MtreeRing

A tool for measuring tree-ring width

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: researchgate.net
✓
Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary

Keywords

dendrochronology forest forestry r shiny-apps shinyapp tree-ring-width tree-rings

Keywords from Contributors

genome http-mock geocode air-pollution taxize agent-based-modeling individual-based-modelling netlogo biomart database-retrieval

Last synced: 6 months ago · JSON representation

Repository

A tool for measuring tree-ring width

Basic Info

Host: GitHub
Owner: ropensci
Language: R
Default Branch: master
Homepage: https://ropensci.github.io/MtreeRing/
Size: 101 MB

Statistics

Stars: 34
Watchers: 4
Forks: 6
Open Issues: 9
Releases: 3

Topics

dendrochronology forest forestry r shiny-apps shinyapp tree-ring-width tree-rings

Created about 7 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Code of conduct Codemeta

MtreeRing

Authors: Jingning Shi, Wei Xiang
License: GPL3

MtreeRing is a tool for automatically measuring tree-ring width using image processing techniques.

Installation

Install the stable version from CRAN

r install.packages("MtreeRing")

or the development version from GitHub

```r

install.packages("devtools")

devtools::install_github("ropensci/MtreeRing") ```

Ring-width measurement

1. Read an image

```r library(MtreeRing)

Read and plot a tree ring image

img.name <- system.file("001.png", package = "MtreeRing") t1 <- ring_read(img = img.name, dpi = 1200, plot = TRUE) ```

ring_read supports commonly used image formats, including png, tiff, jpg and bmp.

