Update datasets in examples and tests

Author: nfrerebeau

DESCRIPTION

@@ -65,7 +65,6 @@ Suggests:
     folio,
     khroma,
     knitr,
-    magrittr,
     rmarkdown,
     testthat (>= 3.0.0),
     vdiffr (>= 1.0.0)

README.Rmd

@@ -64,7 +64,6 @@ remotes::install_github("tesselle/tabula")
 ## Load packages
 library(folio) # Datasets
 library(khroma) # Color scales
-library(magrittr) # Pipes
 library(ggplot2)
 
 library(tabula)
@@ -116,14 +115,14 @@ Measure diversity by comparing to simulated assemblages:
 set.seed(12345)
 
 ## Data from Conkey 1980, Kintigh 1989, p. 28
-chevelon %>%
-  heterogeneity(method = "shannon") %>%
-  simulate() %>%
+chevelon |>
+  heterogeneity(method = "shannon") |>
+  simulate() |>
   plot()
 
-chevelon %>%
-  richness(method = "count") %>%
-  simulate() %>%
+chevelon |>
+  richness(method = "count") |>
+  simulate() |>
   plot()
 ```
 

README.md

@@ -92,7 +92,6 @@ remotes::install_github("tesselle/tabula")
 ## Load packages
 library(folio) # Datasets
 library(khroma) # Color scales
-library(magrittr) # Pipes
 library(ggplot2)
 
 library(tabula)
@@ -163,14 +162,14 @@ Measure diversity by comparing to simulated assemblages:
 set.seed(12345)
 
 ## Data from Conkey 1980, Kintigh 1989, p. 28
-chevelon %>%
-  heterogeneity(method = "shannon") %>%
-  simulate() %>%
+chevelon |>
+  heterogeneity(method = "shannon") |>
+  simulate() |>
   plot()
 
-chevelon %>%
-  richness(method = "count") %>%
-  simulate() %>%
+chevelon |>
+  richness(method = "count") |>
+  simulate() |>
   plot()
 ```
 

codemeta.json

@@ -125,18 +125,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=knitr"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "magrittr",
-      "name": "magrittr",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=magrittr"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -262,7 +250,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1644.741KB",
+  "fileSize": "1888.796KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

inst/examples/ex-diversity.R

@@ -1,9 +1,8 @@
-## Ceramic data
-data("chevelon", package = "folio")
+data("cantabria")
 
 ## Shannon diversity index
-(h <- heterogeneity(chevelon, method = "shannon"))
-(e <- evenness(chevelon, method = "shannon"))
+(h <- heterogeneity(cantabria, method = "shannon"))
+(e <- evenness(cantabria, method = "shannon"))
 
 ## Bootstrap resampling (summary statistics)
 bootstrap(h, f = NULL)

inst/examples/ex-independance.R

@@ -1,12 +1,11 @@
-## Ceramic data
-data("compiegne", package = "folio")
+data("cantabria")
 
 ## Compute EPPM
-counts_eppm <- eppm(compiegne)
+counts_eppm <- eppm(cantabria)
 plot_heatmap(counts_eppm) +
   khroma::scale_fill_YlOrBr(name = "EPPM")
 
 ## Compute PVI
-counts_pvi <- pvi(compiegne)
+counts_pvi <- pvi(cantabria)
 plot_heatmap(counts_pvi) +
   khroma::scale_fill_BuRd(name = "PVI", midpoint = 1)

inst/examples/ex-occurrence.R

@@ -1,6 +1,5 @@
-## Ceramic data
-data("mississippi", package = "folio")
+data("cantabria")
 
 ## Plot spot diagram of a co-occurrence matrix
-occ <- occurrence(mississippi)
+occ <- occurrence(cantabria)
 plot_spot(occ)

inst/examples/ex-plot_diversity.R

@@ -1,14 +1,13 @@
 \donttest{
-## Ceramic data
-data("chevelon", package = "folio")
+data("cantabria")
 
 ## Assemblage diversity size comparison
 ## Warning: this may take a few seconds!
-h <- heterogeneity(chevelon, method = "shannon")
+h <- heterogeneity(cantabria, method = "shannon")
 h_sim <- simulate(h)
 plot(h_sim)
 
-r <- richness(chevelon, method = "count")
+r <- richness(cantabria, method = "count")
 r_sim <- simulate(r)
 plot(r_sim)
 }

inst/examples/ex-plot_matrix.R

@@ -1,9 +1,8 @@
-## Ceramic data
-data("compiegne", package = "folio")
+data("cantabria")
 
 ## Plot matrix diagram...
-plot_heatmap(compiegne)
-plot_heatmap(compiegne, freq = TRUE)
+plot_heatmap(cantabria)
+plot_heatmap(cantabria, freq = TRUE)
 
 ## Presence/absence data
 inc <- sample(0:1, size = 100, replace = TRUE)

inst/examples/ex-plot_rank.R

@@ -1,6 +1,5 @@
-## Ceramic data
-data("compiegne", package = "folio")
+data("cantabria")
 
 ## Plot rank vs abundance
-plot_rank(compiegne)
-plot_rank(compiegne, facet = TRUE)
+plot_rank(cantabria)
+plot_rank(cantabria, facet = TRUE)

inst/examples/ex-plot_spot.R

@@ -1,10 +1,9 @@
-## Ceramic data
-data("mississippi", package = "folio")
+data("cantabria")
 
 ## Plot spot diagram of count data...
 ### ...without threshod
-plot_spot(mississippi)
+plot_spot(cantabria)
 ### ...with the  column means as threshold
-plot_spot(mississippi, threshold = mean)
+plot_spot(cantabria, threshold = mean)
 ### ...with the column medians as threshold
-plot_spot(mississippi, threshold = median)
+plot_spot(cantabria, threshold = median)

inst/examples/ex-rarefaction.R

@@ -1,5 +1,4 @@
-## Engraved Bones data
-data("cantabria", package = "folio")
+data("cantabria")
 
 ## Replicate fig. 3 from Baxter 2011
 rare <- rarefaction(cantabria, sample = 23, method = "baxter")

inst/examples/ex-test.R

@@ -1,5 +1,4 @@
-## Ceramic data
-data("merzbach", package = "folio")
+data("cantabria")
 
 ## Shannon diversity test
-test_diversity(merzbach)
+test_diversity(cantabria)