https://mail.google.com/mail/u/0/?zx=yxdmg1oh1mf4#search/in%3Asent+laoz%40si.edu/162bc4dc2db9f8c1

Request

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:

1. A randomly selected subset of aprox. 1000 tree-tags from one whole-plot.
2. A subset of all trees from at least four quadrats -- 1 hectare would be great.
   I would use the exact same subset of stems in all kinds of tables: tree, stem, ViewFullTable.

Also need all other up-to-date datasets of the same site: ViewTaxonomy, elevation, and whatever else you consider standard for a site.

This will be helpful to train partners in how to deal with raw data.

Useful links:

• to data-raw/database-output/, so the entire collection of files can be downloaded with 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")

• to each individual file in data-raw/, for cases when a single file is what matters for a particular demonstration.

This issue starts to collect ideas for summaries of ForestGEO data which could be included in different tools, for example:

• A bookdown book.
• A shiny app.
• A function that creates a report in different formats.

Feel free to add more ideas as comments below.

Background

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.

Some specific ideas

Patrick would like to visualize data from a site relative to other sites. These are some specific visualizations he proposes:

• Cumulative area versus cumulative number of species. This gives a curve for each plot.
• Same but cumulative number of stems versus cumulative number of species.
• Scatterplot of total number of stems versus total number of species. This gives a point per plot.

Interactivity: Data from the focal plot could be highlighted by clicking on the legend of a plotly graph.

via

---------- 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.

Make it easy to create toy datasets for examples and tests.

Alternatives:

Pre made:

• Pre-make toy datasets and keep them in fgeo.data.
• Paste them to script with an addin, maybe internally using datapasta.

On the fly:

• Create them on the fly with expand.grid or simlar alternative in tidyr and friends.

#13 #14.

tyluRp:

• suggested to add NEWS.md
• Fixed typos and broken links in vignettes.

https://mail.google.com/mail/u/0/?zx=yxdmg1oh1mf4#search/in%3Asent+laoz%40si.edu/162bc4dc2db9f8c1

For easier maintenance, point to data_dictionary instead of repeating the column definitions.

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}.

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

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)

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).

In bciex I had documented datasets generally.

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).

Authorized (via).

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

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

https://github.com/lockedata/optiRum/blob/master/_pkgdown.yml

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  

https://github.com/forestgeo/rtbl/issues/42

Census tables tree and stem are out of date. They don't match with the output of rtbl(). Try recreate them with rtbl().