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-rw-r--r--NEWS.md2
-rw-r--r--R/mkinfit.R2
-rw-r--r--check.log28
-rw-r--r--man/mkinfit.Rd5
-rw-r--r--test.log4
-rw-r--r--tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg26
6 files changed, 20 insertions, 47 deletions
diff --git a/NEWS.md b/NEWS.md
index 22fdf1d4..cd6a1f97 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,8 +4,6 @@
- 'mkinfit': Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals
-- 'mkinfit': The default algorithm for fitting the 'obs' error model is now IRLS
-
- Vignette 'twa.html': Add the maximum time weighted average formulas for the hockey stick model
- Support frameless plots ('frame = FALSE')
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 7e2b8cac..d182f5d0 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -252,7 +252,7 @@ mkinfit <- function(mkinmod, observed,
}
if (error_model_algorithm == "auto") {
error_model_algorithm = switch(err_mod,
- const = "OLS", obs = "IRLS", tc = "d_3")
+ const = "OLS", obs = "d_3", tc = "d_3")
}
errparm_names <- switch(err_mod,
"const" = "sigma",
diff --git a/check.log b/check.log
index b7cccd35..e809af23 100644
--- a/check.log
+++ b/check.log
@@ -24,27 +24,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
-* checking top-level files ... WARNING
-Conversion of ‘README.md’ failed:
-[WARNING] This document format requires a nonempty <title> element.
- Please specify either ‘title’ or ‘pagetitle’ in the metadata.
- Falling back to ‘README’
-Could not fetch https://www.r-pkg.org/badges/version/mkin
-HttpExceptionRequest Request {
- host = "www.r-pkg.org"
- port = 443
- secure = True
- requestHeaders = []
- path = "/badges/version/mkin"
- queryString = ""
- method = "GET"
- proxy = Nothing
- rawBody = False
- redirectCount = 10
- responseTimeout = ResponseTimeoutDefault
- requestVersion = HTTP/1.1
-}
- ConnectionTimeout
+* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
@@ -85,9 +65,5 @@ HttpExceptionRequest Request {
* checking PDF version of manual ... OK
* DONE
-Status: 1 WARNING
-See
- ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
-for details.
-
+Status: OK
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 85b742e8..09af4918 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -176,9 +176,8 @@ mkinfit(mkinmod, observed,
}
\item{error_model_algorithm}{
If "auto", the selected algorithm depends on the error model.
- If the error model is "const", nonlinear least squares fitting ("OLS") is
- selected. If the error model is "obs", iteratively reweighted least squares
- fitting ("IRLS") is selected. If the error model is "tc", the "d_3"
+ If the error model is "const", unweighted nonlinear least squares fitting
+ ("OLS") is selected. If the error model is "obs", or "tc", the "d_3"
algorithm is selected.
The algorithm "d_3" will directly minimize the negative
diff --git a/test.log b/test.log
index 230fbd3b..eb5486e0 100644
--- a/test.log
+++ b/test.log
@@ -3,7 +3,7 @@ Testing mkin
✔ | OK F W S | Context
✔ | 2 | Export dataset for reading into CAKE
✔ | 3 | Confidence intervals and p-values
-✔ | 10 | Error model fitting [37.0 s]
+✔ | 10 | Error model fitting [36.8 s]
✔ | 5 | Calculation of FOCUS chi2 error levels [3.5 s]
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.4 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s]
@@ -23,7 +23,7 @@ Testing mkin
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 69.9 s
+Duration: 69.7 s
OK: 111
Failed: 0
diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
index 88e7aaee..920f70cd 100644
--- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
+++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
@@ -108,7 +108,7 @@
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