Merge pull request #12 from CWWhitney/changes_v1.6

Changes v1.6
CWWhitney · Aug 6, 2019 · db815ef · db815ef
2 parents ccd5a6f + 0a360e9
commit db815ef
Show file tree

Hide file tree

Showing 88 changed files with 72 additions and 1,236 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,6 +3,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^cran-comments.md
-
+^revdep
 
 
diff --git a/R/FCs.R b/R/FCs.R
@@ -4,7 +4,7 @@
 #' @source Prance, G. T., W. Baleé, B. M. Boom, and R. L. Carneiro. “Quantitative Ethnobotany and the Case for Conservation in Amazonia.” Conservation Biology 1, no. 4 (1987): 296–310.
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, number of uses
+#' @keywords quantitative ethnobotany frequency citation
 #' 
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by 

diff --git a/R/FLs.R b/R/FLs.R
@@ -10,7 +10,7 @@
 #' @importFrom dplyr filter summarize select left_join group_by slice
 #' @importFrom assertthat validate_that see_if
 #' 
-#' @keywords ethnobotany, cultural value, use report, fidelity
+#' @keywords ethnobotany cultural value use report fidelity
 #'
 #' @examples
 #' 

diff --git a/R/NUs.R b/R/NUs.R
@@ -4,7 +4,7 @@
 #' @source Prance, G. T., W. Baleé, B. M. Boom, and R. L. Carneiro. “Quantitative Ethnobotany and the Case for Conservation in Amazonia.” Conservation Biology 1, no. 4 (1987): 296–310.
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, number of uses
+#' @keywords quantitative ethnobotany number of uses
 #'
 #' @importFrom stats aggregate
 #' @importFrom assertthat validate_that

diff --git a/R/RFCs.R b/R/RFCs.R
@@ -4,7 +4,7 @@
 #' @source Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <https://doi.org/10.1007/s12231-007-9004-5>
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, number of uses
+#' @keywords quantitative ethnobotany relative frequency citation
 #'
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by

diff --git a/R/RIs.R b/R/RIs.R
@@ -4,7 +4,7 @@
 #' @source Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <https://doi.org/10.1007/s12231-007-9004-5>
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, relative importance
+#' @keywords quantitative ethnobotany relative importance
 #'
 #' @importFrom magrittr %>%
 #' @importFrom stats aggregate

diff --git a/R/Radial_plot.R b/R/Radial_plot.R
@@ -4,7 +4,7 @@
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
 #' @param analysis is one of the quantitative ethnobotany functions from ethnobotanyR, i.e. ethnobotanyR::FCs.
-#' @keywords ethnobotany, cultural value, use report
+#' @keywords ethnobotany visualuzation radial bar plot
 #'
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by 

diff --git a/R/URs.R b/R/URs.R
@@ -4,7 +4,7 @@
 #' @source Prance, G. T., W. Baleé, B. M. Boom, and R. L. Carneiro. “Quantitative Ethnobotany and the Case for Conservation in Amazonia.” Conservation Biology 1, no. 4 (1987): 296–310.
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords ethnobotany, cultural value, use report
+#' @keywords ethnobotany quantitative cultural value use report
 #'
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by 

diff --git a/R/URsum.R b/R/URsum.R
@@ -4,7 +4,7 @@
 #' @source Prance, G. T., W. Baleé, B. M. Boom, and R. L. Carneiro. “Quantitative Ethnobotany and the Case for Conservation in Amazonia.” Conservation Biology 1, no. 4 (1987): 296–310.
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords ethnobotany, use report, quantitative ethnobotany
+#' @keywords ethnobotany use report quantitative ethnobotany
 #'
 #' @importFrom dplyr select
 #' @importFrom assertthat validate_that

diff --git a/R/UVs.R b/R/UVs.R
@@ -4,7 +4,7 @@
 #' @source Tardio, Javier, and Manuel Pardo-de-Santayana. “Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain)1.” Economic Botany 62, no. 1 (May 2008): 24–39. <https://doi.org/10.1007/s12231-007-9004-5>
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, cultural importance
+#' @keywords quantitative ethnobotany cultural importance use value
 #'
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by 

