All files have had permissions changed for some reason. It's really a…

…nnoying. In addition, there is a change to `compile_downloads()` as a result of a user bug report. This fixes an error where a single sample download returns a result with as many rows as columns.
ropensci · Jul 19, 2018 · b85dfda · b85dfda
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diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.gitignore b/.gitignore
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+neotoma 1.7.1
+====================
+o Bugfix for `compile_download`, single sample downloads were failing to compile properly.
+
 neotoma 1.7.0
 ====================
 o Added `plot_leaflet` to allow interactive exploration of downloaded Neotoma data.  Integrates with the Neotoma Explorer.

diff --git a/R/.gitignore b/R/.gitignore
diff --git a/R/Stratiplot.download.R b/R/Stratiplot.download.R
diff --git a/R/ages.R b/R/ages.R
diff --git a/R/bind.R b/R/bind.R
diff --git a/R/browse.R b/R/browse.R
diff --git a/R/clamodel.R b/R/clamodel.R
diff --git a/R/compile_downloads.R b/R/compile_downloads.R
@@ -84,7 +84,7 @@ compile_downloads <- function(downloads) {
                               lat = x$dataset$site$lat,
                               long = x$dataset$site$long,
                               dataset = x$dataset$dataset.meta$dataset.id,
-                              x$counts[good_counts,])
+                              as.data.frame(x$counts)[good_counts,])
     }
     else{
       #  Dummy data for empty sites.
@@ -102,7 +102,6 @@ compile_downloads <- function(downloads) {
     site.info
   }
 
-
   if (inherits(downloads, 'download_list')) {
       site.info <- plyr::ldply(downloads, down.to.df)
   }

diff --git a/R/compile_taxa.R b/R/compile_taxa.R
diff --git a/R/counts.R b/R/counts.R
diff --git a/R/depths.R b/R/depths.R
diff --git a/R/download.R b/R/download.R
diff --git a/R/get_chroncontrol.R b/R/get_chroncontrol.R
diff --git a/R/get_closest.R b/R/get_closest.R
diff --git a/R/get_contact.R b/R/get_contact.R
diff --git a/R/get_dataset.R b/R/get_dataset.R
diff --git a/R/get_download.R b/R/get_download.R
diff --git a/R/get_geochron.R b/R/get_geochron.R
diff --git a/R/get_publication.R b/R/get_publication.R
diff --git a/R/get_site.R b/R/get_site.R
diff --git a/R/get_table.R b/R/get_table.R
diff --git a/R/get_taxa.R b/R/get_taxa.R
diff --git a/R/gp.table.R b/R/gp.table.R
diff --git a/R/param_check.R b/R/param_check.R
diff --git a/R/plot-methods.R b/R/plot-methods.R
diff --git a/R/plot_leaflet.R b/R/plot_leaflet.R
diff --git a/R/pollen.equiv.R b/R/pollen.equiv.R
diff --git a/R/print.chroncontrol.R b/R/print.chroncontrol.R
diff --git a/R/print.dataset.R b/R/print.dataset.R
diff --git a/R/print.dataset_list.R b/R/print.dataset_list.R
diff --git a/R/print.download.R b/R/print.download.R
diff --git a/R/print.download_list.R b/R/print.download_list.R
diff --git a/R/print.geochronologic.R b/R/print.geochronologic.R
diff --git a/R/print.geochronologic_list.R b/R/print.geochronologic_list.R
diff --git a/R/print.site.R b/R/print.site.R
diff --git a/R/read_bacon.R b/R/read_bacon.R
diff --git a/R/read_methods.R b/R/read_methods.R
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/R/taxa.R b/R/taxa.R
@@ -29,7 +29,8 @@
 ##' @export
 ##' @rdname taxa
 `taxa.download` <- function(obj, ...) {
-    ret <- as.data.frame(obj$taxon.list)
+    ret <- as.data.frame(obj$taxon.list,
+                         stringsAsFactors = FALSE)
     class(ret) <- c("neo_taxa", "data.frame")
     ret
 }
@@ -39,14 +40,16 @@
 ##' @rdname taxa
 `taxa.download_list` <- function(obj, collapse = TRUE, hierarchy = FALSE, ...) {
     ret <- lapply(obj, '[[', 'taxon.list')
-    ret <- lapply(ret, as.data.frame, stringsAsFactors = FALSE)
-
+    ret <- lapply(ret,
+                  as.data.frame,
+                  stringsAsFactors = FALSE)
+
     # if (hierarchy == TRUE) {
     #  taxonomy <- get_table("Taxa")
-      
+
       # match_taxa <- function(tax){
       #   row <- match(tax, taxonomy$TaxonName)
-      #   
+      #
       #   output <- taxonomy[row,]
       #   if (taxonomy$TaxonID[row] == taxonomy$HigherTaxonID[row]) {
       #     return(taxonomy[row,])
@@ -56,19 +59,19 @@
       #   }
       #   return(output)
       # }
-        
+
     # }
-    
+
     if (collapse == TRUE) {
       ret <- dplyr::bind_rows(ret)
       ret <- ret[!duplicated(ret[,c(1:3)]),]
-      
+
       # if(hierarchy == TRUE) {
       #   taxonhier <- do.call(rbind.data.frame, lapply(ret$taxon.name, match_taxa))
       #   taxonhier <- taxonhier[!duplicated(taxonhier), c("TaxonID", "TaxonName", "TaxaGroupID", "HigherTaxonID")]
       # }
     }
-    
+
     class(ret) <- c("neo_taxa_list", "list")
     ret
 }
diff --git a/R/taxon.table.R b/R/taxon.table.R
diff --git a/R/translate.table.R b/R/translate.table.R
diff --git a/R/write_agefile.R b/R/write_agefile.R
diff --git a/README.md b/README.md
@@ -61,7 +61,7 @@ More functions are available through the package help.  These represent the core
 + `get_chroncontrol` - Get chronological information used to build the age-depth model for the record. [API](http://api.neotomadb.org/doc/resources/chroncontrol)
 
