Import and manipulate ForestGEO data
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] "/home/mauro/R/x86_64-pc-linux-gnu-library/3.6/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 x 32
#> DBHID PlotName PlotID Family Genus SpeciesName Mnemonic Subspecies SpeciesID
#> <int> <chr> <int> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 385164 luquillo 1 Rubia… Psyc… brachiata PSYBRA <NA> 185
#> 2 385261 luquillo 1 Urtic… Cecr… schreberia… CECSCH <NA> 74
#> 3 384600 luquillo 1 Rubia… Psyc… brachiata PSYBRA <NA> 185
#> 4 608789 luquillo 1 Rubia… Psyc… berteroana PSYBER <NA> 184
#> 5 388579 luquillo 1 Areca… Pres… acuminata PREMON <NA> 182
#> 6 384626 luquillo 1 Arali… Sche… morototoni SCHMOR <NA> 196
#> 7 410958 luquillo 1 Rubia… Psyc… brachiata PSYBRA <NA> 185
#> 8 385102 luquillo 1 Piper… Piper glabrescens PIPGLA <NA> 174
#> 9 353163 luquillo 1 Areca… Pres… acuminata PREMON <NA> 182
#> 10 481018 luquillo 1 Salic… Case… arborea CASARB <NA> 70
#> # … with 490 more rows, and 23 more variables: SubspeciesID <chr>,
#> # 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>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 x 19
#> treeID stemID tag StemTag sp quadrat gx gy MeasureID CensusID
#> <int> <int> <chr> <chr> <chr> <chr> <dbl> <dbl> <int> <int>
#> 1 7624 160987 1089… 175325 TRIP… 722 139. 425. 486675 5
#> 2 19930 117849 1234… 165576 CASA… 425 61.3 496. 471979 5
#> 3 31702 39793 22889 22889 SLOB… 304 53.8 73.8 447307 5
#> 4 35355 44026 27538 27538 SLOB… 1106 203. 110. 449169 5
#> 5 39705 48888 33371 33370 CASS… 1010 184. 194. 451067 5
#> 6 57380 155867 66962 171649 SLOB… 1414 274. 279. 459427 5
#> 7 95656 129113 1315… 131519 OCOL… 402 79.7 22.8 474157 5
#> 8 96051 129565 1323… 132348 HIRR… 1403 278 40.6 474523 5
#> 9 96963 130553 1347… 134707 TETB… 610 114. 182. 475236 5
#> 10 115310 150789 1652… 165286 MANB… 225 24.0 497. 483175 5
#> 11 121424 158579 1707… 170701 CASS… 811 146. 218. 484785 5
#> 12 121689 158871 1712… 171277 INGL… 515 84.2 285. 485077 5
#> 13 121953 159139 1718… 171809 PSYB… 1318 247. 354. 485345 5
#> 14 124522 162698 1742… 174224 CASS… 1411 279. 210. 488386 5
#> 15 125038 163236 1753… 175335 CASS… 822 153. 426. 488924 5
#> 16 126087 NA 1773… <NA> CASA… 521 89.8 408. NA NA
#> 17 126803 NA 1785… <NA> PSYB… 622 113. 426 NA NA
#> 18 126934 NA 1787… <NA> MICR… 324 47 480. NA NA
#> # … with 9 more variables: dbh <dbl>, pom <chr>, hom <dbl>, ExactDate <date>,
#> # DFstatus <chr>, codes <chr>, nostems <dbl>, status <chr>, date <dbl>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_warnings()` to see where this warning was generated.
#> [1] 1000 19add_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 x 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 rowsadd_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 x 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
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