diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/dimethenamid_2018.R | 21 | ||||
| -rw-r--r-- | R/f_time_norm_focus.R | 24 | ||||
| -rw-r--r-- | R/mkinds.R | 3 |
3 files changed, 40 insertions, 8 deletions
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R new file mode 100644 index 00000000..189da618 --- /dev/null +++ b/R/dimethenamid_2018.R @@ -0,0 +1,21 @@ +#' Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 +#' +#' The datasets were extracted from the active substance evaluation dossier +#' published by EFSA. Kinetic evaluations shown for these datasets are intended +#' to illustrate and advance kinetic modelling. The fact that these data and +#' some results are shown here does not imply a license to use them in the +#' context of pesticide registrations, as the use of the data may be +#' constrained by data protection regulations. +#' +#' The R code used to create this data object is installed with this package +#' in the 'dataset_generation' directory. In the code, page numbers are given for +#' specific pieces of information in the comments. +#' +#' @format An [mkindsg] object grouping eight datasets with some meta information +#' @source Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) +#' Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour +#' Rev. 2 - November 2017 +#' \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211} +#' @examples +#' print(dimethenamid_2018) +"dimethenamid_2018" diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R index 66df527e..e7c6f22e 100644 --- a/R/f_time_norm_focus.R +++ b/R/f_time_norm_focus.R @@ -11,7 +11,9 @@ utils::globalVariables("D24_2014") #' @param field_moisture Numeric vector of moisture contents at field capacity #' (pF2) in \\% w/w #' @param study_moisture_ref_source Source for the reference value -#' used to calculate the study moisture +#' used to calculate the study moisture. If 'auto', preference is given +#' to a reference moisture given in the meta information, otherwise +#' the focus soil moisture for the soil class is used #' @param Q10 The Q10 value used for temperature normalisation #' @param walker The Walker exponent used for moisture normalisation #' @param f_na The factor to use for NA values. If set to NA, only factors @@ -65,7 +67,7 @@ f_time_norm_focus.numeric <- function(object, #' @rdname f_time_norm_focus #' @export f_time_norm_focus.mkindsg <- function(object, - study_moisture_ref_source = c("meta", "focus"), + study_moisture_ref_source = c("auto", "meta", "focus"), Q10 = 2.58, walker = 0.7, f_na = NA, ...) { study_moisture_ref_source <- match.arg(study_moisture_ref_source) @@ -79,11 +81,19 @@ f_time_norm_focus.mkindsg <- function(object, meta$field_moisture) } - if (study_moisture_ref_source == "meta") { - study_moisture_ref <- meta$study_moisture_ref + study_moisture_ref_focus <- + focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])] + + if (study_moisture_ref_source == "auto") { + study_moisture_ref <- ifelse (is.na(meta$study_ref_moisture), + study_moisture_ref_focus, + meta$study_ref_moisture) } else { - study_moisture_ref <- - focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])] + if (study_moisture_ref_source == "meta") { + study_moisture_ref <- meta$study_moisture_ref + } else { + study_moisture_ref <- study_moisture_ref_focus + } } if ("study_moisture" %in% names(meta)) { @@ -99,5 +109,5 @@ f_time_norm_focus.mkindsg <- function(object, Q10 = Q10, walker = walker, f_na = f_na) cat("$time_norm was set to\n") print(object$f_time_norm) - return(object$f_time_norm) + invisible(object$f_time_norm) } @@ -140,6 +140,7 @@ mkindsg <- R6Class("mkindsg", self$f_time_norm <- f_time_norm if (!missing(meta)) { + rownames(meta) <- lapply(ds, function(x) x$title) self$meta <- meta } } @@ -157,7 +158,7 @@ mkindsg <- R6Class("mkindsg", print.mkindsg <- function(x, data = FALSE, verbose = data, ...) { cat("<mkindsg> holding", length(x$ds), "mkinds objects\n") cat("Title $title: ", x$title, "\n") - cat("Occurrene of observed compounds $observed_n:\n") + cat("Occurrence of observed compounds $observed_n:\n") print(x$observed_n) if (any(x$f_time_norm != 1)) { cat("Time normalisation factors $f_time_norm:\n") |