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R: Automated and Early Detection of Seasonal Epidemic Onset
...NEWS. Help Pages aedseo Automated and Early Detection of Seasonal Epidemic Onset autoplot Create a complete 'ggplot' appropriate to a particular data type autoplot.aedseo Create a complete 'ggplot'...
/CRAN/refmans/aedseo/html/00Index.html
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R: Automated and Early Detection of Seasonal Epidemic Onset
...Seasonal Epidemic Onset Description This function performs automated and early detection of seasonal epidemic onsets (aedseo) on a time series dataset. It estimates growth rates for consecutive time...
/CRAN/refmans/aedseo/html/aedseo.html
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Automated Detection of Seasonal Epidemic Onset in R
...Seasonal Epidemic Onset in R library(aedseo) library(tibble) library(tidyr) library(dplyr) library(ggplot2) Introduction The methodology used to detect the onset of seasonal respiratory epidemics can...
/CRAN/packages/aedseo/vignettes/aedseo_introduction.html
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R: The Moving Epidemic Method
The Moving Epidemic Method Documentation for package ‘mem’ version 2.18 DESCRIPTION file. Help Pages epimem Deprecated function(s) in the mem package epitiming Deprecated function(s) in the mem...
/CRAN/refmans/mem/html/00Index.html
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R: Functions and Data for "Epidemics: Models and Data in R"
..."Epidemics: Models and Data in R" Documentation for package ‘epimdr’ version 0.6-5 DESCRIPTION file. Help Pages BarabasiAlbert Function to generate a Barabasi-Albert network black Black's measles...
/CRAN/refmans/epimdr/html/00Index.html
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R: Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"
..."Epidemics: Models and Data in R (2nd Edition)" Documentation for package ‘epimdr2’ version 1.0-9 DESCRIPTION file. Help Pages barabasiAlbert Function to generate a Barabasi-Albert network black...
/CRAN/refmans/epimdr2/html/00Index.html
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R: Influenza Epidemic Timing
...the optimal timing of an influenza epidemic in a set of weekly influenza surveillance rates. It provides the start and the end of the epidemic, also it returns a list of pre-epidemic and post-epidemic...
/CRAN/refmans/mem/html/memtiming.html
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R: Creates the surveillance graph of the current season
...season Description Function memsurveillance creates a surveillance graph for the current season. Usage memsurveillance( i.current, i.epidemic.thresholds = NA, i.intensity.thresholds = NA, i.mean...
/CRAN/refmans/mem/html/memsurveillance.html
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R: Simulate Point-Source Epidemics
...Epidemics Description Simulation of epidemics which were introduced by point sources. The basis of this programme is a combination of a Hidden Markov Model (to get random timepoints for outbreaks)...
/CRAN/refmans/surveillance/html/sim.pointSource.html
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R: Methods for influenza modelization
...in the Moving Epidemics Method (MEM) used to monitor influenza activity in a weekly surveillance system. Usage memmodel( i.data, i.seasons = 10, i.type.threshold = 5, i.level.threshold = 0.95, i.tails...
/CRAN/refmans/mem/html/memmodel.html
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hhh4: Endemic-epidemic modeling of areal count time series
...own work. hhh4: Endemic-epidemic modeling of areal count time series Sebastian Meyer∗ Leonhard Held Michael Höhle Friedrich-Alexander-Universität Erlangen-Nürnberg University of Zurich Stockholm...
/CRAN/packages/surveillance/vignettes/hhh4_spacetime.pdf
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'hhh4': An endemic-epidemic modelling framework for infectious disease counts
...modelling and monitoring of epidemic phenomena. This vignette is concerned with the hhh4 modelling framework for univariate and multivariate time series of infectious disease counts proposed by Held...
/CRAN/packages/surveillance/vignettes/hhh4.pdf
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twinstim: An endemic-epidemic modeling framework for spatio-temporal point patterns
...your own work. twinstim: An endemic-epidemic modeling framework for spatio-temporal point patterns Sebastian Meyer∗ Leonhard Held Michael Höhle Friedrich-Alexander-Universität Erlangen-Nürnberg...
/CRAN/packages/surveillance/vignettes/twinstim.pdf
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R: Goodness of fit of the mem
...different indicators related to the goodness of the MEM for detecting the epidemics, using data from the model and using all data in the original dataset. Usage memgoodness( i.data, i.seasons = 10, i...
