• switch DT and datatable in example:

https://seandavi.github.io/sars2pack/reference/param_estimates_published.html

Describe the data resource you'd like to add

Before the COVID-19 pandemic, more than 30 million US workers were employed in six broad industries that are now on the frontlines of the response. They include grocery store clerks, nurses, cleaners, warehouse workers, and bus drivers, among others. They were essential before the pandemic hit, yet also overworked, underpaid, under protected, and under appreciated. The tables below provide a basic demographic profile of workers in these frontline industries.

Access details

• URL: https://github.com/ceprdata/frontline-workers
• Format: to sort out
• Open access: [X] Yes or [ ] No (include additional information)

Additional context
https://cepr.net/a-basic-demographic-profile-of-workers-in-frontline-industries/

Add at least:

• source_url: source url(s)
• download_url: download url(s)
• description: prose description from website/data provider
• license: license, if available

Describe the bug
Vignettes no longer updating. Last update date: May 17, 2020

Expected behavior
Daily updated articles, with at most ~24 H delay

Screenshots

Additional context
Appears to affect all vignettes

Using the yaml file in inst/data_catalog, add dateset details to enhance dataset findability and provenance.

Describe the data resource you'd like to add
Personal measures taken to avoid COVID-19

Access details

• URL: https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/yougov/YouGov-Imperial%20COVID-19%20Behavior%20Tracker.csv
• Format: .csv
• Open access: [X] Yes or [ ] No (include additional information)

Additional context

Looks like:

• Bioconductor BiocManager is now set to use Bioc 3.11
• Bioconductor:Bioconductor_docker is using R 3.6.3, although I think rocker:devel is now running R-devel (R-4.1.0 pre)
• Bioc 3.11 requires R version 4.0

So, bioc supported docker is out-of-sync with bioc versioning. Will likely have to ditch Bioconductor docker images for at least the times around releases, as this is likely to happen again.

Just for a rainy day:

• https://github.com/rich-iannone/pointblank

Description

This is a routinely-maintained data repository for US state-level distancing policies to the 2019 novel coronavirus (SARS-CoV-2), the cause of COVID-19. It was developed and is maintained by researchers at the University of Washington, Seattle, WA, USA.

These data will be useful for US state-level modeling, for example implementing the Imperial College covid19model

Access details

• URL: https://github.com/COVID19StatePolicy/SocialDistancing
• Format: .csv
• Open access: [ X ] Yes or [ ] No (include additional information)

