Release (#142)

* Address devtools::release()
* Add infrastructure
* Suggest pingr
* Suggest tidyr
* Refresh NAMESPACE
* Address release checks on remote servers
* Polish exports

.Rbuildignore

@@ -1,3 +1,4 @@
+^cran-comments\.md$
 ^\.buildignore$
 ^appveyor\.yml$
 ^.*\.Rproj$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fgeo.tool
-Title: Manipulate ForestGEO Data
-Version: 0.0.0.9005
+Title: Import and Manipulate ForestGEO Data
+Version: 1.0.0
 Authors@R: 
     c(person(given = "Mauro",
              family = "Lepore",
@@ -18,8 +18,7 @@ Authors@R:
              role = c("cph", "fnd"),
              email = "[email protected]"))
 Description: Import and manipulate ForestGEO data
-    (\url{http://www.forestgeo.si.edu/}) with functions that expect
-    different classes of ForestGEO data.
+    (<http://www.forestgeo.si.edu/>).
 License: GPL-3
 URL: https://github.com/forestgeo/fgeo.tool
 BugReports: https://github.com/forestgeo/fgeo.tool/issues
@@ -40,11 +39,12 @@ Imports:
 Suggests: 
     covr,
     knitr,
+    pingr,
+    roxygen2,
     spelling,
     stringr,
-    testthat
-VignetteBuilder: 
-    knitr
+    testthat,
+    tidyr
 Remotes: 
     forestgeo/fgeo.x@*release
 Encoding: UTF-8

NAMESPACE

@@ -8,6 +8,7 @@ S3method(flag_if,data.frame)
 S3method(flag_if,default)
 export("%>%")
 export("%||%")
+export(.data)
 export(add_col_row)
 export(add_count)
 export(add_gxgy)
@@ -29,12 +30,13 @@ export(drop_if_na)
 export(drop_status)
 export(ends_with)
 export(enexpr)
+export(enexprs)
 export(enquo)
 export(enquos)
 export(ensym)
+export(ensyms)
 export(everything)
 export(expr)
-export(exprs)
 export(extract_gridsize)
 export(extract_insensitive)
 export(extract_plotdim)
@@ -104,15 +106,14 @@ importFrom(glue,glue_collapse)
 importFrom(magrittr,"%>%")
 importFrom(purrr,quietly)
 importFrom(rlang,"%||%")
-importFrom(rlang,":=")
 importFrom(rlang,.data)
-importFrom(rlang,UQ)
-importFrom(rlang,UQS)
 importFrom(rlang,abort)
 importFrom(rlang,enexpr)
+importFrom(rlang,enexprs)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,ensym)
+importFrom(rlang,ensyms)
 importFrom(rlang,expr)
 importFrom(rlang,exprs)
 importFrom(rlang,has_name)

NEWS.md

@@ -0,0 +1,3 @@
+# fgeo.tool 1.0.0
+
+* Initial release.

R/imports-reeports.R → R/aaa-imports-reeports.R

@@ -8,39 +8,8 @@ rlang::`%||%`
 
 globalVariables(c(".data", "."))
 
-# Tidy eval ---------------------------------------------------------------
+# dplyr -------------------------------------------------------------------
 
-#' Tidy eval helpers
-#'
-#' These functions provide tidy eval-compatible ways to capture
-#' symbols (`sym()`, `syms()`, `ensym()`), expressions (`expr()`,
-#' `exprs()`, `enexpr()`), and quosures (`quo()`, `quos()`, `enquo()`).
-#' To learn more about tidy eval and how to use these tools, read
-#' <http://rlang.tidyverse.org/articles/tidy-evaluation.html>
-#'
-#' @name tidyeval
-#' @keywords internal
-#' @aliases          quo quos enquo sym syms ensym expr exprs enexpr quo_name enquos
-#' @importFrom rlang quo quos enquo sym syms ensym expr exprs enexpr quo_name enquos
-#' @export           quo quos enquo sym syms ensym expr exprs enexpr quo_name enquos
-#' @importFrom rlang UQ UQS .data :=
-NULL
-
-# Reexport most commonly used functions from the tidyverse ----------------
-
-#' Pipe operator
-#'
-#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
-#'
-#' @name %>%
-#' @rdname pipe
-#' @keywords internal
-#' @export
-#' @importFrom magrittr %>%
-#' @usage lhs \%>\% rhs
-NULL
-
-# Main verbs
 #' @importFrom dplyr filter mutate select arrange summarize summarise desc
 NULL
 #' @export
@@ -72,6 +41,8 @@ dplyr::count
 #' @export
 dplyr::add_count
 
