Argument 'legend_x' for 'calplot'

Also, keep check and test logs in the repository.

9 files changed, 112 insertions, 11 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 5491af5..3115cf6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,8 +1,10 @@
 GNUmakefile
 build.log$
+check.log$
 chemCal_.*.tar.gz
 docs
 _pkgdown.yml
 README.html
 .travis.yml
 experimental
+test.log$
diff --git a/DESCRIPTION b/DESCRIPTION
index cacf80c..8858e19 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: chemCal
-Version: 0.2.2
-Date: 2018-07-21
+Version: 0.2.3
+Date: 2021-04-07
 Title: Calibration Functions for Analytical Chemistry
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de",
diff --git a/GNUmakefile b/GNUmakefile
index 7992c5e..9eee6b9 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -37,7 +37,7 @@ install: build
 	"$(RBIN)/R" CMD INSTALL $(TGZ)
 
 check: build
-	"$(RBIN)/R" CMD check --as-cran $(TGZ)
+	"$(RBIN)/R" CMD check --as-cran $(TGZ) 2>&1 | tee check.log
 
 vignettes/%.html: vignettes/%.Rmd vignettes/refs.bib
 	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.Rmd', dir = 'vignettes')"
@@ -56,7 +56,8 @@ winbuilder: build
 	curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/
 
 test: install
-	NOT_CRAN=true "$(RBIN)/Rscript" -e 'devtools::test()'
+	NOT_CRAN=true "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log
+	sed -i -e "s/\r.*\r//" test.log
 
 clean:
 	$(RM) -r vignettes/*_cache
diff --git a/NEWS.md b/NEWS.md
index 04c75b2..dee859d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# chemCal 0.2.3
+
+- 'calplot' gains an argument 'legend_x' for better control of the legend position
+
 # chemCal 0.2.2
 
 - Added the cadmium dataset from Rocke and Lorenzato (1995)
diff --git a/R/calplot.R b/R/calplot.R
index 6aed9c0..fd49a54 100644
--- a/R/calplot.R
+++ b/R/calplot.R
@@ -1,7 +1,8 @@
 calplot <- function(object, 
   xlim = c("auto", "auto"), ylim = c("auto", "auto"), 
-  xlab = "Concentration", ylab = "Response", alpha = 0.05,
-  varfunc = NULL)
+  xlab = "Concentration", ylab = "Response",
+  legend_x = "auto", 
+  alpha = 0.05, varfunc = NULL)
 {
   UseMethod("calplot")
 }
@@ -9,6 +10,7 @@ calplot <- function(object,
 calplot.default <- function(object, 
   xlim = c("auto","auto"), ylim = c("auto","auto"), 
   xlab = "Concentration", ylab = "Response",
+  legend_x = "auto",
   alpha=0.05, varfunc = NULL)
 {
   stop("Calibration plots only implemented for univariate lm objects.")
@@ -16,8 +18,9 @@ calplot.default <- function(object,
 
 calplot.lm <- function(object,
   xlim = c("auto","auto"), ylim = c("auto","auto"), 
-  xlab = "Concentration", ylab = "Response", alpha=0.05,
-  varfunc = NULL)
+  xlab = "Concentration", ylab = "Response",
+  legend_x = "auto", 
+  alpha=0.05, varfunc = NULL)
 {
   if (length(object$coef) > 2)
     stop("More than one independent variable in your model - not implemented")
@@ -47,6 +50,7 @@ calplot.lm <- function(object,
   yrange.auto <- range(c(0,pred.lim))
   if (ylim[1] == "auto") ylim[1] <- yrange.auto[1]
   if (ylim[2] == "auto") ylim[2] <- yrange.auto[2]
+  if (legend_x[1] == "auto") legend_x <- min(object$model[[2]])
   plot(1,
     type = "n", 
     xlab = xlab,
@@ -68,7 +72,7 @@ calplot.lm <- function(object,
   } else {
   matlines(newdata[[1]], conf.lim, lty = c(1, 3, 3), 
     col = c("black", "green4", "green4"))
-  legend(min(x), 
+  legend(legend_x,
     max(pred.lim, na.rm = TRUE), 
     legend = c("Fitted Line", "Confidence Bands", 
         "Prediction Bands"), 
diff --git a/build.log b/build.log
index 738bec1..2fe8e6c 100644
--- a/build.log
+++ b/build.log
@@ -5,5 +5,6 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘chemCal_0.2.2.tar.gz’
+* re-saving image files
+* building ‘chemCal_0.2.3.tar.gz’
 
diff --git a/check.log b/check.log
new file mode 100644
index 0000000..bb10d21
--- /dev/null
+++ b/check.log
@@ -0,0 +1,72 @@
+* using log directory ‘/home/jranke/git/chemCal/chemCal.Rcheck’
+* using R version 4.0.5 (2021-03-31)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--as-cran’
+* checking for file ‘chemCal/DESCRIPTION’ ... OK
+* this is package ‘chemCal’ version ‘0.2.3’
+* package encoding: UTF-8
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
+* checking whether package ‘chemCal’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking for future file timestamps ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking use of S3 registration ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd line widths ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ...
+  Running ‘testthat.R’
+ OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking re-building of vignette outputs ... OK
+* checking PDF version of manual ... OK
+* checking for non-standard things in the check directory ... OK
+* checking for detritus in the temp directory ... OK
+* DONE
+
+Status: OK
+
diff --git a/man/calplot.lm.Rd b/man/calplot.lm.Rd
index 734e696..39f20de 100644
--- a/man/calplot.lm.Rd
+++ b/man/calplot.lm.Rd
@@ -9,7 +9,8 @@
 }
 \usage{
   calplot(object, xlim = c("auto", "auto"), ylim = c("auto", "auto"),
-    xlab = "Concentration", ylab = "Response", alpha=0.05, varfunc = NULL)
+    xlab = "Concentration", ylab = "Response", legend_x = "auto",
+    alpha=0.05, varfunc = NULL)
 }
 \arguments{
   \item{object}{
@@ -29,6 +30,9 @@
   \item{ylab}{
     The label of the y axis.
   }
+  \item{legend_x}{
+    An optional numeric value for adjusting the x coordinate of the legend.
+  }
   \item{alpha}{
     The error tolerance level for the confidence and prediction bands. Note that this 
     includes both tails of the Gaussian distribution, unlike the alpha and beta parameters
diff --git a/test.log b/test.log
new file mode 100644
index 0000000..1da1e42
--- /dev/null
+++ b/test.log
@@ -0,0 +1,13 @@
+Loading chemCal
+Testing chemCal
+✔ |  OK F W S | Context
+✔ |  16       | Compare with investr::calibrate [0.2 s]
+✔ |   5       | Known results for the dataset provided in DIN 32645
+✔ |  15       | Inverse predictions
+✔ |   8       | LOD and LOQ
+✔ |  10       | Known results for the example datasets provided by Massart (1997)
+
+══ Results ═════════════════════════════════════════════════════════════════════
+Duration: 0.4 s
+
+[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]