Merge pull request #13 from lsteinmann/packagedoc

new release

.github/workflows/R-CMD-check.yaml

@@ -4,11 +4,10 @@ on:
   push:
     branches:
       - main
-      - master
-  pull_request:
-    branches:
-      - main
-      - master
+#  pull_request:
+#    branches:
+#      - main
+#      - master
 
 name: R-CMD-check
 

.travis.yml

@@ -5,10 +5,22 @@ language: R
 cache: packages
 latex: false
 
+
+branches:
+  only:
+  - main
+  - packagedoc
+
+
 matrix:
   include:
     - r: 3.3
     - r: release
     - os: osx
-      osx_image: xcode7.3
-      disable_homebrew: true
+
+
+addons:
+  apt:
+    packages:
+      - libgit2-dev
+

DESCRIPTION

@@ -2,8 +2,8 @@ Package: datplot
 Type: Package
 Title: Preparation of object dating ranges for density plots
 Version: 0.2.4
-Author: Lisa Steinmann
-Maintainer: Lisa Steinmann <lisa.steinmann@rub.de>
+Author: anon
+Maintainer: anon <anon@anon.de>
 Description: Converting date ranges into dating 'steps' eases the visualization of changes in e.g. pottery consumption, style and other variables over time. This package provides tools to process and prepare data for visualization.
 License: CC BY-SA 4.0
 Encoding: UTF-8

R/data.R

@@ -53,14 +53,15 @@ NULL
 #' @format A data frame with 2878 rows and 9 variables:
 #' \describe{
 #'   \item{\code{ID}}{character COLUMN_DESCRIPTION}
-#'   \item{\code{ikey}}{character ID at \url{https://inscriptions.packhum.org/}, if available}
+#'   \item{\code{ikey}}{character ID at \url{https://inscriptions.packhum.org/} / \url{https://edh-www.adw.uni-heidelberg.de/home}, if available}
 #'   \item{\code{Location}}{factor Findspot of the Inscription (City)}
 #'   \item{\code{Source}}{character Corpus/Citation of the Inscription}
 #'   \item{\code{Dating}}{character Original Chronological Assesment, may contain inconsistencies}
 #'   \item{\code{Language}}{factor Language of the Inscription, can either be Latin, Greek, or both}
 #'   \item{\code{uncertain_dating}}{logical TRUE if Dating is not certain, FALSE if dating is certain}
 #'   \item{\code{DAT_min}}{integer lower border of the dating timespan, negative values for BCE, positive values for CE}
 #'   \item{\code{DAT_max}}{integer uppper border of the dating timespan, negative values for BCE, positive values for CE}
+#'   \item{\code{URL}}{Link to the inscription (if available) at \url{https://inscriptions.packhum.org/} or \url{https://edh-www.adw.uni-heidelberg.de/home}}
 #'}
 #' @source Weissová, Barbora. 2019. “Regional Economy, Settlement Patterns and the Road System in Bithynia (4th Century BC - 6th Century AD). Spatial and Quantitative Analysis.” Dissertation, Berlin: Freie Universität Berlin. \url{https://refubium.fu-berlin.de/handle/fub188/23730}, partially after \url{https://inscriptions.packhum.org/}
 "Inscr_Bithynia"

README.md

@@ -1,7 +1,7 @@
  <!-- badges: start -->
-  [![R build status](https://github.com/lsteinmann/datplot/workflows/R-CMD-check/badge.svg)](https://github.com/lsteinmann/datplot/actions)
-  [![Travis build status](https://travis-ci.com/lsteinmann/datplot.svg?branch=master)](https://travis-ci.com/lsteinmann/datplot)
-  [![Codecov test coverage](https://codecov.io/gh/lsteinmann/datplot/branch/master/graph/badge.svg)](https://codecov.io/gh/lsteinmann/datplot?branch=master)
+  [![R build status](https://github.com/anonymousgit/datplot/workflows/R-CMD-check/badge.svg)](https://github.com/anonymousgit/datplot/actions)
+  [![Travis Build Status](https://travis-ci.com/anonymousgit/datplot.svg?token=qpxyBQYqepYayg8rYHnD&branch=main)](https://travis-ci.com/anonymousgit/datplot)
+  [![Codecov test coverage](https://codecov.io/gh/anonymousgit/datplot/branch/master/graph/badge.svg)](https://codecov.io/gh/anonymousgit/datplot?branch=main)
   <!-- badges: end -->
 
 datplot
@@ -32,11 +32,11 @@ Installation
 -------
 'datplot' is not currently on CRAN. It can be installed from GitHub with devtools:
 
