various fixes

.Rbuildignore

@@ -24,3 +24,6 @@
 ^Dockerfile$
 ^test_debian.sh$
 ^dev$
+^app\.R$
+^\.covrignore$
+^revdep$

.covrignore

@@ -0,0 +1,9 @@
+R/data_module.R
+R/filter_module.R
+R/NOAA_addin.R
+R/NOAA_app.R
+R/NOAA_data.R
+R/oceanexplorer-package.R
+R/plot_module.R
+R/plot_NOAA.R
+R/table_module.R

.gitignore

@@ -21,3 +21,4 @@ dev/*
 NEWS.md
 CRAN-SUBMISSION
 cran-comments.md
+revdep/

DESCRIPTION

@@ -32,6 +32,7 @@ Suggests:
     curl,
     globals (>= 0.14.0),
     knitr,
+    rmarkdown,
     shinytest (>= 1.5.1),
     spelling,
     testthat (>= 3.1.2),

NAMESPACE

@@ -2,16 +2,10 @@
 
 S3method(reproject,sf)
 S3method(reproject,stars)
-export(":=")
-export(.data)
 export(NOAA_addin)
 export(NOAA_app)
 export(NOAA_server)
-export(as_label)
-export(as_name)
 export(citation_ui)
-export(enquo)
-export(enquos)
 export(env_parm_labeller)
 export(filter_NOAA)
 export(filter_server)
@@ -32,9 +26,3 @@ export(url_parser)
 import(miniUI)
 import(ncmeta)
 import(shiny, except = serverInfo)
-importFrom(rlang,":=")
-importFrom(rlang,.data)
-importFrom(rlang,as_label)
-importFrom(rlang,as_name)
-importFrom(rlang,enquo)
-importFrom(rlang,enquos)

NEWS.md

@@ -1,4 +1,7 @@
-# oceanexplorer (development version)
+# oceanexplorer 0.1.0
+
+* **Feature**: Now one can also use a fuzzy search to select a chemical/physical marine parameters. This is convenient when selecting data near coasts.  
+* Varies updates in the documentation. This includes mainly links as the source and shiny app are no longer hosted at Utrecht University.
 
 # oceanexplorer 0.0.2
 

README.Rmd

@@ -6,7 +6,7 @@ bibliography: "vignettes/packages.bib"
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 
-# The oceanexplorer <a href="https://dplyr.tidyverse.org"><img src="man/figures/logo.png" align="right" height="138" /></a>  
+# The oceanexplorer <a href="https://github.com/MartinSchobben/oceanexplorer"><img src="man/figures/logo.png" align="right" height="138" /></a>  
 
 
 ```{r, include = FALSE}
@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 # following code for loading and writing the bibtex references for the used pkgs
 pkgs <- c(
   # data transformation and visualization
-  "dplyr", "ggplot2", "rlang", "purrr", 
+  "dplyr", "ggplot2", "purrr", 
   # package development
   "devtools", "shinytest", "vdiffr", "roxygen2", "testthat", 
   # documentation
@@ -88,7 +88,7 @@ This project was funded by ERC Starting grant number 802835, OceaNice, awarded t
 
 The construction of the R [@rversion] package *oceanexplorer* and associated documentation was aided by the packages; *devtools* [@devtools], *roxygen2* [@roxygen2], *testthat* [@testthat], *shinytest* [@shinytest], *vdiffr* [@vdiffr], *knitr* [@knitr2014 ; @knitr2015], *rmarkdown* [@rmarkdown2018; @rmarkdown2020], and the superb guidance in the book: *R packages: organize, test, document, and share your code*, by @Wickham2015. 
 
-Data transformation, cleaning and visualization is performed with: *dplyr* [@dplyr], *ggplot2* [@ggplot2], and *rlang* [@rlang].
+Data transformation, cleaning and visualization is performed with: *dplyr* [@dplyr], and *ggplot2* [@ggplot2].
 
 In addition, this package relies on a set of packages for spatial data analysis: *sf* [@sf] and *stars* [@stars].
 
@@ -118,23 +118,23 @@ oxy_global <- get_NOAA("oxygen", 1, "annual")
 
 Slice a specific interval from the array with `filter_NOAA()`, like so:
 
-```{r slice}
+```{r slice, eval=exists("oxy_global")}
 # filter a depth of 200 meters to show OMZs
 (oxy_omz <- filter_NOAA(oxy_global, depth = 200))
 ```
 
 
 In addition, the sliced array can be plotted, like so:
 
-```{r plot1}
+```{r plot1, eval=exists("oxy_omz")}
 # plot the NOAA world ocean atlas for oxygen content
 plot_NOAA(oxy_omz, depth = NULL)
 ```
 
 The same plot can be produced by taking the original data and supplying a value to the `depth` argument and specifying the range of oxygen content to `oxy_omz`.
 
 
-```{r plot2}
+```{r plot2, eval=exists("oxy_global")}
 # plot the NOAA world ocean atlas for oxygen content
 plot_NOAA(oxy_global, depth = 200, rng = range(oxy_omz[[1]]))
 ```
@@ -159,6 +159,6 @@ NOAA_addin()
 
 ## Code of Conduct
 
-Please note that the oceanexplorer project is released with a [Contributor Code of Conduct](https://utrechtuniversity.github.io/oceanexplorer/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the oceanexplorer project is released with a [Contributor Code of Conduct](https://martinschobben.github.io/oceanexplorer/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
 # References

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# The oceanexplorer <a href="https://dplyr.tidyverse.org"><img src="man/figures/logo.png" align="right" height="138" /></a>
+# The oceanexplorer <a href="https://github.com/MartinSchobben/oceanexplorer"><img src="man/figures/logo.png" align="right" height="138" /></a>
 
 <!-- badges: start -->
 
@@ -37,29 +37,29 @@ awarded to Peter Bijl.
 
