Update (#75)

* Examples now run under CRAN's time limit. Also tidy package in general. * dplyr::n() is now imported to avoid `Error in n() : could not find function "n"` ``` Calls: abundance ... .summary -> summarize -> summarise.tbl_df -> summarise_impl ``` * Increment version number
forestgeo · Feb 1, 2019 · 0f405dd · 0f405dd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fgeo.analyze
 Title: Analyze ForestGEO Data
-Version: 1.1.2.9000
+Version: 1.1.3
 Authors@R: 
     c(person(given = "Mauro",
              family = "Lepore",

diff --git a/NAMESPACE b/NAMESPACE
@@ -33,6 +33,7 @@ importFrom(dplyr,count)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,11 @@
 
 * Work in progress.
 
+# fgeo.analyze 1.1.3 (GitHub and drat release)
+
+* Meet CRAN standards.
+* `dplyr::n()` is now imported to avoid [`error could not find function "n"`](https://dplyr.tidyverse.org/news/index.html#breaking-changes).
+
 # fgeo.analyze 1.1.2 (GitHub and drat release)
 
 * Use tidy versions.

diff --git a/R/fgeo_habitat.R b/R/fgeo_habitat.R
@@ -29,27 +29,17 @@
 #'   gridsize = 20, n = 4
 #' )
 #'
-#' # Or
-#' elevation_df <- fgeo.x::elevation$col
-#' habitats <- fgeo_habitat(
-#'   elevation_df,
-#'   gridsize = 20, n = 4,
-#'   xdim = 320, ydim = 500
-#' )
-#'
 #' str(habitats)
+#'
 #' \dontrun{
-#' fgeo_plot_is_installed <- requireNamespace("fgeo.plot", quietly = TRUE)
-#' if (fgeo_plot_is_installed) {
-#'   library(fgeo.plot)
+#' assert_is_installed("fgeo.plot")
+#' library(fgeo.plot)
 #'
-#'   autoplot(habitats)
-#' }
+#' autoplot(habitats)
 #' }
 #'
 #' # Habitat data is useful for calculating species-habitat associations
 #' census <- fgeo.x::tree6_3species
-#'
 #' as_tibble(
 #'   tt_test(census, habitats)
 #' )

diff --git a/R/imports.R b/R/imports.R
@@ -1,5 +1,5 @@
 #' @importFrom dplyr group_by ungroup filter select mutate summarize arrange
-#' @importFrom dplyr count
+#' @importFrom dplyr count n
 #' @importFrom fgeo.tool check_crucial_names is_duplicated is_multiple
 #' @importFrom fgeo.tool rename_matches
 #' @importFrom glue glue glue_collapse
@@ -30,4 +30,4 @@ fgeo.tool::assert_is_installed
 NULL
 
 # Avoid CMD check warnings
-utils::globalVariables(c(".data", ".", "n"))
+utils::globalVariables(c(".data", "."))
diff --git a/R/tt_test.R b/R/tt_test.R
@@ -91,10 +91,6 @@
 #'
 #' some_species <- c("CASARB", "PREMON")
 #' result <- tt_test(census, habitat, sp = some_species)
-#' result
-#'
-#' as_tibble(result)
-#'
 #' summary(result)
 #' @family habitat functions
 #' @export

diff --git a/README.md b/README.md
@@ -484,6 +484,7 @@ habitat <- fgeo_habitat(elevation, gridsize = 20, n = 4)
 tt_test_result <- tt_test(pick, habitat)
 #> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
 #> Using `gridsize = 20`. To change this value see `?tt_test()`.
+#> Warning: Is `census` a tree table (not a stem table)? See `?tt_test()`.
 
