Static documentation rebuilt by pkgdown::build_site()

20 files changed, 112 insertions, 42 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 536ef7d..c7ccaca 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -7,4 +7,5 @@ aux$
 log$
 vignettes/chemCal.tex
 vignettes/chemCal.pdf
+vignettes/chemCal.R
 chemCal_.*.tar.gz
diff --git a/GNUmakefile b/GNUmakefile
index 7c11926..730c460 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -30,8 +30,14 @@ check: build
 check-no-vignettes: build-no-vignettes
 	"$(RBIN)/R" CMD check --as-cran $(TGZ)
 
+vignettes/%.pdf: vignettes/%.Rnw
+	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.Rnw', dir = 'vignettes')"
+
+vignettes: vignettes/chemCal.pdf
+
 pd:
 	"$(RBIN)/Rscript" -e "pkgdown::build_site()"
+	cp vignettes/chemCal.pdf docs/articles
 	git add -A
 	git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index f5eeff8..edc41e2 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -2,3 +2,12 @@ title: chemCal
 
 template:
   bootswatch: spacelab
+
+navbar:
+  title: ~
+  type: default
+  left:
+    - text: Functions and data
+      href: reference/index.html
+    - text: Short manual (pdf)
+      href: articles/chemCal.pdf
diff --git a/docs/articles/chemCal.R b/docs/articles/chemCal.R
new file mode 100644
index 0000000..701db7b
--- /dev/null
+++ b/docs/articles/chemCal.R
@@ -0,0 +1,36 @@
+### R code from vignette source '/home/jranke/git/chemCal/vignettes/chemCal.Rnw'
+
+###################################################
+### code chunk number 1: chemCal.Rnw:38-42
+###################################################
+library(chemCal)
+data(massart97ex3)
+m0 <- lm(y ~ x, data = massart97ex3)
+calplot(m0)
+
+
+###################################################
+### code chunk number 2: chemCal.Rnw:49-50
+###################################################
+plot(m0,which=3)
+
+
+###################################################
+### code chunk number 3: chemCal.Rnw:56-63
+###################################################
+attach(massart97ex3)
+yx <- split(y, x)
+ybar <- sapply(yx, mean)
+s <- round(sapply(yx, sd), digits = 2)
+w <- round(1 / (s^2), digits = 3)
+weights <- w[factor(x)]
+m <- lm(y ~ x, w = weights)
+
+
+###################################################
+### code chunk number 4: chemCal.Rnw:69-71
+###################################################
+inverse.predict(m, 15, ws=1.67)
+inverse.predict(m, 90, ws = 0.145)
+
+
diff --git a/docs/articles/chemCal.pdf b/docs/articles/chemCal.pdf
new file mode 100644
index 0000000..cf1a413
--- /dev/null
+++ b/docs/articles/chemCal.pdf
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 5c6fdad..17c6857 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/authors.html b/docs/authors.html
index 546e902..f4d3c9f 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="reference/index.html">Reference</a>
+  <a href="reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="articles/index.html">Articles</a>
+  <a href="articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/index.html b/docs/index.html
index fda687a..007e710 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -29,10 +29,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
-  <a href="reference/index.html">Reference</a>
+  <a href="reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="articles/index.html">Articles</a>
+  <a href="articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
 <ul class="nav navbar-nav navbar-right"></ul>
diff --git a/docs/reference/calplot.lm.html b/docs/reference/calplot.lm.html
index f66e636..5a33491 100644
--- a/docs/reference/calplot.lm.html
+++ b/docs/reference/calplot.lm.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/chemCal-package.html b/docs/reference/chemCal-package.html
index 18e3822..b720fc9 100644
--- a/docs/reference/chemCal-package.html
+++ b/docs/reference/chemCal-package.html
@@ -50,10 +50,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/din32645.html b/docs/reference/din32645.html
index 1b64592..65a9268 100644
--- a/docs/reference/din32645.html
+++ b/docs/reference/din32645.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b55336a..0c5497d 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/inverse.predict.html b/docs/reference/inverse.predict.html
index 60d169c..af05986 100644
--- a/docs/reference/inverse.predict.html
+++ b/docs/reference/inverse.predict.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/lod.html b/docs/reference/lod.html
index 7c33d47..b9c30e6 100644
--- a/docs/reference/lod.html
+++ b/docs/reference/lod.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/loq.html b/docs/reference/loq.html
index bc62e75..ad7fa86 100644
--- a/docs/reference/loq.html
+++ b/docs/reference/loq.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/massart97ex1.html b/docs/reference/massart97ex1.html
index 9b95a5f..e84c01b 100644
--- a/docs/reference/massart97ex1.html
+++ b/docs/reference/massart97ex1.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/docs/reference/massart97ex3.html b/docs/reference/massart97ex3.html
index 2ec8f6f..2946139 100644
--- a/docs/reference/massart97ex3.html
+++ b/docs/reference/massart97ex3.html
@@ -49,10 +49,10 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../reference/index.html">Functions and data</a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
 </li>
       </ul>
       
diff --git a/inst/staticdocs/index.r b/inst/staticdocs/index.r
deleted file mode 100644
index 4a82ad0..0000000
--- a/inst/staticdocs/index.r
+++ /dev/null
@@ -1,18 +0,0 @@
-sd_section(
-  "Main functions",
-  "Essential functionality",
-  c("inverse.predict", "calplot")
-)
-sd_section(
-  "LOD and LOQ",
-  "Limit of detection and limit of quantification",
-  c("lod",
-    "loq")
-)
-sd_section(
-  "Datasets",
-  "Example data",
-  c("din32645",
-    "massart97ex1",
-    "massart97ex2")
-)
diff --git a/vignettes/chemCal.R b/vignettes/chemCal.R
new file mode 100644
index 0000000..701db7b
--- /dev/null
+++ b/vignettes/chemCal.R
@@ -0,0 +1,36 @@
+### R code from vignette source '/home/jranke/git/chemCal/vignettes/chemCal.Rnw'
+
+###################################################
+### code chunk number 1: chemCal.Rnw:38-42
+###################################################
+library(chemCal)
+data(massart97ex3)
+m0 <- lm(y ~ x, data = massart97ex3)
+calplot(m0)
+
+
+###################################################
+### code chunk number 2: chemCal.Rnw:49-50
+###################################################
+plot(m0,which=3)
+
+
+###################################################
+### code chunk number 3: chemCal.Rnw:56-63
+###################################################
+attach(massart97ex3)
+yx <- split(y, x)
+ybar <- sapply(yx, mean)
+s <- round(sapply(yx, sd), digits = 2)
+w <- round(1 / (s^2), digits = 3)
+weights <- w[factor(x)]
+m <- lm(y ~ x, w = weights)
+
+
+###################################################
+### code chunk number 4: chemCal.Rnw:69-71
+###################################################
+inverse.predict(m, 15, ws=1.67)
+inverse.predict(m, 90, ws = 0.145)
+
+
diff --git a/vignettes/chemCal.pdf b/vignettes/chemCal.pdf
new file mode 100644
index 0000000..cf1a413
--- /dev/null
+++ b/vignettes/chemCal.pdf