diff options
| -rw-r--r-- | .Rbuildignore | 1 | ||||
| -rw-r--r-- | GNUmakefile | 6 | ||||
| -rw-r--r-- | _pkgdown.yml | 9 | ||||
| -rw-r--r-- | docs/articles/chemCal.R | 36 | ||||
| -rw-r--r-- | docs/articles/chemCal.pdf | bin | 0 -> 165600 bytes | |||
| -rw-r--r-- | docs/articles/index.html | 4 | ||||
| -rw-r--r-- | docs/authors.html | 4 | ||||
| -rw-r--r-- | docs/index.html | 4 | ||||
| -rw-r--r-- | docs/reference/calplot.lm.html | 4 | ||||
| -rw-r--r-- | docs/reference/chemCal-package.html | 4 | ||||
| -rw-r--r-- | docs/reference/din32645.html | 4 | ||||
| -rw-r--r-- | docs/reference/index.html | 4 | ||||
| -rw-r--r-- | docs/reference/inverse.predict.html | 4 | ||||
| -rw-r--r-- | docs/reference/lod.html | 4 | ||||
| -rw-r--r-- | docs/reference/loq.html | 4 | ||||
| -rw-r--r-- | docs/reference/massart97ex1.html | 4 | ||||
| -rw-r--r-- | docs/reference/massart97ex3.html | 4 | ||||
| -rw-r--r-- | inst/staticdocs/index.r | 18 | ||||
| -rw-r--r-- | vignettes/chemCal.R | 36 | ||||
| -rw-r--r-- | vignettes/chemCal.pdf | bin | 0 -> 165600 bytes |
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 Binary files differnew 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 Binary files differnew file mode 100644 index 0000000..cf1a413 --- /dev/null +++ b/vignettes/chemCal.pdf |