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diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R new file mode 100644 index 00000000..be5cf583 --- /dev/null +++ b/R/f_time_norm_focus.R @@ -0,0 +1,77 @@ +utils::globalVariables("D24_2014") + +#' Normalisation factors for aerobic soil degradation according to FOCUS guidance +#' +#' Time step normalisation factors for aerobic soil degradation as described +#' in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369). +#' +#' @param object An object containing information used for the calculations +#' @param temperature Numeric vector of temperatures in °C +#' @param moisture Numeric vector of moisture contents in \\% w/w +#' @param field_moisture Numeric vector of moisture contents at field capacity +#' (pF2) in \\% w/w +#' @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 +#' for complete cases will be returned. +#' @param \dots Currently not used +#' @references +#' FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence +#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in +#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +#' FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence +#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in +#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +#' Version 1.1, 18 December 2014 +#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +#' @seealso [focus_soil_moisture] +#' @examples +#' f_time_norm_focus(25, 20, 25) # 1.37, compare p. 184 +#' +#' D24_2014$meta +#' # No moisture normalisation in the first dataset, so we use f_na = 1 to get +#' # Temperature only normalisation as in the EU evaluation +#' f_time_norm_focus(D24_2014, f_na = 1) +#' # Moisture normalisation for the other four soils is one, as soil moisture +#' # is higher than the approximate field capacity derived from the USDA soil +#' # type +#' @export +f_time_norm_focus <- function(object, ...) { + UseMethod("f_time_norm_focus") +} + +#' @rdname f_time_norm_focus +#' @export +f_time_norm_focus.numeric <- function(object, + moisture = NA, field_moisture = NA, + temperature = object, + Q10 = 2.58, walker = 0.7, f_na = NA, ...) +{ + f_temp <- ifelse(is.na(temperature), + f_na, + ifelse(temperature <= 0, + 0, + Q10^((temperature - 20)/10))) + f_moist <- ifelse(is.na(moisture), + f_na, + ifelse(moisture >= field_moisture, + 1, + (moisture / field_moisture)^walker)) + f_time_norm <- f_temp * f_moist + f_time_norm +} + +#' @rdname f_time_norm_focus +#' @export +f_time_norm_focus.mkindsg <- function(object, Q10 = 2.58, walker = 0.7, f_na = NA, ...) { + meta <- object$meta + field_moisture <- focus_soil_moisture[meta$usda_soil_type, "pF2"] + study_moisture <- meta$rel_moisture * meta$moisture_ref + object$f_time_norm <- f_time_norm_focus(meta$temperature, + moisture = study_moisture, field_moisture = field_moisture, + Q10 = Q10, walker = walker, f_na = f_na) + cat("$time_norm was set to\n") + print(object$f_time_norm) +} |