Edits before resubmission (edited license field in description and re…

…moved LICENSE file). Minor edits to readme and vignette.
isakro · Jan 22, 2023 · 8273583 · 8273583
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 1.0.0
-Date: 2023-01-20 15:06:45 UTC
-SHA: 29880918559f59fdc322061b96d42febea1edfce
+Date: 2023-01-21 18:20:06 UTC
+SHA: eaaeacf3d8d90e30aa449119b6b709f7dc0c588e
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -18,7 +18,7 @@ Description: Provides tools for shoreline dating Stone Age sites located on the
   provided, along with basic tools for evaluating the location of sites within 
   the region and corresponding variation in local shoreline displacement.
 Language: en-US
-License: GPL (>= 3) + file LICENSE
+License: GPL (>= 3)
 URL: https://github.com/isakro/shoredate
 BugReports: https://github.com/isakro/shoredate/issues
 Encoding: UTF-8

diff --git a/LICENSE b/LICENSE
diff --git a/README.Rmd b/README.Rmd
@@ -46,7 +46,7 @@ library(shoredate)
 
 ## Geographical and temporal coverage
 
-As the method of shoreline dating is determined by relative sea-level change, it is dependent on reliable geological reconstructions of this development. At present, the method as outlined here is therefore limited to being applicable in the region of south-eastern Norway between Horten in the north east to Arendal in the south west. This region has newly compiled shoreline displacement curves for Horten (Romundset 2021) Larvik (Sørensen et al. 2014; Sørensen et al. 2023), Tvedestrand (Romundset 2018; Romundset et al. 2018) and Arendal (Romundset 2018). The region also formed the study area for Roalkvam (2023), in which the method and its parameters were derived. The spatial coverage is indicated in the maps below. The shoreline isobases in the second figure represent contours along which the shoreline displacement has followed the same trajectory. These correspond to the displacement curves and place names in the third figure, which also indicates the temporal coverage of the package. 
+As the method of shoreline dating is determined by relative sea-level change, it is dependent on reliable geological reconstructions of this development. At present, the method as outlined here is therefore limited to being applicable in the region of south-eastern Norway between Horten in the north east to Arendal in the south west. This region has newly compiled shoreline displacement curves for Horten (Romundset 2021), Porsgrunn (Sørensen et al. 2014; Sørensen et al. 2023), Tvedestrand (Romundset 2018; Romundset et al. 2018) and Arendal (Romundset 2018). The region also formed the study area for Roalkvam (2023), in which the method and its parameters were derived. The spatial coverage is indicated in the maps below. The shoreline isobases in the second figure represent contours along which the shoreline displacement has followed the same trajectory. These correspond to the displacement curves and place names in the third figure, which also indicates the temporal coverage of the package. 
 
 Note that spatial data used with the package should be set to WGS 84 / UTM zone 32N (EPSG:32632).
 

diff --git a/README.md b/README.md
@@ -49,15 +49,15 @@ development. At present, the method as outlined here is therefore
 limited to being applicable in the region of south-eastern Norway
 between Horten in the north east to Arendal in the south west. This
 region has newly compiled shoreline displacement curves for Horten
-(Romundset 2021) Larvik (Sørensen et al. 2014; Sørensen et al. 2023),
-Tvedestrand (Romundset 2018; Romundset et al. 2018) and Arendal
-(Romundset 2018). The region also formed the study area for Roalkvam
-(2023), in which the method and its parameters were derived. The spatial
-coverage is indicated in the maps below. The shoreline isobases in the
-second figure represent contours along which the shoreline displacement
-has followed the same trajectory. These correspond to the displacement
-curves and place names in the third figure, which also indicates the
-temporal coverage of the package.
+(Romundset 2021), Porsgrunn (Sørensen et al. 2014; Sørensen et
+al. 2023), Tvedestrand (Romundset 2018; Romundset et al. 2018) and
+Arendal (Romundset 2018). The region also formed the study area for
+Roalkvam (2023), in which the method and its parameters were derived.
+The spatial coverage is indicated in the maps below. The shoreline
+isobases in the second figure represent contours along which the
+shoreline displacement has followed the same trajectory. These
+correspond to the displacement curves and place names in the third
+figure, which also indicates the temporal coverage of the package.
 
 Note that spatial data used with the package should be set to WGS 84 /
 UTM zone 32N (EPSG:32632).

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,23 +1,14 @@
 ## Release summary
 
-Third re-submission of the package after automatic rejection on first attempts.
-Handled notes pertaining to possible misspelling, possibly incorrect URIs and 
-long run-time for examples and tests.
+Resubmission. Removed LICENSE file and "+ file LICENSE" in the description. 
 
