The CafriplotsR Apps at a Glance
apps-overview.RmdIntroduction
CafriplotsR ships ten interactive applications. They cover the whole life cycle of an inventory dataset — exploring it, standardizing its taxonomy, importing it, correcting it, and linking it to herbarium specimens — without writing any R code beyond the one line that launches the app.
Each app opens on the same login screen. What differs is who may use it: three apps can be opened without any credentials, the other seven need your own account because they write to the database. One of the three, the taxonomic matching app, goes further still and also runs offline.
One of the three does not need R at all. The taxonomic name standardization app is also hosted, at https://cafri-taxomatch.lab.sspcloud.fr — open it in a browser and it behaves exactly like the local app, public login included. Use it to try the package out, or to point a colleague at the workflow without asking them to install anything.
Which app do I need?
| App | Launch with | Access |
|---|---|---|
| Taxonomic name standardization | launch_taxonomic_match_app() |
public, account, or offline |
| Taxonomic backbone | launch_taxo_backbone_app() |
public to browse, account to edit |
| Plot querying | launch_query_plots_app() |
public or account |
| Plot data import | launch_import_wizard() |
account |
| Plot features and censuses | launch_feature_wizard() |
account |
| Record-by-record corrections | launch_data_update_app() |
account |
| Taxa-level trait import | launch_taxa_traits_import() |
account |
| Herbarium specimen import | launch_specimen_import_wizard() |
account |
| Specimen identifications | launch_specimen_identification_app() |
account |
| Individual ↔︎ specimen linking | launch_individual_specimen_linking_app() |
account |
Working without an account
The login screen of the three read-only apps offers a Connect as public user button. It signs you in through a shared, read-only account that reaches the taxonomy and the species-level traits. Nothing you do in that mode can change the database, and the editing controls are hidden rather than disabled.
This is enough to:
- standardize your own species list against the Central African backbone,
- browse the backbone, its synonymy and the traits attached to a taxon,
- explore the inventories that their owners have opened to everyone.
It is not enough to import data, correct records, or manage specimens. Those apps do not show the public button at all, because a read-only account cannot complete a single one of their workflows.
Working without a network
One app goes further and runs with no database at all: the taxonomic name standardization app offers a Use offline (cached backbone) button. It works from a copy of the taxonomic backbone saved on your own machine, so you can standardize a species list from a field station, a plane or any other place without a route to the server.
Two things are worth knowing before you rely on it:
- The button only appears once a cache exists. The cache is written the first time you run the matching app online, so run it connected once before you leave.
- Offline, you get automatic matching, fuzzy suggestions and manual review. The traits enrichment tab is hidden, because traits live in the database and nothing local can stand in for them.
The other nine apps never show this button. Offline mode leaves the app with no connection, and none of them has anything to work on in that state — they import, correct or query live data. If you were expecting the button somewhere else, that is why it is not there.
Explore and standardize
Taxonomic name standardization
Matches your own list of species names against the Central African
plant taxonomic backbone: automatic matching with fuzzy search, manual
review of whatever the matcher could not resolve on its own, and export
of the standardized list. The result gives each of your names a stable
taxon identifier (idtax_n), which is what lets you join
traits and inventories later on.
Start here if you arrive with a species list from your own fieldwork. This is also the one app that runs offline, from a cached copy of the backbone.
And it is the only one you can use without installing
anything: https://cafri-taxomatch.lab.sspcloud.fr serves the same
application from SSP Cloud. The hosted copy talks to the same database,
so a standardized list exported there carries the same
idtax_n values as one produced locally.
Taxonomic backbone
Browses and manages the taxonomic backbone itself: searching taxa, inspecting synonymy relationships, and generating the R code for the query you just built by hand. With an account, it also adds new taxa, updates existing records and maintains synonymy. As a public user you get the browsing and code-generation half; the editing controls do not appear.
Plot querying
An interactive front end to query_plots(): filter plots
by country, method or other criteria, see them on a map, drill down to
the individual trees, and export the result. Which plots you see depends
on the account you used — row-level security policies decide, and a
public user sees only the inventories their owners have opened to
everyone.
Import and update
These apps all require your own account, and they only ever touch the plots your account is entitled to.
Plot data import
The complete import workflow for plots and individual measurements: upload a file, map its columns to the database fields, validate, preview what will be written, and execute. It wraps the package’s import functions, so the checks you would otherwise run by hand are applied for you.
Plot features and censuses
Adds features to plots that already exist — either a new census, with its dates and the people involved, or arbitrary plot-level features.
Record-by-record corrections
Corrects plot metadata and individual records one at a time. It is
the friendly counterpart to update_records(), which is more
powerful but expects you to already know which table a value lives
in.
Herbarium specimens
Specimen identifications
Updates the identifications recorded for specimens, wrapping
update_ident_specimens().