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Import and manipulate ForestGEO data

lifecycle Coverage status CRAN status R-CMD-check Codecov test coverage R-CMD-check

fgeo.tool helps you to import and manipulate ForestGEO data.

Installation

Install the latest stable version of fgeo.tool from CRAN with:

install.packages("fgeo.tool")

Install the development version of fgeo.tool from GitHub with:

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

Or install all fgeo packages in one step.

Example

library(fgeo.tool)
#> 
#> Attaching package: 'fgeo.tool'
#> The following object is masked from 'package:stats':
#> 
#>     filter
# Helps access data for examples
library(fgeo.x)

example_path() allows you to access datasets stored in your R libraries.

example_path()
#>  [1] "csv"           "mixed_files"   "rdata"         "rdata_one"    
#>  [5] "rds"           "taxa.csv"      "tsv"           "vft_4quad.csv"
#>  [9] "view"          "weird"         "xl"

(vft_file <- example_path("view/vft_4quad.csv"))
#> [1] "/usr/local/lib/R/site-library/fgeo.x/extdata/view/vft_4quad.csv"

read_vft() and read_taxa() import a ViewFullTable and ViewTaxonomy from .tsv or .csv files.

read_vft(vft_file)
#> # A tibble: 500 × 32
#>     DBHID PlotName PlotID Family   Genus Speci…¹ Mnemo…² Subsp…³ Speci…⁴ Subsp…⁵
#>     <int> <chr>     <int> <chr>    <chr> <chr>   <chr>   <chr>     <int> <chr>  
#>  1 385164 luquillo      1 Rubiace… Psyc… brachi… PSYBRA  <NA>        185 <NA>   
#>  2 385261 luquillo      1 Urticac… Cecr… schreb… CECSCH  <NA>         74 <NA>   
#>  3 384600 luquillo      1 Rubiace… Psyc… brachi… PSYBRA  <NA>        185 <NA>   
#>  4 608789 luquillo      1 Rubiace… Psyc… berter… PSYBER  <NA>        184 <NA>   
#>  5 388579 luquillo      1 Arecace… Pres… acumin… PREMON  <NA>        182 <NA>   
#>  6 384626 luquillo      1 Araliac… Sche… moroto… SCHMOR  <NA>        196 <NA>   
#>  7 410958 luquillo      1 Rubiace… Psyc… brachi… PSYBRA  <NA>        185 <NA>   
#>  8 385102 luquillo      1 Piperac… Piper glabre… PIPGLA  <NA>        174 <NA>   
#>  9 353163 luquillo      1 Arecace… Pres… acumin… PREMON  <NA>        182 <NA>   
#> 10 481018 luquillo      1 Salicac… Case… arborea CASARB  <NA>         70 <NA>   
#> # … with 490 more rows, 22 more variables: QuadratName <chr>, QuadratID <int>,
#> #   PX <dbl>, PY <dbl>, QX <dbl>, QY <dbl>, TreeID <int>, Tag <chr>,
#> #   StemID <int>, StemNumber <int>, StemTag <int>, PrimaryStem <chr>,
#> #   CensusID <int>, PlotCensusNumber <int>, DBH <dbl>, HOM <dbl>,
#> #   ExactDate <date>, Date <int>, ListOfTSM <chr>, HighHOM <int>,
#> #   LargeStem <chr>, Status <chr>, and abbreviated variable names ¹​SpeciesName,
#> #   ²​Mnemonic, ³​Subspecies, ⁴​SpeciesID, ⁵​SubspeciesID
#> # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names

pick_dbh_under(), drop_status() and friends pick and drop rows from a ForestGEO ViewFullTable or census table.

