Fix imports from dimensio and arkhe

DESCRIPTION

@@ -24,11 +24,11 @@ URL: https://packages.tesselle.org/kairos/,
     https://github.com/tesselle/kairos
 BugReports: https://github.com/tesselle/kairos/issues
 Depends: 
-    R (>= 3.5)
+    R (>= 3.5),
+    dimensio (>= 0.6.0)
 Imports: 
     aion (>= 1.0.2),
-    arkhe (>= 1.5.0),
-    dimensio (>= 0.5.0),
+    arkhe (>= 1.6.0),
     extraDistr,
     grDevices,
     methods,

NAMESPACE

@@ -23,10 +23,9 @@ export(BCE)
 export(BP)
 export(CE)
 export(b2k)
-export(bootstrap)
 export(calendar)
-export(jackknife)
 export(remove_NA)
+export(remove_constant)
 export(remove_zero)
 export(replace_NA)
 export(replace_zero)
@@ -66,6 +65,9 @@ exportMethods(time)
 exportMethods(weights)
 import(aion)
 import(arkhe)
+importClassesFrom(aion,RataDie)
+importClassesFrom(aion,TimeSeries)
+importClassesFrom(dimensio,CA)
 importFrom(aion,AD)
 importFrom(aion,BC)
 importFrom(aion,BCE)
@@ -77,18 +79,11 @@ importFrom(aion,end)
 importFrom(aion,start)
 importFrom(aion,time)
 importFrom(aion,year_axis)
-importFrom(arkhe,bootstrap)
-importFrom(arkhe,jackknife)
 importFrom(arkhe,remove_NA)
+importFrom(arkhe,remove_constant)
 importFrom(arkhe,remove_zero)
 importFrom(arkhe,replace_NA)
 importFrom(arkhe,replace_zero)
-importFrom(dimensio,ca)
-importFrom(dimensio,get_coordinates)
-importFrom(dimensio,get_data)
-importFrom(dimensio,get_eigenvalues)
-importFrom(dimensio,get_replications)
-importFrom(dimensio,predict)
 importFrom(extraDistr,ptnorm)
 importFrom(grDevices,xy.coords)
 importFrom(methods,.valueClassTest)
@@ -100,3 +95,5 @@ importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,validObject)
+importMethodsFrom(arkhe,bootstrap)
+importMethodsFrom(arkhe,jackknife)

NEWS.md

@@ -1,4 +1,6 @@
 # kairos 2.0.2.9000
+## Internals
+* List **dimensio** in `Depends`.
 
 # kairos 2.0.2
 ## Internals

R/AllClasses.R

@@ -1,7 +1,13 @@
 # CLASSES DEFINITION AND INITIALIZATION
 NULL
 
-# MeanDate ======================================================================
+# Import classes ===============================================================
+#' @importClassesFrom aion TimeSeries
+#' @importClassesFrom aion RataDie
+#' @importClassesFrom dimensio CA
+NULL
+
+# MeanDate =====================================================================
 #' Mean Date
 #'
 #' An S4 class to store the weighted mean date (e.g. Mean Ceramic Date) of
@@ -141,7 +147,7 @@ NULL
   contains = "TimeSeries"
 )
 
-# CountApportion ==================================================================
+# CountApportion ===============================================================
 #' Count Apportioning
 #'
 #' An S4 class to represent an artifact apportioning results. Gives the

R/AllGenerics.R

@@ -2,9 +2,10 @@
 #' @include AllClasses.R
 NULL
 
-# S4 dispatch to S3 generics ===================================================
-setGeneric("jackknife", package = "arkhe")
-setGeneric("bootstrap", package = "arkhe")
+# Import S4 generics ===========================================================
+#' @importMethodsFrom arkhe jackknife
+#' @importMethodsFrom arkhe bootstrap
+NULL
 
 # Mutators =====================================================================
 ## Subset ----------------------------------------------------------------------

R/kairos-package.R

@@ -10,6 +10,8 @@
 #'  `kairos` uses the following [options()] to configure behavior:
 #'  * `kairos.progress`: a [`logical`] scalar. Should progress bars be
 #'    displayed?
+#'  * `kairos.calendar`: a [`aion::TimeScale-class`] object (default calendar
+#'    for printing).
 #'
 #' @author
 #' **Full list of authors and contributors** (alphabetic order)
@@ -39,8 +41,6 @@
 
