Release 1.1.1 (#70)

* Suggest not import fgeo.x
* Remove has_table_names

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fgeo.analyze
 Title: Analyze ForestGEO Data
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: 
     c(person(given = "Mauro",
              family = "Lepore",
@@ -55,7 +55,6 @@ Depends:
 Imports: 
     dplyr,
     fgeo.tool,
-    fgeo.x,
     glue,
     graphics,
     grDevices,
@@ -70,6 +69,7 @@ Imports:
     withr
 Suggests: 
     covr,
+    fgeo.x,
     ggplot2,
     knitr,
     measurements,

NAMESPACE

@@ -18,6 +18,7 @@ export("%>%")
 export(abundance)
 export(abundance_byyr)
 export(as_tibble)
+export(assert_is_installed)
 export(basal_area)
 export(basal_area_byyr)
 export(fgeo_habitat)
@@ -35,6 +36,7 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
+importFrom(fgeo.tool,assert_is_installed)
 importFrom(fgeo.tool,check_crucial_names)
 importFrom(fgeo.tool,is_duplicated)
 importFrom(fgeo.tool,is_multiple)

NEWS.md

@@ -2,6 +2,10 @@
 
 * Work in progress.
 
+# fgeo.analyze 1.1.1 (GitHub release)
+
+* fgeo.x no longer is imported but suggested.
+
 # fgeo.analyze 1.1.0 (GitHub release)
 
 * Import fgeo packages via `Additional_repositories` served at <https://forestgeo.github.io/drat/>

R/abund_index.R

@@ -19,6 +19,7 @@
 #' is a rowname.
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
 #' abund_index(fgeo.x::tree6, plotdim = c(1000, 500), gridsize = 20)
 #' @family functions for abundance and basal area
 #' @noRd

R/abundance.R

@@ -49,6 +49,7 @@
 #' abundance(stem)
 #' \dontrun{
 #' # Similar but more realistic
+#' assert_is_installed("fgeo.x")
 #' stem <- fgeo.x::download_data("luquillo_stem5_random")
 #'
 #' abundance(stem)

R/add_cluster.R

@@ -13,6 +13,7 @@
 #'   argument `k` to [stats::cutree()]).
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
 #' elev_ls <- fgeo.x::elevation
 #' topo <- fgeo_topography(elev_ls, gridsize = 20)
 #' add_cluster(topo, n = 4)

R/demography_ctfs.R

@@ -74,37 +74,39 @@
 #' * `date2`, mean date in census 2.
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
+#'
 #' census1 <- fgeo.x::tree5
 #' census2 <- fgeo.x::tree6
-#' 
+#'
 #' as_tibble(
 #'   recruitment_ctfs(census1, census2)
 #' )
-#' 
+#'
 #' # Use `interaction(...)` to aggregate by any number of grouping variables
 #' sp_quadrat <- interaction(census1$sp, census1$quadrat)
-#' 
+#'
 #' recruitment <- recruitment_ctfs(
 #'   census1, census2,
 #'   split1 = sp_quadrat,
 #'   quiet = TRUE
 #' )
 #' as_tibble(recruitment)
-#' 
+#'
 #' mortality <- mortality_ctfs(
 #'   census1, census2,
 #'   split1 = sp_quadrat, quiet = TRUE
 #' )
 #' as_tibble(mortality)
-#' 
+#'
 #' growth <- growth_ctfs(census1, census2, split1 = sp_quadrat, quiet = TRUE)
 #' as_tibble(growth)
-#' 
+#'
 #' # Easy way to separate grouping variables
 #' tidyr_is_installed <- requireNamespace("tidyr", quietly = TRUE)
 #' if (tidyr_is_installed) {
 #'   library(tidyr)
-#' 
+#'
 #'   as_tibble(growth) %>%
 #'     separate(groups, into = c("sp", "quadrat"))
 #' }

R/fgeo_habitat.R

@@ -20,6 +20,8 @@
 #'   as many distinct integer values as determined by the argument `n`.
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
+#'
 #' # Input a ForestGEO-like elevation list or dataframe
 #' elevation_ls <- fgeo.x::elevation
 #' habitats <- fgeo_habitat(

R/fgeo_topography.R

@@ -18,6 +18,8 @@
 #' Thanks to Jian Zhang for reporting a bug (issue 59).
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
+#'
 #' elev_list <- fgeo.x::elevation
 #' fgeo_topography(elev_list, gridsize = 20)
 #'
@@ -102,6 +104,8 @@ abort_if_xdim_ydim_is_null <- function(xdim, ydim) {
 #' @seealso [calcslope()], [quadslope()]
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
+#'
 #' # The input to elev is very specific; you may need to tweak it.
 #' elev <- fgeo.x::elevation
 #' result <- allquadratslopes(

R/imports.R

@@ -12,6 +12,11 @@
 #' @importFrom tibble tibble as.tibble as_tibble
 NULL
 
+#' @importFrom fgeo.tool assert_is_installed
+#' @export
+#' @keywords internal
+fgeo.tool::assert_is_installed
+
 #' Pipe operator
 #'
 #' See \code{magrittr::\link[magrittr]{\%>\%}} for details.

R/summary.R

@@ -10,6 +10,8 @@
 #' @seealso [tt_test()], [base::summary()].
 #'
 #' @examples
+#' assert_is_installed("fgeo.x")
+#'
 #' tt_result <- tt_test(fgeo.x::tree6_3species, fgeo.x::habitat)
 #'
 #' summary(tt_result)

R/tt_test.R

@@ -67,6 +67,7 @@
 #'
 #' @examples
 #' library(fgeo.tool)
+#' assert_is_installed("fgeo.x")
 #'
 #' # Example data
 #' tree <- fgeo.x::tree6_3species
@@ -406,7 +407,13 @@ rename_to_xy <- function(x) {
 }
 
 check_tt_test <- function(census, habitat, sp, plotdim, gridsize) {
-  has_stem_names <- !has_table_names(fgeo.x::tree6)(census)
+  tree_names <- c(
+  "treeID", "stemID", "tag", "StemTag", "sp", "quadrat", "gx", "gy",
+  "MeasureID", "CensusID", "dbh", "pom", "hom", "ExactDate", "DFstatus",
+  "codes", "nostems", "status", "date"
+  )
+  has_stem_names <- !all(names(census) %in% tree_names)
+
   msg <- "Is `census` a tree table (not a stem table)? See `?tt_test()`."
   if (has_stem_names) warn(msg)