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rangeMapper

A platform for the study of macroecology of life history traits

https://github.com/mpio-be/rangemapper

Science Score: 33.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

assemblage-level ecology global life-history-traits r raster-cell species
Last synced: 10 months ago · JSON representation

Repository

A platform for the study of macroecology of life history traits

Basic Info
Statistics
  • Stars: 7
  • Watchers: 3
  • Forks: 3
  • Open Issues: 2
  • Releases: 0
Topics
assemblage-level ecology global life-history-traits r raster-cell species
Created over 12 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.Rmd 

---
output: github_document
---





```{r, echo = FALSE, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/"
)
```


# rangeMapper 



[![R-CMD-check](https://github.com/mpio-be/rangeMapper/workflows/R-CMD-check/badge.svg)](https://github.com/mpio-be/rangeMapper/actions)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/rangeMapper)](https://CRAN.R-project.org/package=rangeMapper)
[![status](https://tinyverse.netlify.com/badge/rangeMapper)](https://CRAN.R-project.org/package=rangeMapper)
[![Codecov test coverage](https://codecov.io/gh/mpio-be/rangeMapper/branch/master/graph/badge.svg)](https://codecov.io/gh/mpio-be/rangeMapper?branch=master)





    
A framework for the study of macroecological patterns of life-history traits.  




### `rangeMapper` builds upon three types of data:   
 1. __Species distribution ranges__   
 2. __Life-history datasets__   
 3. __Environmental rasters__  

### `rangeMapper` is build on three concepts:  
 1. __The canvas__   which is a regular grid of squares or hexagons.   
 2. __The subsets__  which are defined by combinations of life-history datasets and map data.   
 3. __The maps__     representing one or several variables summarised on the canvas.   


```{r, example, echo=FALSE, message=FALSE,  fig.height=5}
require(rangeMapper)
require(sf)
require(data.table)
require(ggplot2)
require(patchwork)


con = rmap_connect()
rmap_add_ranges(con, x = wrens, ID = 'sci_name')
rmap_prepare(con, 'hex', cellsize = 500)
rmap_add_bio(con, wrens, 'sci_name')
rmap_save_map(con, fun= 'avg', v = 'clutch_size', src='wrens', dst='cs')
cs = rmap_to_sf(con, 'cs')
cnv = rmap_to_sf(con, 'wkt_canvas')

thm = theme_bw() +theme(plot.margin = unit(c(0,0,0,0), "cm") )

g1 = 
ggplot() + 
  geom_sf(data = wrens, aes(),  alpha= 0.2, size  = 0.3) + 
   thm +  ggtitle('Distribution ranges') + 
   scale_y_continuous(position = "right") + ylab('⇧') + theme(axis.title=element_text(size=30, color = "grey60") )

g2 = 
ggplot() + 
  geom_sf(data = cnv, aes(),  size  = 0.3) + 
  thm + ggtitle('Canvas') + 
  scale_y_continuous(position = "right") + ylab('⇧') + theme(axis.title=element_text(size=30, color = "grey60") )

g3 = 
ggplot(cs) + 
  geom_sf(aes(fill = avg_clutch_size),  size= 0.05, color = 'grey90', show.legend = FALSE) + 
  scale_fill_gradientn(colours = viridis::viridis(10, option = 'E') ) + 
  thm  + ggtitle('Map')

x = data.frame(Species = c('S1', 'S2', 'S3', '...', 'Si'), Trait = c('t1', 't2', 't3', '...', 'ti'))  

T = ggplot() +
  ggpmisc::annotate(geom = "table", x = 0, y = 0, size= 5, label = list(x) ) + 
  scale_x_continuous(position = "top") + xlab('⇧') + 
  guides(x = "none", y = "none") + ylab(NULL) +
  theme_minimal() + theme(axis.title=element_text(size=30, color = "grey60") ) 

(g1 + g2 + g3)/(plot_spacer() +T + plot_spacer()) 


```

### File format

`rangeMapper`'s project containers are `sqlite` files.



### Installation

```{r, eval = FALSE}
# Install release version from CRAN
install.packages("rangeMapper")

# Install development version from GitHub
remotes::install_github("mpio-be/rangeMapper")
```

Owner

  • Name: Department of Ornithology
  • Login: mpio-be
  • Kind: organization
  • Location: Seewiesen, Germany

Max Planck Institute for Biological Intelligence,Department of Ornithology

GitHub Events

Total
Last Year

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 182
  • Total Committers: 2
  • Avg Commits per committer: 91.0
  • Development Distribution Score (DDS): 0.022
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
mihai v****u@o****e 178
Joan Maspons j****s@c****t 4
Committer Domains (Top 20 + Academic)
creaf.uab.cat: 1 orn.mpg.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 5
  • Average time to close issues: 11 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.4
  • Average comments per pull request: 0.2
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • HenrikBengtsson (3)
  • rsbivand (2)
Pull Request Authors
  • jmaspons (4)
  • HenrikBengtsson (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 361 last-month
  • Total docker downloads: 855
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 19
  • Total maintainers: 1
cran.r-project.org: rangeMapper

A Platform for the Study of Macro-Ecology of Life History Traits

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 361 Last month
  • Docker Downloads: 855
Rankings
Forks count: 14.3%
Stargazers count: 18.4%
Dependent repos count: 19.5%
Average: 20.1%
Downloads: 20.5%
Dependent packages count: 27.9%
Maintainers (1)
valcu@orn.mpg.de
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • DBI * imports
  • RSQLite * imports
  • data.table * imports
  • exactextractr * imports
  • future * imports
  • future.apply * imports
  • glue * imports
  • graphics * imports
  • magrittr * imports
  • methods * imports
  • progressr * imports
  • raster * imports
  • sf * imports
  • ggplot2 * suggests
  • igraph * suggests
  • knitr * suggests
  • nlme * suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • spdep * suggests
  • testthat * suggests
  • viridis * suggests