diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinfit.Rd | 3 | ||||
| -rw-r--r-- | man/multistart.Rd | 4 | ||||
| -rw-r--r-- | man/plot.mixed.mmkin.Rd | 2 | ||||
| -rw-r--r-- | man/saem.Rd | 5 |
4 files changed, 10 insertions, 4 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f96b4d22..edec9546 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -39,7 +39,8 @@ model to be fitted to the data, or one of the shorthand names ("SFO", parent only degradation model is generated for the variable with the highest value in \code{observed}.} -\item{observed}{A dataframe with the observed data. The first column called +\item{observed}{A dataframe or an object coercible to a dataframe +(e.g. a \code{tibble}) with the observed data. The first column called "name" must contain the name of the observed variable for each data point. The second column must contain the times of observation, named "time". The third column must be named "value" and contain the observed values. diff --git a/man/multistart.Rd b/man/multistart.Rd index 0df29bfa..d3c23bcf 100644 --- a/man/multistart.Rd +++ b/man/multistart.Rd @@ -77,7 +77,7 @@ dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) f_saem_full <- saem(f_mmkin) f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -parplot(f_saem_full_multi, lpos = "topleft") +parplot(f_saem_full_multi, lpos = "topleft", las = 2) illparms(f_saem_full) f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") @@ -87,7 +87,7 @@ illparms(f_saem_reduced) library(parallel) cl <- makePSOCKcluster(12) f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) -parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2)) +parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2), las = 2) stopCluster(cl) } } diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd index 1e264db3..3c44510d 100644 --- a/man/plot.mixed.mmkin.Rd +++ b/man/plot.mixed.mmkin.Rd @@ -25,7 +25,7 @@ nrow.legend = ceiling((length(i) + 1)/ncol.legend), rel.height.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, - pch_ds = 1:length(i), + pch_ds = c(1:25, 33, 35:38, 40:41, 47:57, 60:90)[1:length(i)], col_ds = pch_ds + 1, lty_ds = col_ds, frame = TRUE, diff --git a/man/saem.Rd b/man/saem.Rd index fd19fe59..5d42f1b1 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -22,6 +22,7 @@ saem(object, ...) omega.init = "auto", covariates = NULL, covariate_models = NULL, + center_covariates = c(NA, "median", "mean"), no_random_effect = NULL, error.init = c(1, 1), nbiter.saemix = c(300, 100), @@ -101,6 +102,10 @@ initialisation of \link[saemix:saemixModel]{saemix::saemixModel} is used for ome variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available in the 'covariates' data frame.} +\item{center_covariates}{Either NA, for no centering, or your +preferred function for calculating the center, currently either +median or mean.} + \item{no_random_effect}{Character vector of degradation parameters for which there should be no variability over the groups. Only used if the covariance model is not explicitly specified.} |