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| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-03 16:41:31 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-03 18:18:19 +0100 |
| commit | f0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch) | |
| tree | 03af20e730330e148acf3a7c008d82387dbe52eb /R/plot.mixed.mmkin.R | |
| parent | 82814b17ec182467c25325d747fffa8ffbe4bb33 (diff) | |
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'R/plot.mixed.mmkin.R')
| -rw-r--r-- | R/plot.mixed.mmkin.R | 23 |
1 files changed, 1 insertions, 22 deletions
diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index 1674d855..5a0b7412 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -2,7 +2,7 @@ utils::globalVariables("ds") #' Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object #' -#' @param x An object of class [mixed.mmkin], [saem.mmkin] or [nlme.mmkin] +#' @param x An object of class [mixed.mmkin], [nlme.mmkin] #' @param i A numeric index to select datasets for which to plot the individual predictions, #' in case plots get too large #' @inheritParams plot.mkinfit @@ -39,15 +39,6 @@ utils::globalVariables("ds") #' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) #' plot(f_nlme) #' -#' f_saem <- saem(f, transformations = "saemix") -#' plot(f_saem) -#' -#' # We can overlay the two variants if we generate predictions -#' pred_nlme <- mkinpredict(dfop_sfo, -#' f_nlme$bparms.optim[-1], -#' c(parent = f_nlme$bparms.optim[[1]], A1 = 0), -#' seq(0, 180, by = 0.2)) -#' plot(f_saem, pred_over = list(nlme = pred_nlme)) #' } #' @export plot.mixed.mmkin <- function(x, @@ -91,18 +82,6 @@ plot.mixed.mmkin <- function(x, type = ifelse(standardized, "pearson", "response")) } - if (inherits(x, "saem.mmkin")) { - if (x$transformations == "saemix") backtransform = FALSE - degparms_i <- saemix::psi(x$so) - rownames(degparms_i) <- ds_names - degparms_i_names <- setdiff(x$so@results@name.fixed, names(fit_1$errparms)) - colnames(degparms_i) <- degparms_i_names - residual_type = ifelse(standardized, "standardized", "residual") - residuals <- x$data[[residual_type]] - degparms_pop <- x$so@results@fixed.effects - names(degparms_pop) <- degparms_i_names - } - degparms_fixed <- fit_1$fixed$value names(degparms_fixed) <- rownames(fit_1$fixed) degparms_all <- cbind(as.matrix(degparms_i), |