/CRAN/refmans/mem/html/memgoodness.html
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R: Example dataset for a multi-group SIR model
sir_example {simode} R Documentation Example dataset for a multi-group SIR model Description A model for the spread of a seasonal influenza epidemics in two groups over five seasons. Usage sir_example...
/CRAN/refmans/simode/html/sir_example.html
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R: Evolution of estimators
...mem estimators Usage memevolution( i.data, i.evolution.seasons = 10, i.evolution.method = "sequential", ... ) Arguments i.data Data frame of input data. i.evolution.seasons Maximum number of seasons...
/CRAN/refmans/mem/html/memevolution.html
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R: Creates the animated graph of the surveillance of the current...
...the current season Description Function memsurveillance.animated creates an animated surveillance graph for the current season. Usage memsurveillance.animated( i.current, i.epidemic.thresholds = NA, i...
/CRAN/refmans/mem/html/memsurveillance.animated.html
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R: Thresholds for influenza intensity
...historical records (surveillance rates). Usage memintensity(i.flu) Arguments i.flu An object of class mem. Details This method is based on the Moving Epidemics Method (MEM) used to monitor influenza...
/CRAN/refmans/mem/html/memintensity.html
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R: Stability of indicators
Details Shows the stability of the main indicators according the number of seasons used to calculate them. That allows to decide the minimum and maximum number of seasons to be included in the model...
/CRAN/refmans/mem/html/memstability.html
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R: Predictions from a 'hhh4' Model
...fitted hhh4 model (class "hhh4"). newSubset subset of time points for which to return the predictions. Defaults to the subset used for fitting the model, and must be a subset of 1:nrow(object$stsObj).
/CRAN/refmans/surveillance/html/hhh4_predict.html
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R: Methods for influenza trend calculation
...trend. Usage memtrend( i.flu, i.type = 1, i.level = 0.95, i.type.boot = "norm", i.iter.boot = 10000 ) Arguments i.flu An object of class mem. i.type Type of confidence interval to calculate the trend...
/CRAN/refmans/mem/html/memtrend.html
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R: Plots for Fitted 'hhh4'-models
...hhh4-models Description There are six types of plots for fitted hhh4 models: Plot the "fitted" component means (of selected units) along time along with the observed counts. Plot the estimated "season"...
/CRAN/refmans/surveillance/html/hhh4_plot.html
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R: Data transformation
...frame of input data. i.range.x First and last surveillance week. i.name Name of the column to transform. i.max.na.per maximum percentage of na's in a season allowable, otherwise, the season is removed ...
/CRAN/refmans/mem/html/transformdata.html
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R: Data transformation
...i.fun = mean ) Arguments i.data Data frame of input data. i.name Name of the column that contains the values. i.cutoff.original Cutoff point between seasons when they have two years i.range.x.final...
/CRAN/refmans/mem/html/transformdata.back.html
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R: Creates the historical series graph of the datasets
...file = T, i.graph.file.name = "", i.plot.timing = F, i.plot.intensity = F, i.alternative.thresholds = NA, i.color.pattern = c("#C0C0C0", "#606060", "#000000", "#808080", "#000000", "#001933", "#00C000", ...
/CRAN/refmans/mem/html/full.series.graph.html
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R: Transformation of series of data
...to be used by functions to fit two waves. Details Input data must be a data.frame with each column a surveillance season and each row a week. Transformation options: 1 No transformation 2 Odd 3 Fill ...
/CRAN/refmans/mem/html/transformseries.html
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R: Model for Landscape Epidemiology & Evolution
...dispersal, inits, seed, cultivars_param, basic_patho_param, genes_param, treatment_param ) Arguments time_param list of simulation parameters: Nyears = number cropping seasons, nTSpY = ...
/CRAN/refmans/landsepi/html/model_landsepi.html
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R: mcmctsir
...runs the TSIR model using a MCMC estimation. The susceptibles are still reconstructed in the same way as the regular tsir model, however beta, alpha, and sbar (or whatever combination you enter) are...
/CRAN/refmans/tsiR/html/mcmctsir.html
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R: Fitting HHH Models with Random Effects and Neighbourhood...
...negative binomial model to a univariate or multivariate time series of counts. The characteristic feature of hhh4 models is the additive decomposition of the conditional mean into epidemic and endemic...
