vegtable

Handling vegetation-plot data sets

https://github.com/kamapu/vegtable

Science Score: 46.0%

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Low similarity (15.7%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

Handling vegetation-plot data sets

Basic Info

Host: GitHub
Owner: kamapu
Language: HTML
Default Branch: main
Homepage: http://kamapu.github.io/vegtable/
Size: 22.1 MB

Statistics

Stars: 7
Watchers: 1
Forks: 0
Open Issues: 18
Releases: 8

Created about 10 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog

The aim of vegtable is to provide a way for handling databases stored in Turboveg. This package incorporates many concepts and some functions included in the package vegdata but defining an homonymous S4 class containing all elements of a database in just one object. The package vegtable also contains several methods for this object class.

Species lists in vegtable objects are handled by the package taxlist, thus I will recommend to take a look on it.

This package has been developed as a tool handling data stored in SWEA-Dataveg. Further development is running in the context of the project GlobE-wetlands.

An important source of inspiration for vegtable have been the enthusiastic discussions during several versions of the Meetings on Vegetation Databases.

Updating to the last version of vegtable

The very first step is to install the package devtools and dependencies. Then you just need to execute following commands in your R-session:

r library(devtools) install_github("kamapu/vegtable")

Some examples

The current version of vegtable includes an example data, which corresponds to a subset from SWEA-Dataveg. This data set contains plot observations done in Kenya imported from 5 sources.

``` r library(vegtable)

> Loading required package: taxlist

>

> Attaching package: 'taxlist'

> The following objects are masked from 'package:base':

>

> levels, levels<-, print

data(Kenya_veg)

validate and explore

validObject(Kenya_veg)

> [1] TRUE

summary(Kenya_veg)

> ## Metadata

> db_name: Sweadataveg

> sp_list: Easplist

> dictionary: Swea

> object size: 9501 Kb

> validity: TRUE

>

> ## Content

> number of plots: 1946

> plots with records: 1946

> variables in header: 34

> number of relations: 3

>

> ## Taxonomic List

> taxon names: 3164

> taxon concepts: 2392

> validity: TRUE

```

Among others, the object contains plot observations done in the Aberdare National Park (Kenya) by Schmitt (1991). We can make a subset including the plots classified by the mentioned author into the Juniperus procera-Podocarpus latifolius community (IDs 780 to 798).

``` r JPcomm <- subset(Kenya_veg, ReleveID %in% c(780:798)) summary(JPcomm)

> ## Metadata

> db_name: Sweadataveg

> sp_list: Easplist

> dictionary: Swea

> object size: 717.4 Kb

> validity: TRUE

>

> ## Content

> number of plots: 19

> plots with records: 19

> variables in header: 17

> number of relations: 3

>

> ## Taxonomic List

> taxon names: 3164

> taxon concepts: 2392

> validity: TRUE

```

If you have geo-referenced plot observations, you can use the coordinates to produce a map of the distribution of your plots by using the package leaflet.

r library(leaflet) leaflet(JPcomm@header) %>% addTiles() %>% addCircleMarkers( lng = ~LONGITUDE, lat = ~LATITUDE, color = "red", opacity = 0.3, radius = 1 )

Further readings

Owner

Name: Miguel Alvarez
Login: kamapu
Kind: user

Website: https://kamapu.net/people.html#miguel-alvarez
Repositories: 54
Profile: https://github.com/kamapu

Vegetation Ecologist and software developer.

GitHub Events

Total

Last Year

Committers

Last synced: over 2 years ago

All Time

Total Commits: 263
Total Committers: 20
Avg Commits per committer: 13.15
Development Distribution Score (DDS): 0.445

Past Year

Commits: 5
Committers: 1
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Miguel Alvarez	k**8@g**m	146
Miguel Alvarez	m**z@u**e	75
ma	ma@m****0	13
m_alvarez	m**z@1**3	4
PC 7	P**7@1**9	3
m_alvarez	m**z@1**7	3
m_alvarez	m**z@1**4	3
m_alvarez	m**z@1**1	2
m_alvarez	m**z@m**P	2
miguel	m**l@m**0	2
m_alvarez	m**z@1**0	1
m_alvarez	m**z@1**3	1
m_alvarez	m**z@1**4	1
m_alvarez	m**z@1**2	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1

Committer Domains (Top 20 + Academic)

192.168.2.102: 1 131.220.203.124: 1 131.220.194.63: 1 10.5.107.200: 1 192.168.2.111: 1 131.220.246.54: 1 131.220.206.147: 1 131.220.67.49: 1 131.220.245.43: 1 uni-bonn.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 39
Total pull requests: 16
Average time to close issues: 7 months
Average time to close pull requests: 3 days
Total issue authors: 3
Total pull request authors: 1
Average comments per issue: 0.62
Average comments per pull request: 0.0
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 1
Average time to close issues: 37 minutes
Average time to close pull requests: less than a minute
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

kamapu (37)
orb16 (1)

Pull Request Authors

kamapu (18)

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 280 last-month

Total dependent packages: 0
Total dependent repositories: 2
Total versions: 9
Total maintainers: 1

cran.r-project.org: vegtable

Handling Vegetation Data Sets

Homepage: https://github.com/kamapu/vegtable
Documentation: http://cran.r-project.org/web/packages/vegtable/vegtable.pdf
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Latest release: 0.1.8
published about 3 years ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 280 Last month

Rankings

Dependent repos count: 19.3%

Stargazers count: 23.6%

Average: 27.7%

Forks count: 27.9%

Dependent packages count: 28.8%

Downloads: 39.2%

Maintainers (1)

kamapu78@gmail.com

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
taxlist * depends
foreign * imports
methods * imports
qdapRegex * imports
sp * imports
stringi * imports
vegdata * imports
biblio * suggests
knitr * suggests
rmarkdown * suggests
sf * suggests
testthat * suggests
vegan * suggests

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