+# tidyselect --------------------------------------------------------------
+
 # Unleash the power of dplyr::select(). See ?tidyselect::select_helpers
 #' @importFrom tidyselect starts_with ends_with contains matches num_range
 #' @importFrom tidyselect one_of everything last_col 
@@ -93,8 +64,9 @@ tidyselect::everything
 #' @export
 tidyselect::last_col
 
-# Handle large datasets; print more info than dataframes and nicer
-#' @importFrom tibble tibble tribble as_tibble
+# tibble ------------------------------------------------------------------
+
+#' @importFrom tibble as_tibble tibble tribble
 NULL
 #' @export
 tibble::tibble
@@ -103,3 +75,7 @@ tibble::tribble
 #' @export
 tibble::as_tibble
 
+# Other -------------------------------------------------------------------
+
+# rlang: See utils-tidy-eval.R
+# magrittr: See utils-pipe.R

R/aaa-utils-pipe.R

@@ -0,0 +1,11 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+NULL

R/aaa-utils-tidy-eval.R

@@ -0,0 +1,45 @@
+#' Tidy eval helpers
+#'
+#' @description
+#'
+#' * \code{\link[rlang]{sym}()} creates a symbol from a string and
+#'   \code{\link[rlang]{syms}()} creates a list of symbols from a
+#'   character vector.
+#'
+#' * \code{\link[rlang]{expr}()} and \code{\link[rlang]{quo}()} quote
+#'   one expression. `quo()` wraps the quoted expression in a quosure.
+#'
+#'   The plural variants [rlang::exprs()] and
+#'   \code{\link[rlang]{quos}()} return a list of quoted expressions or
+#'   quosures.
+#'
+#' * \code{\link[rlang]{enexpr}()} and \code{\link[rlang]{enquo}()}
+#'   capture the expression supplied as argument by the user of the
+#'   current function (`enquo()` wraps this expression in a quosure).
+#'
+#'   \code{\link[rlang]{enexprs}()} and \code{\link[rlang]{enquos}()}
+#'   capture multiple expressions supplied as arguments, including
+#'   `...`.
+#'
+#' `exprs()` is not exported to avoid conflicts with `Biobase::exprs()`,
+#' therefore one should always use `rlang::exprs()`.
+#'
+#' To learn more about tidy eval and how to use these tools, visit
+#' <http://rlang.r-lib.org> and the [Metaprogramming
+#' section](https://adv-r.hadley.nz/introduction-16.html) of [Advanced
+#' R](https://adv-r.hadley.nz).
+#'
+#' @md
+#' @name     tidyeval
+#' @keywords internal
+#' @importFrom rlang quo quos enquo enquos quo_name sym ensym syms
+#'                   ensyms expr exprs enexpr enexprs .data
+#' @aliases  quo quos enquo enquos quo_name
+#'           sym ensym syms ensyms
+#'           expr exprs enexpr enexprs
+#'           .data
+#' @export   quo quos enquo enquos quo_name
+#' @export   sym ensym syms ensyms
+#' @export   expr enexpr enexprs
+#' @export   .data
+NULL

R/add_status_tree.R

@@ -1,3 +1,7 @@
+#' @importFrom tibble tribble
+#' @export
+tibble::tribble
+
 #' Add column `status_tree` based on the status of all stems of each tree.
 #'
 #' @template x_fgeo

R/add_subquad.R

@@ -117,7 +117,7 @@ add_subquad <- function(df,
 #' @return A modified version of the input.
 #' 
 #' @examples
-#' first_subquad_11 <- tibble::tibble(subquadrat = c("11", "12", "22"))
+#' first_subquad_11 <- tibble(subquadrat = c("11", "12", "22"))
 #' first_subquad_11
 #'
 #' first_subquad_01 <- recode_subquad(first_subquad_11, offset = -1)

