#'

                     
                   
                   
-                    666
+                    665
                     
                     
                       
#' }

                     
                   
                   
-                    667
+                    666
                     
                     
                       
pai <- R6Class("pai",

                     
                   
                   
-                    668
+                    667
                     
                     
                       
  inherit = chent,

                     
                   
                   
-                    669
+                    668
                     
                     
                       
  public = list(

                     
                   
                   
-                    670
+                    669
                     
                     
                       

                     
                   
                   
-                    671
+                    670
                     
                     
                       
    #' @field iso ISO common name of the active ingredient according to ISO 1750

                     
                   
                   
-                    672
+                    671
                     
                     
                       
    iso = NULL,

                     
                   
                   
-                    673
+                    672
                     
                     
                       

                     
                   
                   
-                    674
+                    673
                     
                     
                       
    #' @field bcpc Information retrieved from the BCPC compendium available online

                     
                   
                   
-                    675
+                    674
                     
                     
                       
    #' at <pesticidecompendium.bcpc.org>

                     
                   
                   
-                    676
+                    675
                     
                     
                       
    bcpc = NULL,

                     
                   
                   
-                    677
+                    676
                     
                     
                       

                     
                   
                   
-                    678
+                    677
                     
                     
                       
    #' @description

                     
                   
                   
-                    679
+                    678
                     
                     
                       
    #' Create a new pai object

                     
                   
                   
-                    680
+                    679
                     
                     
                       
    #' @param iso The ISO common name to be used in the query of the

                     
                   
                   
-                    681
+                    680
                     
                     
                       
    #' BCPC compendium

                     
                   
                   
-                    682
+                    681
                     
                     
                       
    #' @param identifier Alternative identifier used for querying pubchem

                     
                   
                   
-                    683
+                    682
                     
                     
                       
    #' @param smiles Optional user provided SMILES code

                     
                   
                   
-                    684
+                    683
                     
                     
                       
    #' @param inchikey Optional user provided InChI Key

                     
                   
                   
-                    685
+                    684
                     
                     
                       
    #' @param bcpc Should the BCPC compendium be queried?

                     
                   
                   
-                    686
+                    685
                     
                     
                       
    #' @param pubchem Should an attempt be made to retrieve chemical

                     
                   
                   
-                    687
+                    686
                     
                     
                       
    #' information from PubChem via the webchem package?

                     
                   
                   
-                    688
+                    687
                     
                     
                       
    #' @param pubchem_from Possibility to select the argument

                     
                   
                   
-                    689
+                    688
                     
                     
                       
    #' that is used to query pubchem

                     
                   
                   
-                    690
+                    689
                     
                     
                       
    #' @param rdkit Should an attempt be made to retrieve chemical

                     
                   
                   
-                    691
+                    690
                     
                     
                       
    #' information from a local rdkit installation via python

                     
                   
                   
-                    692
+                    691
                     
                     
                       
    #' and the reticulate package?

                     
                   
                   
-                    693
+                    692
                     
                     
                       
    #' @param template An optional SMILES code to be used as template for RDKit

                     
                   
                   
-                    694
+                    693
                     
                     
                       
    #' @param chyaml Should we look for a identifier.yaml file in the working

                     
                   
                   
-                    695
+                    694
                     
                     
                       
    initialize = function(iso, identifier = iso,

                     
                   
                   
-                    696
+                    695
                     
                     
                       
      smiles = NULL, inchikey = NULL, bcpc = TRUE,

                     
                   
                   
-                    697
+                    696
                     
                     
                       
      pubchem = TRUE, pubchem_from = 'auto',

                     
                   
                   
-                    698
+                    697
                     
                     
                       
      rdkit = TRUE, template = NULL,

                     
                   
                   
-                    699
+                    698
                     
                     
                       
      chyaml = FALSE)

                     
                   
                   
-                    700
+                    699
                     
                     
                       
    {

                     
                   
                   
-                    701
+                    700
                     
                     
                       

                     
                   
                   
-                    702
+                    701
                     1x
                     
                       
      if (!is.null(inchikey)) {

                     
                   
                   
-                    703
+                    702
                     !
                     
                       
        self$inchikey = inchikey

                     
                   
                   
-                    704
+                    703
                     !
                     
