From 0b419c94910d7ac1d5717f7861b35cc25972117e Mon Sep 17 00:00:00 2001 From: Mauro Lepore Date: Mon, 28 Jan 2019 15:06:45 -0600 Subject: [PATCH] Release (#26) * Rename first argument to meet tidyverse principles * Prepare next release * Increment version number --- DESCRIPTION | 2 +- NEWS.md | 6 +- R/download_data.R | 10 +- README.Rmd | 4 +- README.md | 4 +- docs/CODE_OF_CONDUCT.html | 2 +- docs/CONTRIBUTING.html | 2 +- docs/ISSUE_TEMPLATE.html | 2 +- docs/LICENSE.html | 2 +- docs/README.knit.html | 333 ++++++++++++++++++++++++++++++++++++++ docs/SUPPORT.html | 2 +- docs/authors.html | 2 +- docs/index.html | 6 +- docs/news/index.html | 16 +- inst/WORDLIST | 5 + man/download_data.Rd | 6 +- 16 files changed, 377 insertions(+), 27 deletions(-) create mode 100644 docs/README.knit.html diff --git a/DESCRIPTION b/DESCRIPTION index d3aeddd..b261ae5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: fgeo.x Title: Access Small ForestGEO Datasets For Examples -Version: 1.0.1.9000 +Version: 1.1.0 Authors@R: c(person(given = "Mauro", family = "Lepore", diff --git a/NEWS.md b/NEWS.md index 43f6df6..6baf8aa 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,11 @@ * Work in progress. -# fgeo.x 1.0.1 (GitHub release) +# fgeo.x 1.1.0 (GithHub release) + +* First argument of most visible functions are now named following tidyverse principles () + +# fgeo.x 1.0.1 (GitHub and drat release) * Review documentation. diff --git a/R/download_data.R b/R/download_data.R index bd382d8..f89e954 100644 --- a/R/download_data.R +++ b/R/download_data.R @@ -1,7 +1,7 @@ #' Access data stored online. #' -#' @param .data A string giving the name of the dataset to download. The name of -#' any dataset listed [here]( +#' @param x A string giving the name of the dataset to download. The name +#' of any dataset listed [here]( #' https://github.com/forestgeo/fgeo.data/tree/master/data) (without the #' extension). #' @@ -14,14 +14,14 @@ #' } #' @family datasets #' @export -download_data <- function(.data) { +download_data <- function(x) { tmp <- tempfile() - utils::download.file(data_url(.data), tmp) + utils::download.file(data_url(x), tmp) e <- new.env() load(tmp, envir = e) - e[[.data]] + e[[x]] } data_url <- function(x) { diff --git a/README.Rmd b/README.Rmd index 7c8c7fe..ae97b23 100644 --- a/README.Rmd +++ b/README.Rmd @@ -26,8 +26,8 @@ Access small example datasets from [Luquillo](https://forestgeo.si.edu/sites/nor Install the latest stable version of **fgeo.x** with: ```R -# install.packages("devtools") -devtools::install_github("forestgeo/fgeo.x@*release") +these_repos <- c(getOption("repos"), "https://forestgeo.github.io/drat") +install.packages("fgeo.x", repos = these_repos) ``` Install the development version of **fgeo.x** with: diff --git a/README.md b/README.md index ec70912..bec8ef8 100644 --- a/README.md +++ b/README.md @@ -18,8 +18,8 @@ ForestGEO site in Puerto Rico. Install the latest stable version of **fgeo.x** with: ``` r -# install.packages("devtools") -devtools::install_github("forestgeo/fgeo.x@*release") +these_repos <- c(getOption("repos"), "https://forestgeo.github.io/drat") +install.packages("fgeo.x", repos = these_repos) ``` Install the development version of **fgeo.x** with: diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index ed24d25..83d3e55 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index 95f2aaf..5c6f1da 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index 9750769..dc1a83f 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 0d7c34b..068fae7 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/README.knit.html b/docs/README.knit.html new file mode 100644 index 0000000..99bd48a --- /dev/null +++ b/docs/README.knit.html @@ -0,0 +1,333 @@ + + + + + + + + + Small ForestGEO datasets for examples • fgeo.x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Small ForestGEO datasets for examples

+
+ + +
+

output: github_document editor_options: chunk_output_type: console —

+
+ +

lifecycle Travis build status

+

Access small example datasets from Luquillo, a ForestGEO site in Puerto Rico.