/CRAN/refmans/surveillance/html/hhh4.html
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R: Plots for Fitted 'algo.twins' Models
...Fitted algo.twins Models Description Plot results of fitting a twins model using MCMC output. Plots similar to those in the Held et al. (2006) paper are generated. Usage ## S3 method for class 'atwins'...
/CRAN/refmans/surveillance/html/plot.atwins.html
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R: Analysis of different indicators to find the optimum value of...
...indicators to find the optimum value of the window parameter Description Function roc.analysis perform a ROC analysis Usage roc.analysis( i.data, i.param.values = seq(1, 5, 0.1), i.min.seasons = 6, i...
/CRAN/refmans/mem/html/roc.analysis.html
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R: runtsir
..."deterministic", inits.fit = FALSE, epidemics = "cont", pred = "forward", threshold = 1, seasonality = "standard", add.noise.sd = 0, mul.noise.sd = 0, printon = F, fit = NULL, fittype = NULL...
/CRAN/refmans/tsiR/html/runtsir.html
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R: Generation of epidemiological and economic model outputs
...model outputs Description Generates epidemiological and economic outputs from model simulations. Usage epid_output( types = "all", time_param, Npatho, area, rotation, croptypes, cultivars_param...
/CRAN/refmans/landsepi/html/epid_output.html
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/CRAN/packages/landsepi/vignettes/list_of_parameters.pdf
...spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. Assumptions: In orange...
/CRAN/packages/landsepi/vignettes/list_of_parameters.pdf
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MGDrivE2: Simulation of Time-inhomogeneous Stochastic Processes (Seasonality)
...Petri Net Equilibrium Conditions and Hazard Functions Simulation of Fully Specified SPN Model Simulation: ODE Models Simulation: CTMC Models Results References Preface The Stochastic Petri net (SPN)...
/CRAN/packages/MGDrivE2/vignettes/inhomogeneous.html
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4 - Running a simple simulation with a pathogen with mixed reproduction system
...a simple simulation for details on basic parameterisation. ## Initialisation of the simulation simul_params <- createSimulParams(outputDir = getwd()) ## Seed simul_params@Seed simul_params <- setSeed...
/CRAN/packages/landsepi/vignettes/O4-run_sex_repro.html
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R: Landscape Epidemiology and Evolution
...spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. Details Package: landsepi Type...
/CRAN/refmans/landsepi/html/landsepi-package.html
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/CRAN/packages/landsepi/vignettes/landsepi_poster.pdf
Modelling plant resistance deployment: the R package landsepi The R package landsepi provides a general modelling framework to help compare plant resistance deployment strategies and understand the...
/CRAN/packages/landsepi/vignettes/landsepi_poster.pdf
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SPARSE-MOD SEIR Model
...-MOD SEIR Model. SEIR stands for the numbers (not fractions) of Susceptible-Exposed-Infectious-Removed hosts, which define the state variables of the model. The differential equations of this model are: ...
/CRAN/packages/SPARSEMODr/vignettes/seir-model.html
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shinySIR: Interactive plotting for infectious disease models
...models shinySIR provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ODE models (such as the SIR, SIRS, and SIS models)...
/CRAN/packages/shinySIR/vignettes/Vignette.html
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R: Simulation with input parameters as data.frames.
...-genetic model simulating the spread and evolution of a pathogen in a heterogeneous landscape and generating a wide range of epidemiological, evolutionary and economic outputs. Usage simul_landsepi...
/CRAN/refmans/landsepi/html/simul_landsepi.html
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R: Simulates the spread of Ascochyta blight in a chickpea field
...a chickpea paddock over a growing season. Both host and pathogen activities are simulated in one square metre cells. Usage trace_asco( weather, paddock_length, paddock_width, sowing_date, harvest_date...
/CRAN/refmans/ascotraceR/html/trace_asco.html
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R: Print, Summary and other Standard Methods for '"hhh4"'...
...some standard extraction methods defined for objects of class "hhh4" resulting from a call to hhh4. The implementation is illustrated in Meyer et al. (2017, Section 5), see vignette("hhh4_spacetime").