Data elements

• File: "USstatesCov19distancingpolicy.csv". Prior datasets are archived with date stamps in the format of YYYYMMDD.
• location_id: State-level unique identifier per the Global Burden of Disease (GBD) study.
• StateFIPS: State-level Federal Information Processing Standard (FIPS) code.
• StatePostal: Two-letter state postal code. This corresponds to StatePostal in the "state_id.csv".
• StateName: State name. This corresponds to StateName in "state_id.csv".
• StatePolicy : String variable of state policies, as described below:
  - EmergDec: Emergency declaration; currently includes State of Emergency, Public Health Emergency, and Public Health Disaster declarations.
  - GathRecomAny: Any recommendation of against gathering that stops short of a formal mandate or restriction of gatherings. Includes uses phrasing such as "advises against mass gatherings" and "constituents should avoid gatherings of more than 100" that imply a recommendation versus restriction.
  - GathRestrictAny: Restriction of any gathering; includes formal mandate or an executive order that uses phrasing such as "prohibits all mass gatherings" (per definition of mass gathering) and "constituents must avoid gatherings of more than 100". The first issuance of a gathering restriction of any size is coded with this date.
  - GathRestrict1000: Restriction of any gathering exceeding 1000 persons; coding followed the "GathRestrict" criteria. Some mandates include exceptions for essential businesses and organizations; these cases are still coded as a restriction applicable to the general public.
  - GathRestrict500: Restriction of any gathering exceeding 500 persons; coding followed the "GathRestrict" criteria and used the same coding approach as "GathRestrict1000" (i.e., considered a restriction if applicable to the general public).
  - GathRestrict250: Restriction of any gathering exceeding 250 persons; coding followed the same criteria as above.
  - GathRestrict100: Restriction of any gathering exceeding 100 persons; coding followed the same criteria as above.
  - GathRestrict50: Restriction of any gathering exceeding 50 persons; coding followed the same criteria as above.
  - GathRestrict25: Restriction of any gathering exceeding 25 persons; coding followed the same criteria as above.
  - GathRestrict10: Restriction of any gathering exceeding 10 persons; coding followed the same criteria as above.
  - GathRestrict5: Restriction of any gathering exceeding 5 persons; coding followed the same criteria as above.
  - SchoolClose: Formal closing of (at minimum) public schools. Where possible, additional information on types of school closings are provided in "PolicyCodingNotes".
  - RestaurantRestrict: Restriction or limitation of restaurants and other venues where food is consumed on-premises. Coding a case as a restriction requires a formal restriction on operations (e.g., offsite consumption only, limiting services to only take-away, delivery, or curbside drop-off) or mandate for substantially reducing operations (e.g., restaurant closure must occur unless 10 or fewer patrons are dining at at time).
  - OtherBusinessClose: Mandate to fully close operations of any category of business. Coding a case as an other business closure requires the executive order to use phrasing indicative of a mandate (e.g., "casinos must close", "operations at fitness centers and entertainment venues must cease by date"). A given state may have multiple cases of other business closures as they often occurred in phases (e.g., fitness centers and gyms on March 13, 2020; casinos and entertainment venues on March 15, 2020; personal service businesses like barbers and nail salons on March 19, 2020); thus, where possible, separate entries are provided for each mandate.
  - NEBusinessClose: Mandate to close all non-essential businesses. Coding a case as a closure order requires the executive order to use phrasing indicative of a mandate (e.g., "non-essential businesses are required to close", "non-essential businesses must cease operations by date"). Coding does not distinguish among states' classification of essential versus non-essential businesses, as they vary substantially by state.
  - StayAtHome: Mandate for individuals to stay at home for all non-essential activities. Coding a case as a stay-at-home order mandate requires the executive order to using phrasing indicative of a mandate (e.g., "must stay at home"); otherwise it is coded as 0 for the "Mandate" variable if it uses advisory phrasing. Coding does not distinguish among states' classification of essential versus non-essential activities, as they vary substantially by state. Shelter-in-place and stay-at-home orders are considered to be equivalent.
  - StateCurfew: Mandates specific curfews at which residents are not to be outside their homes unless performing essential activities, as defined by the state. Coding a case as a state curfew requires specific curfew times (thus "stay-at-home" mandates were not considered curfews).
  -Quarantine: Quarantines mandated for people entering the state, requiring a period of self-isolation. Quarantines may be imposed on all people entering the state, out-of-state residents, or travelers from a particular state or city. Quarantine length and who is covered by the policy can be found in the "PolicyNotes" variable. This policy type was added April 3, 2020.
  -TravelRestrictIntra: Restrictions on travel within the state. These restrictions can be between cities or counties or within them. The "StateWide" variable reflects whether these restrictions are applicable to across the state (coded as 1) or only for local areas (coded as 0). This policy type was added April 3, 2020.
  -TravelRestrictExit: Policies which prohibit residents of a state from leaving the state. These policies may have exceptions for essential businesses. This policy type was added April 3, 2020.
  - TravelRestrictEntry: Travel restriction mandates that limit non-residents from entering a given state. These policies may have exceptions or exemptions for essential businesses or their employees, and they may include restrictions for commercial lodging for non-residents. This policy type was added April 8, 2020.
• Mandate: Binary variable indicating whether the policy applied is a mandate (1) or is advisory or a recommendation (0). This is coded on the basis of the order's phrasing (e.g., "residents are advised to stay at home and avoid unnecessary travel" would be coded as 0 for mandate as a "StayAtHome" policy). This variable was added on March 30, 2020.
• DateIssued: Date of policy issuance. The date of signing of the policy document (e.g., executive order) was used wherever possible. Format is YYYYMMDD (e.g., March 16, 2020 is 20200316). Entries are not currently included for most non-statewide policies; this documentation is in-progress.
• DateEnacted: Date of policy enactment: the date of when the policy would be enforced, per descriptions available in policy documents. The format is YYYYMMDD. Entries are not currently included for most non-statewide policies; this documentation is in-progress.
• DateExpiry: Date of policy expiry, if or as provided in the policy issuance or executive order. This date is meant to reflect when the policy or order would be in effect until or unless additional action is taken to extend, amend, or halt its status. The format is YYYYMMDD. This documentation is in-progress, as it was added on March 29, 2020 as a variable of interest.
• DateEnded: Date the policy is ended. This date is meant to reflect when a policy is ended, particularly if it is halted or reversed prior to its expiry date. The format is YYYYMMDD. This documentation is in-progress.
• PolicyCodingNotes: Coder notes. Information on specific businesses closed, type of emergency declaration, potential exceptions, etc., are provided here.
• PolicySource: Currently available source for each policy issued. Sourcing by hard-copy PDF versus hyperlinks is in-progress.
• StateWide: Binary variable indicating whether the policy applied statewide (1) or for local areas (0).
• LastUpdated: Date of last update for the given state-policy observation. The format is YYYYMMDD.
• LastUpdatedNotes: Coder notes on last updates. This reflects notable changes since the last update, especially if a date has been recoded (e.g., switching to coding orders enacted at 11:59 pm on date1 to date1+1 for its enactment timing) or the "StatePolicy" type has been amended (e.g., some initial coding of "NEBusinessClose" policies were applicable to non-essential in-person retail businesses only, not all non-essential businessess as defined by state).

