Adapt tests, vignettes and examples

- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit

1 files changed, 8 insertions, 4 deletions

diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
index 7529c5f2..c4d6bfe4 100644
--- a/tests/testthat/test_from_max_mean.R
+++ b/tests/testthat/test_from_max_mean.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2018 Johannes Ranke
+# Copyright (C) 2018,2019 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -21,15 +21,19 @@ context("Test fitting the decline of metabolites from their maximum")
 test_that("Fitting from maximum mean value works", {
   SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"),
                      m1 = mkinsub("SFO"))
-  expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, from_max_mean = TRUE))
+  expect_warning(
+    expect_error(mkinfit(SFO_SFO, FOCUS_2006_D, from_max_mean = TRUE),
+      "only implemented for models with a single observed variable"),
+    "Observations with value of zero were removed")
   
   # We can either explicitly create a model for m1, or subset the data
   SFO_m1 <- mkinmod(m1 = mkinsub("SFO"))
-  f.1 <- mkinfit(SFO_m1, FOCUS_2006_D, from_max_mean = TRUE, quiet = TRUE)
+  f.1 <- expect_warning(mkinfit(SFO_m1, FOCUS_2006_D, from_max_mean = TRUE, quiet = TRUE))
   expect_equivalent(endpoints(f.1)$distimes["m1", ], c(170.8, 567.5), 
                     scale = 1, tolerance = 0.1)
 
-  f.2 <- mkinfit("SFO", subset(FOCUS_2006_D, name == "m1"), from_max_mean = TRUE, quiet = TRUE)
+  f.2 <- expect_warning(mkinfit("SFO", subset(FOCUS_2006_D, name == "m1"), 
+                                from_max_mean = TRUE, quiet = TRUE))
   expect_equivalent(endpoints(f.2)$distimes["m1", ], c(170.8, 567.5), 
                     scale = 1, tolerance = 0.1)
 })