R/from_var_to_var.R

@@ -105,7 +105,7 @@ index_to_rowcol <- function(index, gridsize, plotdim) {
 #' @export
 gxgy_to_index <- function(gx, gy, gridsize, plotdim) {
   if (missing(plotdim)) {
-    plotdim <- guess_plotdim(tibble::tibble(gx = gx, gy = gy))
+    plotdim <- guess_plotdim(tibble(gx = gx, gy = gy))
   }
 
   badgxgy <- (gx < 0 | gy < 0 | gx >= plotdim[1] | gy >= plotdim[2] |
@@ -123,7 +123,7 @@ gxgy_to_index <- function(gx, gy, gridsize, plotdim) {
 #' @export
 gxgy_to_lxly <- function(gx, gy, gridsize, plotdim) {
   if (missing(plotdim)) {
-    plotdim <- guess_plotdim(tibble::tibble(gx, gy))
+    plotdim <- guess_plotdim(tibble(gx, gy))
   }
 
   rc <- gxgy_to_rowcol(gx, gy, gridsize, plotdim) - 1
@@ -147,7 +147,7 @@ gxgy_to_qxqy <- function(gx, gy, gridsize, plotdim) {
 #' @export
 gxgy_to_rowcol <- function(gx, gy, gridsize, plotdim) {
   if (missing(plotdim)) {
-    plotdim <- guess_plotdim(tibble::tibble(gx, gy))
+    plotdim <- guess_plotdim(tibble(gx, gy))
   }
 
   index <- gxgy_to_index(gx, gy, gridsize, plotdim)
@@ -158,7 +158,7 @@ gxgy_to_rowcol <- function(gx, gy, gridsize, plotdim) {
 #' @export
 gxgy_to_hectindex <- function(gx, gy, plotdim) {
   if (missing(plotdim)) {
-    plotdim <- guess_plotdim(tibble::tibble(gx = gx, gy = gy))
+    plotdim <- guess_plotdim(tibble(gx = gx, gy = gy))
   }
 
   if (at_or_beyond_edge(gx, gy, plotdim)) {

R/nms_manipulate_names.R

@@ -56,7 +56,7 @@ nms_try_rename <- function(x, want, try) {
 #' * `nms_restore()` Returns the object `x` with original (restored) names.
 #'
 #' @examples
-#' cns <- tibble::tibble(CensusID = 1, status = "A")
+#' cns <- tibble(CensusID = 1, status = "A")
 #' original <- cns
 #' original
 #'

R/read_fgeo.R

@@ -44,7 +44,7 @@ read_delim_ <- function(delim, file, col_types, na, ...) {
 #'
 #' @seealso [readr::read_delim()], [type_vft()], [type_taxa()].
 #'
-#' @return A dataframe (or tibble).
+#' @return A dataframe (or [tibble][tibble::tibble-package]).
 #'
 #' @examples
 #' library(fgeo.x)

R/type_ensure.R

@@ -10,7 +10,7 @@
 #'   of type `type`.
 #'
 #' @examples
-#' dfm <- tibble::tibble(
+#' dfm <- tibble(
 #'   w = c(NA, 1, 2),
 #'   x = 1:3, 
 #'   y = as.character(1:3), 

cran-comments.md

@@ -0,0 +1,38 @@
+## Test environments
+
+* local windows 10 x64, R 3.5.2
+* ubuntu 14.04 (on travis-ci), R 3.5.1
+* win-builder (devel and release)
+
+## R CMD check results
+
+0 errors | 0 warnings | 3 notes
+Platform:	Ubuntu Linux 16.04 LTS, R-release, GCC
+Build ID:	fgeo.tool_1.0.0.tar.gz-0f72e41e51a84fcabc6c05c80881c26d
+* New submission
+* Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’
+* Strong dependencies not in mainstream repositories: fgeo.x
+
+0 errors | 3 warnings | 0 notes
+Platform:	Fedora Linux, R-devel, clang, gfortran
+Build ID:	fgeo.tool_1.0.0.tar.gz-0714fa14002648d29d3d6799b2295e7f
+* New submission
+* Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’
+* Strong dependencies not in mainstream repositories: fgeo.x
+
+0 errors | 3 warnings | 0 notes
+Platform:	Windows Server 2008 R2 SP1, R-devel, 32/64 bit
+Build ID:	fgeo.tool_1.0.0.tar.gz-f58d4077e55b47c9a6c7cf738664c1f4
+* New submission
+* Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’
+* Strong dependencies not in mainstream repositories: fgeo.x
+
+0 errors | 3 warnings | 0 notes
+using R Under development (unstable) (2019-01-07 r75958)
+* New submission
+* Unknown, possibly mis-spelled, fields in DESCRIPTION: 'Remotes'
+* Strong dependencies not in mainstream repositories: fgeo.x
+
+## Downstream dependencies
+
+There are currently no downstream dependencies for this package.