Package: naomi.utils 0.0.13

Jeffrey Eaton

naomi.utils: Utility Functions For Naomi Datasets

This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.

Authors:Jeffrey Eaton [aut, cre]

naomi.utils_0.0.13.tar.gz
naomi.utils_0.0.13.zip(r-4.5)naomi.utils_0.0.13.zip(r-4.4)naomi.utils_0.0.13.zip(r-4.3)
naomi.utils_0.0.13.tgz(r-4.4-any)naomi.utils_0.0.13.tgz(r-4.3-any)
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naomi.utils.pdf |naomi.utils.html✨
naomi.utils/json (API)
NEWS

# Install 'naomi.utils' in R:
install.packages('naomi.utils', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mrc-ide/naomi.utils/issues

On CRAN:

1.60 score 1 stars 10 scripts 41 exports 190 dependencies

Last updated 8 months agofrom:855662cde1 (on master). Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 12 2024
R-4.5-winERROROct 12 2024
R-4.5-linuxERROROct 12 2024
R-4.4-winERROROct 12 2024
R-4.4-macERROROct 12 2024
R-4.3-winERROROct 12 2024
R-4.3-macERROROct 12 2024

Exports:%>%allocate_areas_survey_regionsassert_area_id_checkassert_pop_age_groupassert_pop_data_checkassign_dhs_cluster_areascalc_survey_hiv_indicatorscheck_boundariescheck_pjnz_shiny90compare_boundariescopy_pjnz_extractcreate_individual_hiv_dhscreate_survey_biomarker_dhscreate_survey_boundaries_dhscreate_survey_circumcision_dhscreate_survey_clusters_dhscreate_survey_individuals_dhscreate_survey_meta_dhscreate_survey_regions_dhscreate_surveys_dhsgather_areasgenerate_area_idget_age_groupsget_mid_calendar_quarterhintr_inputs_readynaomi_debugnaomi_extract_gpwnaomi_extract_worldpopplot_area_hierarchy_summaryplot_survey_coordinate_checkread_pjnz_region_coderead_sf_zipread_sf_zip_listread_shiny90_countryrecode_naomi1_age_grouprecode_naomi1_ancrecode_naomi1_artsurveys_add_dhs_regvarvalidate_naomi_populationvalidate_survey_region_areaswrite_sf_shp_zip

Dependencies:abindanclikaskpassassertthatbase64encbeersBHbigDbinombitbit64bitopsbootbriobslibcachemcallrcellrangerclassclassIntclicliprcolorspacecommonmarkcpp11crayoncrosstalkcrulcurldata.tabledata.treeDBIdeldirdigestdocoptdplyre1071ellipsiseppeppasmevaluateexactextractrfansifarverfastmapfastmatchfirst90fontawesomeforcatsforeignfsgenericsgeojsongeojsoniogeojsonsfgeometriesgetPassggplot2gluegtgtablehavenhighrhintrhmshtmltoolshtmlwidgetshttpcodehttpuvhttridsiotoolsisobandjqrjquerylibjsonifyjsonlitejsonvalidatejuicyjuiceKernSmoothknitrlabelinglaterlatticelazyevallgrlifecyclelogwatchlubridatemagrittrmarkdownMASSMatrixmemoisemgcvmimeminqamitoolsmunsellmvtnormnaominaomi.optionsnlmenumDerivopensslopenxlsxpillarpkgconfigplotlyplumberplyrporcelainprettyunitsprocessxprogresspromisesprotoliteproxypspurrrqdapRegexqsR6rapidjsonrRApiSerializerappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrdhsreactablereactRreadrreadxlreduxrematchreshape2rlangrmarkdownrrqrstudioapis2sassscalessfsfheaderssodiumspspDataspdepspeciospudstorrstringfishstringistringrsurveysurvivalswaggersysterratibbletidyrtidyselecttimechangetinytexTMBtraduiretriebeardtzdbunitsurltoolsutf8uuidV8vctrsviridisLitevroomwebutilswithrwkwritexlxfunxml2yamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Allocate areas to survey regionsallocate_areas_survey_regions
Checks for consistent area IDs between two datasetsassert_area_id_check
Checks valid age groupsassert_pop_age_group
Data validation for input population dataassert_pop_data_check
Assign survey clusters to dataset areasassign_dhs_cluster_areas
Calculate age/sex/area stratified survey estimates for biomarker outcomescalc_survey_hiv_indicators
Check full and aggregated boundariescheck_boundaries
Check whether PJNZ contains .shiny90 filecheck_pjnz_shiny90
Compare boundaries of two shapefiles by overlaying themcompare_boundaries
Extract the .DP and .PJN from a Spectrum PJNZcopy_pjnz_extract
Create individual HIV outcomes dataset from DHScreate_individual_hiv_dhs
Create survey region boundaries dataset from DHS spatial data repositorycreate_survey_boundaries_dhs
Create male circumcision outcomes dataset from DHScreate_survey_circumcision_dhs
Create survey clusters datasetcreate_survey_clusters_dhs
Create survey individuals and biomarker dataset from DHS extractcreate_survey_biomarker_dhs create_survey_individuals_dhs
Create DHS survey meta data tablecreate_survey_meta_dhs
Create survey regions dataset from DHScreate_survey_regions_dhs
Create surveys dataset from DHS APIcreate_surveys_dhs
Convert nested hierarchy from wide to long formatgather_areas
Generate single Naomi area idgenerate_area_id
Find Calendar Quarter Midpoint of Two Datesget_mid_calendar_quarter
Prepare output from hintr debug rds for debugginghintr_inputs_ready
Download debug from server and upload into sharepointnaomi_debug
Extract Gridded Population of the World (GPW) raster datanaomi_extract_gpw
Extract WorldPop raster datanaomi_extract_worldpop
Plot area hierarchy levelsplot_area_hierarchy_summary
Summary plot of survey cluster coordinates outside boundariesplot_survey_coordinate_check
Read Spectrum region code from PJNZ fileread_pjnz_region_code
Read shape file from ZIPread_sf_zip
Read Multiple Shape Files in ZIP Archiveread_sf_zip_list
Read country from .zip.shiny90 fileread_shiny90_country
Recode age group from Naomi 1 to Naomi 2recode_naomi1_age_group
Update ART and ANC programme data set to Naomi 2.0 specificationsrecode_naomi1_anc recode_naomi1_art
Add REGVAR to surveys datasetsurveys_add_dhs_regvar
Validate naomi population datasetvalidate_naomi_population
Validation of mapping to survey region areasvalidate_survey_region_areas
Save sf object to zipped ESRI .shp filewrite_sf_shp_zip