-    devtools::install_github("lsteinmann/datplot")
+    devtools::install_github("anonymousgit/datplot")
 
 Or via downloading the latest release and installing from the file: 
 
-    install_local(path = "../datplot_0.2.4.tar.gz")
+    devtools::install_local(path = "../datplot_0.2.4.tar.gz")
 
 Contact
 -------

data-raw/Inscr_Bithynia.R

@@ -5,6 +5,20 @@ library(tidyverse)
 
 inscriptions <- readxl::read_excel(system.file('extdata', 'Bithynia_Inscriptions.xlsx', package = 'datplot', mustWork = TRUE))
 
+inscriptions <- inscriptions %>%
+  mutate(ikey = na_if(ikey, "N / A"),
+         ikey = gsub("2PH", "PH", ikey),
+         ikey = gsub("v", "PH", ikey),
+         URL = NA)
+
+repl <- grep("HD", inscriptions$ikey)
+inscriptions$URL[repl] <- paste("https://edh-www.adw.uni-heidelberg.de/edh/inschrift/",
+                                gsub("HD", "", inscriptions$ikey[repl]), sep = "")
+repl <- grep("PH", inscriptions$ikey)
+inscriptions$URL[repl] <- paste("https://epigraphy.packhum.org/text/",
+                                gsub("PH", "", inscriptions$ikey[repl]), sep = "")
+
+
 inscriptions$ID <- paste("I_", 1:nrow(inscriptions), sep = "")
 inscriptions <- inscriptions %>%
   rename(Dating = `Chronological Frame`) %>%
@@ -127,7 +141,7 @@ for (r in sel) {
 
 join_dating <- rbind(join_dating, num_dating[!is.na(num_dating$DAT_min),])
 num_dating <- num_dating[which(is.na(num_dating$DAT_min)),]
-unique(num_dating$Dating)[1:20]
+#unique(num_dating$Dating)[1:20]
 
 join_dating$DAT_min[which(join_dating$DAT_min == 0)] <- 1
 join_dating$DAT_max[which(join_dating$DAT_max == 0)] <- -1
@@ -153,7 +167,10 @@ inscriptions <- left_join(inscriptions, join_dating, by = "Dating")
 inscriptions[which(inscriptions$ID == "I_1162"),"DAT_max"] <- 63
 inscriptions[which(inscriptions$ID == "I_2725"),c("DAT_min", "DAT_max")] <- inscriptions[which(inscriptions$ID == "I_2725"),c("DAT_max", "DAT_min")]
 
-inscriptions <- inscriptions[,c(6,1:5,7:9)]
+
+
+inscriptions <- inscriptions[,c(7,1:5,8:10,6)]
+
 
 attr(inscriptions, "contact") <-
   "Anonymous Anonymous ([email protected]), Anonymous Anonymous ([email protected])"
@@ -172,6 +189,7 @@ attr(inscriptions$uncertain_dating, "descr") <-
   "TRUE if Dating is not certain, FALSE if dating is certain"
 attr(inscriptions$DAT_min, "descr") <- "lower border of the dating timespan"
 attr(inscriptions$DAT_max, "descr") <- "uppper border of the dating timespan"
+attr(inscriptions$URL, "descr") <- "Link to the Inscription at https://inscriptions.packhum.org/"
 
 #write.table(inscriptions, file = "inscriptions.csv",
 #            fileEncoding = "UTF-8", sep = ";", row.names = FALSE)

inst/literatur.bib

@@ -1,9 +1,9 @@
 % Encoding: UTF-8
 
 @Www{BAPD,
-  title     = {Beazley Archive Pottery Database (BAPD)},
-  owner     = {University of Oxford},
-  timestamp = {2018-04-27},
+  title     = {Beazley Archive Pottery Database ({{BAPD}})},
+  author     = {University of Oxford},
+  urldate = {2018-04-27},
   url       = {https://www.beazley.ox.ac.uk/pottery/default.htm},
 }
 
