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Package: nfidd 1.0.0

NFIDD course contributors

nfidd: Material to support course on nowcasting and forecasting of infectious disease dynamics

Resources to support a short course on nowcasting and forecasting of infectious disease dynamics.

Authors:NFIDD course contributors [cre, aut]

nfidd_1.0.0.tar.gz
nfidd_1.0.0.zip(r-4.5)nfidd_1.0.0.zip(r-4.4)nfidd_1.0.0.zip(r-4.3)
nfidd_1.0.0.tgz(r-4.4-any)nfidd_1.0.0.tgz(r-4.3-any)
nfidd_1.0.0.tar.gz(r-4.5-noble)nfidd_1.0.0.tar.gz(r-4.4-noble)
nfidd_1.0.0.tgz(r-4.4-emscripten)nfidd_1.0.0.tgz(r-4.3-emscripten)
nfidd.pdf |nfidd.html✨
nfidd/json (API)
NEWS

# Install 'nfidd' in R:

install.packages('nfidd', repos = c('https://epiforecasts.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nfidd/nfidd/issues

Datasets:

infection_times - Infection times
mech_forecasts - Forecasts from a mechanistic model
rw_forecasts - Forecasts from a semi-mechanistic model
stat_forecasts - Forecasts from a semi-mechanistic model with additional statistical complexity

On CRAN:

delay-estimation epidemics forecasting infectious-disease-dynamics learning nowcasting outbreak-analysis outbreaks

4.87 score 14 stars 16 exports 21 dependencies

Last updated 2 months agofrom:d01678e108 (on v1.0.0). Checks:OK: 3 NOTE: 4. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 05 2024
R-4.5-win	NOTE	Dec 05 2024
R-4.5-linux	NOTE	Dec 05 2024
R-4.4-win	NOTE	Dec 05 2024
R-4.4-mac	NOTE	Dec 05 2024
R-4.3-win	OK	Dec 05 2024
R-4.3-mac	OK	Dec 05 2024

Exports:add_delays censored_delay_pmf convolve_with_delay geometric_diff_ar geometric_random_walk make_daily_infections make_gen_time_pmf make_ip_pmf nfidd_cmdstan_model nfidd_load_stan_functions nfidd_stan_function_files nfidd_stan_functions nfidd_stan_models nfidd_stan_path renewal simulate_onsets

Dependencies:cli cpp11 dplyr fansi generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Simulate symptom onset and hospitalization times from infection times	add_delays
Discretise a Continuous Delay Distribution	censored_delay_pmf
Convolve a Time Series with a Delay Distribution	convolve_with_delay
Geometric Differenced Autoregressive Process	geometric_diff_ar
Geometric Random Walk	geometric_random_walk
Infection times	infection_times
Convert infection times to a daily time series	make_daily_infections
Generate a probability mass function for the generation time	make_gen_time_pmf
Generate a probability mass function for the incubation period	make_ip_pmf
Forecasts from a mechanistic model	mech_forecasts
Create a CmdStanModel with NFIDD Stan functions	nfidd_cmdstan_model
Load Stan functions as a string	nfidd_load_stan_functions
Get Stan files containing specified functions	nfidd_stan_function_files
Get Stan function names from Stan files	nfidd_stan_functions
List Available Stan Models in NFIDD	nfidd_stan_models
Get the path to Stan code	nfidd_stan_path
Simulate Infections using the Renewal Equation	renewal
Forecasts from a semi-mechanistic model	rw_forecasts
Simulate symptom onsets from daily infection counts	simulate_onsets
Forecasts from a semi-mechanistic model with additional statistical complexity	stat_forecasts