Package: iidda.analysis 1.0.0

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_1.0.0.tar.gz
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iidda.analysis_1.0.0.tgz(r-4.4-any)iidda.analysis_1.0.0.tgz(r-4.3-any)
iidda.analysis_1.0.0.tar.gz(r-4.5-noble)iidda.analysis_1.0.0.tar.gz(r-4.4-noble)
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iidda.analysis.pdf |iidda.analysis.html
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'))

Peer review:

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

On CRAN:

5.40 score 1 scripts 71 exports 71 dependencies

Last updated 2 days agofrom:a34ec14fa0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:%>%add_user_entriesbrowse_pipeline_dependenciesca_iso_3166_2check_dateclean_canmod_cdiComputeMovingAveragecreate_bin_descfactor_time_scalefind_unaccounted_casesgenerate_empty_dfgenerate_user_tableget_implied_zerosget_unit_labelsgrid_datesHandleMissingValuesHandleZeroValuesiidda_get_metadataiidda_plot_bariidda_plot_boxiidda_plot_heatmapiidda_plot_highlightiidda_plot_maiidda_plot_rohani_heatmapiidda_plot_scalesiidda_plot_settingsiidda_plot_waveletiidda_prep_bariidda_prep_boxiidda_prep_maiidda_prep_rohaniiidda_prep_seasonal_heatmapiidda_prep_seriesiidda_prep_waveletiidda_themeiidda_theme_aboveiidda_theme_heatjoin_lookup_tablejoin_user_tablelog1p_modified_translookup_joinmake_time_transmid_datesmid_timesmutate_time_varsnames_to_join_bynormalize_disease_hierarchynormalize_duplicate_sourcesnormalize_locationnormalize_populationnormalize_time_scalesnum_daysnum_days_utilperiod_averagerPeriodAggregatorquantile_transread_iidda_datasetresolve_joinSeriesHarmonizertime_scale_pickerTimeScalePickertitleizeTrimSeriesunion_seriesvalid_time_varsWaveletDeheaperWaveletInterpolatorWaveletJoinerWaveletNormalizerWaveletTransformeryear_end_fix

Dependencies:bitbit64cachemclicliprcolorspacecpp11crayondotCall64dplyrEMDfansifarverfastmapfieldsgenericsggforceggplot2gluegtablehmsiiddaisobandjanitorjsonlitelabelinglatticelifecyclelocfitlubridatemagrittrmapsMASSMatrixmemoisemgcvmunsellnlmepatchworkpillarpitonpkgconfigpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrrlangscalessnakecasespamstringistringrsystemfontstibbletidyrtidyselecttidyxltimechangetweenrtzdbutf8vctrsviridisLitevroomWaveletCompwithr

flexi_filter

Rendered fromflexi_filter.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

plot_rohani

Rendered fromplot_rohani.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Add entries to user tableadd_user_entries
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
Create age bin descriptionscreate_bin_desc
Data Prep Constructorsdata_prep_constructors
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 Implied Zerosget_implied_zeros
Get time unit labelsget_unit_labels
Create a grid of dates starting at the first day in grid unitgrid_dates
Handle Missing Values in Series VariableHandleMissingValues
Handle Zero Values in Series VariableHandleZeroValues
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
Scale series dataiidda_plot_scales
Plot Time Seriesiidda_plot_series
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 Moving Average Plotiidda_prep_ma
Prep Data for Rohani Plotiidda_prep_rohani
Prep Data for seasonal heatmapiidda_prep_seasonal_heatmap
Prep Data for Time Seriesiidda_prep_series
Prep Data for Wavelet Plotiidda_prep_wavelet
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
Quantile Transformationquantile_trans
Read IIDDA Dataset into a Dataframeread_iidda_dataset
Resolve left_joinresolve_join
Wavelet Series HarmonizerSeriesHarmonizer
Time Extenttime_extent
Default Time Scale Pickertime_scale_picker
Time unitstime_units
Time Scale PickerTimeScalePicker
Titleizetitleize
Trim Time SeriesTrimSeries
Union Time Seriesunion_series
Get unique tokens from iidda metadataunique_entries
Validate time variablesvalid_time_vars
De-heaping time seriesWaveletDeheaper
Wavelet InterpolatorWaveletInterpolator
Wavelet JoinerWaveletJoiner
Wavelet NormalizerWaveletNormalizer
Wavelet TransformerWaveletTransformer
Year End Fixyear_end_fix