 ## R CMD check results
 There were no ERRORs or WARNINGs. 
 
 There was 1 NOTE:
 
 * checking CRAN incoming feasibility ... NOTE
-  Maintainer: ‘Isak Roalkvam <isakroa@protonmail.com>’
 
   New submission
-
-  License components with restrictions and base license permitting such:
-    GPL (>= 3) + file LICENSE
-  File 'LICENSE':
-    YEAR: 2022
-    COPYRIGHT HOLDER: shoredate authors
 
 
diff --git a/man/figures/interpolated_curve-1.png b/man/figures/interpolated_curve-1.png
diff --git a/man/figures/target_location-1.png b/man/figures/target_location-1.png
diff --git a/vignettes/shore-multipoint-1.png b/vignettes/shore-multipoint-1.png
diff --git a/vignettes/shore-plot_example_isobases-1.png b/vignettes/shore-plot_example_isobases-1.png
diff --git a/vignettes/shore-plot_example_isobases-2.png b/vignettes/shore-plot_example_isobases-2.png
diff --git a/vignettes/shore-plot_intcurve-1.png b/vignettes/shore-plot_intcurve-1.png
diff --git a/vignettes/shore-plot_location-1.png b/vignettes/shore-plot_location-1.png
diff --git a/vignettes/shore-plot_sum_isobases-1.png b/vignettes/shore-plot_sum_isobases-1.png
diff --git a/vignettes/shoredate.Rmd b/vignettes/shoredate.Rmd
@@ -22,7 +22,7 @@ vignette: >
 # Introduction
 The concept of dating sites based on their present-day elevation with reference to past shoreline displacement has been an important tool for archaeologists in northern Scandinavia since the early 1900s (e.g. Brøgger 1905). This is based on the observation that Stone Age sites in the region tend to have been located close to the contemporaneous shoreline when they were in use. Furthermore, following the retreat of the Fennoscandian Ice Sheet, the isostatic uplift has been so severe that despite corresponding eustatic sea-level rise, the relative sea-level has been falling throughout prehistory in large parts of this region. Within any given area where this is the case, the general pattern is thus that older sites will be located at higher altitudes than younger sites.
 
-This vignette describes the R package *shoredate* which provides tools for shoreline dating Stone Age sites located on the Norwegian Skagerrak coast using the approach presented in Roalkvam (2023). This is based on the an empirical evaluation of the likely elevation of the sites above sea-level when they were in use, and the local trajectory of past relative sea-level change. Due to the geographical contingency of the method, and the dependency on geological reconstructions of shoreline displacement, the package is at present limited to coastal sites located in the region stretching from Horten county in the north east, to Arendal county in the south west.
+This vignette describes the R package *shoredate* which provides tools for shoreline dating Stone Age sites located on the Norwegian Skagerrak coast using the approach presented in Roalkvam (2023). This is based on an empirical evaluation of the likely elevation of the sites above sea-level when they were in use, and the local trajectory of past relative sea-level change. Due to the geographical contingency of the method, and the dependency on geological reconstructions of shoreline displacement, the package is at present limited to coastal sites located in the region stretching from Horten county in the north east, to Arendal county in the south west.
 
 ## Geographical and temporal coverage
 
@@ -140,7 +140,7 @@ A more sparse version can also be plotted by specifying what elements are to be
 
 
 ```r
-shoredate_plot(target_date,  elevation_distribution = FALSE,
+shoredate_plot(target_date, elevation_distribution = FALSE,
                displacement_curve = FALSE, highest_density_region = FALSE)
 ```
 
@@ -284,16 +284,21 @@ While the range of the typically employed isobase directions generally result in
 
 
 ```r
+# Add a name to the example site
+target_point <- sf::st_as_sf(target_point, crs = 32632)
+target_point$name <- "Example site"
+
 # Using the same target point and elevation as above, but specifying two different directions
 # for the isobases when dating
-iso_date <- shoreline_date(site = target_point, elevation = elev_raster, isobase_direction = c(325, 338))
+iso_date <- shoreline_date(site = target_point, elevation = elev_raster,
+                           isobase_direction = c(325, 338))
 
 iso_date
 ```
 
 ```
 ## ===============
-## Site:  1
+## Site:  Example site
 ## Elevation:  58.51383 
 ## 
 ## Isobase direction:  325 
@@ -313,7 +318,7 @@ In the call to plot it can then be specified that the direction of the isobases
 
 
 ```r
-shoredate_plot(iso_date, isobase_direction = TRUE)
+shoredate_plot(iso_date, site_name = TRUE, isobase_direction = TRUE)
 ```
 
 <img src="shore-plot_example_isobases-1.png" alt="plot of chunk plot_example_isobases" style="display: block; margin: auto;" /><img src="shore-plot_example_isobases-2.png" alt="plot of chunk plot_example_isobases" style="display: block; margin: auto;" />
@@ -324,23 +329,15 @@ As an alternative to keeping the two shoreline dates of the site separate, the p
 
 
 ```r
-target_point$name <- "Example site"
-
 sum_iso_date <- shoreline_date(site = target_point, elevation = elev_raster,
                                isobase_direction = c(325, 338), sum_isobase_directions = TRUE)
-```
 
