Package: sitrep 0.2.3

Alexander Spina

sitrep: Report templates and helper functions for applied epidemiology

Report templates and helper functions for applied epidemiology

Authors:Alexander Spina [aut, cre], Zhian N. Kamvar [aut], Dirk Schumacher [aut], Kate Doyle [aut], Chris Jarvis [aut], Lukas Richter [aut], Annick Lenglet [cph], Neale Batra [ctb]

sitrep_0.2.3.tar.gz
sitrep_0.2.3.zip(r-4.5)sitrep_0.2.3.zip(r-4.4)sitrep_0.2.3.zip(r-4.3)
sitrep_0.2.3.tgz(r-4.4-any)sitrep_0.2.3.tgz(r-4.3-any)
sitrep_0.2.3.tar.gz(r-4.5-noble)sitrep_0.2.3.tar.gz(r-4.4-noble)
sitrep_0.2.3.tgz(r-4.4-emscripten)sitrep_0.2.3.tgz(r-4.3-emscripten)
sitrep.pdf |sitrep.html✨
sitrep/json (API)
NEWS

# Install 'sitrep' in R:

install.packages('sitrep', repos = c('https://r4epi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/r4epi/sitrep/issues

Datasets:

AJS_linelist_internal - Example outbreak data for Hepatatis E virus or Acute Jaundice Syndrome
AJS_pop_internal - Example population data for Hepatatis E virus or Acute Jaundice Syndrome
shape_block_internal - Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome
shape_quartier_internal - Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome

On CRAN:

epidemiology msf outbreaks report-generator

4.08 score 40 stars 9 scripts 52 exports 159 dependencies

Last updated 2 years agofrom:b96906b87b. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win	WARNING	Oct 25 2024
R-4.5-linux	WARNING	Oct 25 2024
R-4.4-win	WARNING	Oct 25 2024
R-4.4-mac	WARNING	Oct 25 2024
R-4.3-win	WARNING	Oct 25 2024
R-4.3-mac	WARNING	Oct 25 2024

Exports:add_ar add_cfr add_crosstabs add_mr add_weights_cluster add_weights_strata age_categories age_pyramid assert_positive_timespan attack_rate augment_redundant available_sitrep_templates case_fatality_rate case_fatality_rate_df check_sitrep_templates constrain_dates data_frame_from_2x2 dots_to_charlist download_kobo download_outbreak_linelist download_outbreak_pop download_shape_block download_shape_quartier download_survey fac_from_num find_breaks find_date_cause find_end_date find_start_date fmt_ci fmt_ci_df fmt_count fmt_pci fmt_pci_df gen_data gen_polygon gen_population group_age_categories gt_mh_odds gt_remove_stat merge_ci_df merge_pci_df mortality_rate msf_dict msf_dict_rename_helper msf_dict_survey rename_redundant tab_linelist tab_survey tab_univariate unite_ci zcurve

Dependencies:abind anthro anytime apyramid askpass backports base64enc BH bigD binom bit bit64 bitops broom bslib cachem cards cellranger class classInt cli clipr colorspace commonmark cpp11 crayon curl data.table DBI digest dplyr e1071 ellipsis epidict epikit epitabulate evaluate fansi farver fastmap flextable fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreign fs gdtools generics ggalluvial ggplot2 ggspatial glue gt gtable gtsummary haven here highr hms htmltools htmlwidgets isoband janitor jpeg jquerylib jsonlite juicyjuice KernSmooth knitr labeling labelled lattice lazyeval lifecycle lubridate magrittr markdown MASS matchmaker Matrix memoise mgcv mime minqa mitools munsell nlme numDeriv officer openssl pacman parsedate patchwork pillar pkgconfig png prettyunits progress proxy purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs RColorBrewer Rcpp RcppArmadillo reactable reactR readr readxl rematch remotes rio rlang rmarkdown rosm rprojroot rstudioapi s2 sass scales sf slider snakecase srvyr stringi stringr survey survival sys systemfonts textshaping tibble tidyr tidyselect timechange tinytex tsibble tzdb units utf8 uuid V8 vctrs viridisLite vroom warp withr wk writexl xfun xml2 yaml zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Functions re-exported from apyramid	age_pyramid
Example outbreak data for Hepatatis E virus or Acute Jaundice Syndrome (AJS)	AJS_linelist_internal
Example population data for Hepatatis E virus or Acute Jaundice Syndrome (AJS)	AJS_pop_internal
Display the available sitrep templates	available_sitrep_templates
Access kobo data dictionary	download_kobo
Access AJS outbreak linelist	download_outbreak_linelist
Access AJS outbreak population data	download_outbreak_pop
Access Am Timan blocks shapefile	download_shape_block
Access Am Timan quartier shapefile	download_shape_quartier
Access fake mortality survey data	download_survey
Internal function (not exported - i.e. not userfacing) to reduce code duplication	generic_download
Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome (AJS)	shape_block_internal
Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome (AJS)	shape_quartier_internal