                       
        attr(self$inchikey, "source") <- "user"

                     
                   
                   
-                    705
+                    704
                     
                     
                       
      }

                     
                   
                   
-                    706
+                    705
                     
                     
                       

                     
                   
                   
-                    707
+                    706
                     1x
                     
                       
      if (!missing(iso) & bcpc) {

                     
                   
                   
-                    708
+                    707
                     1x
                     
-                      
        message("BCPC:")

+                      
        message("Querying BCPC for ", identifier, " ...")

                     
                   
                   
-                    709
+                    708
                     1x
                     
                       
        bcpc_result = webchem::bcpc_query(identifier, from = "name")

                     
                   
                   
-                    710
+                    709
                     
                     
                       

                     
                   
                   
-                    711
+                    710
                     
                     
                       
        # Use first element of list, as we passed a query of length one

                     
                   
                   
-                    712
+                    711
                     1x
                     
                       
        if (is.na(bcpc_result[[1]][1])) {

                     
                   
                   
-                    713
+                    712
                     !
                     
                       
          message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem")

                     
                   
                   
-                    714
+                    713
                     
                     
                       
        } else {

                     
                   
                   
-                    715
+                    714
                     1x
                     
                       
          self$bcpc = bcpc_result[[1]]

                     
                   
                   
-                    716
+                    715
                     1x
                     
                       
          self$iso = self$bcpc$cname

                     
                   
                   
-                    717
+                    716
                     1x
                     
                       
          attr(self$iso, "source") <- "bcpc"

                     
                   
                   
-                    718
+                    717
                     1x
                     
                       
          attr(self$iso, "status") <- self$bcpc$status

                     
                   
                   
-                    719
+                    718
                     1x
                     
                       
          bcpc_ik = self$bcpc$inchikey

                     
                   
                   
-                    720
+                    719
                     1x
                     
                       
          if (length(bcpc_ik) == 1 && !is.na(bcpc_ik)) {

                     
                   
                   
-                    721
+                    720
                     1x
                     
                       
            if (is.null(self$inchikey)) {

                     
                   
                   
-                    722
+                    721
                     1x
                     
                       
              self$inchikey = substr(self$bcpc$inchikey, 1, 27)

                     
                   
                   
-                    723
+                    722
                     1x
                     
                       
              attr(self$inchikey, "source") <- "bcpc"

                     
                   
                   
-                    724
+                    723
                     
                     
                       
            } else {

                     
                   
                   
-                    725
+                    724
                     !
                     
                       
              if (bcpc_ik == self$inchikey) {

                     
                   
                   
-                    726
+                    725
                     !
                     
                       
                attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc")

                     
                   
                   
-                    727
+                    726
                     
                     
                       
              } else {

                     
                   
                   
-                    728
+                    727
                     !
                     
                       
                warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org")

                     
                   
                   
-                    729
+                    728
                     
                     
                       
              }

                     
                   
                   
-                    730
+                    729
                     
                     
                       
            }

                     
                   
                   
-                    731
+                    730
                     
                     
                       
          }

                     
                   
                   
-                    732
+                    731
                     
                     
                       
        }

                     
                   
                   
-                    733
+                    732
                     
                     
                       
      }

                     
                   
                   
-                    734
+                    733
                     
                     
                       

                     
                   
                   
-                    735
+                    734
                     
                     
                       
      # Set pubchem_from if not specified

                     
                   
                   
-                    736
+                    735
                     1x
                     
                       
      if (pubchem_from == 'auto') {

                     
                   
                   
-                    737
+                    736
                     1x
                     
                       
        pubchem_from = 'name'

                     
                   
                   
-                    738
+                    737
                     1x
                     
                       
        if (!is.null(self$inchikey)) {

                     
                   
                   
-                    739
+                    738
                     1x
                     
                       
          pubchem_from = 'inchikey'

                     
                   
                   
-                    740
+                    739
                     
                     
                       
        }

                     
                   
                   
-                    741
+                    740
                     
                     
                       
      }

                     
                   
                   
-                    742
+                    741
                     
                     
                       

                     
                   
                   
-                    743
+                    742
                     1x
                     
                       
      super$initialize(identifier = identifier,

                     
                   
                   
-                    744
+                    743
                     1x
                     
                       
        smiles = smiles, inchikey = self$inchikey,

                     
                   
