diff options
Diffstat (limited to 'man')
| -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 |
3 files changed, 22 insertions, 4 deletions
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 |