Start polishing vignettes for pkgdown

R/calibration.R

@@ -8,8 +8,8 @@
 #' (LOD) and limit of quantification (LOQ) in accordance with DIN 32645 (2008).
 #' 
 #' The LOD is defined as the lowest quantity of a substance that can be
-#' distinguished from the absence of that substance (blank value) within a
-#' given confidence level (\code{alpha}). The LOQ is defined as the lowest quantity of
+#' distinguished from the absence of that substance (blank value) within a given
+#' confidence level (\code{alpha}). The LOQ is defined as the lowest quantity of
 #' a substance that can be quantified/distinguished from another sample given
 #' with respect to a defined confidence level (\code{k}).
 #'
@@ -47,10 +47,10 @@
 #' 
 #' @return
 #' \code{calibration} returns an object of \code{\link[base]{class}}
-#' '\code{calibration}'. \code{print()} calls the function parameters together with the
-#' respective LOD and LOQ. \code{plot()} plots the respective calibration curve
-#' together with the measurement values. \code{summary()} may be used to retrieve
-#' the summary of the underlying model.
+#' '\code{calibration}'. \code{print()} calls the function parameters together
+#' with the respective LOD and LOQ. \code{plot()} plots the respective
+#' calibration curve together with the measurement values. \code{summary()} may
+#' be used to retrieve the summary of the underlying model.
 #' 
 #' @author 
 #' Zacharias Steinmetz
@@ -69,8 +69,8 @@
 #' 215-222. \doi{10.1016/S1570-0232(02)00244-1}.
 #' 
 #' Currie, L.A. (1999). Nomenclature in evaluation of analytical methods
-#' including detection and quantification capabilities:
-#' (IUPAC Recommendations 1995). \emph{Analytica Chimica Acta} \bold{391}, 105-126.
+#' including detection and quantification capabilities: (IUPAC Recommendations
+#' 1995). \emph{Analytica Chimica Acta} \bold{391}, 105-126.
 #' 
 #' DIN 32645 (2008). \emph{Chemical analysis - Decision limit, detection limit
 #' and determination limit under repeatability conditions - Terms, methods,
@@ -106,7 +106,8 @@ calibration <- function(formula, data = NULL, blanks = NULL, weights = NULL,
     }
   }
 
-  model <- do.call(model, list(formula = formula, data = newdata, weights = newweights, ...))
+  model <- do.call(model, list(formula = formula, data = newdata,
+                               weights = newweights, ...))
   model$call <- match.call(expand.dots = F)
   model$formula <- formula
 
@@ -177,9 +178,11 @@ plot.calibration <- function(x, interval = "conf", level = 0.95, ...) {
   model <- x$model
 
   conc <- model$model[,2]
-  new <- data.frame(conc = seq(min(conc), max(conc), length.out = 100 * length(conc)))
+  new <- data.frame(conc = seq(min(conc), max(conc),
+                               length.out = 100 * length(conc)))
   names(new) <- all.vars(model$formula)[2]
-  pred <- data.frame(new, predict(x$model, new, interval = interval, level = level))
+  pred <- data.frame(new, predict(x$model, new, interval = interval,
+                                  level = level))
 
   plot(model$formula, data = model$model, ...)
   lines(pred[, 2] ~ pred[, 1])

R/theme_publish.R

@@ -15,9 +15,9 @@
 #' Zacharias Steinmetz
 #' 
 #' @examples
-#' require(ggplot2)
+#' library(ggplot2)
 #' p <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg,
-#'      colour=factor(gear))) + facet_wrap( ~ am)
+#'      colour = factor(gear))) + facet_wrap( ~ am)
 #' p
 #' p + theme_publish()
 #'

README.md

@@ -17,12 +17,12 @@ analysis in environmental chemistry and ecotoxicology. Provides, for example,
 `calibration()` to calculate calibration curves and corresponding limits of
 detection (LODs) and limits of quantification (LOQs) according to German DIN
 32645 (2008). `texture()` makes it easy to estimate soil particle size
-distributions from hydrometer measurements (ASTM D422-63, 2007).
-Some functions of the package require **ggplot2** or **drc**.
+distributions from hydrometer measurements (ASTM D422-63, 2007). Some functions
+of the package require **ggplot2** or **drc**.
 
