R-universe search: exports:region

Showing 10 of total 10 results (show query)

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 22 hours ago.

popgen population-genetics simulations spatial-statistics

56 stars 9.13 score 88 scripts

ropensci

rsat:Dealing with Multiplatform Satellite Images

Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).

Maintained by Unai Pérez - Goya. Last updated 12 months ago.

satellite-images

54 stars 7.45 score 52 scripts

edwbaker

sonicscrewdriver:Bioacoustic Analysis and Publication Tools

Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.

Maintained by Ed Baker. Last updated 3 days ago.

bioacoustics ecoacoustics

6 stars 7.04 score 26 scripts

mrjoh3

c3:'C3.js' Chart Library

Create interactive charts with the 'C3.js' <http://c3js.org/> charting library. All plot types in 'C3.js' are available and include line, bar, scatter, and mixed geometry plots. Plot annotations, labels and axis are highly adjustable. Interactive web based charts can be embedded in R Markdown documents or Shiny web applications.

Maintained by Matt Johnson. Last updated 4 years ago.

chart htmlwidget plots

39 stars 6.45 score 72 scripts

stanfill

rotations:Working with Rotation Data

Tools for working with rotational data, including simulation from the most commonly used distributions on SO(3), methods for different Bayes, mean and median type estimators for the central orientation of a sample, confidence/credible regions for the central orientation based on those estimators and a novel visualization technique for rotation data. Most recently, functions to identify potentially discordant (outlying) values have been added. References: Bingham, Melissa A. and Nordman, Dan J. and Vardeman, Steve B. (2009), Bingham, Melissa A and Vardeman, Stephen B and Nordman, Daniel J (2009), Bingham, Melissa A and Nordman, Daniel J and Vardeman, Stephen B (2010), Leon, C.A. and Masse, J.C. and Rivest, L.P. (2006), Hartley, R and Aftab, K and Trumpf, J. (2011), Stanfill, Bryan and Genschel, Ulrike and Hofmann, Heike (2013), Maonton, Jonathan (2004), Mardia, KV and Jupp, PE (2000, ISBN:9780471953333), Rancourt, D. and Rivest, L.P. and Asselin, J. (2000), Chang, Ted and Rivest, Louis-Paul (2001), Fisher, Nicholas I. (1996, ISBN:0521568900).

Maintained by Bryan Stanfill. Last updated 1 years ago.

openblas cpp

5.23 score 57 scripts 1 dependents

bioc

MSA2dist:MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies.

Maintained by Kristian K Ullrich. Last updated 1 days ago.

alignment sequencing genetics go cpp

4.95 score 7 scripts 1 dependents

bergsmat

metaplot:Data-Driven Plot Design

Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditioning variables to metaplot() to generate density plots, boxplots, mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. The user may choose between trellis and ggplot output. Compact syntax and integrated metadata promote workflow scalability.

Maintained by Tim Bergsma. Last updated 1 years ago.

2 stars 4.49 score 52 scripts 1 dependents

chuxinyuan

CNID:Get Basic Information from Chinese ID Number

The Chinese ID number contains a lot of information, this package helps you get the region, date of birth, age, age based on year, gender, zodiac, constellation information from the Chinese ID number.

Maintained by Xinyuan Chu. Last updated 12 days ago.

3.00 score 1 scripts

mrc-ide

moz.utils:Utility functions

Utility functions, for useful utilitarian uses.

Maintained by Oli Stevens. Last updated 2 months ago.

2.26 score 18 scripts

rwalke

eoR:Data Management Package (Exposure and Occurrence Data in R)

This data management package provides some helper classes for publicly available data sources (HMD, DESTATIS) in Demography. Similar to ideas developed in the Bioconductor project <https://bioconductor.org> we strive to encapsulate data in easy to use S4 objects. If original data is provided in a text file, the resulting S4 object contains all information from that text file. But the information is somehow structured (header, footer, etc). Further the classes provide methods to make a subset for selected calendar years or selected regions. The resulting subset objects still contain the original header and footer information.

Maintained by Rainer Walke. Last updated 5 years ago.

1.70 score 4 scripts