diff options
| -rw-r--r-- | R/intervals.R | 5 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 13 | ||||
| -rw-r--r-- | tests/testthat/summary_hfit_sfo_tc.txt | 58 | ||||
| -rw-r--r-- | tests/testthat/test_mhmkin.R | 11 |
4 files changed, 81 insertions, 6 deletions
diff --git a/R/intervals.R b/R/intervals.R index 258eb4ad..705ef6eb 100644 --- a/R/intervals.R +++ b/R/intervals.R @@ -77,8 +77,9 @@ intervals.saem.mmkin <- function(object, level = 0.95, backtransform = TRUE, ... attr(confint_ret, "label") <- "Fixed effects:" # Random effects - ranef_ret <- as.matrix(conf.int[paste0("SD.", pnames), c("lower", "est.", "upper")]) - rownames(ranef_ret) <- paste0(gsub("SD\\.", "sd(", rownames(ranef_ret)), ")") + sdnames <- intersect(rownames(conf.int), paste("SD", pnames, sep = ".")) + ranef_ret <- as.matrix(conf.int[sdnames, c("lower", "est.", "upper")]) + rownames(ranef_ret) <- paste0(gsub("SD\\.", "sd(", sdnames), ")") attr(ranef_ret, "label") <- "Random effects:" diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index fa52a579..f41e7e20 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -73,7 +73,12 @@ #' f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, #' quiet = TRUE, error_model = "tc", cores = 5) #' f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) -#' summary(f_saem_dfop_sfo, data = TRUE) +#' print(f_saem_dfop_sfo) +#' illparms(f_saem_dfop_sfo) +#' f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, covariance.model = diag(c(0, 0, 1, 1, 1, 0))) +#' illparms(f_saem_dfop_sfo_2) +#' intervals(f_saem_dfop_sfo_2) +#' summary(f_saem_dfop_sfo_2, data = TRUE) #' } #' #' @export @@ -138,8 +143,8 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = list(pnames, pnames)) # Random effects - rnames <- paste0("SD.", pnames) - confint_ranef <- as.matrix(conf.int[rnames, c("estimate", "lower", "upper")]) + sdnames <- intersect(rownames(conf.int), paste0("SD.", pnames)) + confint_ranef <- as.matrix(conf.int[sdnames, c("estimate", "lower", "upper")]) colnames(confint_ranef)[1] <- "est." # Error model @@ -202,7 +207,7 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) cat("\nModel predictions using solution type", x$solution_type, "\n") cat("\nFitted in", x$time[["elapsed"]], "s\n") - cat("Using", paste(x$so@options$nbiter.saemix, collapse = ", "), + cat("Using", paste(x$so@options$nbiter.saemix, collapse = ", "), "iterations and", x$so@options$nb.chains, "chains\n") cat("\nVariance model: ") diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt new file mode 100644 index 00000000..ad701cee --- /dev/null +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -0,0 +1,58 @@ +saemix version used for fitting: Dummy 0.0 for testing +mkin version used for pre-fitting: Dummy 0.0 for testing +R version used for fitting: Dummy R version for testing +Date of fit: Dummy date for testing +Date of summary: Dummy date for testing + +Equations: +d_parent/dt = - k_parent * parent + +Data: +106 observations of 1 variable(s) grouped in 6 datasets + +Model predictions using solution type analytical + +Fitted in test time 0 s +Using 300, 100 iterations and 9 chains + +Variance model: Two-component variance function + +Mean of starting values for individual parameters: + parent_0 log_k_parent + 101 -3 + +Fixed degradation parameter values: +None + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 533 531 -261 + +Optimised parameters: + est. lower upper +parent_0 101 100 102 +log_k_parent -3 -4 -3 + +Correlation: + pr_0 +log_k_parent 0.1 + +Random effects: + est. lower upper +SD.log_k_parent 0.3 0.1 0.4 + +Variance model: + est. lower upper +a.1 0.91 0.64 1.17 +b.1 0.05 0.04 0.06 + +Backtransformed parameters: + est. lower upper +parent_0 1e+02 1e+02 1e+02 +k_parent 4e-02 3e-02 4e-02 + +Estimated disappearance times: + DT50 DT90 +parent 19 64 diff --git a/tests/testthat/test_mhmkin.R b/tests/testthat/test_mhmkin.R index e059948a..eced5583 100644 --- a/tests/testthat/test_mhmkin.R +++ b/tests/testthat/test_mhmkin.R @@ -29,4 +29,15 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", { hfit_sfo_tc <- update(hfits[["SFO", "tc"]], covariance.model = diag(c(0, 1))) expect_equal(illparms(hfit_sfo_tc), character(0)) + + test_summary <- summary(hfit_sfo_tc) + test_summary$saemixversion <- "Dummy 0.0 for testing" + test_summary$mkinversion <- "Dummy 0.0 for testing" + test_summary$Rversion <- "Dummy R version for testing" + test_summary$date.fit <- "Dummy date for testing" + test_summary$date.summary <- "Dummy date for testing" + test_summary$time <- c(elapsed = "test time 0") + + expect_known_output(print(test_summary, digits = 1), + "summary_hfit_sfo_tc.txt") }) |