                   
-                    745
+                    744
                     1x
                     
                       
        pubchem = pubchem, pubchem_from = pubchem_from,

                     
                   
                   
-                    746
+                    745
                     1x
                     
                       
        rdkit = rdkit, template = template, chyaml = chyaml)

                     
                   
                   
-                    747
+                    746
                     
                     
                       

                     
                   
                   
-                    748
+                    747
                     1x
                     
                       
      invisible(self)

                     
                   
                   
-                    749
+                    748
                     
                     
                       
    }

                     
                   
                   
-                    750
+                    749
                     
                     
                       
  )

                     
                   
                   
-                    751
+                    750
                     
                     
                       
)

                     
                   
                   
-                    752
+                    751
                     
                     
                       

                     
                   
                   
-                    753
+                    752
                     
                     
                       
#' Printing method for pai objects (pesticidal active ingredients)

                     
                   
                   
-                    754
+                    753
                     
                     
                       
#'

                     
                   
                   
-                    755
+                    754
                     
                     
                       
#' @param x The chent object to be printed

                     
                   
                   
-                    756
+                    755
                     
                     
                       
#' @param ... Further arguments for compatibility with the S3 method

                     
                   
                   
-                    757
+                    756
                     
                     
                       
#' @export

                     
                   
                   
-                    758
+                    757
                     
                     
                       
print.pai = function(x, ...) {

                     
                   
                   
-                    759
+                    758
                     !
                     
                       
  cat("<pai> with ISO common name $iso", x$iso, "\n")

                     
                   
                   
-                    760
+                    759
                     !
                     
                       
  print.chent(x)

                     
                   
                   
-                    761
+                    760
                     !
                     
                       
  if (length(x$TPs) > 0) {

                     
                   
                   
-                    762
+                    761
                     !
                     
                       
    cat("\nTransformation products:\n")

                     
                   
                   
-                    763
+                    762
                     !
                     
                       
    print(x$TPs)

                     
                   
                   
-                    764
+                    763
                     
                     
                       
  }

                     
                   
                   
-                    765
+                    764
                     !
                     
                       
  if (nrow(x$transformations) > 0) {

                     
                   
                   
-                    766
+                    765
                     !
                     
                       
    cat("\nTransformations:\n")

                     
                   
                   
-                    767
+                    766
                     !
                     
                       
    print(x$transformations)

                     
                   
                   
-                    768
+                    767
                     
                     
                       
  }

                     
                   
                   
-                    769
+                    768
                     
                     
                       
}

                     
                   
                   
-                    770
+                    769
                     
                     
                       

                     
                   
                   
-                    771
+                    770
                     
                     
                       
#' @title R6 class for a plant protection product with at least one active ingredient

                     
                   
                   
-                    772
+                    771
                     
                     
                       
#'

                     
                   
                   
-                    773
+                    772
                     
                     
                       
#' @description Contains basic information about the active ingredients in the

                     
                   
                   
-                    774
+                    773
                     
                     
                       
#' product

                     
                   
                   
-                    775
+                    774
                     
                     
                       
#'

                     
                   
                   
-                    776
+                    775
                     
                     
                       
#' @export

                     
                   
                   
-                    777
+                    776
                     
                     
                       
#' @format An [R6::R6Class] generator object.

                     
                   
                   
-                    778
+                    777
                     
                     
                       
ppp <- R6Class("ppp",

                     
                   
                   
-                    779
+                    778
                     
                     
                       
  public = list(

                     
                   
                   
-                    780
+                    779
                     
                     
                       

                     
                   
                   
-                    781
+                    780
                     
                     
                       
    #' @field name The name of the product

                     
                   
                   
-                    782
+                    781
                     
                     
                       
    name = NULL,

                     
                   
                   
-                    783
+                    782
                     
                     
                       

                     
                   
                   
-                    784
+                    783
                     
                     
                       
    #' @field ais A list of active ingredients

                     
                   
                   
-                    785
+                    784
                     
                     
                       
    ais = list(),

                     
                   
                   
-                    786
+                    785
                     
                     
                       

                     
                   
                   
-                    787
+                    786
                     
                     
                       
    #' @field concentrations The concentration of the ais

                     
                   
