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Morphoscape

Morphoscape: An R package for the contruction and analysis of adaptive landscapes

https://github.com/blakedickson/morphoscape

Science Score: 26.0%

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Repository

Morphoscape: An R package for the contruction and analysis of adaptive landscapes

Basic Info
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 3
  • Open Issues: 14
  • Releases: 1
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = FALSE,
  warning = FALSE,
  message = FALSE,
  tidy = FALSE,
  fig.align='center',
  comment = "#>",
  fig.path = "man/figures/README-",
  R.options = list(width = 200)
)
```
# Morphoscape: An R package for the contruction and analysis of adaptive landscapes

------

`Morphoscape` is a package designed for the constructions, analysis and visualization of spatially organized trait data into adaptive landscapes. `Morphoscape` provides a pipeline for combining spatial coordinate data derived from an ordinated morphospace, such as a PCA, with performance trait data; and finding 'optimum' adaptive landscapes from the combination of those trait data.

`Morphoscape` does not provide tools for the generation of morphospaces. For shape analyses and tools to ordinate multivariate phenotypic data, see the `Geomorph` or `Morpho` packages. 

For an in-depth guide on using `Morphoscape`, and some discussion on morphospace design, see the vignette.  

To install `Morphoscape` from GitHub you will need to install the
`devtools` package and run `install_github("blakedickson/Morphoscape")`:

```{r, eval=FALSE}
install.packages("devtools")
devtools::install_github("blakedickson/Morphoscape")
```

The point of entry into `Morphoscape` is a dataframe containing two columns of XY coordinate data followed by columns containing performance variables. See the `warps` data object for an example. An additional dataframe `turtles` with specimen coordinates and grouping variables is also provided.

``` {r} 
library(Morphoscape)
data('warps')
str(warps)

data('turtles')
str(turtles)
```

This dataframe is input into the `as_fnc_df()` which will coerce coordinate data into the correct format, and rescale performance variables to unit range.

```{r}
warps_fnc <- as_fnc_df(warps, func.names = c("hydro", "curve", "mech", "fea"))
```

Performance surfaces are calculated using `krige_surf()`, and can be used to just calculate surfaces, or also predict performance of `new_data` points.

```{r}
kr_surf <- krige_surf(warps_fnc, hull = NULL, new_data = turtles)
plot(kr_surf)
```

To calculate adaptive landscapes based on groupings, first a population of landscapes is generated using `generate_weights()` and `calc_all_lscps()`:

```{r}
weights <- generate_weights(n = 10, data = kr_surf)
all_landscapes <- calc_all_lscps(kr_surf, grid_weights = weights)
all_landscapes
```

Optimal landscapes for groups are then calculated using `calcWprimeBy()` and can be statistically compared using `multi.lands.grp.test()`:

```{r}
wprime_by_Group <- calcWprimeBy(all_landscapes, by = ~Ecology)

wprime_by_Group
summary(wprime_by_Group)
plot(wprime_by_Group, ncol = 2)

tests <- multi.lands.grp.test(wprime_by_Group)
tests
```

To cite `Morphoscape`, please run `citation("Morphoscape")`.

Owner

  • Name: Blake V Dickson
  • Login: blakedickson
  • Kind: user

GitHub Events

Total
  • Watch event: 1
  • Push event: 4
Last Year
  • Watch event: 1
  • Push event: 4

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 87
  • Total Committers: 3
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.241
Top Committers
Name Email Commits
blakedickson b****n@g****m 66
Noah Greifer n****r@g****m 19
blakedickson 3****n@u****m 2

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 14
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 26 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.17
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • blakedickson (14)
Pull Request Authors
  • blakedickson (8)
  • rjbrocklehurst (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 122 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: Morphoscape

Computation and Visualization of Adaptive Landscapes

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 122 Last month
Rankings
Forks count: 14.9%
Average: 27.2%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
b.dickson@unsw.edu.au
Last synced: about 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • automap * imports
  • concaveman * imports
  • ggplot2 * imports
  • sp * imports
  • spatial * imports
  • viridis * imports
  • alphahull * suggests
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite