Avoid using cat() for default output, tests

5 files changed, 29 insertions, 21 deletions

diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R
index e7c6f22e..259dd131 100644
--- a/R/f_time_norm_focus.R
+++ b/R/f_time_norm_focus.R
@@ -107,7 +107,6 @@ f_time_norm_focus.mkindsg <- function(object,
   object$f_time_norm <- f_time_norm_focus(meta$temperature,
     moisture = study_moisture, field_moisture = field_moisture,
     Q10 = Q10, walker = walker, f_na = f_na)
-  cat("$time_norm was set to\n")
-  print(object$f_time_norm)
+  message("$f_time_norm was (re)set to normalised values")
   invisible(object$f_time_norm)
 }
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 4da39841..bf164c3f 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -646,8 +646,8 @@ mkinfit <- function(mkinmod, observed,
 
       if (cost < cost.current) {
         assign("cost.current", cost, inherits = TRUE)
-        if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),
-                        " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")
+        if (!quiet) message(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),
+                        " at call ", calls, ": ", signif(cost.current, 6), "\n")
       }
     }
     return(cost)
diff --git a/test.log b/test.log
index b044e6a0..a2217f49 100644
--- a/test.log
+++ b/test.log
@@ -3,22 +3,22 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [4.3s]
+✔ |         5 | Analytical solutions for coupled models [4.4s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         2 | Export dataset for reading into CAKE
-✔ |        12 | Confidence intervals and p-values [1.1s]
+✔ |        12 | Confidence intervals and p-values [1.0s]
 ⠋ |         1 | Dimethenamid data from 2018                                     
-✔ |     1  25 | Dimethenamid data from 2018 [49.7s]
+✔ |     1  25 | Dimethenamid data from 2018 [49.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:147:3): 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 [7.0s]
+✔ |        14 | Error model fitting [6.9s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.8s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.5s]
-✔ |         1 | Fitting the logistic model [0.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.2s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.6s]
+✔ |         1 | Fitting the logistic model [0.4s]
 ⠴ |         6 | Nonlinear mixed-effects models                                  
 ✔ |     1  15 | Nonlinear mixed-effects models [2.4s]
 ────────────────────────────────────────────────────────────────────────────────
@@ -27,16 +27,16 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
 ✔ |        10 | Special cases of mkinfit calls [0.6s]
-✔ |         1 | mkinfit features [0.5s]
+✔ |         3 | mkinfit features [1.1s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |         3 | Model predictions with mkinpredict [0.3s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.1s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [9.2s]
 ✔ |        16 | Plotting [1.5s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix_parent [30.4s]
+✔ |        23 | saemix_parent [29.2s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s]
-✔ |         7 | Fitting the SFORB model [4.5s]
+✔ |         7 | Fitting the SFORB model [4.4s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s]
@@ -44,10 +44,10 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 133.2 s
+Duration: 132.0 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)
 
-[ FAIL 0 | WARN 0 | SKIP 2 | PASS 235 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 237 ]
diff --git a/tests/testthat/test_f_time_norm.R b/tests/testthat/test_f_time_norm.R
index c5e0607c..d5b89902 100644
--- a/tests/testthat/test_f_time_norm.R
+++ b/tests/testthat/test_f_time_norm.R
@@ -5,13 +5,12 @@ test_that("Simple temperature and moisture normalisation works", {
 })
 
 test_that("Time step normalisation for a dataset works", {
-  expect_output(f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1),
-    "was set to")
+  expect_message(f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1))
   expect_equal(round(D24_2014$f_time_norm, 3), c(1.606, 0.712, 0.716, 0.716, 0.898))
-  expect_output(f_time_norm_focus(dimethenamid_2018), "was set to")
+  expect_message(f_time_norm_focus(dimethenamid_2018))
 
   # Reference values from Dimethenamid RAR 2018 Vol3 B.8
-  expect_equal(round(dimethenamid_2018$f_time_norm, 3), 
+  expect_equal(round(dimethenamid_2018$f_time_norm, 3),
     c(1,
       0.971,                           # p. 56
       rep(round(1.329 * 0.924, 3), 2), # p. 51
diff --git a/tests/testthat/test_mkinfit.R b/tests/testthat/test_mkinfit.R
index fb81c3d8..11b6111a 100644
--- a/tests/testthat/test_mkinfit.R
+++ b/tests/testthat/test_mkinfit.R
@@ -8,3 +8,13 @@ test_that("Specifying initial values for state variables works correctly", {
   # also affecting AIC calculations
   expect_equal(logLik(f_1), logLik(f_2))
 })
+
+test_that("We get messages and output from mkinfit if desired", {
+  # For progress info we use message()
+  expect_message(mkinfit("SFO", FOCUS_2006_A, quiet = FALSE))
+
+  # trace_parms uses cat()
+  out <- capture.output(
+    tmp <- mkinfit("SFO", FOCUS_2006_A, trace_parms = TRUE, quiet = TRUE))
+  expect_true(length(out) > 10)
+})