+
+

+Installation

+

Install the latest stable version of fgeo.x with:

+
these_repos <- c(getOption("repos"), "https://forestgeo.github.io/drat")
+install.packages("fgeo.x", repos = these_repos)
+

Install the development version of fgeo.x with:

+ +

Or install all fgeo packages in one step.

+
+
+

+Example

+
library(fgeo.x)
+

Some datasets available in fgeo.x:

+
str(elevation)
+#> List of 4
+#>  $ col :Classes 'tbl_df', 'tbl' and 'data.frame':    6565 obs. of  3 variables:
+#>   ..$ x   : int [1:6565] 0 0 0 0 0 0 0 0 0 0 ...
+#>   ..$ y   : int [1:6565] 0 5 10 15 20 25 30 35 40 45 ...
+#>   ..$ elev: num [1:6565] 364 364 363 363 363 ...
+#>  $ mat : num [1:101, 1:65] 364 364 363 363 363 ...
+#>  $ xdim: int 320
+#>  $ ydim: int 500
+
+str(habitat)
+#> Classes 'fgeo_habitat', 'tbl_df', 'tbl' and 'data.frame':    400 obs. of  3 variables:
+#>  $ gx      : num  0 0 0 0 0 0 0 0 0 0 ...
+#>  $ gy      : num  0 20 40 60 80 100 120 140 160 180 ...
+#>  $ habitats: int  1 1 1 1 1 1 1 1 1 1 ...
+
+str(tree5)
+#> Classes 'tbl_df', 'tbl' and 'data.frame':    30 obs. of  19 variables:
+#>  $ treeID   : int  7624 8055 19930 23746 31702 35355 35891 39705 50184 57380 ...
+#>  $ stemID   : int  160987 10036 117849 29677 39793 44026 44634 48888 60798 155867 ...
+#>  $ tag      : chr  "108958" "109482" "123493" "14473" ...
+#>  $ StemTag  : chr  "175325" "109482" "165576" "14473" ...
+#>  $ sp       : chr  "TRIPAL" "CECSCH" "CASARB" "PREMON" ...
+#>  $ quadrat  : chr  "722" "522" "425" "617" ...
+#>  $ gx       : num  138.7 94.8 61.3 100.3 53.8 ...
+#>  $ gy       : num  425.3 424.4 495.7 328 73.8 ...
+#>  $ MeasureID: int  486675 468874 471979 442571 447307 449169 434266 451067 437645 459427 ...
+#>  $ CensusID : int  5 5 5 5 5 5 5 5 5 5 ...
+#>  $ dbh      : num  10.9 165 23.6 170 67 50 269 67 240 16.6 ...
+#>  $ pom      : chr  "1.3" "1.3" "1.3" "1.3" ...
+#>  $ hom      : num  1.3 1.3 1.3 1.32 1.37 1.4 1.26 1.5 1.3 1.3 ...
+#>  $ ExactDate: Date, format: "2012-02-01" "2012-01-30" ...
+#>  $ DFstatus : chr  "alive" "alive" "alive" "alive" ...
+#>  $ codes    : chr  "SPROUT;A" "MAIN;A" "SPROUT;A" "MAIN;A" ...
+#>  $ nostems  : num  2 1 2 1 1 1 1 5 1 3 ...
+#>  $ status   : chr  "A" "A" "A" "A" ...
+#>  $ date     : num  19024 19022 19051 18967 18821 ...
+
+str(stem5)
+#> Classes 'tbl_df', 'tbl' and 'data.frame':    30 obs. of  19 variables:
+#>  $ treeID   : int  4832 9689 23686 23903 24526 24978 25534 30954 32644 34407 ...
+#>  $ stemID   : int  5905 12178 29616 29911 30750 31380 32193 38949 40902 42945 ...
+#>  $ tag      : chr  "10554" "111528" "14406" "14637" ...
+#>  $ StemTag  : chr  "10554" "111528" "14406" "14637" ...
+#>  $ sp       : chr  "MANBID" "CORBOR" "PREMON" "PREMON" ...
+#>  $ quadrat  : chr  "212" "1524" "417" "1017" ...
+#>  $ gx       : num  30.8 289 69 193.7 194.2 ...
+#>  $ gy       : num  235 465 335 334 359 ...
