README.md

fgeo.scbi

Lifecycle:
experimental Travis build
status Coveralls test
coverage CRAN
status

The goal of fgeo.scbi is to provide easy access to data from the Smithsonian Conservation Biology Institute (SCBI) ForestGEO plot. For now, this is an experimental package to test a new approach to sharing ForestGEO data.

Installation

# install.packages("devtools")
devtools::install_github("forestgeo/fgeo.scbi")

Example

Access data from dryad (https://doi.org/10.5061/dryad.6nc8c).

Access data from the public data portal on GitHub.

library(purrr)

github_path <- 
  "SCBI-ForestGEO/SCBI-ForestGEO-Data/tree_main_census/data/census-csv-files"

download_urls <- ghr::ghr_ls_download_url(github_path)
download_urls %>% 
  purrr::map(readr::read_csv) %>% 
  purrr::set_names(fs::path_file(download_urls))
#> $census3_coord_local_plot.csv
#> # A tibble: 55,295 x 9
#>    treeid stemid   tag stemtag quadratname    qx    qy    px    py
#>     <dbl>  <dbl> <dbl>   <dbl>       <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1      1      1 10079       1         104   3.7  13     3.7  73  
#>  2      2      2 10168       1         103  17.3  18.9  17.3  58.9
#>  3      3      3 10567       1         110   9    17.1   9   197. 
#>  4      4      4 12165       1         122  14.2   8.5  14.2 428. 
#>  5      5      5 12190       1         122   9.4  16.4   9.4 436. 
#>  6      6      6 12192       1         122   1.3  14     1.3 434  
#>  7      7      7 12212       1         123  17.8   7.1  17.8 447. 
#>  8      8      8 12261       1         125  18     3.7  18   484. 
#>  9      9      9 12456       1         130  18    17.8  18   598. 
#> 10     10     10 12551       1         132   5.6   7.7   5.6 628. 
#> # ... with 55,285 more rows
#> 
#> $scbi.full1.csv
#> # A tibble: 40,283 x 20
#>    treeID stemID   tag StemTag sp    quadrat    gx    gy DBHID CensusID
#>     <dbl>  <dbl> <dbl>   <dbl> <chr> <chr>   <dbl> <dbl> <dbl>    <dbl>
#>  1      1      1 10079       1 libe  0104     3.70  73       1        1
#>  2      2      2 10168       1 libe  0103    17.3   58.9     3        1
#>  3      3      3 10567       1 libe  0110     9    197.      5        1
#>  4      4      4 12165       1 nysy  0122    14.2  428.      7        1
#>  5      5      5 12190       1 havi  0122     9.40 436.      9        1
#>  6      6      6 12192       1 havi  0122     1.30 434      13        1
#>  7      7      7 12212       1 unk   0123    17.8  447.     15        1
#>  8      8      8 12261       1 libe  0125    18    484.     17        1
#>  9      9      9 12456       1 vipr  0130    18    598.     19        1
#> 10     10     10 12551       1 astr  0132     5.60 628.     22        1
#> # ... with 40,273 more rows, and 10 more variables: dbh <dbl>, pom <dbl>,
#> #   hom <dbl>, ExactDate <date>, DFstatus <chr>, codes <chr>,
#> #   nostems <dbl>, date <dbl>, status <chr>, agb <dbl>
#> 
#> $scbi.full2.csv
#> # A tibble: 40,283 x 20
#>    treeID stemID   tag StemTag sp    quadrat    gx    gy DBHID CensusID
#>     <dbl>  <dbl> <dbl>   <dbl> <chr> <chr>   <dbl> <dbl> <dbl>    <dbl>
#>  1      1      1 10079       1 libe  0104     3.70  73   41801        2
#>  2      2      2 10168       1 libe  0103    17.3   58.9 41723        2
#>  3      3      3 10567       1 libe  0110     9    197.  42501        2
#>  4      4      4 12165       1 nysy  0122    14.2  428.  42869        2
#>  5      5      5 12190       1 havi  0122     9.40 436.  42904        2
#>  6      6      6 12192       1 havi  0122     1.30 434   42909        2
#>  7      7  31200 12212       2 unk   0123    17.8  447.  42946        2
#>  8      8  31201 12261       2 libe  0125    18    484.  43023        2
