updated documentation for v1.0.2

mchevalier2 · Apr 25, 2022 · 92ce882 · 92ce882
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: crestr
 Title: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets
-Version: 1.0.1
+Version: 1.0.2
 Authors@R:
     person(given = "Manuel",
            family = "Chevalier",
@@ -12,7 +12,7 @@ Description: Applies the CREST climate reconstruction
              through the package or by importing private data. An ensemble of
              graphical outputs were designed to facilitate the use of the
              package and the interpretation of the results. More information can
-             be obtained from Chevalier (2021) <doi:10.5194/cp-2021-153>.
+             be obtained from Chevalier (2022) <doi:10.5194/cp-18-821-2022>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

diff --git a/NEWS.md b/NEWS.md
@@ -24,6 +24,10 @@
 
 * Excluding all the distribution grid cells without any climate data.
 
+* Replaced class(dat) == 'RasterLayer' by inherits(dat, 'RasterLayer')
+
+* Improved documentation
+
 
 # crestr 1.0.0
 

diff --git a/R/plot.utils.R b/R/plot.utils.R
@@ -78,7 +78,7 @@ plot_map_eqearth <- function(dat, ext=raster::extent(dat), zlim=range(raster::va
                         )
 
     M2 <- sp::spTransform(M1, PROJ)
-    if (class(dat) == 'RasterLayer')  dat <- raster::projectRaster(from=dat, crs=PROJ)
+    if (inherits(dat, 'RasterLayer'))  dat <- raster::projectRaster(from=dat, crs=PROJ)
 
     if ('Raster' %in% methods::is(top_layer)) top_layer <- raster::projectRaster(from=top_layer, crs=PROJ)
 
@@ -120,7 +120,7 @@ plot_map_eqearth <- function(dat, ext=raster::extent(dat), zlim=range(raster::va
     raster::crs(Sl1) <- sp::CRS("+init=epsg:4326")
     bckg.eqearth <- sp::spTransform(Sl1, raster::crs(PROJ))
 
-    if (class(dat) == 'RasterLayer')  dat <- raster::mask(dat, bckg.eqearth)
+    if (inherits(dat, 'RasterLayer'))  dat <- raster::mask(dat, bckg.eqearth)
 
     ext <- raster::extent(bckg.eqearth)
     ext_factor_x <- max(graphics::strwidth(paste0('     ', round(as.numeric(names(horizontals.eqearth)),2)), units='inches', cex=6/8))
@@ -184,7 +184,7 @@ plot_map_eqearth <- function(dat, ext=raster::extent(dat), zlim=range(raster::va
         sp::plot(verticals.eqearth,col='white',lwd=0.5, add=TRUE )
 
         sp::plot(M2, col='black', border=NA, add=TRUE)
-        if (class(dat) == 'RasterLayer') {
+        if (inherits(dat, 'RasterLayer')) {
             raster::image(dat, colNa='black', add=TRUE, interpolate=FALSE, zlim=zlim, col=col)
             sp::plot(M2, border='black', lwd=0.5, add=TRUE)
         }

diff --git a/README.Rmd b/README.Rmd
@@ -33,7 +33,7 @@ These responses take the form of probability density functions (*PDFs*). The
 details of the method have been described in
 [Chevalier *et al.* (2014)](http://www.doi.org/10.5194/cp-10-2081-2014), the
 calibrated data are presented in
-[Chevalier (2019)](http://www.doi.org/10.1016/j.gloplacha.2019.01.016) and the package is fully described in [Chevalier (2021)](https://cp.copernicus.org/preprints/cp-2021-153/).
+[Chevalier (2019)](http://www.doi.org/10.1016/j.gloplacha.2019.01.016) and the package is fully described in [Chevalier (2022)](https://cp.copernicus.org/articles/18/821/2022/).
 
 
 ## Installation
@@ -193,5 +193,8 @@ unlink(file.path(getwd(), 'crest-test'), recursive=TRUE)
    SofTware): a probability density function (PDF)-based quantitative climate
    reconstruction method. *Clim. Past* 10, 2081–2098. [10.5194/cp-10-2081-2014](http://www.doi.org/10.5194/cp-10-2081-2014)
  - Chevalier, M., 2019. Enabling possibilities to quantify past climate from
-   fossil assemblages at a global scale. *Glob. Planet. Change* 175, 27–35. [10.1016/j.gloplacha.2019.01.016](http://www.doi.org/10.1016/j.gloplacha.2019.01.016)
- - Chevalier, M., 2021. _crestr_ An R package to perform probabilistic climate reconstructions using fossil proxies. *Clim. Past Disc.*. [10.5194/cp-2021-153](http://www.doi.org/10.5194/cp-2021-153)
+   fossil assemblages at a global scale. *Glob. Planet. Change* 175, 27–35.
+   [10.1016/j.gloplacha.2019.01.016](http://www.doi.org/10.1016/j.gloplacha.2019.01.016)
+ - Chevalier, M., 2022. _crestr_ an R package to perform probabilistic climate
+   reconstructions from palaeoecological datasets. Clim. Past
+   [doi:10.5194/cp-18-821-2022](https://www.doi.org/10.5194/cp-18-821-2022)
diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ functions (*PDFs*). The details of the method have been described in
 the calibrated data are presented in [Chevalier
 (2019)](http://www.doi.org/10.1016/j.gloplacha.2019.01.016) and the
 package is fully described in [Chevalier
-(2021)](https://cp.copernicus.org/preprints/cp-2021-153/).
+(2022)](https://cp.copernicus.org/articles/18/821/2022/).
 