+#>  $ MeasureID: int  440357 469305 442528 442708 443140 443418 435148 446883 447786 435787 ...
+#>  $ CensusID : int  5 5 5 5 5 5 5 5 5 5 ...
+#>  $ dbh      : num  148 NA 154 195 360 185 328 15.7 60 124 ...
+#>  $ pom      : chr  "1.5" NA "1.3" "1.2" ...
+#>  $ hom      : num  1.48 NA 1.3 1.2 1.4 1.4 1.5 1.3 1.29 1.35 ...
+#>  $ ExactDate: Date, format: "2011-09-30" "2012-02-17" ...
+#>  $ DFstatus : chr  "alive" "stem dead" "alive" "alive" ...
+#>  $ codes    : chr  "MAIN;A" "MAIN;A;LS;DP;ST" "MAIN;A" "MAIN;A" ...
+#>  $ countPOM : num  1 1 1 1 1 1 1 1 1 1 ...
+#>  $ status   : chr  "A" "G" "A" "A" ...
+#>  $ date     : num  18900 19040 18966 19010 19009 ...
+
+str(vft_4quad)
+#> Classes 'tbl_df', 'tbl' and 'data.frame':    500 obs. of  32 variables:
+#>  $ DBHID           : int  480614 467103 466804 388646 481054 388453 411794 411798 411761 388160 ...
+#>  $ PlotName        : chr  "luquillo" "luquillo" "luquillo" "luquillo" ...
+#>  $ PlotID          : int  1 1 1 1 1 1 1 1 1 1 ...
+#>  $ Family          : chr  "Fabaceae-mimosoideae" "Salicaceae" "Meliaceae" "Salicaceae" ...
+#>  $ Genus           : chr  "Inga" "Casearia" "Guarea" "Casearia" ...
+#>  $ SpeciesName     : chr  "laurina" "sylvestris" "guidonia" "arborea" ...
+#>  $ Mnemonic        : chr  "INGLAU" "CASSYL" "GUAGUI" "CASARB" ...
+#>  $ Subspecies      : chr  NA NA NA NA ...
+#>  $ SpeciesID       : int  128 73 117 70 70 185 184 117 184 70 ...
+#>  $ SubspeciesID    : chr  NA NA NA NA ...
+#>  $ QuadratName     : chr  "721" "621" "721" "622" ...
+#>  $ QuadratID       : int  327 326 327 342 343 342 343 343 342 343 ...
+#>  $ PX              : num  126 115 127 110 126 ...
+#>  $ PY              : num  413 405 412 431 420 ...
+#>  $ QX              : num  5.75 14.59 6.64 9.9 5.66 ...
+#>  $ QY              : num  13.1 4.9 11.9 10.7 0.5 ...
+#>  $ TreeID          : int  108604 2092 871 8811 109474 8475 109467 109471 109438 7843 ...
+#>  $ Tag             : chr  "154809" "102365" "100975" "110415" ...
+#>  $ StemID          : int  143326 2555 114203 11057 144288 115993 144281 144285 144248 115875 ...
+#>  $ StemNumber      : int  0 0 0 0 0 0 0 0 0 0 ...
+#>  $ StemTag         : int  154809 102365 154808 110415 156286 156210 156268 156281 156223 156272 ...
+#>  $ PrimaryStem     : chr  NA NA NA NA ...
+#>  $ CensusID        : int  5 5 5 4 5 4 4 4 4 4 ...
+#>  $ PlotCensusNumber: int  5 5 5 4 5 4 4 4 4 4 ...
+#>  $ DBH             : num  30.8 74 22.3 NA 33.8 NA NA 16.5 NA 44.6 ...
+#>  $ HOM             : num  1.3 1.3 1.3 NA 1.3 NA NA 1.3 NA 1.3 ...
+#>  $ ExactDate       : Date, format: "2012-01-31" "2012-01-30" ...
+#>  $ Date            : int  19023 19022 19023 17122 19024 17125 17126 17126 17125 17126 ...
+#>  $ ListOfTSM       : chr  "MAIN;A" "MAIN;A" "SPROUT;A" "MAIN;A;LS;B" ...
+#>  $ HighHOM         : int  1 1 1 1 1 1 1 1 1 1 ...
+#>  $ LargeStem       : chr  NA NA NA NA ...
+#>  $ Status          : chr  "alive" "alive" "alive" "broken below" ...
+