#>  9      9  31202 12456       2 vipr  0130    18    598.  43249        2
#> 10     10     10 12551       1 astr  0132     5.60 628.  43346        2
#> # ... with 40,273 more rows, and 10 more variables: dbh <dbl>, pom <dbl>,
#> #   hom <dbl>, ExactDate <date>, DFstatus <chr>, codes <chr>,
#> #   nostems <dbl>, date <dbl>, status <chr>, agb <dbl>
#> 
#> $scbi.spptable.csv
#> # A tibble: 73 x 10
#>    sp    Latin Genus Species Family SpeciesID Authority IDLevel syn   subsp
#>    <chr> <chr> <chr> <chr>   <chr>      <dbl> <chr>     <chr>   <lgl> <lgl>
#>  1 acne  Acer~ Acer  negundo Sapin~         1 <NA>      species NA    NA   
#>  2 acpl  Acer~ Acer  platan~ Sapin~         2 <NA>      species NA    NA   
#>  3 acru  Acer~ Acer  rubrum  Sapin~         3 <NA>      species NA    NA   
#>  4 acsp  Acer~ Acer  sp      Sapin~         4 <NA>      Multip~ NA    NA   
#>  5 aial  Aila~ Aila~ altiss~ Simar~         5 <NA>      species NA    NA   
#>  6 amar  Amel~ Amel~ arborea Rosac~         6 <NA>      species NA    NA   
#>  7 astr  Asim~ Asim~ triloba Annon~         7 <NA>      species NA    NA   
#>  8 beth  Berb~ Berb~ thunbe~ Berbe~         8 <NA>      species NA    NA   
#>  9 caca  Carp~ Carp~ caroli~ Betul~         9 <NA>      species NA    NA   
#> 10 caco  Cary~ Carya cordif~ Jugla~        10 <NA>      species NA    NA   
#> # ... with 63 more rows
#> 
#> $scbi.stem1.csv
#> # A tibble: 55,295 x 20
#>    treeID stemID   tag StemTag sp    quadrat    gx    gy DBHID CensusID
#>     <dbl>  <dbl> <dbl>   <dbl> <chr> <chr>   <dbl> <dbl> <dbl>    <dbl>
#>  1      1      1 10079       1 libe  0104     3.70  73       1        1
#>  2      1  31194 10079       2 libe  0104     3.70  73       2        1
#>  3      2      2 10168       1 libe  0103    17.3   58.9     3        1
#>  4      2  31195 10168       2 libe  0103    17.3   58.9     4        1
#>  5      3      3 10567       1 libe  0110     9    197.      5        1
#>  6      3  31196 10567       2 libe  0110     9    197.      6        1
#>  7      3  40394 10567       3 libe  0110     9    197.     NA       NA
#>  8      4      4 12165       1 nysy  0122    14.2  428.      7        1
#>  9      4  31197 12165       2 nysy  0122    14.2  428.      8        1
#> 10      5      5 12190       1 havi  0122     9.40 436.      9        1
#> # ... with 55,285 more rows, and 10 more variables: dbh <dbl>, pom <dbl>,
#> #   hom <dbl>, ExactDate <date>, DFstatus <chr>, codes <chr>,
#> #   countPOM <dbl>, date <dbl>, status <chr>, agb <dbl>
#> 
#> $scbi.stem2.csv
#> # A tibble: 55,295 x 20
#>    treeID stemID   tag StemTag sp    quadrat    gx    gy DBHID CensusID
#>     <dbl>  <dbl> <dbl>   <dbl> <chr> <chr>   <dbl> <dbl> <dbl>    <dbl>
#>  1      1      1 10079       1 libe  0104     3.70  73   41801        2
#>  2      1  31194 10079       2 libe  0104     3.70  73   41802        2
#>  3      2      2 10168       1 libe  0103    17.3   58.9 41723        2
#>  4      2  31195 10168       2 libe  0103    17.3   58.9 41724        2
#>  5      3      3 10567       1 libe  0110     9    197.  42501        2
#>  6      3  31196 10567       2 libe  0110     9    197.  42502        2
#>  7      3  40394 10567       3 libe  0110     9    197.  80573        2
#>  8      4      4 12165       1 nysy  0122    14.2  428.  42869        2
#>  9      4  31197 12165       2 nysy  0122    14.2  428.  42870        2
#> 10      5      5 12190       1 havi  0122     9.40 436.  42904        2
#> # ... with 55,285 more rows, and 10 more variables: dbh <dbl>, pom <dbl>,
#> #   hom <dbl>, ExactDate <date>, DFstatus <chr>, codes <chr>,
#> #   countPOM <dbl>, date <dbl>, status <chr>, agb <dbl>


forestgeo/fgeo.scbi documentation built on May 31, 2019, 10:02 a.m.