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-rw-r--r--R/intervals.R5
-rw-r--r--R/summary.saem.mmkin.R13
-rw-r--r--tests/testthat/summary_hfit_sfo_tc.txt58
-rw-r--r--tests/testthat/test_mhmkin.R11
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")
})

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