Package: iidda.analysis 2.0.0

Steven Walker

iidda.analysis: Tools for Analyzing IIDDA Datasets

This package contains tools for working with data obtained from the International Infectious Disease Data Archive.

Authors:Steven Walker

iidda.analysis_2.0.0.tar.gz
iidda.analysis_2.0.0.zip(r-4.7)iidda.analysis_2.0.0.zip(r-4.6)iidda.analysis_2.0.0.zip(r-4.5)
iidda.analysis_2.0.0.tgz(r-4.6-any)iidda.analysis_2.0.0.tgz(r-4.5-any)
iidda.analysis_2.0.0.tar.gz(r-4.7-any)iidda.analysis_2.0.0.tar.gz(r-4.6-any)
iidda.analysis_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
iidda.analysis/json (API)

# Install 'iidda.analysis' in R:
install.packages('iidda.analysis', repos = c('https://canmod.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/canmod/iidda-tools/issues

On CRAN:

Conda:

4.98 score 27 scripts 104 exports 67 dependencies

Last updated from:4e958088c4. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING193
source / vignettesOK224
linux-release-x86_64WARNING193
macos-release-arm64WARNING137
macos-oldrel-arm64WARNING107
windows-develWARNING232
windows-releaseWARNING172
windows-oldrelWARNING166
wasm-releaseOK125

Exports:%>%add_user_entriesAttachAvailabilitybasal_groupBasalGroupAdderbrowse_pipeline_dependenciesca_iso_3166_2check_dateclean_canmod_cdicompute_moving_average_defaultComputeMovingAveragecount_aggregator_defaultCountAggregatorcreate_bin_descCustomDataPrepDataDictionaryConverterDeheaperdeheaper_defaultfactor_time_scalefind_unaccounted_casesgenerate_empty_dfgenerate_user_tableget_iidda_attrget_implied_zerosget_unit_labelsgrid_dateshandle_missing_values_defaulthandle_zero_values_defaultHandleMissingValuesHandleZeroValuesharmonize_plotsHierarchicalBalancerHierarchyNormalizeriidda_attach_availabilityiidda_attach_bariidda_attach_seriesiidda_availabilityiidda_bariidda_defaultsiidda_defaults_rmiidda_get_metadataiidda_maiidda_plot_bariidda_plot_boxiidda_plot_heatmapiidda_plot_highlightiidda_plot_maiidda_plot_rohani_heatmapiidda_plot_settingsiidda_plot_waveletiidda_prep_availabiliyiidda_prep_bariidda_prep_boxiidda_prep_maiidda_prep_rohaniiidda_prep_seasonal_heatmapiidda_prep_seriesiidda_prep_waveletiidda_render_plotiidda_seriesiidda_set_column_typesiidda_themeiidda_theme_aboveiidda_theme_availability_barsiidda_theme_availability_heatmapiidda_theme_heatjoin_lookup_tablejoin_user_tablelog1p_modified_translookup_joinmagnitudemake_time_transmid_datesmid_timesmutate_time_varsnames_to_join_bynormalize_disease_hierarchynormalize_duplicate_sourcesnormalize_locationnormalize_populationnormalize_time_scalesnum_daysnum_days_utilperiod_aggregator_defaultperiod_averagerperiod_describer_defaultPeriodAggregatorPeriodDescriberquantile_transread_iidda_datasetresolve_joinseries_harmonizer_defaultSeriesHarmonizerSkipperTimeRangeDescriberTimeScalePickerTimeVariableConverterTitleGuessertitleizetrim_series_defaultTrimSeriesunion_seriesvalid_time_varsyear_end_fix

Dependencies:base64encbitbit64cachemclicliprcpp11crayoncurldotCall64dplyrEMDfarverfastmapfieldsgenericsggforceggplot2gluegtablehmsiiddaisobandjanitorjsonlitelabelinglatticelifecyclelocfitlubridatemagrittrmapsMASSmemoisepatchworkpillarpitonpkgconfigpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangS7scalessnakecasespamstringistringrsystemfontstibbletidyrtidyselecttidyxltimechangetweenrtzdbutf8vctrsviridisLitevroomWaveletCompwithr

plot_rohani
Plotting Infectious Disease Time-Series | Example Data | Generalizing Rohani, Earn, and Grenfell
Rendered fromplot_rohani.Rmdusingknitr::rmarkdown

