Showing 27 of total 27 results (show query)
slwu89
MicroMoB:Discrete Time Simulation of Mosquito-Borne Pathogen Transmission
Provides a framework based on S3 dispatch for constructing models of mosquito-borne pathogen transmission which are constructed from submodels of various components (i.e. immature and adult mosquitoes, human populations). A consistent mathematical expression for the distribution of bites on hosts means that different models (stochastic, deterministic, etc.) can be coherently incorporated and updated over a discrete time step.
Maintained by Sean L. Wu. Last updated 2 years ago.
120.4 match 4.16 score 32 scripts
marshalllab
MGDrivE2:Mosquito Gene Drive Explorer 2
A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.
Maintained by Sean L. Wu. Last updated 4 years ago.
37.4 match 6 stars 6.33 score 30 scripts
mrc-ide
malariasimulation:An individual based model for malaria
Specifies the latest and greatest malaria model.
Maintained by Giovanni Charles. Last updated 28 days ago.
22.0 match 16 stars 8.17 score 146 scripts
mattmar
dynamAedes:A Unified Mechanistic Model for the Population Dynamics of Invasive Aedes Mosquitoes
Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.
Maintained by Matteo Marcantonio. Last updated 1 years ago.
ecologyinvasive-speciesmodellingmosquitoespathogens
20.3 match 7 stars 5.59 score 11 scriptsmarshalllab
MGDrivE:Mosquito Gene Drive Explorer
Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.
Maintained by Hรฉctor Manuel Sรกnchez Castellanos. Last updated 4 years ago.
12.5 match 6 stars 7.06 score 61 scripts
momx
Momocs:Morphometrics using R
The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.
Maintained by Vincent Bonhomme. Last updated 1 years ago.
7.2 match 51 stars 7.42 score 346 scripts
geomorphr
geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Maintained by Dean Adams. Last updated 1 months ago.
4.0 match 76 stars 12.05 score 700 scripts 6 dependents
middleton-lab
abd:The Analysis of Biological Data
The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Maintained by Kevin M. Middleton. Last updated 11 months ago.
7.8 match 6 stars 5.53 score 182 scripts 1 dependents
tdaverse
ripserr:Calculate Persistent Homology with Ripser-Based Engines
Ports the Ripser <https://arxiv.org/abs/1908.02518> and Cubical Ripser <https://arxiv.org/abs/2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.
Maintained by Jason Cory Brunson. Last updated 6 hours ago.
algebraic-topologycohomologycppcubical-complexpersistent-homologypixelpoint-cloudr-languager-programmingrcpprips-complexripsersimplicial-complexsimplicial-homologytopological-data-analysistopologyvietoris-complexvoxelcpp
6.2 match 7 stars 5.98 score 6 scripts
metabocomp
MUVR2:Multivariate Methods with Unbiased Variable Selection
Predictive multivariate modelling for metabolomics. Types: Classification and regression. Methods: Partial Least Squares, Random Forest ans Elastic Net Data structures: Paired and unpaired Validation: repeated double cross-validation (Westerhuis et al. (2008)<doi:10.1007/s11306-007-0099-6>, Filzmoser et al. (2009)<doi:10.1002/cem.1225>) Variable selection: Performed internally, through tuning in the inner cross-validation loop.
Maintained by Yingxiao Yan. Last updated 6 months ago.
7.2 match 2 stars 4.04 score 1 scripts
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
3.8 match 5 stars 7.32 score 310 scripts 3 dependents
ghislainv
jSDM:Joint Species Distribution Models
Fits joint species distribution models ('jSDM') in a hierarchical Bayesian framework (Warton and al. 2015 <doi:10.1016/j.tree.2015.09.007>). The Gibbs sampler is written in 'C++'. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize computation efficiency.
Maintained by Ghislain Vieilledent. Last updated 2 years ago.
4.5 match 11 stars 5.87 score 68 scripts
cidm-ph
ggmapinset:Add Inset Panels to Maps
Helper to add insets based on geom_sf() from 'ggplot2'. This package gives you a drop-in replacement for geom_sf() that supports adding a zoomed inset map without having to create and embed a separate plot.
