diff options
| -rw-r--r-- | NAMESPACE | 2 | ||||
| -rw-r--r-- | R/illparms.R | 24 | ||||
| -rw-r--r-- | log/check.log | 6 | ||||
| -rw-r--r-- | log/test.log | 61 | ||||
| -rw-r--r-- | man/illparms.Rd | 7 | ||||
| -rw-r--r-- | tests/testthat/test_mhmkin.R | 3 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 1 |
7 files changed, 80 insertions, 24 deletions
@@ -44,7 +44,9 @@ S3method(plot,mkinfit) S3method(plot,mmkin) S3method(plot,nafta) S3method(print,illparms.mhmkin) +S3method(print,illparms.mkinfit) S3method(print,illparms.mmkin) +S3method(print,illparms.saem.mmkin) S3method(print,mhmkin) S3method(print,mixed.mmkin) S3method(print,mkinds) diff --git a/R/illparms.R b/R/illparms.R index 931d8f05..003c6db1 100644 --- a/R/illparms.R +++ b/R/illparms.R @@ -22,8 +22,9 @@ #' tested? #' @return For [mkinfit] or [saem] objects, a character vector of parameter #' names. For [mmkin] or [mhmkin] objects, a matrix like object of class -#' 'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable -#' printing method. +#' 'illparms.mmkin' or 'illparms.mhmkin'. +#' @note All objects have printing methods. For the single fits, printing +#' does not output anything in the case no ill-defined parameters are found. #' @export illparms <- function(object, ...) { @@ -39,7 +40,18 @@ illparms.mkinfit <- function(object, conf.level = 0.95, ...) { p_values <- suppressWarnings(summary(object)$bpar[, "Pr(>t)"]) na <- is.na(p_values) failed <- p_values > 1 - conf.level - names(parms(object))[na | failed] + ret <- names(parms(object))[na | failed] + class(ret) <- "illparms.mkinfit" + return(ret) +} + +#' @rdname +#' @export +print.illparms.mkinfit <- function(x, ...) { + class(x) <- NULL + if (length(x) > 0) { + print(as.character(x)) + } } #' @rdname illparms @@ -82,7 +94,7 @@ print.illparms.mmkin <- function(x, ...) { #' @export illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) { if (inherits(object, "try-error")) { - return(NA) + failed <- NA } else { ints <- intervals(object, conf.level = conf.level) failed <- NULL @@ -95,9 +107,13 @@ illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod failed <- c(failed, names(which(failed_errmod))) } } + class(failed) <- "illparms.saem.mmkin" return(failed) } +#' @export +print.illparms.saem.mmkin <- print.illparms.mkinfit + #' @rdname illparms #' @export illparms.mhmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) { diff --git a/log/check.log b/log/check.log index 36bd30ca..4092108e 100644 --- a/log/check.log +++ b/log/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.2.1 (2022-06-23) +* using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -43,7 +43,7 @@ The Date field is over a month old. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... OK +* checking R code for possible problems ... [14s/14s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -59,7 +59,7 @@ The Date field is over a month old. * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... OK +* checking examples ... [15s/15s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK diff --git a/log/test.log b/log/test.log index bb81dd43..7152c3fe 100644 --- a/log/test.log +++ b/log/test.log @@ -5,18 +5,27 @@ ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.9s] +✔ | 1 12 | Dimethenamid data from 2018 [31.6s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [4.9s] +✔ | 14 | Error model fitting [4.8s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [15.8s] +✖ | 1 7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s] +──────────────────────────────────────────────────────────────────────────────── +Failure (test_mhmkin.R:27:3): Multiple hierarchical kinetic models can be fitted and diagnosed +illparms(hfit_sfo_tc) not equal to character(0). +Attributes: < Modes: list, NULL > +Attributes: < Lengths: 1, 0 > +Attributes: < names for target but not for current > +Attributes: < current is not list-like > +target is illparms.saem.mmkin, current is character +──────────────────────────────────────────────────────────────────────────────── ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits @@ -27,14 +36,38 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 7 | Multistart method for saem.mmkin models [36.