@@ -20,7 +20,7 @@ @article{datplotarticle
 
 @thesis{weissova2019,
   title = {Regional Economy, Settlement Patterns and the Road System in {{Bithynia}} (4th century {{BC}} - 6th century {{AD}}). {{Spatial}} and {{Quantitative Analysis}}},
-  author = {Weissov\'a, Barbora},
+  author = {Weissova, Barbora},
   date = {2019},
   institution = {{Freie Universit\"at Berlin}},
   location = {{Berlin}},
@@ -33,7 +33,7 @@ @thesis{weissova2019
 @article{weissova_HinterlandNikaiaNicaea_2019,
   title = {The {{Hinterland}} of {{Nikaia}}/{{Nicaea}}/{{Iznik}}: {{Analyzing}} the {{Hellenistic Roman}} and {{Late Antique Bithynian Landscape}} through {{Remote Sensing}} and {{GIS Techniques}}},
   shorttitle = {The {{Hinterland}} of {{Nikaia}}/{{Nicaea}}/{{Iznik}}},
-  author = {Weissov\'a, Barbora and Brigand, Robin and Polla, Silvia},
+  author = {Weissova, Barbora and Brigand, Robin and Polla, Silvia},
   date = {2019},
   journaltitle = {eTopoi Journal for Ancient Studies},
   volume = {8},
@@ -68,10 +68,9 @@ @article{orton_CatchUnitResearch_2017
 }
 
 @incollection{johnson_AoristicAnalysisSeeds_2004,
-  ids = {:unknunknown\_AoristicAnalysisSeeds\_2004},
   title = {Aoristic Analysis: Seeds of a New Approach to Mapping Archaeological Distributions through Time},
   booktitle = {2003 - Enter the Past. The E-way into the four Dimensions of Cultural Heritage. CAA 2003. Computer Applications and Quantitative Methods in Archaeology},
-  author = {Johnson, I.},
+  author = {Johnson, Ian},
   editor = {B\"orner, W. and Goriany, M.},
   date = {2004},
   publisher = {Archaeopress},
@@ -81,6 +80,52 @@ @incollection{johnson_AoristicAnalysisSeeds_2004
 
 
 
+@article{baxter_ReinventingwheelModelling_2016,
+  title = {Reinventing the Wheel? Modelling temporal uncertainty with applications to brooch distributions in Roman Britain},
+  shorttitle = {Reinventing the wheel?},
+  author = {Baxter, Mike J. and Cool, H.E.M.},
+  date = {2016-02},
+  journaltitle = {Journal of Archaeological Science},
+  volume = {66},
+  pages = {120--127},
+  doi = {10.1016/j.jas.2015.12.007}
+}
+
+@article{crema_probabilisticframeworkassessing_2010,
+  title = {A probabilistic framework for assessing spatio-temporal point patterns in the archaeological record},
+  author = {Crema, Enrico R. and Bevan, Andrew and Lake, Mark W.},
+  date = {2010-05},
+  journaltitle = {Journal of Archaeological Science},
+  volume = {37},
+  pages = {1118--1130},
+  doi = {10.1016/j.jas.2009.12.012},
+  number = {5}
+}
+
+
+
+
+@book{shennan_Quantifyingarchaeology_1988,
+  title = {Quantifying Archaeology},
+  author = {Shennan, Stephen},
+  date = {1988},
+  publisher = {Edinburgh University Press},
+  location = {Edinburgh}
+}
+
+
+@article{baxter_histogramimprovedapproachessimple_1996,
+  title = {Beyond the Histogram -- Improved Approaches to Simple Data Display in Archaeology using Kernel Density Estimates},
+  author = {Baxter, Mike J. and Beardah, Christian C.},
+  date = {1996},
+  journaltitle = {Archeologia e calcolatori},
+  volume = {7},
+  pages = {397--408},
+  number = {1}
+}
+
+
+