Describe the data resource you'd like to add
Our dataset on non-pharmaceutical interventions, including school closings, public venue closings, etc., by county

• US
• county-leve
• non-geospatial
• curated, updated

Access details

• URL: https://raw.githubusercontent.com/Keystone-Strategy/covid19-intervention-data/master/complete_npis_inherited_policies.csv
• Format: .csv,
• Open access: [X] Yes or [ ] No (include additional information)

Additional context
Came from SafeGraph datasets channel in slack.

Describe the bug
covidtracker_data() fails to download the expected data. I think the cause is that they started versioning their API, so the correct URL to the csv is now "http://covidtracking.com/api/v1/states/daily.csv"

To Reproduce
covidtracker_data() returns the following error:

Error: Can't subset columns that don't exist.
x The columns `date`, `state`, `positive`, `negative`, `pending`, etc. don't exist.

Ouptput of sessionInfo

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] plotly_4.9.2               sars2pack_0.0.47           sf_0.9-2                   R0_1.2-6                  
 [5] MASS_7.3-51.6              geofacet_0.1.10            tidyquant_1.0.0            quantmod_0.4-15           
 [9] TTR_0.23-5                 PerformanceAnalytics_2.0.4 xts_0.11-2                 zoo_1.8-6                 
[13] lubridate_1.7.8            ggplot2_3.3.0              purrr_0.3.4                tidyr_1.0.2               
[17] dplyr_0.8.5                Cairo_1.5-10               knitr_1.24                