/CRAN/refmans/surveillance/html/hhh4_methods.html
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R: Run a simulation
...demo-genetic model simulating the spread and evolution of a pathogen in a heterogeneous landscape and generating a wide range of epidemiological, evolutionary and economic outputs. Usage runSimul...
/CRAN/refmans/landsepi/html/runSimul.html
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Getting started
...take into account the effect of numerous covariates, taken individually or in the form of interactions, on the epidemic process, without having to use advanced mathematics to formalize the model into...
/CRAN/packages/nosoi/vignettes/nosoi.html
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/CRAN/refmans/pomp/help/macros/citations.Rd
...{\Anderson2001}{J.L. Anderson. An ensemble adjustment Kalman filter for data assimilation. \emph{Monthly Weather Review} \bold{129}, 2884--2903, 2001.} \newcommand{\Andrieu2009}{C. Andrieu and G.O....
/CRAN/refmans/pomp/help/macros/citations.Rd
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Introduction to excessmort
...Rafael Irizarry and Rolando Acosta 2024-03-13 This document is an introduction to the excessmort package for analyzing time series count data. The packages was designed to help estimate excess...
/CRAN/packages/excessmort/vignettes/excessmort.html
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Getting started with outbreak detection
...various endemic-epidemic modelling frameworks for surveillance data (hhh4, twinSIR, and twinstim), as well as more outbreak detection methods (glrnb, boda, and farringtonFlexible). These new features...
/CRAN/packages/surveillance/vignettes/surveillance.pdf
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/CRAN/refmans/spatPomp/help/macros/cite.Rd
...Assimilation. \emph{Monthly Weather Review} \bold{129}, 2884--2903, 2001.} \newcommand{\arulampalam2002}{Arulampalam, M. S., Maskell, S., Gordon, N. and Clapp, T. (2002) A Tutorial on Particle Filters...
/CRAN/refmans/spatPomp/help/macros/cite.Rd
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R: Power-Law and Nonparametric Neighbourhood Weights for...
...-Models Description Set up power-law or nonparametric weights for the neighbourhood component of hhh4-models as proposed by Meyer and Held (2014). Without normalization, power-law weights are w_{ji}...
/CRAN/refmans/surveillance/html/hhh4_W.html
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CRAN Task View: Time Series Analysis
...Maintainer: Rob J Hyndman, Rebecca Killick Contact: Rob.Hyndman at monash.edu Version: 2023-04-04 URL: https://CRAN.R-project.org/view=TimeSeries Source: https://github.com/cran-task-views/TimeSeries/...
/CRAN/views/TimeSeries.html
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R: Measles in UK spatPomp generator
...Generate a spatPomp object for measles in the top-U most populous cities in England and Wales. The model is adapted from He et al. (2010) with gravity transport following Park and Ionides (2020). The...
/CRAN/refmans/spatPomp/html/measles.html
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SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations
...Sweden Uppsala University Sweden Abstract We present the R package SimInf which provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large...
/CRAN/packages/SimInf/vignettes/SimInf.pdf
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R: Nonlinear forecasting
...fail.value = NA_real_, params, rinit, rprocess, rmeasure, ..., verbose = getOption("verbose") ) ## S4 method for signature 'pomp' nlf_objfun( data, est = character(0), lags, nrbf = 4, ti, tf, seed...
/CRAN/refmans/pomp/html/nlf.html
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R: Occurrence of Invasive Meningococcal Disease in Germany
...location of 636 cases of invasive meningococcal disease (IMD) caused by the two most common meningococcal finetypes in Germany, ‘B:P1.7-2,4:F1-5’ (of serogroup B) and ‘C:P1.5,2:F3-3...
/CRAN/refmans/surveillance/html/imdepi.html
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SpTe2M: Nonparametric Modeling and Monitoring of Spatio-Temporal Data
SpTe2M: Nonparametric Modeling and Monitoring of Spatio-Temporal Data Kai Yang, Peihua Qiu September 29, 2023 Introduction Florida ILI Data Load ILI data Create ILI maps ILI Data Modeling Estimate...
/CRAN/packages/SpTe2M/vignettes/SpTe2M.html
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Monitoring Count Time Series in R: Aberration Detection in Public Health Surveillance
...2016;70(10):1–35. doi:10.18637/jss.v070.i10. Monitoring Count Time Series in R: Aberration Detection in Public Health Surveillance Maëlle Salmon Dirk Schumacher Michael Höhle Robert Koch Institute...