 ## Functions
 
-Currently, the following functions are available:
+The following functions are available:
 
 ### Data manipulation and analysis
 
@@ -34,8 +34,7 @@ Currently, the following functions are available:
 * Determine particle size distributions and soil texture classes (DIN/USDA)
   measured with a soil hydrometer in accordance with ASTM D422-63 (2007) using
   `texture()`; see
-  [vignette](https://htmlpreview.github.io/?https://github.com/zsteinmetz/envalysis/blob/master/vignettes/texture.html)
-  for details
+  [vignette](https://zsteinmetz.de/envalysis/articles/texture.html) for details
 * Confidence intervals `CI()`, standard errors `se()`, and root mean square
   errors `rmse()`
 * Various sorption isotherms `sorption()`
@@ -48,7 +47,7 @@ Currently, the following functions are available:
   significant digit, using `signifig()`
 * Clean, black-and-white ggplot2 theme for scientific publications
   `theme_publish()`; a preview is available
-  [here](https://htmlpreview.github.io/?https://github.com/zsteinmetz/envalysis/blob/master/vignettes/theme_publish.html)
+  [here](https://zsteinmetz.de/envalysis/articles/theme_publish.html)
 
 ## Installation
 
@@ -57,7 +56,7 @@ Currently, the following functions are available:
 ### Install from CRAN (stable version)
 
 You can install the released version of **envalysis** from
-[CRAN](https://CRAN.R-project.org) with:
+[CRAN](https://cran.r-project.org/package=envalysis) with:
 
 ```r
 install.packages("envalysis")

vignettes/texture.R

@@ -19,7 +19,6 @@ tex <- texture(reading ~ blank + time + temperature, clayloam, plot = T)
 tex
 
 ## ----classify-----------------------------------------------------------------
-# Load soiltexture
 library(soiltexture)
 
 # Prepare data

vignettes/texture.Rmd

@@ -1,5 +1,7 @@
 ---
-title: "Particle size estimation using the hydrometer method modified from ASTM D422-63 (2007) and Bouyoucos (1927)"
+title: "Particle size estimation with `texture()`"
+subtitle: > 
+  Based on the hydrometer method by ASTM D422-63 (2007) and Bouyoucos (1927)
 author: "Zacharias Steinmetz"
 date: "`r Sys.Date()`"
 output:
@@ -49,36 +51,33 @@ knitr::opts_chunk$set(
 
 ### Dispersing solution
 
-Dissolve 40 g of SHMP in 1 L of deionized water.
-To facilitate complete dissolution, fill a 1 L volumetric flask with about
-500 mL of deionized water and add the SHMP step-by-step
-while stirring the solution with a magnetic stirrer.
-The solution is stable for at least one month.
+Dissolve 40 g of SHMP in 1 L of deionized water. To facilitate complete
+dissolution, fill a 1 L volumetric flask with about 500 mL of deionized water
+and add the SHMP step-by-step while stirring the solution with a magnetic
+stirrer. The solution is stable for at least one month.
 
 ### Calibration
 
-Hydrometers are graduated to be read at the bottom of the meniscus.
-However, readings may need be taken at the top of the meniscus in opaque
-soil suspensions.
+Hydrometers are graduated to be read at the bottom of the meniscus. However,
+readings may need be taken at the top of the meniscus in opaque soil
+suspensions.
 
-Lower the hydrometer into a 1 L cylinder filled with 125 mL of SHMP solution
-and 875 mL of deionized water.
-When stabilized (after about 20 s), record both the reading at the bottom (zero
-or composite correction factor) and at the top of the meniscus
-(meniscus correction factor).
+Lower the hydrometer into a 1 L cylinder filled with 125 mL of SHMP solution and
+875 mL of deionized water. When stabilized (after about 20 s), record both the
+reading at the bottom (zero or composite correction factor) and at the top of
+the meniscus (meniscus correction factor).
 
 ### Sample pretreatment
 
-If the soil sample contains primarily clay or silt, weigh out 50 g of
-soil (accuracy ± 0.01 g) in a 500 mL screw bottle (in 3-fold
-replication). If the sample is sandy, take 100 g each. Add 125 mL SHMP solution
-to the soil. Agitate the mixture for 16 h (or overnight) in a horizontal shaker.
+If the soil sample contains primarily clay or silt, weigh out 50 g of soil
+(accuracy ± 0.01 g) in a 500 mL screw bottle (in 3-fold replication). If the
+sample is sandy, take 100 g each. Add 125 mL SHMP solution to the soil. Agitate
+the mixture for 16 h (or overnight) in a horizontal shaker.
 
-Completely transfer the soil slurry into the 1 L sedimentation cylinder
-using a squirt bottle. Fill up to the 1 L mark with deionized water.
-Cap the cylinder with parafilm (ensure tightness).
-Agitate the slurry by turning the cylinder upside down and back 30 times
-during 1 min.
+Completely transfer the soil slurry into the 1 L sedimentation cylinder using a
+squirt bottle. Fill up to the 1 L mark with deionized water. Cap the cylinder
+with parafilm (ensure tightness). Agitate the slurry by turning the cylinder
+upside down and back 30 times during 1 min.
 
 ### Measurement
 
@@ -117,11 +116,10 @@ The following table may serve as a sample template to record the data
 
 ### Data evaluation
 
-A complete description of how to calculate the particle size
-distribution from the recorded hydrometer readings is available in the
-respective ASTM guideline (ASTM D422-63, 2007). The
-algorithm has also been implemented into this package using the `texture()`
-function:
+A complete description of how to calculate the particle size distribution from
+the recorded hydrometer readings is available in the respective ASTM guideline
+(ASTM D422-63, 2007). The algorithm has also been implemented into this package
+using the `texture()` function.
 
