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maurolepore committed Jan 27, 2024
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Expand Up @@ -69,26 +69,25 @@ from .tsv or .csv files.
``` r
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>,
#> 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
#> # ℹ 490 more rows
#> # ℹ 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>, 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
#> # LargeStem <chr>, Status <chr>
```

`pick_dbh_under()`, `drop_status()` and friends pick and drop rows from
Expand All @@ -100,30 +99,28 @@ 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
#> treeID stemID tag StemTag sp quadrat gx gy MeasureID CensusID
#> <int> <int> <chr> <chr> <chr> <chr> <dbl> <dbl> <int> <int>
#> 1 7624 160987 108958 175325 TRIPAL 722 139. 425. 486675 5
#> 2 19930 117849 123493 165576 CASARB 425 61.3 496. 471979 5
#> 3 31702 39793 22889 22889 SLOBER 304 53.8 73.8 447307 5
#> 4 35355 44026 27538 27538 SLOBER 1106 203. 110. 449169 5
#> 5 39705 48888 33371 33370 CASSYL 1010 184. 194. 451067 5
#> 6 57380 155867 66962 171649 SLOBER 1414 274. 279. 459427 5
#> 7 95656 129113 131519 131519 OCOLEU 402 79.7 22.8 474157 5
#> 8 96051 129565 132348 132348 HIRRUG 1403 278 40.6 474523 5
#> 9 96963 130553 134707 134707 TETBAL 610 114. 182. 475236 5
#> 10 115310 150789 165286 165286 MANBID 225 24.0 497. 483175 5
#> 11 121424 158579 170701 170701 CASSYL 811 146. 218. 484785 5
#> 12 121689 158871 171277 171277 INGLAU 515 84.2 285. 485077 5
#> 13 121953 159139 171809 171809 PSYBRA 1318 247. 354. 485345 5
#> 14 124522 162698 174224 174224 CASSYL 1411 279. 210. 488386 5
#> 15 125038 163236 175335 175335 CASSYL 822 153. 426. 488924 5
#> 16 126087 NA 177394 <NA> CASARB 521 89.8 408. NA NA
#> 17 126803 NA 178513 <NA> PSYBER 622 113. 426 NA NA
#> 18 126934 NA 178763 <NA> MICRAC 324 47 480. NA NA
#> # ℹ 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
Expand All @@ -135,10 +132,6 @@ 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
```

Expand All @@ -162,8 +155,7 @@ stem %>%
#> 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
#> # ℹ 1,310 more rows
```

`add_index()` and friends add columns to a ForestGEO-like dataframe.
Expand All @@ -187,15 +179,14 @@ stem %>%
#> 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
#> # ℹ 1,310 more rows
```

[Get started with **fgeo**](https://forestgeo.github.io/fgeo/)

## Information

- [Getting help](https://forestgeo.github.io/fgeo.tool/SUPPORT.html).
- [Contributing](https://forestgeo.github.io/fgeo.tool/CONTRIBUTING.html).
- [Contributor Code of
Conduct](https://forestgeo.github.io/fgeo.tool/CODE_OF_CONDUCT.html).
- [Getting help](https://forestgeo.github.io/fgeo.tool/SUPPORT.html).
- [Contributing](https://forestgeo.github.io/fgeo.tool/CONTRIBUTING.html).
- [Contributor Code of
Conduct](https://forestgeo.github.io/fgeo.tool/CODE_OF_CONDUCT.html).

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