diff --git a/R/ethnoChord.R b/R/ethnoChord.R
@@ -16,7 +16,7 @@
 #' @importFrom assertthat see_if
 #' @importFrom cowplot plot_grid
 #' 
-#' @keywords ethnobotany, cultural value, use report
+#' @keywords quantitative ethnobotany cultural value use report chord diagram
 #'
 #' @examples
 #' 

diff --git a/R/ethnoChordUser.R b/R/ethnoChordUser.R
@@ -12,7 +12,7 @@
 #' @importFrom graphics strwidth
 #' @importFrom assertthat validate_that see_if
 #' 
-#' @keywords ethnobotany, cultural value, use report
+#' @keywords quantitative ethnobotany cultural value use report chord diagram
 #'
 #' @examples
 #' 

diff --git a/R/ethnobotanyChord.R b/R/ethnobotanyChord.R
@@ -15,7 +15,7 @@
 #' @importFrom assertthat validate_that
 #' @importFrom assertthat see_if
 #' 
-#' @keywords ethnobotany, cultural value, use report
+#' @keywords ethnobotany
 #'
 #' @examples
 #' 

diff --git a/R/simple_UVs.R b/R/simple_UVs.R
@@ -4,7 +4,8 @@
 #' @source Albuquerque, U. P., R. F. P. Lucena, J. M. Monteiro, A. T. N. Florentino, and C. F. C. B. R. Almeida. 2006. Evaluating Two Quantitative Ethnobotanical Techniques. Ethnobotany Research and Applications 4:51–60. <http://hdl.handle.net/10125/237>
 #' @param data is an ethnobotany data set with column 1 'informant' and 2 'sp_name' as row identifiers of informants and of species names respectively.
 #' The rest of the columns are the identified ethnobotany use categories. The data should be populated with counts of uses per person (should be 0 or 1 values).
-#' @keywords quantitative ethnobotany, cultural importance
+#' 
+#' @keywords quantitative ethnobotany cultural importance use value
 #'
 #' @importFrom magrittr %>%
 #' @importFrom dplyr filter summarize select left_join group_by 

diff --git a/cran-comments.md b/cran-comments.md
@@ -5,10 +5,12 @@ devtools::release()
 
 ## R CMD check results
 There were no ERRORs, WARNINGs or NOTEs
+I checked the package with `devtools::check()`
+All is well
 I checked spelling with `devtools::spell_check()`
 All is fine
 I checked R-hub with `devtools::check_rhub()`
-All is well
+All is great
 checked win-builder with `devtools::check_win_devel()`
 All is ok
 

diff --git a/man/FCs.Rd b/man/FCs.Rd
diff --git a/man/FLs.Rd b/man/FLs.Rd
diff --git a/man/NUs.Rd b/man/NUs.Rd
diff --git a/man/RFCs.Rd b/man/RFCs.Rd
diff --git a/man/RIs.Rd b/man/RIs.Rd
diff --git a/man/Radial_plot.Rd b/man/Radial_plot.Rd
diff --git a/man/URs.Rd b/man/URs.Rd
diff --git a/man/URsum.Rd b/man/URsum.Rd
diff --git a/man/UVs.Rd b/man/UVs.Rd
diff --git a/man/ethnoChord.Rd b/man/ethnoChord.Rd
diff --git a/man/ethnoChordUser.Rd b/man/ethnoChordUser.Rd
diff --git a/man/ethnobotanyChord.Rd b/man/ethnobotanyChord.Rd
diff --git a/man/simple_UVs.Rd b/man/simple_UVs.Rd
diff --git a/revdep/README.md b/revdep/README.md
diff --git a/revdep/checks.noindex/libraries.csv b/revdep/checks.noindex/libraries.csv
diff --git a/revdep/data.sqlite b/revdep/data.sqlite
diff --git a/revdep/failures.md b/revdep/failures.md
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/DESCRIPTION b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/DESCRIPTION
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/INDEX b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/INDEX
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/Rd.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/Rd.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/data.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/data.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/features.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/features.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/hsearch.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/hsearch.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/links.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/links.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/nsInfo.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/nsInfo.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/package.rds b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/Meta/package.rds
diff --git a/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/NAMESPACE b/revdep/library.noindex/ethnobotanyR/new/ethnobotanyR/NAMESPACE