/CRAN/packages/surveillance/vignettes/monitoringCounts.pdf
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R: A real data example for 'recur.bart'.
...xdm.train, can be obtained online at https://www.mcw.edu/-/media/MCW/Departments/Biostatistics/tr064zip.zip There are 488 patients in the full cohort: 235 in the training set and 253 in the testing ...
/CRAN/refmans/BART/html/xdm20.train.html
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'algo.glrnb': Count data regression charts using the generalized likelihood ratio statistic
...statistic Valentin Wimmer(1,2)∗ and Michael Höhle(1,2) (1) Department of Statistics, University of Munich, Germany (2) MC-Health – Munich Center of Health Sciences 6 June 2008 Abstract The aim of...
/CRAN/packages/surveillance/vignettes/glrnb.pdf
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1 - Running a simple simulation
...model, assumptions and available functions. See also the vignette list of parameters for a detailed description of all model parameters. Take a quick overview of what landsepi can do. Initialisation...
/CRAN/packages/landsepi/vignettes/O1-run_simple_simul.html
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/CRAN/packages/dynr/vignettes/NonlinearContinuousTimeModels.pdf
...-Miin Chow November 27, 2023 This le demonstrates the utilization of dynr in tting single-regime and regime-switching nonlinear dynamic models. As extensions of linear models, nonlinear dynamic models...
/CRAN/packages/dynr/vignettes/NonlinearContinuousTimeModels.pdf
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Molecular Clock Dating of Influenza H3N2
...Clock Dating of Influenza H3N2 Erik Volz 2020-01-26 Introduction treedater fits a strict or relaxed molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.
/CRAN/packages/treedater/vignettes/h3n2.html
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Spread of a pathogen in a homogeneous population
Spread of a pathogen in a homogeneous population Sebastian Lequime 2024-02-09 nosoi can accommodate a wide range of epidemiological transmission scenarios. It hence relies on many parameters, that need...
/CRAN/packages/nosoi/vignettes/none.html
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tscount: An R Package for Analysis of Count Time Series Following Generalized Linear Models
...tscount provides likelihood-based estimation methods for analysis and modeling of count time series following generalized linear models. This is a flexible class of models which can describe serial...
/CRAN/packages/tscount/vignettes/tsglm.pdf
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CRAN Task View: Agricultural Science
...Task View: Agricultural Science Maintainer: Julia Piaskowski, Adam Sparks, Adrian Correndo Contact: julia.piask at gmail.com Version: 2024-04-19 URL: https://CRAN.R-project.org/view=Agriculture Source...
/CRAN/views/Agriculture.html
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CRAN Task View: Bayesian Inference
CRAN Task View: Bayesian Inference Maintainer: Jong Hee Park, Michela Cameletti, Xun Pang, Kevin M. Quinn Contact: jongheepark at snu.ac.kr Version: 2023-07-17 URL: https://CRAN.R-project.org/view...
/CRAN/views/Bayesian.html
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/CRAN/packages/ETAS/vignettes/usingETASWeapper.pdf
...Model to Earthquake Data Abdollah Jalilian Razi University Abstract The epidemic-type aftershock sequence (ETAS) model is the most widely used statistical model to describe earthquake catalogs. ETAS...
/CRAN/packages/ETAS/vignettes/usingETASWeapper.pdf
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Quotes on Statistics, Data Visualization and Science
...a lot, just by looking. – Yogi Berra (#data visualization,vision) Did you ever see such a thing as a drawing of a muchness? – Lewis Carroll, Alice in Wonderland (#data visualization) The critical...
/CRAN/packages/statquotes/vignettes/statquotes.html
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Codes for the GHO Dimension
Codes for the GHO Dimension 2024-01-19 Available codes for the GHO dimension: Code Title Adult_curr_cig_smoking Prevalence of current cigarette smoking among adults (%) Adult_curr_e-cig Prevalence of...
/CRAN/packages/rgho/vignettes/c-values-gho.html
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GHO indicators
GHO indicators 2024-01-19 Available codes for the COUNTRY dimension: IndicatorCode IndicatorName Language AIR_61 Household and ambient air pollution attributable DALYs (per 100 000 capita) EN AIR_8...
/CRAN/packages/rgho/vignettes/e-indicators.html
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