diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/dimethenamid_2018.R | 10 | ||||
| -rw-r--r-- | R/mean_degparms.R | 8 | ||||
| -rw-r--r-- | R/plot.mixed.mmkin.R | 18 | ||||
| -rw-r--r-- | man/dimethenamid_2018.Rd | 10 | ||||
| -rw-r--r-- | man/mean_degparms.Rd | 12 | ||||
| -rw-r--r-- | man/plot.mixed.mmkin.Rd | 4 |
8 files changed, 53 insertions, 15 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index db40d511..73547d2c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.1.0 -Date: 2022-03-07 +Date: 2022-04-09 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -6,6 +6,10 @@ - 'saem()': Slightly improve speed in the case that no analytical solution for saemix is implemented, activate a test of the respective code +- 'mean_degparms': New argument 'default_log_parms' that makes it possible to supply a surrogate value (default) for log parameters that fail the t-test + +- 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data + # mkin 1.1.0 (2022-03-14) ## Mixed-effects models diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R index 2fdd1981..00ed9073 100644 --- a/R/dimethenamid_2018.R +++ b/R/dimethenamid_2018.R @@ -49,12 +49,16 @@ #' # look more plausible, but the truth is likely to be in #' # between these variants #' plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE) -#' # Therefore we use nonlinear mixed-effects models +#' # We can also specify a default value for the failing +#' # log parameters, to mimic FOCUS guidance +#' plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE, +#' default_log_parms = log(2)/1000) +#' # As these attempts are not satisfying, we use nonlinear mixed-effects models #' # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc) #' # nlme reaches maxIter = 50 without convergence #' f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc) #' # I am commenting out the convergence plot as rendering them -#' # with pkgdown fails (at least without further tweaks to the +#' # with pkgdown fails (at least without further tweaks to the #' # graphics device used) #' #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence") #' summary(f_dmta_saem_tc) @@ -65,6 +69,6 @@ #' # covariance.model = diag(c(0, rep(1, 7)))) #' # saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence") #' # This does not perform better judged by AIC and BIC -#' saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) +#' # saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) #' } "dimethenamid_2018" diff --git a/R/mean_degparms.R b/R/mean_degparms.R index ec20c068..fdcc5c00 100644 --- a/R/mean_degparms.R +++ b/R/mean_degparms.R @@ -11,8 +11,12 @@ #' rate constants) pass the t-test for significant difference from zero. #' @param conf.level Possibility to adjust the required confidence level #' for parameter that are tested if requested by 'test_log_parms'. +#' @param default_log_parms If set to a numeric value, this is used +#' as a default value for the tested log parameters that failed the +#' t-test. #' @export -mean_degparms <- function(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6) +mean_degparms <- function(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6, + default_log_parms = NA) { if (nrow(object) > 1) stop("Only row objects allowed") parm_mat_trans <- sapply(object, parms, transformed = TRUE) @@ -33,7 +37,7 @@ mean_degparms <- function(object, random = FALSE, test_log_parms = FALSE, conf.l parm_mat_trans_OK <- parm_mat_trans for (trans_parm in log_parm_trans_names) { parm_mat_trans_OK[trans_parm, ] <- ifelse(t_test_back_OK[trans_parm, ], - parm_mat_trans[trans_parm, ], NA) + parm_mat_trans[trans_parm, ], default_log_parms) } } else { parm_mat_trans_OK <- parm_mat_trans diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index 2903a05c..3a444253 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -14,6 +14,8 @@ utils::globalVariables("ds") #' [mixed.mmkin] object #' @param conf.level Passed to [mean_degparms] in the case of an #' [mixed.mmkin] object +#' @param default_log_parms Passed to [mean_degparms] in the case of an +#' [mixed.mmkin] object #' @param rel.height.legend The relative height of the legend shown on top #' @param rel.height.bottom The relative height of the bottom plot row #' @param ymax Vector of maximum y axis values @@ -69,6 +71,7 @@ plot.mixed.mmkin <- function(x, pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, + default_log_parms = NA, ymax = "auto", maxabs = "auto", ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), nrow.legend = ceiling((length(i) + 1) / ncol.legend), @@ -87,7 +90,8 @@ plot.mixed.mmkin <- function(x, backtransform = TRUE if (identical(class(x), "mixed.mmkin")) { - degparms_pop <- mean_degparms(x$mmkin, test_log_parms = test_log_parms, conf.level = conf.level) + degparms_pop <- mean_degparms(x$mmkin, test_log_parms = test_log_parms, + conf.level = conf.level, default_log_parms = default_log_parms) degparms_tmp <- parms(x$mmkin, transformed = TRUE) degparms_i <- as.data.frame(t(degparms_tmp[setdiff(rownames(degparms_tmp), names(fit_1$errparms)), ])) @@ -247,8 +251,7 @@ plot.mixed.mmkin <- function(x, par(mar = c(3.0, 4.1, 1.1, 2.1)) } - plot(pred_pop$time, pred_pop[[obs_var]], - type = "l", lwd = 2, lty = lty_pop, + plot(0, type = "n", xlim = xlim, ylim = ylim_row, xlab = xlab, ylab = paste("Residues", obs_var), frame = frame) @@ -267,6 +270,9 @@ plot.mixed.mmkin <- function(x, col = col_ds[ds_i], lty = lty_ds[ds_i]) } + lines(pred_pop$time, pred_pop[[obs_var]], + type = "l", lwd = 2, lty = lty_pop) + if (identical(maxabs, "auto")) { maxabs = max(abs(observed_row$residual), na.rm = TRUE) } @@ -274,7 +280,8 @@ plot.mixed.mmkin <- function(x, if (identical(resplot, "time")) { plot(0, type = "n", xlim = xlim, xlab = "Time", ylim = c(-1.2 * maxabs, 1.2 * maxabs), - ylab = if (standardized) "Standardized residual" else "Residual") + ylab = if (standardized) "Standardized residual" else "Residual", + frame = frame) abline(h = 0, lty = 2) @@ -289,7 +296,8 @@ plot.mixed.mmkin <- function(x, xlim = c(0, max(pred_ds[[obs_var]])), xlab = "Predicted", ylim = c(-1.2 * maxabs, 1.2 * maxabs), - ylab = if (standardized) "Standardized residual" else "Residual") + ylab = if (standardized) "Standardized residual" else "Residual", + frame = frame) abline(h = 0, lty = 2) diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd index 6c28ab7b..20d2dc1b 100644 --- a/man/dimethenamid_2018.Rd +++ b/man/dimethenamid_2018.Rd @@ -62,12 +62,16 @@ plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = FALSE) # look more plausible, but the truth is likely to be in # between these variants plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE) -# Therefore we use nonlinear mixed-effects models +# We can also specify a default value for the failing +# log parameters, to mimic FOCUS guidance +plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE, + default_log_parms = log(2)/1000) +# As these attempts are not satisfying, we use nonlinear mixed-effects models # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc) # nlme reaches maxIter = 50 without convergence f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc) # I am commenting out the convergence plot as rendering them -# with pkgdown fails (at least without further tweaks to the +# with pkgdown fails (at least without further tweaks to the # graphics device used) #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence") summary(f_dmta_saem_tc) @@ -78,7 +82,7 @@ summary(f_dmta_saem_tc) # covariance.model = diag(c(0, rep(1, 7)))) # saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence") # This does not perform better judged by AIC and BIC -saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) +# saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) } } \keyword{datasets} diff --git a/man/mean_degparms.Rd b/man/mean_degparms.Rd index 5e2b4b0f..bc986d35 100644 --- a/man/mean_degparms.Rd +++ b/man/mean_degparms.Rd @@ -4,7 +4,13 @@ \alias{mean_degparms} \title{Calculate mean degradation parameters for an mmkin row object} \usage{ -mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6) +mean_degparms( + object, + random = FALSE, + test_log_parms = FALSE, + conf.level = 0.6, + default_log_parms = NA +) } \arguments{ \item{object}{An mmkin row object containing several fits of the same model to different datasets} @@ -17,6 +23,10 @@ rate constants) pass the t-test for significant difference from zero.} \item{conf.level}{Possibility to adjust the required confidence level for parameter that are tested if requested by 'test_log_parms'.} + +\item{default_log_parms}{If set to a numeric value, this is used +as a default value for the tested log parameters that failed the +t-test.} } \value{ If random is FALSE (default), a named vector containing mean values diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd index d87ca22c..33b4a67f 100644 --- a/man/plot.mixed.mmkin.Rd +++ b/man/plot.mixed.mmkin.Rd @@ -15,6 +15,7 @@ pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, + default_log_parms = NA, ymax = "auto", maxabs = "auto", ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), @@ -57,6 +58,9 @@ from \link{mkinpredict} with a compatible \link{mkinmod}.} \item{conf.level}{Passed to \link{mean_degparms} in the case of an \link{mixed.mmkin} object} +\item{default_log_parms}{Passed to \link{mean_degparms} in the case of an +\link{mixed.mmkin} object} + \item{ymax}{Vector of maximum y axis values} \item{maxabs}{Maximum absolute value of the residuals. This is used for the |