2. Detect ring borders

After plotting the image, the automatic detection of ring borders can be performed using three alternative methods: (1) watershed algorithm; (2) Canny edge detector; (3) a linear detection algorithm from R package measuRing.

```r

Split a long core sample into 2 pieces to

get better display performance and use the

watershed algorithm to detect ring borders:

t2 <- ring_detect(ring.data = t1, seg = 2, method = 'watershed') ```

Figure 1. The automatic detection of ring borders

3. Calculate ring-width series

If all ring borders are correctly identified, you can generate a ring-width series in data frame format. Use write.rwl to export the ring-width series to an rwl file.

r rw.df <- ring_calculate(ring.data = t2, seriesID = "940220") library(dplR) # A dendrochronological analysis package fn <- tempfile(fileext=".rwl") write.rwl(rwl.df = rw.df, fname = fn, format = "tucson")

Shiny application

If you are not familiar with R and its command line interface, the shiny-based app is a good alternative.

r MtreeRing::ring_app_launch()

This command allows to run a Shiny-based application within the system's default web browser. The app provides a beginner-friendly graphical interface and supports more flexible mouse-based interactions, allowing image files to be uploaded up to 150 MB in size.

The dashboard has three components: a header, sidebar and body, like this

A workflow for the Shiny app can be found at https://ropensci.github.io/MtreeRing/articles/app-MtreeRing.html. Most steps are demonstrated with a gif to make the workflow more understandable.

Ring width correction

If an increment borer is used to extract samples, it is well known that the auger sometimes fails to traverse the pith of the sampled tree but passes through one side of the pith at a certain distance. Tangent lines of rings close to the pith are therefore not perpendicular to the horizontal path, which may lead to considerable errors in ring widths.

Under such conditions, you can create two paths by setting the argument incline = TRUE, or by ticking the checkbox Inclined tree rings. See this example.

The line segment connecting two dots on the same ring should match the tangent of a tree ring border. The corrected ring width is estimated from the distance between adjacent rings and orientation of ring borders.

Support

Any feedback, bug reports or suggestions are welcomed. If you have a comment on MtreeRing, or you find a bug in the released or beta versions, please submit bugs and/or feature requests at https://github.com/ropensci/MtreeRing/issues. Include the package version, OS, and any command-line required to reproduce the problem.

Code of conduct

I will try to add new features based on user feedback. It is hoped that others will contribute additional useful features. Please note that the 'MtreeRing' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

CodeMeta (codemeta.json)

{
  "@context": [
    "https://doi.org/10.5063/schema/codemeta-2.0",
    "http://schema.org"
  ],
  "@type": "SoftwareSourceCode",
  "identifier": "MtreeRing",
  "description": "Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.",
  "name": "MtreeRing: A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images",
  "codeRepository": "https://github.com/ropensci/MtreeRing",
  "issueTracker": "https://github.com/ropensci/MtreeRing/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "1.3",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "version": "3.5.2",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 3.5.2 (2018-12-20)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Jingning",
      "familyName": "Shi",
      "email": "snow940220@bjfu.edu.cn"
    },
    {
      "@type": "Person",
      "givenName": "Wei",
      "familyName": "Xiang"
    }
  ],
  "contributor": {},
  "copyrightHolder": {},
  "funder": {},
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Jingning",
      "familyName": "Shi",
      "email": "snow940220@bjfu.edu.cn"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shinytest",
      "name": "shinytest"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "mockery",
      "name": "mockery"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling"
    }
  ],
  "softwareRequirements": [
    {
      "@type": "SoftwareApplication",
      "identifier": "magrittr",
      "name": "magrittr",
      "version": ">= 1.5"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "png",
      "name": "png"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "jpeg",
      "name": "jpeg"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tiff",
      "name": "tiff"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "bmp",
      "name": "bmp"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "magick",
      "name": "magick"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "imager",
      "name": "imager"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "dplR",
      "name": "dplR"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spatstat",
      "name": "spatstat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "measuRing",
      "name": "measuRing"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shiny",
      "name": "shiny"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shinydashboard",
      "name": "shinydashboard"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shinyWidgets",
      "name": "shinyWidgets"
    }
  ],
  "readme": "https://github.com/ropensci/MtreeRing/blob/master/README.md",
  "fileSize": "22396.559KB",
  "contIntegration": [
    "https://travis-ci.org/ropensci/MtreeRing.svg?branch=master",
    "https://ci.appveyor.com/project/JingningShi/mtreering/branch/master",
    "https://codecov.io/gh/ropensci/MtreeRing"
  ],
  "releaseNotes": "https://github.com/ropensci/MtreeRing/blob/master/NEWS.md"
}

GitHub Events

Total

Issues event: 1
Watch event: 4

Last Year

Issues event: 1
Watch event: 4

Committers

Last synced: over 1 year ago

All Time

Total Commits: 423
Total Committers: 6
Avg Commits per committer: 70.5
Development Distribution Score (DDS): 0.487

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Jingning Shi	3****i	217
Jingning Shi	3****i	188
Jingning Shi	s**0@b**n	13
Jeroen Ooms	j**s@g**m	2
Maëlle Salmon	m**n@y**e	2
rOpenSci Bot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

bjfu.edu.cn: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 9
Total pull requests: 6
Average time to close issues: about 21 hours
Average time to close pull requests: 10 months
Total issue authors: 6
Total pull request authors: 4
Average comments per issue: 1.78
Average comments per pull request: 0.83
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

maelle (3)
lgsmith295 (2)
mariasimone308 (1)
condwanaland (1)
christopherbeatty (1)
stefaniebutland (1)

Pull Request Authors

maelle (3)
LaertesPecker (2)
JingningShi (1)
rorynolan (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 157 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 7
Total maintainers: 1

cran.r-project.org: MtreeRing

A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images

Homepage: https://docs.ropensci.org/MtreeRing
Documentation: http://cran.r-project.org/web/packages/MtreeRing/MtreeRing.pdf
License: GPL-3
Status: removed
Latest release: 1.4.5
published almost 5 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 157 Last month

Rankings

Forks count: 10.1%

Stargazers count: 11.6%

Average: 25.2%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Downloads: 39.0%

Maintainers (1)

snow940220@bjfu.edu.cn

Last synced: 8 months ago

Dependencies

DESCRIPTION cran

bmp * imports
dplR * imports
dplyr * imports
imager * imports
jpeg * imports
magick * imports
magrittr >= 1.5 imports
measuRing * imports
png * imports
shiny * imports
shinyWidgets * imports
shinydashboard * imports
spatstat.geom * imports
tiff * imports
knitr * suggests
mockery * suggests
shinytest * suggests
spelling * suggests
testthat * suggests