Last update: 2024-03-15
Started: 2023-01-30

flexi_filter
What is flexi_filter for? | What does flexi_filter return? | What you can search
Rendered fromflexi_filter.Rmdusingknitr::rmarkdown

Last update: 2022-11-05
Started: 2022-11-05

Readme and manuals

Help Manual

Help pageTopics
Add entries to user tableadd_user_entries
Basal Groupbasal_group
Basal Group AdderBasalGroupAdder
Browse Pipeline Dependenciesbrowse_pipeline_dependencies
Order Canadian Provinces Geographicallyca_iso_3166_2
Test if x is a Date, coerce if notcheck_date
Clean CANMOD CDI Dataclean_canmod_cdi
Compute Moving Average of Time SeriesComputeMovingAverage
Count AggregatorCountAggregator
Create age bin descriptionscreate_bin_desc
Custom Data Prep FunctionCustomDataPrep
Data Prep Constructorsdata_prep_constructors
Data Dictionary ConverterDataDictionaryConverter
De-heaping time seriesDeheaper
Factor Time Scalefactor_time_scale
Find Unaccounted Casesfind_unaccounted_cases
Data for a Particular Diseasegenerate_disease_df
Create empty table with column namesgenerate_empty_df
Create user-defined lookup tablegenerate_user_table
Get IIDDA Attributeget_iidda_attr
Get Implied Zerosget_implied_zeros
Get time unit labelsget_unit_labels
Create a grid of dates starting at the first day in grid unitgrid_dates
Data Prep Default Functionscompute_moving_average_default count_aggregator_default data_prep_default deheaper_default handle_missing_values_default handle_zero_values_default period_aggregator_default period_describer_default series_harmonizer_default trim_series_default
Handle Missing Values in Series VariableHandleMissingValues
Handle Zero Values in Series VariableHandleZeroValues
Attach Bar Plot to Datasetiidda_attach_bar
Get IIDDA metadataiidda_get_metadata
Plot Bar Graphiidda_plot_bar
Plot Box Plotiidda_plot_box
Plot Heatmapiidda_plot_heatmap
Add Plot Highlightiidda_plot_highlight
Plot Moving Average Time Seriesiidda_plot_ma
Plot Rohani Heatmapiidda_plot_rohani_heatmap
LBoM plot settingsiidda_plot_settings
Plot Waveletiidda_plot_wavelet
Prep Data for Bar Graphiidda_prep_bar
Prep Data for Box plotiidda_prep_box
Prep Data for Rohani Plotiidda_prep_rohani
Prep Data for seasonal heatmapiidda_prep_seasonal_heatmap
Render a Plotiidda_render_plot
Plot a time seriesiidda_attach_series iidda_prep_ma iidda_prep_series iidda_series
Themes for ggplot2iidda_theme iidda_theme_above iidda_theme_heat iidda_theme_time
Join lookup tablejoin_lookup_table
Join user-defined lookup tablejoin_user_table
Log1p Scale Transformationlog1p_modified_trans
Left join for lookup tableslookup_join
Lubridate functionslubridate_funcs
Get time transformationmake_time_trans
Period Mid-Dates and Mid-Timesmid_dates mid_dates_times mid_times
Mutate time variablesmutate_time_vars
Column names to join bynames_to_join_by
Normalize Disease Hierarchynormalize_disease_hierarchy
Normalize Duplicate Sourcesnormalize_duplicate_sources
Normalize Locationnormalize_location
Normalize Populationnormalize_population
Normalize Time Scalesnormalize_time_scales
Numbers of Daysnum_days num_days_util
Obtain period midpoints and average daily rates for count dataperiod_averager
Period AggregatorPeriodAggregator
Period DescriberPeriodDescriber
Quantile Transformationquantile_trans
Read IIDDA Dataset into a Dataframeread_iidda_dataset
Resolve left_joinresolve_join
Series HarmonizerSeriesHarmonizer
Skip Pipeline StepSkipper
Series variablesstd_series_variables
Time unitsstd_time_units
Time variablesstd_time_variables
Time Extenttime_extent
Time Range DesciberTimeRangeDescriber
Time Scale PickerTimeScalePicker
Time Variable ConverterTimeVariableConverter
Title GuesserTitleGuesser
Titleizetitleize
Trim Time SeriesTrimSeries
Union Time Seriesunion_series
Get unique tokens from iidda metadataunique_entries
Validate time variablesvalid_time_vars
Prep Data for Wavelet Plotwavelet_something
Year End Fixyear_end_fix