 ## Installation
 
@@ -299,6 +299,6 @@ list.files(file.path(getwd(), 'crest-test'))
     from fossil assemblages at a global scale. *Glob. Planet. Change*
     175, 27–35.
     [10.1016/j.gloplacha.2019.01.016](http://www.doi.org/10.1016/j.gloplacha.2019.01.016)
--   Chevalier, M., 2021. *crestr* An R package to perform probabilistic
-    climate reconstructions using fossil proxies. *Clim. Past Disc.*.
-    [10.5194/cp-2021-153](http://www.doi.org/10.5194/cp-2021-153)
+-   Chevalier, M., 2022. *crestr* an R package to perform probabilistic
+    climate reconstructions from palaeoecological datasets. Clim. Past
+    [doi:10.5194/cp-18-821-2022](https://www.doi.org/10.5194/cp-18-821-2022)
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,10 +1,61 @@
 ---
 title: "cran-comments"
 author: "Manuel Chevalier"
-date: "03/11/2021"
+date: "25/04/2022"
 output: github_document
 ---
 
+
+
+# Submission of crestr v1.0.2 (25/04/2022)
+
+This version contains very small adjustements of the package, as described below. Most changes are aestetic in nature and relate to the design of the plots.
+
+## List of changes
+
+* Minor bugs fixed on the plots
+    * Title of the LOO plot adapted from 'variable name [unit]' to 'Leave-one-out anomalies for\nvariable name [unit]'
+    * Title of stratigraphic diagrams can spread across many lines now
+    * The thickness of the lines on the samplePDFs plot has been revised to show a greater range.
+    * Labels added to the y-axes on the histograms of the climate space plot.
+    * Labels added to the y-axis of the histograms and pdf plots of the taxaCharacteristics figure.
+    * Adding caption on LOO diagram (+ and - anomalies)
+    * Fixing title problem on plot_diagram()
+    * Adding a colouring option for hiatus(es) on plot.crestObj()
+    * Fixed problem of opening empty plotting windows when exporting the figures to files
+    * Changing default value for bar_width in plot_loo() and plot_diagram()
+
+* Replacing the parameter fullPosterior by fullUncertainties in export().
+
+* Typos in the documentation have been fixed.
+
+* The text of the vignettes was updated to reflect changes in the manuscript. Nothing really significant.
+
+* Fixing bug related to ai.sqrt in crest.get_modern_data(). Only the climate space data were transformed.
+
+* Excluding all the distribution grid cells without any climate data.
+
+* Replaced class(dat) == 'RasterLayer' by inherits(dat, 'RasterLayer')
+
+* Improved documentation
+
+## Tests
+
+I ran the same tests as I did to release v1.0.0, and did not get any ERRORS or WARNINGS. Some tests gave NOTES, but these are not things I can or should fix.
+
+* Possibly misspelled words in DESCRIPTION: Palaeoecological (3:9)
+    * This is the proper spelling of the word in British English, and it is in the title of the reference. It cannot be changed.
+* Found the following (possibly) invalid URLs: URL: https://doi.org/10.1002/joc.5086 and URL: https://www.doi.org/10.1002/jqs.2850. Status: 503. Message: Service Unavailable
+    * These links function perfectly. The note only appeared for one test.
+* checking for detritus in the temp directory ... NOTE Found the following files/directories: lastMiKTeXException'
+    * Not sure how to act on that.
+
+
+
+
+
+
+
 # Re-submission #2
 
 Thank you for the tips on how to ameliorate the package. I have now included all your suggestions, including:

diff --git a/crestr_1.0.1.pdf b/crestr_1.0.1.pdf
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/calibration-data.html b/docs/articles/calibration-data.html
diff --git a/docs/articles/get-started.html b/docs/articles/get-started.html
diff --git a/docs/articles/get-started_files/figure-html/plot-1.png b/docs/articles/get-started_files/figure-html/plot-1.png
diff --git a/docs/articles/get-started_files/figure-html/plot-2.png b/docs/articles/get-started_files/figure-html/plot-2.png
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/limpopo.html b/docs/articles/limpopo.html
diff --git a/docs/articles/technicalities.html b/docs/articles/technicalities.html
diff --git a/docs/articles/theory.html b/docs/articles/theory.html
diff --git a/docs/authors.html b/docs/authors.html