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1      ellipsis_0.3.0        class_7.3-17          base64enc_0.1-3       rstudioapi_0.10      
  [6] npsurv_0.4-0          MatrixModels_0.4-1    ggrepel_0.8.1         bit64_0.9-7           fansi_0.4.1          
 [11] xml2_1.3.1            splines_3.6.3         lsei_1.2-0            jsonlite_1.6.1        mcmc_0.9-7           
 [16] dbplyr_1.4.2          png_0.1-7             rgeos_0.5-2           shiny_1.4.0.2         BiocManager_1.30.10  
 [21] readr_1.3.1           compiler_3.6.3        httr_1.4.1            lazyeval_0.2.2        assertthat_0.2.1     
 [26] Matrix_1.2-18         fastmap_1.0.1         cli_2.0.2             later_1.0.0           htmltools_0.4.0      
 [31] quantreg_5.54         tools_3.6.3           coda_0.19-3           gtable_0.3.0          glue_1.4.0           
 [36] reshape2_1.4.3        rappdirs_0.3.1        Rcpp_1.0.4.6          cellranger_1.1.0      imguR_1.0.3          
 [41] webdriver_1.0.5       vctrs_0.2.4           countrycode_1.1.2     debugme_1.1.0         crosstalk_1.0.0      
 [46] xfun_0.8              stringr_1.4.0         ps_1.3.0              openxlsx_4.1.4        rvest_0.3.5          
 [51] mime_0.7              lifecycle_0.2.0       scales_1.0.0          BiocStyle_2.14.4      hms_0.5.0            
 [56] promises_1.1.0        coarseDataTools_0.6-5 SparseM_1.77          yaml_2.2.1            curl_4.3             
 [61] memoise_1.1.0         gridExtra_2.3         incidence_1.7.1       stringi_1.4.3         RSQLite_2.1.2        
 [66] highr_0.8             e1071_1.7-3           zip_2.0.4             rlang_0.4.5           pkgconfig_2.0.3      
 [71] geogrid_0.1.1         evaluate_0.14         lattice_0.20-41       labeling_0.3          htmlwidgets_1.5.1    
 [76] bit_1.1-15.2          tidyselect_1.0.0      processx_3.4.1        showimage_1.0.0       plyr_1.8.4           
 [81] magrittr_1.5          R6_2.4.1              generics_0.0.2        DBI_1.1.0             pillar_1.4.3         
 [86] withr_2.1.2           fitdistrplus_1.0-14   units_0.6-4           survival_3.1-12       sp_1.3-1             
 [91] tibble_3.0.1          crayon_1.3.4          Quandl_2.10.0         KernSmooth_2.23-17    utf8_1.1.4           
 [96] BiocFileCache_1.10.2  rmarkdown_2.1         jpeg_0.1-8.1          rnaturalearth_0.1.0   grid_3.6.3           
[101] readxl_1.3.1          data.table_1.12.6     blob_1.2.1            callr_3.3.1           digest_0.6.25        
[106] classInt_0.4-1        xtable_1.8-4          httpuv_1.5.2          MCMCpack_1.4-6        munsell_0.5.0        
[111] viridisLite_0.3.0     EpiEstim_2.2-1        quadprog_1.5-7

Describe the data resource you'd like to add
Florida up-to-date line list for all deaths and cases.

Access details

• URL: https://opendata.arcgis.com/datasets/37abda537d17458bae6677b8ab75fcb9_0.csv
• Format: .csv, .tsv, .json, etc.
• Open access: [X] Yes or [ ] No (include additional information)

Additional context
Add any other context or screenshots about the data request here.

Please consider a pull request in addition to or in place of this feature request.

Lots of added features should be noted.

Hadley says....

Describe the bug

Webdriver package installs phantomjs, but R cannot find it.

To Reproduce
Only a problem when running gh-actions

Expected behavior
Working gh-pages pushes with phantomjs functionality.

Screenshots

Additional context
Consider switching to Rselenium package.

Nice data resource from kaggle competition

https://www.kaggle.com/koryto/countryinfo#covid19countryinfo.csv

Link to #7 so that we can standardize dataset tests.

Looks like the process is exceeding memory when running the google_mobility_data example.

I have tried several times to install but failed

Describe the data resource you'd like to add
Include:

Access details

• URL: https://covid19risk.eastus.cloudapp.azure.com/#tab-7292-3
• Format: will likely need to be reconstructed from original data
• Open access: NA (see format)

Additional context
https://covid19risk.eastus.cloudapp.azure.com/#tab-7292-3

Implement tests for data sources that look like:

• check column names
• check column types

Looks like this will work; nice improvements since I last looked.

For all the _data functions, use a layer of BiocFileCache between the user and the download.

Need to check what resources have viable metadata (to see that expiration occurs in a timely manner). Consider adding a "default timeout" option for these resources, as many are updated one or more times per day.

https://www.cdc.gov/nhsn/covid19/report-patient-impact.html#anchor_1594393649

This site has an API for US data, including positive and negative tests with data at county level.