Some other datasets that install with fgeo.x:

+
example_path()
+#>  [1] "csv"           "mixed_files"   "rdata"         "rdata_one"    
+#>  [5] "rds"           "taxa.csv"      "tsv"           "vft_4quad.csv"
+#>  [9] "view"          "weird"         "xl"
+
+dir(example_path("view"))
+#> [1] "taxa.csv"      "vft_4quad.csv"
+
+str(read.csv(example_path("vft_4quad.csv")))
+#> 'data.frame':    500 obs. of  32 variables:
+#>  $ DBHID           : int  385164 385261 384600 608789 388579 384626 410958 385102 353163 481018 ...
+#>  $ PlotName        : Factor w/ 1 level "luquillo": 1 1 1 1 1 1 1 1 1 1 ...
+#>  $ PlotID          : int  1 1 1 1 1 1 1 1 1 1 ...
+#>  $ Family          : Factor w/ 20 levels "Araliaceae","Arecaceae",..: 17 20 17 17 2 1 17 15 2 19 ...
+#>  $ Genus           : Factor w/ 30 levels "Alchornea","Alchorneopsis",..: 25 6 25 25 24 27 25 23 24 5 ...
+#>  $ SpeciesName     : Factor w/ 36 levels " hirsuta","acuminata",..: 9 29 9 7 2 23 9 14 2 4 ...
+#>  $ Mnemonic        : Factor w/ 37 levels "ALCFLO","ALCLAT",..: 32 7 32 31 30 34 32 28 30 5 ...
+#>  $ Subspecies      : logi  NA NA NA NA NA NA ...
+#>  $ SpeciesID       : int  185 74 185 184 182 196 185 174 182 70 ...
+#>  $ SubspeciesID    : logi  NA NA NA NA NA NA ...
+#>  $ QuadratName     : int  621 621 721 621 622 721 721 621 722 622 ...
+#>  $ QuadratID       : int  326 326 327 326 342 327 327 326 343 342 ...
+#>  $ PX              : num  119 109 133 117 113 ...
+#>  $ PY              : num  414 411 416 412 424 ...
+#>  $ QX              : num  19 9.4 12.9 16.6 12.6 ...
+#>  $ QY              : num  13.64 10.52 15.9 11.58 3.62 ...
+#>  $ TreeID          : int  1990 2177 797 124957 84880 862 108712 1848 26708 109413 ...
+#>  $ Tag             : int  102244 102466 100889 175166 110271 100964 154949 102088 17576 156180 ...
+#>  $ StemID          : int  2419 114525 981 163153 103483 1068 143443 2248 33769 144222 ...
+#>  $ StemNumber      : int  0 0 0 0 0 0 0 0 0 0 ...
+#>  $ StemTag         : int  102244 154442 100888 175166 110271 100964 154949 102088 17576 156180 ...
+#>  $ PrimaryStem     : logi  NA NA NA NA NA NA ...
+#>  $ CensusID        : int  4 4 4 6 4 4 4 4 4 5 ...
+#>  $ PlotCensusNumber: int  4 4 4 6 4 4 4 4 4 5 ...
+#>  $ DBH             : num  NA NA NA 34.6 171 NA NA NA 163 36.2 ...
+#>  $ HOM             : num  NA NA NA 1.3 1.3 NA NA NA 1.35 1.3 ...
+#>  $ ExactDate       : Factor w/ 14 levels "2006-11-16","2006-11-17",..: 2 2 4 10 2 4 5 1 3 7 ...
+#>  $ Date            : int  17122 17122 17126 20662 17122 17126 17127 17121 17125 19023 ...
+#>  $ ListOfTSM       : Factor w/ 16 levels "MAIN;A","MAIN;A;C",..: 8 14 14 1 1 8 8 8 1 1 ...
+#>  $ HighHOM         : int  1 1 1 1 1 1 1 1 1 1 ...
+#>  $ LargeStem       : logi  NA NA NA NA NA NA ...
+#>  $ Status          : Factor w/ 4 levels "alive","broken below",..: 3 4 4 1 1 3 3 3 1 1 ...
+