 ### Recent Changes
-+ unreleased: Added the `taxa` function to extract taxa lists from large download objects.
++ 1.7.1: Bugfix for `compile_download`, single sample downloads were failing to compile properly, added the `taxa` function to extract taxa lists from large download objects.
 + 1.7.0: Added `plot_leaflet` to allow interactive exploration of downloaded Neotoma data.  Integrates with the Neotoma Explorer.  Minor bugfix for `get_download` to allow records to be sent to Neotoma and to be filtered.
 + 1.6.2: Improved the basic `plot` method based on tests against Tilia files in the Neotoma Holding Tank & built more robust interpolation in `read_bacon` so that age models without interpolated dates can still be imported. `browse` now opens multiple datastes in the Neotoma Explorer at once.
 + 1.6.1: New `Stratiplot` method, using the `analogue` package to plot dataset diagrams from `download` and `download_list` objects, bug fixes for `write_agefile` and a new function, `read_bacon`, to read in and integrate Bacon chronologies into `download` objects.

diff --git a/appveyor.yml b/appveyor.yml
diff --git a/code_of_conduct.md b/code_of_conduct.md
diff --git a/cran-comments.md b/cran-comments.md
diff --git a/download.out b/download.out
diff --git a/inst/CITATION b/inst/CITATION
diff --git a/inst/Cores/THREEPINES/THREEPINES.csv b/inst/Cores/THREEPINES/THREEPINES.csv
diff --git a/inst/Cores/THREEPINES/THREEPINES_depths.txt b/inst/Cores/THREEPINES/THREEPINES_depths.txt
diff --git a/inst/crystal.tlx b/inst/crystal.tlx
diff --git a/inst/img/histogramplot.png b/inst/img/histogramplot.png
diff --git a/inst/img/inkspot_neotoma.gif b/inst/img/inkspot_neotoma.gif
diff --git a/inst/img/mammothsites.png b/inst/img/mammothsites.png
diff --git a/man/Stratiplot.download.Rd b/man/Stratiplot.download.Rd
diff --git a/man/Stratiplot.download_list.Rd b/man/Stratiplot.download_list.Rd
diff --git a/man/ages.Rd b/man/ages.Rd
diff --git a/man/bind.Rd b/man/bind.Rd
diff --git a/man/browse.Rd b/man/browse.Rd
diff --git a/man/browse.dataset.Rd b/man/browse.dataset.Rd
diff --git a/man/browse.dataset_list.Rd b/man/browse.dataset_list.Rd
diff --git a/man/browse.default.Rd b/man/browse.default.Rd
diff --git a/man/browse.download.Rd b/man/browse.download.Rd
diff --git a/man/browse.download_list.Rd b/man/browse.download_list.Rd
diff --git a/man/compile_downloads.Rd b/man/compile_downloads.Rd
diff --git a/man/compile_taxa.Rd b/man/compile_taxa.Rd
diff --git a/man/counts.Rd b/man/counts.Rd
diff --git a/man/depths.Rd b/man/depths.Rd
diff --git a/man/download.Rd b/man/download.Rd
diff --git a/man/get_chroncontrol.Rd b/man/get_chroncontrol.Rd
diff --git a/man/get_chroncontrol.dataset.Rd b/man/get_chroncontrol.dataset.Rd
diff --git a/man/get_chroncontrol.dataset_list.Rd b/man/get_chroncontrol.dataset_list.Rd
diff --git a/man/get_chroncontrol.default.Rd b/man/get_chroncontrol.default.Rd
diff --git a/man/get_chroncontrol.download.Rd b/man/get_chroncontrol.download.Rd
diff --git a/man/get_chroncontrol.download_list.Rd b/man/get_chroncontrol.download_list.Rd
diff --git a/man/get_closest.Rd b/man/get_closest.Rd
diff --git a/man/get_contact.Rd b/man/get_contact.Rd
diff --git a/man/get_dataset.Rd b/man/get_dataset.Rd
diff --git a/man/get_dataset.default.Rd b/man/get_dataset.default.Rd
diff --git a/man/get_dataset.download.Rd b/man/get_dataset.download.Rd
diff --git a/man/get_dataset.download_list.Rd b/man/get_dataset.download_list.Rd
diff --git a/man/get_dataset.geochronologic.Rd b/man/get_dataset.geochronologic.Rd
diff --git a/man/get_dataset.geochronologic_list.Rd b/man/get_dataset.geochronologic_list.Rd