 ## Credits
 
-The construction of the R (R Core Team 2022) package *oceanexplorer* and
-associated documentation was aided by the packages; *devtools* (Wickham
-et al. 2021), *roxygen2* (Wickham, Danenberg, et al. 2022), *testthat*
-(Wickham 2022), *shinytest* (Chang, Csárdi, and Wickham 2021), *vdiffr*
-(Henry et al. 2022), *knitr* (Xie 2014 ; Xie 2015), *rmarkdown* (Xie,
-Allaire, and Grolemund 2018; Xie, Dervieux, and Riederer 2020), and the
-superb guidance in the book: *R packages: organize, test, document, and
-share your code*, by Wickham (2015).
+The construction of the R (R Core Team 2023) package *oceanexplorer* and
+associated documentation was aided by the packages; *devtools* (Wickham,
+Hester, et al. 2022), *roxygen2* (Wickham, Danenberg, et al. 2022),
+*testthat* (Wickham 2023), *shinytest* (Chang, Csárdi, and Wickham
+2023), *vdiffr* (Henry et al. 2023), *knitr* (Xie 2014 ; Xie 2015),
+*rmarkdown* (Xie, Allaire, and Grolemund 2018; Xie, Dervieux, and
+Riederer 2020), and the superb guidance in the book: *R packages:
+organize, test, document, and share your code*, by Wickham (2015).
 
 Data transformation, cleaning and visualization is performed with:
-*dplyr* (Wickham, François, et al. 2022), *ggplot2* (Wickham, Chang, et
-al. 2022), and *rlang* (Henry and Wickham 2022).
+*dplyr* (Wickham, François, et al. 2023), and *ggplot2* (Wickham, Chang,
+et al. 2023).
 
 In addition, this package relies on a set of packages for spatial data
-analysis: *sf* (Pebesma 2022a) and *stars* (Pebesma 2022b).
+analysis: *sf* (Pebesma 2023a) and *stars* (Pebesma 2023b).
 
 The app is build with *shiny* (Chang et al. 2022) and the guidance in
 the book: *Mastering Shiny: Build Interactive Apps, Reports &
 Dashboards* (Wickham 2020) was a great help in learning how to develop
 such applications. Furthermore, the packages *shinyjs* (Attali 2021),
-*waiter* (Coene 2022), *bslib* (Sievert and Cheng 2022) and *thematic*
-(Sievert, Schloerke, and Cheng 2021) ensure user-friendliness of the
-interface and visually pleasing graphics.
+*waiter* (Coene 2022), *bslib* (Sievert, Cheng, and Aden-Buie 2023) and
+*thematic* (Sievert, Schloerke, and Cheng 2023) ensure user-friendliness
+of the interface and visually pleasing graphics.
 
 ## Installation
 
@@ -139,7 +139,7 @@ NOAA_addin()
 
 Please note that the oceanexplorer project is released with a
 [Contributor Code of
-Conduct](https://utrechtuniversity.github.io/oceanexplorer/CODE_OF_CONDUCT.html).
+Conduct](https://martinschobben.github.io/oceanexplorer/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
 
 # References
@@ -158,75 +158,67 @@ Shiny Apps in Seconds*. <https://deanattali.com/shinyjs/>.
 Chang, Winston, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke,
 Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert, and Barbara
 Borges. 2022. *Shiny: Web Application Framework for r*.
-<https://shiny.rstudio.com/>.
+<https://shiny.posit.co/>.
 
 </div>
 
 <div id="ref-shinytest" class="csl-entry">
 
-Chang, Winston, Gábor Csárdi, and Hadley Wickham. 2021. *Shinytest: Test
+Chang, Winston, Gábor Csárdi, and Hadley Wickham. 2023. *Shinytest: Test
 Shiny Apps*. <https://github.com/rstudio/shinytest>.
 
 </div>
 
 <div id="ref-waiter" class="csl-entry">
 
 Coene, John. 2022. *Waiter: Loading Screen for Shiny*.
-<https://CRAN.R-project.org/package=waiter>.
+<https://waiter.john-coene.com/>.
 
 </div>
 
 <div id="ref-vdiffr" class="csl-entry">
 
 Henry, Lionel, Thomas Lin Pedersen, T Jake Luciani, Matthieu Decorde,
-and Vaudor Lise. 2022. *Vdiffr: Visual Regression Testing and Graphical
-Diffing*. <https://CRAN.R-project.org/package=vdiffr>.
-
-</div>
-
-<div id="ref-rlang" class="csl-entry">
-
-Henry, Lionel, and Hadley Wickham. 2022. *Rlang: Functions for Base
-Types and Core r and Tidyverse Features*.
-<https://CRAN.R-project.org/package=rlang>.
+and Vaudor Lise. 2023. *Vdiffr: Visual Regression Testing and Graphical
+Diffing*. <https://vdiffr.r-lib.org/>.
 
 </div>
 
 <div id="ref-sf" class="csl-entry">
 
-Pebesma, Edzer. 2022a. *Sf: Simple Features for r*.
-<https://CRAN.R-project.org/package=sf>.
+Pebesma, Edzer. 2023a. *Sf: Simple Features for r*.
+<https://r-spatial.github.io/sf/>.
 
 </div>
 
 <div id="ref-stars" class="csl-entry">
 
-———. 2022b. *Stars: Spatiotemporal Arrays, Raster and Vector Data
-Cubes*. <https://CRAN.R-project.org/package=stars>.
+———. 2023b. *Stars: Spatiotemporal Arrays, Raster and Vector Data
+Cubes*. <https://r-spatial.github.io/stars/>.
 
 </div>
 
 <div id="ref-rversion" class="csl-entry">
 
-R Core Team. 2022. *R: A Language and Environment for Statistical
+R Core Team. 2023. *R: A Language and Environment for Statistical
 Computing*. Vienna, Austria: R Foundation for Statistical Computing.
 <https://www.R-project.org/>.
 
 </div>
 
 <div id="ref-bslib" class="csl-entry">
 
-Sievert, Carson, and Joe Cheng. 2022. *Bslib: Custom Bootstrap ’Sass’
-Themes for Shiny and Rmarkdown*.
-<https://CRAN.R-project.org/package=bslib>.
+Sievert, Carson, Joe Cheng, and Garrick Aden-Buie. 2023. *Bslib: Custom
+Bootstrap ’Sass’ Themes for Shiny and Rmarkdown*.
+<https://rstudio.github.io/bslib/>.
 
 </div>
 
 <div id="ref-thematic" class="csl-entry">
 
-Sievert, Carson, Barret Schloerke, and Joe Cheng. 2021. *Thematic:
+Sievert, Carson, Barret Schloerke, and Joe Cheng. 2023. *Thematic:
 Unified and Automatic Theming of Ggplot2, Lattice, and Base r Graphics*.
-<https://CRAN.R-project.org/package=thematic>.
+<https://rstudio.github.io/thematic/>.
 
 </div>
 
@@ -246,41 +238,40 @@ Dashboards.* O’Reilly Media, Inc. <https://mastering-shiny.org/>.
 
 <div id="ref-testthat" class="csl-entry">
 
-———. 2022. *Testthat: Unit Testing for r*.
-<https://CRAN.R-project.org/package=testthat>.
+———. 2023. *Testthat: Unit Testing for r*. <https://testthat.r-lib.org>.
 
 </div>
 
 <div id="ref-ggplot2" class="csl-entry">
 
 Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen,
 Kohske Takahashi, Claus Wilke, Kara Woo, Hiroaki Yutani, and Dewey
-Dunnington. 2022. *Ggplot2: Create Elegant Data Visualisations Using the
-Grammar of Graphics*. <https://CRAN.R-project.org/package=ggplot2>.
+Dunnington. 2023. *Ggplot2: Create Elegant Data Visualisations Using the
+Grammar of Graphics*. <https://ggplot2.tidyverse.org>.
 
 </div>
 
 <div id="ref-roxygen2" class="csl-entry">
 
 Wickham, Hadley, Peter Danenberg, Gábor Csárdi, and Manuel Eugster.
 2022. *Roxygen2: In-Line Documentation for r*.
-<https://CRAN.R-project.org/package=roxygen2>.
+<https://roxygen2.r-lib.org/>.
 
 </div>
 
 <div id="ref-dplyr" class="csl-entry">
 
-Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2022.
-*Dplyr: A Grammar of Data Manipulation*.
-<https://CRAN.R-project.org/package=dplyr>.
+Wickham, Hadley, Romain François, Lionel Henry, Kirill Müller, and Davis
+Vaughan. 2023. *Dplyr: A Grammar of Data Manipulation*.
+<https://dplyr.tidyverse.org>.
 
 </div>
 
 <div id="ref-devtools" class="csl-entry">
 
-Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan. 2021.
+Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan. 2022.
 *Devtools: Tools to Make Developing r Packages Easier*.
-<https://CRAN.R-project.org/package=devtools>.
+<https://devtools.r-lib.org/>.
 
 </div>
 
@@ -289,7 +280,7 @@ Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan. 2021.
 Xie, Yihui. 2014. “Knitr: A Comprehensive Tool for Reproducible Research
 in R.” In *Implementing Reproducible Computational Research*, edited by
 Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman;
-Hall/CRC. <http://www.crcpress.com/product/isbn/9781466561595>.
+Hall/CRC.
 
 </div>