tree5 <- fgeo.x::tree5

tree5 %>% 
  pick_dbh_under(100)
#> # A tibble: 18 × 19
#>    treeID stemID tag    StemTag sp     quadrat    gx    gy Measu…¹ Censu…²   dbh
#>     <int>  <int> <chr>  <chr>   <chr>  <chr>   <dbl> <dbl>   <int>   <int> <dbl>
#>  1   7624 160987 108958 175325  TRIPAL 722     139.  425.   486675       5  10.9
#>  2  19930 117849 123493 165576  CASARB 425      61.3 496.   471979       5  23.6
#>  3  31702  39793 22889  22889   SLOBER 304      53.8  73.8  447307       5  67  
#>  4  35355  44026 27538  27538   SLOBER 1106    203.  110.   449169       5  50  
#>  5  39705  48888 33371  33370   CASSYL 1010    184.  194.   451067       5  67  
#>  6  57380 155867 66962  171649  SLOBER 1414    274.  279.   459427       5  16.6
#>  7  95656 129113 131519 131519  OCOLEU 402      79.7  22.8  474157       5  23.6
#>  8  96051 129565 132348 132348  HIRRUG 1403    278    40.6  474523       5  12.9
#>  9  96963 130553 134707 134707  TETBAL 610     114.  182.   475236       5  18.6
#> 10 115310 150789 165286 165286  MANBID 225      24.0 497.   483175       5  14.6
#> 11 121424 158579 170701 170701  CASSYL 811     146.  218.   484785       5  20.2
#> 12 121689 158871 171277 171277  INGLAU 515      84.2 285.   485077       5  13.4
#> 13 121953 159139 171809 171809  PSYBRA 1318    247.  354.   485345       5  14  
#> 14 124522 162698 174224 174224  CASSYL 1411    279.  210.   488386       5  13.1
#> 15 125038 163236 175335 175335  CASSYL 822     153.  426.   488924       5  14.5
#> 16 126087     NA 177394 <NA>    CASARB 521      89.8 408.       NA      NA  NA  
#> 17 126803     NA 178513 <NA>    PSYBER 622     113.  426        NA      NA  NA  
#> 18 126934     NA 178763 <NA>    MICRAC 324      47   480.       NA      NA  NA  
#> # … with 8 more variables: pom <chr>, hom <dbl>, ExactDate <date>,
#> #   DFstatus <chr>, codes <chr>, nostems <dbl>, status <chr>, date <dbl>, and
#> #   abbreviated variable names ¹​MeasureID, ²​CensusID
#> # ℹ Use `colnames()` to see all variable names

pick_main_stem() and pick_main_stemid() pick the main stem or main stemid(s) of each tree in each census.

stem <- download_data("luquillo_stem6_random")

dim(stem)
#> [1] 1320   19
dim(pick_main_stem(stem))
#> Warning: The `add` argument of `group_by()` is deprecated as of dplyr 1.0.0.
#> Please use the `.add` argument instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> [1] 1000   19

add_status_tree() adds the column status_tree based on the status of all stems of each tree.

stem %>% 
  select(CensusID, treeID, stemID, status) %>% 
  add_status_tree()
#> # A tibble: 1,320 × 5
#>    CensusID treeID stemID status status_tree
#>       <int>  <int>  <int> <chr>  <chr>      
#>  1        6    104    143 A      A          
#>  2        6    119    158 A      A          
#>  3       NA    180    222 G      A          
#>  4       NA    180    223 G      A          
#>  5        6    180    224 G      A          
#>  6        6    180    225 A      A          
#>  7        6    602    736 A      A          
#>  8        6    631    775 A      A          
#>  9        6    647    793 A      A          
#> 10        6   1086   1339 A      A          
#> # … with 1,310 more rows
#> # ℹ Use `print(n = ...)` to see more rows

add_index() and friends add columns to a ForestGEO-like dataframe.

stem %>% 
  select(gx, gy) %>% 
  add_index()
#> Guessing: plotdim = c(320, 500)
#> * If guess is wrong, provide the correct argument `plotdim`
#> # A tibble: 1,320 × 3
#>       gx    gy index
#>    <dbl> <dbl> <dbl>
#>  1  10.3  245.    13
#>  2 183.   410.   246
#>  3 165.   410.   221
#>  4 165.   410.   221
#>  5 165.   410.   221
#>  6 165.   410.   221
#>  7 149.   414.   196
#>  8  38.3  245.    38
#>  9 143.   411.   196
#> 10  68.9  253.    88
#> # … with 1,310 more rows
#> # ℹ Use `print(n = ...)` to see more rows

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