diff --git a/man/get_dataset.site.Rd b/man/get_dataset.site.Rd
diff --git a/man/get_download.Rd b/man/get_download.Rd
diff --git a/man/get_download.dataset.Rd b/man/get_download.dataset.Rd
diff --git a/man/get_download.dataset_list.Rd b/man/get_download.dataset_list.Rd
diff --git a/man/get_download.default.Rd b/man/get_download.default.Rd
diff --git a/man/get_download.site.Rd b/man/get_download.site.Rd
diff --git a/man/get_geochron.Rd b/man/get_geochron.Rd
diff --git a/man/get_publication.Rd b/man/get_publication.Rd
diff --git a/man/get_publication.dataset.Rd b/man/get_publication.dataset.Rd
diff --git a/man/get_publication.dataset_list.Rd b/man/get_publication.dataset_list.Rd
diff --git a/man/get_publication.default.Rd b/man/get_publication.default.Rd
diff --git a/man/get_publication.download.Rd b/man/get_publication.download.Rd
diff --git a/man/get_publication.download_list.Rd b/man/get_publication.download_list.Rd
diff --git a/man/get_site.Rd b/man/get_site.Rd
diff --git a/man/get_site.dataset.Rd b/man/get_site.dataset.Rd
diff --git a/man/get_site.dataset_list.Rd b/man/get_site.dataset_list.Rd
diff --git a/man/get_site.default.Rd b/man/get_site.default.Rd
diff --git a/man/get_site.download.Rd b/man/get_site.download.Rd
diff --git a/man/get_site.download_list.Rd b/man/get_site.download_list.Rd
diff --git a/man/get_site.geochronologic.Rd b/man/get_site.geochronologic.Rd
diff --git a/man/get_site.geochronologic_list.Rd b/man/get_site.geochronologic_list.Rd
diff --git a/man/get_table.Rd b/man/get_table.Rd
diff --git a/man/get_taxa.Rd b/man/get_taxa.Rd
diff --git a/man/gp.table.Rd b/man/gp.table.Rd
diff --git a/man/param_check.Rd b/man/param_check.Rd
diff --git a/man/plot_leaflet.Rd b/man/plot_leaflet.Rd
diff --git a/man/pollen.equiv.Rd b/man/pollen.equiv.Rd
diff --git a/man/read.tilia.Rd b/man/read.tilia.Rd
diff --git a/man/read_bacon.Rd b/man/read_bacon.Rd
diff --git a/man/taxa.Rd b/man/taxa.Rd
diff --git a/man/taxon.list.Rd b/man/taxon.list.Rd
diff --git a/man/translate.table.Rd b/man/translate.table.Rd
diff --git a/man/write_agefile.Rd b/man/write_agefile.Rd
diff --git a/package_check.R b/package_check.R
diff --git a/revdep/.gitignore b/revdep/.gitignore
diff --git a/revdep/check.R b/revdep/check.R
diff --git a/tests/.gitignore b/tests/.gitignore
diff --git a/tests/local_dont_run/download_tester.R b/tests/local_dont_run/download_tester.R
diff --git a/tests/local_dont_run/error_tests.RDS b/tests/local_dont_run/error_tests.RDS
diff --git a/tests/test-all.R b/tests/test-all.R
diff --git a/tests/testthat/test_examples.R b/tests/testthat/test_examples.R
diff --git a/tests/testthat/test_neotoma.R b/tests/testthat/test_neotoma.R
@@ -4,6 +4,14 @@
 #  library("testthat")
 #  library("neotoma")
 #
+# context('Get closest is working')
+# test_that('the right number of samples are returned',
+#           {
+#             cl_smp <- get_closest(x = c(-89.4012, 43.0731), n = 5, buffer = 5, datasettype = "pollen")
+#             expect_is(cl_smp, 'dataset_list')
+#             expect_equal(length(cl_smp), 5)
+#           })
+#
 # context('The API itself is working properly')
 # test_that('The API is returning data as expected from its documentation',
 #       {
@@ -136,6 +144,8 @@
 #   expect_is(compile_downloads(get_download(4559:4564)), 'data.frame')
 #   expect_is(compile_taxa(get_download(100), 'P25'), 'download_list')
 #   expect_is(compile_taxa(get_download(100)[[1]], 'P25'), 'download')
+#   expect_equal(nrow(compile_downloads(get_download(4565))), 1)
+#   
 # })
 #
 # #-----------------------------------------------------

diff --git a/tests/testthat/test_simple_paper.R b/tests/testthat/test_simple_paper.R