diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | NAMESPACE | 2 | ||||
| -rw-r--r-- | R/mixed.mmkin.R | 3 | ||||
| -rw-r--r-- | R/nlme.R | 4 | ||||
| -rw-r--r-- | R/plot.mixed.mmkin.R | 5 | ||||
| -rw-r--r-- | R/saem.R | 1 |
6 files changed, 11 insertions, 8 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 118ceaae..6734a43c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.1.2 -Date: 2022-07-21 +Date: 2022-09-14 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -24,7 +24,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, purpose. Depends: R (>= 2.15.1), Imports: stats, graphics, methods, parallel, deSolve, R6, inline (>= 0.3.19), - numDeriv, lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix (>= 3.1) + numDeriv, lmtest, pkgbuild, nlme (>= 3.1-151), saemix (>= 3.1), rlang, vctrs Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, benchmarkme, tibble, stats4 License: GPL @@ -135,7 +135,7 @@ importFrom(nlme,intervals) importFrom(parallel,detectCores) importFrom(parallel,mclapply) importFrom(parallel,parLapply) -importFrom(purrr,map_dfr) +importFrom(rlang,"!!!") importFrom(stats,AIC) importFrom(stats,BIC) importFrom(stats,aggregate) diff --git a/R/mixed.mmkin.R b/R/mixed.mmkin.R index 682a9a34..fd6d975f 100644 --- a/R/mixed.mmkin.R +++ b/R/mixed.mmkin.R @@ -1,5 +1,6 @@ #' Create a mixed effects model from an mmkin row object #' +#' @importFrom rlang !!! #' @param object An [mmkin] row object #' @param method The method to be used #' @param \dots Currently not used @@ -65,7 +66,7 @@ mixed.mmkin <- function(object, method = c("none"), ...) { function(x) x$data[c("variable", "time", "observed", "predicted", "residual")]) names(ds_list) <- ds_names - res$data <- purrr::map_dfr(ds_list, function(x) x, .id = "ds") + res$data <- vctrs::vec_rbind(!!!ds_list, .names_to = "ds") names(res$data)[1:4] <- c("ds", "name", "time", "value") res$data$name <- as.character(res$data$name) res$data$ds <- ordered(res$data$ds, levels = unique(res$data$ds)) @@ -125,7 +125,7 @@ nlme_function <- function(object) { } #' @rdname nlme -#' @importFrom purrr map_dfr +#' @importFrom rlang !!! #' @return A \code{\link{groupedData}} object #' @export nlme_data <- function(object) { @@ -134,7 +134,7 @@ nlme_data <- function(object) { ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")]) names(ds_list) <- ds_names - ds_nlme <- purrr::map_dfr(ds_list, function(x) x, .id = "ds") + ds_nlme <- vctrs::vec_rbind(!!!ds_list, .names_to = "ds") ds_nlme$variable <- as.character(ds_nlme$variable) ds_nlme$ds <- ordered(ds_nlme$ds, levels = unique(ds_nlme$ds)) ds_nlme_renamed <- data.frame(ds = ds_nlme$ds, name = ds_nlme$variable, diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index 3a444253..6815bfd2 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -153,7 +153,7 @@ plot.mixed.mmkin <- function(x, outtimes <- sort(unique(c(x$data$time, seq(xlim[1], xlim[2], length.out = 50)))) - pred_ds <- purrr::map_dfr(i, function(ds_i) { + pred_list <- lapply(i, function(ds_i) { odeparms_trans <- degparms_all[ds_i, odeparms_names] names(odeparms_trans) <- odeparms_names # needed if only one odeparm if (backtransform) { @@ -171,8 +171,9 @@ plot.mixed.mmkin <- function(x, out <- mkinpredict(x$mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, atol = fit_1$atol, rtol = fit_1$rtol) - return(cbind(as.data.frame(out), ds = ds_names[ds_i])) }) + names(pred_list) <- ds_names[i] + pred_ds <- vctrs::vec_rbind(!!!pred_list, .names_to = "ds") odeparms_pop_trans <- degparms_all_pop[odeparms_names] @@ -559,6 +559,7 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk } #' @rdname saem +#' @importFrom rlang !!! #' @return An [saemix::SaemixData] object. #' @export saemix_data <- function(object, verbose = FALSE, ...) { |