 # A list or matrices
 tt_test_result

diff --git a/cran-comments.md b/cran-comments.md
@@ -6,91 +6,32 @@
 
 ## R CMD check results
 
-1.1.2
-
-WARNING
-New submission
-Strong dependencies not in mainstream repositories:
-  fgeo.tool
-Suggests or Enhances not in mainstream repositories:
-  fgeo.x
-Availability using Additional_repositories specification:
-  fgeo.tool   yes   https://forestgeo.github.io/drat/
-  fgeo.x      yes   https://forestgeo.github.io/drat/
-
-NOTE
-Examples with CPU or elapsed time > 5s
-              user system elapsed
-tt_test      2.000  0.004   5.274
-fgeo_habitat 1.896  0.060   5.320
-
-
-ERROR
-Running examples in 'fgeo.analyze-Ex.R' failed
-The error most likely occurred in:
-```R
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: abundance
-> ### Title: Abundance and basal area, optionally by groups.
-> ### Aliases: abundance basal_area
-> 
-> ### ** Examples
-> 
-> library(fgeo.tool)
-
-Attaching package: 'fgeo.tool'
-
-The following object is masked from 'package:stats':
-
-    filter
-
-> 
-> # abundance() -------------------------------------------------------------
-> 
-> abundance(data.frame(1))
-Error in n() : could not find function "n"
-Calls: abundance ... .summary -> summarize -> summarise.tbl_df -> summarise_impl
-Execution halted
-** running examples for arch 'x64' ... ERROR
-Running examples in 'fgeo.analyze-Ex.R' failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: abundance
-> ### Title: Abundance and basal area, optionally by groups.
-> ### Aliases: abundance basal_area
-> 
-> ### ** Examples
-> 
-> library(fgeo.tool)
-
-Attaching package: 'fgeo.tool'
-
-The following object is masked from 'package:stats':
-
-    filter
-
-> 
-> # abundance() -------------------------------------------------------------
-> 
-> abundance(data.frame(1))
-Error in n() : could not find function "n"
-Calls: abundance ... .summary -> summarize -> summarise.tbl_df -> summarise_impl
-Execution halted
-* checking for unstated dependencies in 'tests' ... OK
-* checking tests ...
-** running tests for arch 'i386' ... [21s] OK
-  Running 'spelling.R' [0s]
-  Running 'testthat.R' [20s]
-** running tests for arch 'x64' ... [23s] OK
-  Running 'spelling.R' [0s]
-  Running 'testthat.R' [22s]
-* checking PDF version of manual ... OK
-* DONE
-Status: 2 ERRORs, 1 WARNING
-```
-
-
+* using R version 3.4.4 (2018-03-15)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* this is package ‘fgeo.analyze’ version ‘1.1.3’
+
+Status: 2 NOTEs
+* NOTE 1 raises if the package is built using R v3.5. (<https://ropensci.github.io/dev_guide/building.html#authorship>).
+* NOTE 2 is safe to ignore.
+
+NOTE 1
+* Authors@R field gives persons with non-standard roles:
+* Gabriel Arellano [aut, rev]: rev
+* Suzanne Lao [aut, rev]: rev
+* KangMin Ngo [rev]: rev
+* Haley Overstreet [rev]: rev
+* Sabrina Russo [aut, rev]: rev
+* Daniel Zuleta [aut, rev]: rev
+
+NOTE 2
+* New submission
+* Strong dependencies not in mainstream repositories:
+* fgeo.tool
+* Suggests or Enhances not in mainstream repositories:
+* fgeo.x
+* Availability using Additional_repositories specification:
+* fgeo.tool yes https://forestgeo.github.io/drat/
+* fgeo.x yes https://forestgeo.github.io/drat/
 
 ## Downstream dependencies
 

diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/siteonly/tt_test.html b/docs/articles/siteonly/tt_test.html
diff --git a/docs/articles/siteonly/tt_test_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/siteonly/tt_test_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/siteonly/tt_test_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/siteonly/tt_test_files/figure-html/unnamed-chunk-8-1.png
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/abundance.html b/docs/reference/abundance.html
diff --git a/docs/reference/abundance_byyr.html b/docs/reference/abundance_byyr.html
diff --git a/docs/reference/fgeo.analyze-package.html b/docs/reference/fgeo.analyze-package.html