Download data from fgeo.data:

+ +

Get started with fgeo

+
+
+

+Information

+ +
+
+ + +
+ +
+ + + +
+ + + + + + diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html index d22d4ad..ffc1144 100644 --- a/docs/SUPPORT.html +++ b/docs/SUPPORT.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/authors.html b/docs/authors.html index cd3020b..68a7bd9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 diff --git a/docs/index.html b/docs/index.html index ebb4c3e..403c758 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 @@ -91,8 +91,8 @@

Installation

Install the latest stable version of fgeo.x with:

- +
these_repos <- c(getOption("repos"), "https://forestgeo.github.io/drat")
+install.packages("fgeo.x", repos = these_repos)

Install the development version of fgeo.x with:

diff --git a/docs/news/index.html b/docs/news/index.html index c63b009..cf9eaf2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ fgeo.x - 1.0.1.9000 + 1.1.0 @@ -112,9 +112,16 @@

Changelog

Source: NEWS.md -
+

-fgeo.x 1.0.1 (GitHub release)

+fgeo.x 1.1.0 (GithHub release) +
    +
  • First argument of most visible functions are now named following tidyverse principles (http://bit.ly/2TfDcfX)
    • +
+
+
+

+fgeo.x 1.0.1 (GitHub and drat release)

  • Review documentation.
@@ -132,7 +139,8 @@

Contents

diff --git a/inst/WORDLIST b/inst/WORDLIST index bdacdaf..4ed567f 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -5,8 +5,13 @@ fgeo forestgeo ForestGEO funder +GithHub +http https lifecycle luquillo Luquillo +ly si +TfDcfX +tidyverse diff --git a/man/download_data.Rd b/man/download_data.Rd index 4bbf82a..4f8ca6a 100644 --- a/man/download_data.Rd +++ b/man/download_data.Rd @@ -4,11 +4,11 @@ \alias{download_data} \title{Access data stored online.} \usage{ -download_data(.data) +download_data(x) } \arguments{ -\item{.data}{A string giving the name of the dataset to download. The name of -any dataset listed \href{https://github.com/forestgeo/fgeo.data/tree/master/data}{here} (without the +\item{x}{A string giving the name of the dataset to download. The name +of any dataset listed \href{https://github.com/forestgeo/fgeo.data/tree/master/data}{here} (without the extension).} } \value{