 ```{r texture}
 # Load envalysis
@@ -140,7 +138,6 @@ Further soil classification and plotting may be done with the **soiltexture**
 package.
 
 ```{r classify}
-# Load soiltexture
 library(soiltexture)
 
 # Prepare data
@@ -162,16 +159,19 @@ The analyzed soil is a clay loam (German: "Toniger Lehm", Lt2).
 
 ## References
 
-Ashworth, J., Keyes, D., Kirk, R., & Lessard, R. (2001). Standard Procedure in the 
-Hydrometer Method for Particle Size Analysis. *Communications in Soil Science and 
-Plant Analysis* **32**, 633-642. DOI: [10.1081/CSS-100103897](https://doi.org/10.1081/CSS-100103897).
+Ashworth, J., Keyes, D., Kirk, R., & Lessard, R. (2001). Standard Procedure in
+the Hydrometer Method for Particle Size Analysis. *Communications in Soil
+Science and Plant Analysis* **32**, 633-642. DOI:
+[10.1081/CSS-100103897](https://doi.org/10.1081/CSS-100103897).
 
-ASTM D422-63 (2007). *Standard Test Method for Particle-Size Analysis of 
-Soils*. Technical standard. ASTM International, West Conshohocken, PA.
+ASTM D422-63 (2007). *Standard Test Method for Particle-Size Analysis of Soils*.
+Technical standard. ASTM International, West Conshohocken, PA.
 
-Bouyoucos, G.J., (1927). The hydrometer as a new method for the mechanical 
+Bouyoucos, G.J., (1927). The hydrometer as a new method for the mechanical
 analysis of soils. Soil Science 23, 343–354.
 
 Moeys, J., Shangguan, W., Petzold, R., Minasny, B., Rosca, B., Jelinski, N.,
-Zelazny, W., Souza, R.M.S., Safanelli, J.L., & ten Caten, A. (2018). *soiltexture:
-Functions for Soil Texture Plot, Classification and Transformation*. URL: [https://CRAN.R-project.org/package=soiltexture](https://CRAN.R-project.org/package=soiltexture).
+Zelazny, W., Souza, R.M.S., Safanelli, J.L., & ten Caten, A. (2018).
+*soiltexture: Functions for Soil Texture Plot, Classification and
+Transformation*. URL:
+[https://CRAN.R-project.org/package=soiltexture](https://CRAN.R-project.org/package=soiltexture).

vignettes/texture.html

@@ -11,9 +11,9 @@
 
 <meta name="author" content="Zacharias Steinmetz" />
 
-<meta name="date" content="2023-07-27" />
+<meta name="date" content="2023-09-05" />
 
-<title>Particle size estimation using the hydrometer method modified from ASTM D422-63 (2007) and Bouyoucos (1927)</title>
+<title>Particle size estimation with texture()</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -350,11 +350,12 @@
 
 
 
-<h1 class="title toc-ignore">Particle size estimation using the
-hydrometer method modified from ASTM D422-63 (2007) and Bouyoucos
-(1927)</h1>
+<h1 class="title toc-ignore">Particle size estimation with
+<code>texture()</code></h1>
+<h3 class="subtitle"><p>Based on the hydrometer method by ASTM D422-63
+(2007) and Bouyoucos (1927)</p></h3>
 <h4 class="author">Zacharias Steinmetz</h4>
-<h4 class="date">2023-07-27</h4>
+<h4 class="date">2023-09-05</h4>
 
 </div>
 
@@ -528,7 +529,7 @@ <h3>Data evaluation</h3>
 distribution from the recorded hydrometer readings is available in the
 respective ASTM guideline (ASTM D422-63, 2007). The algorithm has also
 been implemented into this package using the <code>texture()</code>
-function:</p>
+function.</p>
 <pre class="r"><code># Load envalysis
 library(envalysis)
 
@@ -574,8 +575,7 @@ <h3>Data evaluation</h3>
 # &gt; Std. Error 0.0131 0.0226 0.00954</code></pre>
 <p>Further soil classification and plotting may be done with the
 <strong>soiltexture</strong> package.</p>
-<pre class="r"><code># Load soiltexture
-library(soiltexture)
+<pre class="r"><code>library(soiltexture)
 
 # Prepare data
 germansoil &lt;- data.frame(t(tex$din[&quot;Estimate&quot;,] * 100))