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epimodel

EpiModel:Mathematical Modeling of Infectious Disease Dynamics

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Maintained by Samuel Jenness. Last updated 2 months ago.

agent-based-modelingepidemicsepidemiologyinfectious-diseasesnetwork-graphcpp

250 stars 11.43 score 315 scripts

r-arcgis

arcgislayers:An Interface to ArcGIS Data Services

Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or 'ArcGIS Platform' to read, write, publish, or manage vector and raster data via ArcGIS location services REST API endpoints <https://developers.arcgis.com/rest/>.

Maintained by Josiah Parry. Last updated 13 days ago.

arcgisesrigisr-spatial

50 stars 8.07 score 38 scripts 4 dependents

maliny12

sugarglider:Create Glyph-Maps of Spatiotemporal Data

Provides 'ggplot2' extensions to construct glyph-maps for visualizing seasonality in spatiotemporal data. See the Journal of Statistical Software reference: Zhang, H. S., Cook, D., Laa, U., Langrené, N., & Menéndez, P. (2024) <doi:10.18637/jss.v110.i07>. The manuscript for this package is currently under preparation and can be found on GitHub at <https://github.com/maliny12/paper-sugarglider>.

Maintained by Maliny Po. Last updated 3 months ago.

data-visualization

11 stars 6.68 score 7 scripts

burch-cm

altfuelr:Provides an Interface to the NREL Alternate Fuels Locator

Provides a number of functions to access the National Energy Research Laboratory Alternate Fuel Locator API <https://developer.nrel.gov/docs/transportation/alt-fuel-stations-v1/>. The Alternate Fuel Locator shows the location of alternate fuel stations in the United States and Canada. This package also includes the data from the US Department of Energy Alternate Fuel database as a data set.

Maintained by Christopher Burch. Last updated 4 years ago.

2 stars 3.00 score 5 scripts

j-mitchel

scITD:Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Maintained by Jonathan Mitchel. Last updated 2 years ago.

cpp

1.98 score 19 scripts

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