-```
-## Error in UseMethod("st_bbox"): no applicable method for 'st_bbox' applied to an object of class "list"
-```
-
-```r
 sum_iso_date
 ```
 
 ```
 ## ===============
-## Site:  1
+## Site:  Example site
 ## Elevation:  58.51383 
 ## 
 ## Sum of isobase directions:  325 338 

diff --git a/vignettes/shoredate.Rmd.orig b/vignettes/shoredate.Rmd.orig
@@ -38,7 +38,7 @@ spatial_limit <- sf::st_read(system.file("extdata/spatial_limit.gpkg",
 # Introduction
 The concept of dating sites based on their present-day elevation with reference to past shoreline displacement has been an important tool for archaeologists in northern Scandinavia since the early 1900s (e.g. Brøgger 1905). This is based on the observation that Stone Age sites in the region tend to have been located close to the contemporaneous shoreline when they were in use. Furthermore, following the retreat of the Fennoscandian Ice Sheet, the isostatic uplift has been so severe that despite corresponding eustatic sea-level rise, the relative sea-level has been falling throughout prehistory in large parts of this region. Within any given area where this is the case, the general pattern is thus that older sites will be located at higher altitudes than younger sites.
 
-This vignette describes the R package *shoredate* which provides tools for shoreline dating Stone Age sites located on the Norwegian Skagerrak coast using the approach presented in Roalkvam (2023). This is based on the an empirical evaluation of the likely elevation of the sites above sea-level when they were in use, and the local trajectory of past relative sea-level change. Due to the geographical contingency of the method, and the dependency on geological reconstructions of shoreline displacement, the package is at present limited to coastal sites located in the region stretching from Horten county in the north east, to Arendal county in the south west.
+This vignette describes the R package *shoredate* which provides tools for shoreline dating Stone Age sites located on the Norwegian Skagerrak coast using the approach presented in Roalkvam (2023). This is based on an empirical evaluation of the likely elevation of the sites above sea-level when they were in use, and the local trajectory of past relative sea-level change. Due to the geographical contingency of the method, and the dependency on geological reconstructions of shoreline displacement, the package is at present limited to coastal sites located in the region stretching from Horten county in the north east, to Arendal county in the south west.
 
 ## Geographical and temporal coverage
 
@@ -131,7 +131,7 @@ shoredate_plot(target_date,  greyscale = TRUE)
 A more sparse version can also be plotted by specifying what elements are to be excluded.
 
 ```{r sparse, fig.width = 4.4, fig.height = 3.7}
-shoredate_plot(target_date,  elevation_distribution = FALSE,
+shoredate_plot(target_date, elevation_distribution = FALSE,
                displacement_curve = FALSE, highest_density_region = FALSE)
 ```
 
@@ -224,26 +224,29 @@ The direction of the shoreline gradient is specified by the isobases that run pe
 While the range of the typically employed isobase directions generally result in minor differences in the resulting shoreline dates, it is possible to specify other and multiple directions for these, and perform the shoreline date using each individual direction. This can be useful either for evaluating the sensitivity of a date or if one believes there is reason suspect a different direction than the default in a particular case.
 
 ```{r example_site_isobases, message = FALSE}
+# Add a name to the example site
+target_point <- sf::st_as_sf(target_point, crs = 32632)
+target_point$name <- "Example site"
+
 # Using the same target point and elevation as above, but specifying two different directions
 # for the isobases when dating
-iso_date <- shoreline_date(site = target_point, elevation = elev_raster, isobase_direction = c(325, 338))
+iso_date <- shoreline_date(site = target_point, elevation = elev_raster,
+                           isobase_direction = c(325, 338))
 
 iso_date
 ```
 
 In the call to plot it can then be specified that the direction of the isobases is printed with each date. Note that it is not possible use `multiplot` when having used multiple isobase directions when dating the sites. The following thus also shows the default behaviour when plotting multiple dates at once and not setting `multiplot = TRUE`.
 
 ```{r plot_example_isobases, fig.width = 4, fig.height = 3.5}
-shoredate_plot(iso_date, isobase_direction = TRUE)
+shoredate_plot(iso_date, site_name = TRUE, isobase_direction = TRUE)
 ```
 
 ## Sum the probability of dates across isobase directions
 
 As an alternative to keeping the two shoreline dates of the site separate, the parameter `sum_isobase_directions` can be set to `TRUE` when calling `shoreline_date()` to sum the probability of the dates. Again, by default this is normalised to sum to unity.
 
 ```{r example_sum_isobases, message = FALSE}
-target_point$name <- "Example site"
-
 sum_iso_date <- shoreline_date(site = target_point, elevation = elev_raster,
                                isobase_direction = c(325, 338), sum_isobase_directions = TRUE)