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.9s] -✔ | 16 | Plotting [9.9s] +✔ | 7 | Multistart method for saem.mmkin models [35.7s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s] +✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [72.6s] +✖ | 3 1 34 | saemix parent models [70.9s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem +Failure (test_saemix_parent.R:12:3): Parent fits using saemix are correctly implemented +illparms(sfo_saem_1) not equal to "sd(parent_0)". +Attributes: < Modes: list, NULL > +Attributes: < Lengths: 1, 0 > +Attributes: < names for target but not for current > +Attributes: < current is not list-like > +target is illparms.saem.mmkin, current is character + +Failure (test_saemix_parent.R:14:3): Parent fits using saemix are correctly implemented +illparms(sfo_saem_1_reduced) not equal to character(0). +Attributes: < Modes: list, NULL > +Attributes: < Lengths: 1, 0 > +Attributes: < names for target but not for current > +Attributes: < current is not list-like > +target is illparms.saem.mmkin, current is character + +Failure (test_saemix_parent.R:25:3): Parent fits using saemix are correctly implemented +illparms(sfo_saem_1_mkin) not equal to "sd(parent_0)". +Attributes: < Modes: list, NULL > +Attributes: < Lengths: 1, 0 > +Attributes: < names for target but not for current > +Attributes: < current is not list-like > +target is illparms.saem.mmkin, current is character + +Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] @@ -42,16 +75,16 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 7 | Fitting the SFORB model [3.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.1s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] +✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 209.2 s +Duration: 204.9 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) • Fitting with saemix takes around 10 minutes when using deSolve (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 3 | PASS 261 ] +[ FAIL 4 | WARN 0 | SKIP 3 | PASS 259 ] diff --git a/man/illparms.Rd b/man/illparms.Rd index 90adf2bb..ebc3185a 100644 --- a/man/illparms.Rd +++ b/man/illparms.Rd @@ -41,8 +41,7 @@ tested?} \value{ For \link{mkinfit} or \link{saem} objects, a character vector of parameter names. For \link{mmkin} or \link{mhmkin} objects, a matrix like object of class -'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable -printing method. +'illparms.mmkin' or 'illparms.mhmkin'. } \description{ The method for generalised nonlinear regression fits as obtained @@ -59,6 +58,10 @@ effects expressed as standard deviations include zero, and if the confidence intervals for the error model parameters include zero. } +\note{ +All objects have printing methods. For the single fits, printing +does not output anything in the case no ill-defined parameters are found. +} \examples{ fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE) illparms(fit) diff --git a/tests/testthat/test_mhmkin.R b/tests/testthat/test_mhmkin.R index fc588473..72b81fec 100644 --- a/tests/testthat/test_mhmkin.R +++ b/tests/testthat/test_mhmkin.R @@ -25,6 +25,7 @@ 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)) + expect_silent(print(illparms(hfit_sfo_tc))) test_summary <- summary(hfit_sfo_tc) test_summary$saemixversion <- "Dummy 0.0 for testing" @@ -37,7 +38,7 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", { expect_known_output(print(test_summary, digits = 1), "summary_hfit_sfo_tc.txt") - # It depends on the platform exactly which of the + # It depends on the platform exactly which of the # SFO datasets fail to converge with FOMC skip_on_travis() diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 39efa18f..e7574b01 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -12,6 +12,7 @@ test_that("Parent fits using saemix are correctly implemented", { expect_equal(illparms(sfo_saem_1), "sd(parent_0)") # So we have also done a fit without this variance expect_equal(illparms(sfo_saem_1_reduced), character(0)) + expect_silent(print(illparms(sfo_saem_1_reduced))) # We cannot currently do the fit with completely fixed initial values mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100)) |