Maintained by Carl Suster. Last updated 3 months ago.
data-visualizationgeospatialggplot-extensionggplot2
3.5 match 36 stars 6.21 score 9 scripts 1 dependents
e-kotov
alboFr:Get French Data on Tiger Mosquito Colonisation
Get French Data on Tiger Mosquito (Aedes Albopictus) colonisation in France from the online map at <https://signalement-moustique.anses.fr/signalement_albopictus/colonisees>.
Maintained by Egor Kotov. Last updated 22 days ago.
aedes-albopictusdatafrancetiger-mosquito
12.6 match 1.70 score 3 scripts
cran
epiDisplay:Epidemiological Data Display Package
Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at '<https://medipe.psu.ac.th/epicalc/>'.
Maintained by Virasakdi Chongsuvivatwong. Last updated 3 years ago.
3.5 match 1 stars 5.44 score 758 scripts 2 dependents
ptaconet
modisfast:Fast and Efficient Access to MODIS Earth Observation Data
Programmatic interface to several NASA Earth Observation 'OPeNDAP' servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).
Maintained by Paul Taconet. Last updated 6 days ago.
data-cubeearth-science-dataenvironmental-datagpmlandmodisnasaopendapprecipitation-datatemperature-datavegetation-dataviirs
3.3 match 29 stars 5.60 score 13 scripts
daijiang
neonDivData:Standardized NEON Organismal Data for Biodiversity Research
Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).
Maintained by Daijiang Li. Last updated 10 months ago.
4.3 match 15 stars 4.18 score 17 scripts
thiyangt
denguedatahub:A Tidy Format Datasets of Dengue by Country
Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Maintained by Thiyanga S. Talagala. Last updated 1 months ago.
3.2 match 11 stars 5.12 score 34 scriptscran
mosqcontrol:Mosquito Control Resource Optimization
This project aims to make an accessible model for mosquito control resource optimization. The model uses data provided by users to estimate the mosquito populations in the sampling area for the sampling time period, and the optimal time to apply a treatment or multiple treatments.
Maintained by Travis Byrum. Last updated 5 years ago.
5.7 match 2.70 score 4 scripts
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 5 days ago.
2.4 match 1 stars 5.76 score 11 scriptscran
vectorsurvR:Data Access and Analytical Tools for 'VectorSurv' Users
Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Maintained by Christina De Cesaris. Last updated 2 months ago.
3.8 match 3.30 score
claudiofronterre
RiskMap:Geo-Statistical Modeling of Spatially Referenced Data
Provides functions for geo-statistical analysis of both continuous and count data using maximum likelihood methods. The models implemented in the package use stationary Gaussian processes with Matern correlation function to carry out spatial prediction in a geographical area of interest. The underpinning theory of the methods implemented in the package are found in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).
Maintained by Emanuele Giorgi. Last updated 6 months ago.
3.8 match 3.18 score 5 scripts
cran
GAD:Analysis of Variance from General Principles
Analysis of complex ANOVA models with any combination of orthogonal/nested and fixed/random factors, as described by Underwood (1997). There are two restrictions: (i) data must be balanced; (ii) fixed nested factors are not allowed. Homogeneity of variances is checked using Cochran's C test and 'a posteriori' comparisons of means are done using Student-Newman-Keuls (SNK) procedure. For those terms with no denominator in the F-ratio calculation, pooled mean squares and quasi F-ratios are provided. Magnitute of effects are assessed by components of variation.
Maintained by Leonardo Sandrini-Neto. Last updated 11 months ago.
3.3 match 2.00 score
malaria-atlas-project
malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Maintained by Mauricio van den Berg. Last updated 8 months ago.
0.5 match 44 stars 9.10 score 118 scripts 3 dependents
moshejasper
kindisperse:Simulate and Estimate Close-Kin Dispersal Kernels
Functions for simulating and estimating kinship-related dispersal. Based on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito". Assumes an additive variance model of dispersal in two dimensions, compatible with Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, as well as the functions needed to estimate parent-offspring dispersal for simulated or empirical data, and to undertake sampling design for future field studies of dispersal. For ease of use an integrated Shiny app is also included.
Maintained by Moshe-Elijah Jasper. Last updated 5 months ago.
0.5 match 1 stars 3.70 score 5 scripts