 #' @import arkhe
 #' @import aion
-#' @importFrom dimensio ca get_coordinates get_data get_eigenvalues
-#' get_replications predict
 #' @importFrom extraDistr ptnorm
 #' @importFrom grDevices xy.coords
 #' @importFrom methods as callGeneric callNextMethod new setClass setGeneric

R/reexport.R

@@ -1,13 +1,5 @@
 # REEXPORT FROM ARKHE
 
-#' @importFrom arkhe bootstrap
-#' @export
-arkhe::bootstrap
-
-#' @importFrom arkhe jackknife
-#' @export
-arkhe::jackknife
-
 #' @importFrom arkhe replace_NA
 #' @export
 arkhe::replace_NA
@@ -24,6 +16,10 @@ arkhe::remove_NA
 #' @export
 arkhe::remove_zero
 
+#' @importFrom arkhe remove_constant
+#' @export
+arkhe::remove_constant
+
 #' @importFrom aion calendar
 #' @export
 aion::calendar

paper.md

@@ -0,0 +1,33 @@
+---
+title: 'kairos: An R Package for the Analysis of Chronological Patterns from Archaeological Count Data'
+tags:
+  - archaeology
+  - time series
+  - chronology
+authors:
+  - name: Nicolas Frerebeau
+    orcid: 0000-0001-5759-4944
+    affiliation: 1
+affiliations:
+  - name: UMR 6034 Archéosciences Bordeaux (CNRS, Université Bordeaux Montaigne, Université de Bordeaux, EPHE)
+    index: 1
+date: 27 November 2023
+bibliography: paper.bib
+---
+
+# Summary
+
+# Statement of need
+
+# Functionality
+
+A toolkit for absolute and relative dating and analysis of
+chronological patterns. This package includes functions for
+chronological modeling and dating of archaeological assemblages from
+count data. It provides methods for matrix seriation. It also allows
+to compute time point estimates and density estimates of the
+occupation and duration of an archaeological site.
+
+# Acknowledgements
+
+# References

vignettes/seriation.Rmd

@@ -121,7 +121,7 @@ tabula::plot_ford(zuni)
 (zun_indices <- seriate_average(zuni, margin = c(1, 2)))
 
 ## Plot CA results
-dimensio::biplot(zun_indices)
+biplot(zun_indices)
 ```
 
 ```{r ca-permutation, fig.width=7, fig.height=7}
@@ -142,17 +142,17 @@ According to @peeples2012, "[this] point removal procedure [results in] a reduce
 ```{r bootstrap, fig.width=7, fig.height=7, out.width='50%', fig.show='hold'}
 ## Partial bootstrap CA
 ## Warning: this may take a few seconds!
-zuni_boot <- dimensio::bootstrap(zun_indices, n = 30)
+zuni_boot <- bootstrap(zun_indices, n = 30)
 
 ## Bootstrap CA results for the rows
 ## (add convex hull)
 zuni_boot |> 
-  dimensio::viz_rows(col = "lightgrey", pch = 16, legend = NULL) |> 
-  dimensio::viz_hull(col = adjustcolor("#004488", alpha = 0.2))
+  viz_rows(col = "lightgrey", pch = 16, legend = NULL) |> 
+  viz_hull(col = adjustcolor("#004488", alpha = 0.2))
 
 ## Bootstrap CA results for the columns
 zuni_boot |> 
-  dimensio::viz_columns(pch = 16, legend = list(x = "topright"))
+  viz_columns(pch = 16, legend = list(x = "topright"))
 ```
 
 ```{r refine, fig.width=7, fig.height=7}
@@ -164,7 +164,7 @@ fun <- function(x) { mean(x) + sd(x) }
 (zuni_refine <- seriate_refine(zun_indices, cutoff = fun, margin = 1))
 
 ## Plot CA results for the rows
-dimensio::viz_rows(zuni_refine, highlight = "observation", pch = c(16, 15))
+viz_rows(zuni_refine, highlight = "observation", pch = c(16, 15))
 ```
 
 ```{r refine-histogram, fig.width=5, fig.height=5}