                   
-                    788
+                    787
                     
                     
                       
    concentrations = NULL,

                     
                   
                   
-                    789
+                    788
                     
                     
                       

                     
                   
                   
-                    790
+                    789
                     
                     
                       
    #' @field concentration_units Defaults to g/L

                     
                   
                   
-                    791
+                    790
                     
                     
                       
    concentration_units = NULL,

                     
                   
                   
-                    792
+                    791
                     
                     
                       

                     
                   
                   
-                    793
+                    792
                     
                     
                       
    #' @field density The density of the product

                     
                   
                   
-                    794
+                    793
                     
                     
                       
    density = NULL,

                     
                   
                   
-                    795
+                    794
                     
                     
                       

                     
                   
                   
-                    796
+                    795
                     
                     
                       
    #' @field density_units Defaults to g/L

                     
                   
                   
-                    797
+                    796
                     
                     
                       
    density_units = "g/L",

                     
                   
                   
-                    798
+                    797
                     
                     
                       

                     
                   
                   
-                    799
+                    798
                     
                     
                       
    #' @description

                     
                   
                   
-                    800
+                    799
                     
                     
                       
    #' Creates a new instance of this [R6][R6::R6Class] class.

                     
                   
                   
-                    801
+                    800
                     
                     
                       
    #' @param name The name of the product

                     
                   
                   
-                    802
+                    801
                     
                     
                       
    #' @param ... Identifiers of the active ingredients

                     
                   
                   
-                    803
+                    802
                     
                     
                       
    #' @param concentrations Concentrations of the active ingredients

                     
                   
                   
-                    804
+                    803
                     
                     
                       
    #' @param concentration_units Defaults to g/L

                     
                   
                   
-                    805
+                    804
                     
                     
                       
    #' @param density The density

                     
                   
                   
-                    806
+                    805
                     
                     
                       
    #' @param density_units Defaults to g/L

                     
                   
                   
-                    807
+                    806
                     
                     
                       
    initialize = function(name, ..., concentrations, concentration_units = "g/L",

                     
                   
                   
-                    808
+                    807
                     
                     
                       
      density = 1000, density_units = "g/L")

                     
                   
                   
-                    809
+                    808
                     
                     
                       
    {

                     
                   
                   
-                    810
+                    809
                     !
                     
                       
      self$name <- name

                     
                   
                   
-                    811
+                    810
                     !
                     
                       
      self$ais <- list(...)

                     
                   
                   
-                    812
+                    811
                     !
                     
                       
      self$concentrations <- concentrations

                     
                   
                   
-                    813
+                    812
                     !
                     
                       
      self$density <- density

                     
                   
                   
-                    814
+                    813
                     !
                     
                       
      self$density_units <- density_units

                     
                   
                   
-                    815
+                    814
                     !
                     
                       
      names(self$concentrations) <- names(self$ais)

                     
                   
                   
-                    816
+                    815
                     !
                     
                       
      self$concentration_units <- concentration_units

                     
                   
                   
-                    817
+                    816
                     
                     
                       
    }

                     
                   
                   
-                    818
+                    817
                     
                     
                       
  )

                     
                   
                   
-                    819
+                    818
                     
                     
                       
)

                     
                   
                   
-                    820
+                    819
                     
                     
                       

                     
                   
                   
-                    821
+                    820
                     
                     
                       
#' Printing method for ppp objects (plant protection products)

                     
                   
                   
-                    822
+                    821
                     
                     
                       
#'

                     
                   
                   
-                    823
+                    822
                     
                     
                       
#' @param x The chent object to be printed

                     
                   
                   
-                    824
+                    823
                     
                     
                       
#' @param ... Further arguments for compatibility with the S3 method

                     
                   
                   
-                    825
+                    824
                     
                     
                       
#' @export

                     
                   
                   
-                    826
+                    825
                     
                     
                       
print.ppp = function(x, ...) {

                     
                   
                   
-                    827
+                    826
                     !
                     
                       
  cat("<pp> named", x$name, "\n")

                     
                   
                   
-                    828
+                    827
                     
                     
                       
}

                     
                   
                   
-                    829
+                    828
                     
                     
                       
# vim: set ts=2 sw=2 expandtab:

-- 
cgit v1.2.3