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View Code? Open in Web Editor NEWOpen Datasets of ForestGEO
Home Page: https://forestgeo.github.io/fgeo.data/
License: Other
Open Datasets of ForestGEO
Home Page: https://forestgeo.github.io/fgeo.data/
License: Other
library(tidyverse)
library(fgeo.data)
tables <- c("bci_stem6_random", "bci_tree6_random", "bci_vft_random")
tables %>%
map(get) %>%
set_names(tables) %>%
map(select, matches("status")) %>%
map(unique) %>%
map(pull) %>%
map(paste, collapse = ", ")
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"
#>
#> $bci_tree6_random
#> [1] "A, D, P"
#>
#> $bci_vft_random
#> [1] "alive, broken below, dead, missing"
Created on 2018-04-16 by the reprex package (v0.2.0).
library(tidyverse)
#> -- Attaching packages -------------------------------------------- tidyverse 1.2.1 --
#> v ggplot2 2.2.1 v purrr 0.2.4
#> v tibble 1.4.2 v dplyr 0.7.4
#> v tidyr 0.8.0 v stringr 1.3.0
#> v readr 1.1.1 v forcats 0.3.0
#> -- Conflicts ----------------------------------------------- tidyverse_conflicts() --
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag() masks stats::lag()
# Good
list(
census1 = fgeo.data::luquillo_stem_random %>% filter(CensusID == 5),
census2 = fgeo.data::luquillo_stem_random %>% filter(CensusID == 6)
) %>%
map(nrow)
#> $census1
#> [1] 1324
#>
#> $census2
#> [1] 1324
# Bad
list(
census1 = fgeo.data::luquillo_stem_random_tiny %>% filter(CensusID == 5),
census2 = fgeo.data::luquillo_stem_random_tiny %>% filter(CensusID == 6)
) %>%
map(nrow)
#> $census1
#> [1] 13
#>
#> $census2
#> [1] 9
Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on https://stackoverflow.com/, https://community.rstudio.com/, https://github.com/forestgeo/forum/ or email Mauro Lepore at [email protected].
Please include a minimal reproducible example (AKA a reprex). If you've never heard of a reprex before, start by reading https://www.tidyverse.org/help/#reprex.
Brief description of the problem
# insert reprex here
In bciex I had documented datasets generally.
Authorized (via).
Census tables tree and stem are out of date. They don't match with the output of rtbl()
. Try recreate them with rtbl()
.
For easier maintenance, point to data_dictionary
instead of repeating the column definitions.
Make it easy to create toy datasets for examples and tests.
Alternatives:
Pre made:
On the fly:
From: Mauro Lepore [[email protected]]
Sent: Monday, March 19, 2018 9:43 AM
To: Davies, Stuart J.; Lao, Suzanne
Subject: Can you please send me the current BCI dataset?
Can you please send me the current BCI dataset?
...
I would specifically use these two pieces:
Also need all other up-to-date datasets of the same site: ViewTaxonomy, elevation, and whatever else you consider standard for a site.
The documentation of the fgeo.data package is available at https://forestgeo.github.io/fgeo.data. To suggest edits please add your comments below or create a pull request.
If you have any question, please ask me by referring to me as @maurolepore.
Search related issues on https://github.com with: label:hacktoberfest maurolepore
Columns definitions may change and fall out of sync relative to definitions hard-wired in the package.
Scrap definitions from the web, and provide a single dataset of variables and definitions for users to find their own definitions.
Use fixed vft in data-raw\private\ViewFullTable_luquillo to remake all affected data.
# Subject: RE: Why there may be more than one tag per TreeID?
# > In the case of Luquillo, which is a relatively clean dataset, there
# shouldn’t be # duplicate tree tags.
# > I have fixed the errors. Please download the ViewFullTable
all(is.na(fgeo.data::luquillo_tree5_random$date))
#> [1] TRUE
all(is.na(fgeo.data::luquillo_stem5_random$date))
#> [1] TRUE
# Is the problem comming from rtbl?
all(is.na(fgeo.data::luquillo_vft_4quad$Date))
#> [1] FALSE
Created on 2018-09-28 by the reprex package (v0.2.1)
This will be helpful to train partners in how to deal with raw data.
Useful links:
usethis::use_course()
. This includes a .Rproj file and a data-raw/ directory, to show learners how to organize a project.For example:
A zip file that lives here:
https://github.com/forestgeo/fgeo.opendata/blob/dev/inst/database-output.zip
Can be downloaded with (note that blob
is replaced by raw
):
use_course("https://github.com/forestgeo/fgeo.opendata/raw/dev/inst/database-output.zip")
Labelled with FIXME.
SubspeciesID FIXME: Foreign Key to FIXME table.
Date FIXME: Integer representing the number of days since 1 Jan 1960.
HighHOM FIXME: Define HighHOM
LargeStem FIXME: Define LargeStem
tyluRp:
This issue starts to collect ideas for summaries of ForestGEO data which could be included in different tools, for example:
Feel free to add more ideas as comments below.
Today I discussed with Patrick Jansen the idea of developing tools to summarize ForestGEO data that could be used to gain some insight about plot data short after it's been collected.
This idea related to building the new generation of ForestGEO plot-books (online, interactive, built with pkgdown), which @teixeirak is working on. She started a repository to work on such a book, and that seems to be the best place to discuss this issue. But I discuss it here because that repository is now private.
Patrick would like to visualize data from a site relative to other sites. These are some specific visualizations he proposes:
Interactivity: Data from the focal plot could be highlighted by clicking on the legend of a plotly graph.
library(tidyverse)
stem <- fgeo.data::luquillo_stem6_1ha
dups <- c("100223", "116681", "118059", "119589", "17112", "18174")
stem %>%
select(treeID, tag) %>%
unique() %>%
filter(tag %in% dups) %>%
arrange(tag)
#> # A tibble: 12 x 2
#> treeID tag
#> <int> <chr>
#> 1 224 100223
#> 2 125584 100223
#> 3 14122 116681
#> 4 125589 116681
#> 5 15349 118059
#> 6 125590 118059
#> 7 16687 119589
#> 8 125591 119589
#> 9 26248 17112
#> 10 125552 17112
#> 11 27280 18174
#> 12 125564 18174
Created on 2018-06-22 by the reprex package (v0.2.0).
DONE
bit.ly
url <- "http://bit.ly/fgeo-opendata-taxa-bci"
url <- "http://bit.ly/fgeo-data-bci-taxa"
#' Raw .csv file available at \url{http://bit.ly/fgeo-opendata-vft-random-bci}).
#' Raw .csv file available at \url{http://bit.ly/fgeo-data-bci-vft-random}).
#' \url{http://bit.ly/fgeo-opendata-vft-1ha-bci}.
#' \url{http://bit.ly/fgeo-data-bci-vft-1ha}.
#' \url{http://bit.ly/fgeo-opendata-elevation-bci}.
#' \url{http://bit.ly/fgeo-data-bci-elevation}.
---------- Forwarded message ----------
From: Lao, Suzanne <[email protected]>
Date: Mon, Apr 16, 2018 at 2:20 PM
Subject: RE: Can you please send me the current BCI dataset?
To: Mauro Lepore <[email protected]>
...you should keep it in the Stem files. This is just the Status variable from ViewFullTable. In other words, DFstatus in the R stem file is exactly Status in the ViewFullTable.
You don’t need it in the Tree R files because DFstatus refers to the stem, not the tree.
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