• https://covidtracking.com/

This will make generating meaningful overviews easier.

I'm talking about imports into the namespace, not Imports from the DESCRIPTION file. Consider using :: notation instead of imports to clean up namespace.

Describe the bug

test failure

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (???): us_state_distancing_policy column names match ────────────────
`cnames` not equal to names(dsets[[dset]]$columns).
Lengths differ: 43 is not 39
── Failure (???): us_state_distancing_policy column types match ────────────────
`ctypes` not equal to dsets[[dset]]$columns.
Length mismatch: comparison on first 39 components
Component "curfew": 1 string mismatch

• Caching using biocfilecache
• Documentation style
• Data catalog entry
• Basic testing
  • URL exists
  • column names
  • sanity checks
  • data type checks on columns like date and geometry

Describe the bug
When running the CI on GH actions, runs time out (intermittently) when min_bic example run.

Expected behavior
Have min_bic either gracefully terminate after some number of iterations, or recode....

Currently, I disabled the example. Needs to be reenabled when fixed.

Describe the data resource you'd like to add
Include:
The COVID19 Government Measures Dataset puts together all the measures implemented by governments worldwide in response to the Coronavirus pandemic. Data collection includes secondary data review. The researched information available falls into five categories:

Social distancing
Movement restrictions
Public health measures
Social and economic measures
Lockdowns

Each category is broken down into several types of measures.

ACAPS consulted government, media, United Nations, and other organisations sources.

Access details

• URL: https://www.acaps.org/covid19-government-measures-dataset
• Format: Excel
• Open access: [X] Yes or [ ] No (include additional information)

Inference of transmission tree from a dated phylogeny

https://cran.r-project.org/web/packages/TransPhylo/vignettes/infer.html

Excellent work @seandavi and team, an useful resource. A small typo in the Preface section's affiliation subsection

1. Harard Medical School..

Thanks for the great package.
I cannot figure out how to update the data.
I checked that the data have been updated on usafacts.org, but not updated neither by rerunning usa_facts_data() or reinstalling the package.

eesi(nytdat) when used with "Georgia" as input results in:

Hi Sean,

I love this package! I noticed tonight that when I call cdc_excess_deaths, the dates aren't parsing correctly unless I use ymd rather than mdy on the "date" (Week Ending Date) column. Looks like the CDC's format might have changed on you?

Thanks again for making covid data analysis with R so simple,
--Nancy

Include in a table format:

• column names
• dimensions
• column descriptions
• ? example data
• description
• source
• relationships (could do this programmatically to look for columns that have similar names and/or values between datasets

Describe the bug
A clear and concise description of what the bug is.

To Reproduce

Ideally, submit a reproducible example with code and error. If that is not possible, submit what you can.
I can't install this sars2pack package, I have a screenshot for this error.
Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Ouptput of sessionInfo
Type sessionInfo() into your R session and paste the results here surrounded by '```' above and below.

Additional context
Add any other context about the problem here.

Describe the data resource you'd like to add

The 2019 Revision of World Population Prospects is the twenty-sixth round of official United Nations population estimates and projections that have been prepared by the Population Division of the Department of Economic and Social Affairs of the United Nations Secretariat.

These CSV files are encoded in UTF-8 and all of them have the following columns:

LocID (numeric): numeric code for the location; for countries and areas, it follows the ISO 3166-1 numeric standard
Location (string): name of the region, subregion, country or area
VarID (numeric): numeric code for the variant
Variant (string): projection variant name (Medium is the most used); for more information see Definition of projection variants
Time (string): label identifying the single year (e.g. 1950) or the period of the data (e.g. 1950-1955)
MidPeriod (numeric): numeric value identifying the mid period of the data, with the decimal representing the month (e.g. 1950.5 for July 1950)
Use the LocID, VarID and Time columns to link the data accross the different files, if necessary. Note that Time differs between single year (e.g. 1950) and period (e.g. 1950-1955) data.

Access details

• URL: https://population.un.org/wpp/Download/Standard/CSV/
• Format: .csv
• Open access: [X] Yes or [ ] No (include additional information)

Additional context
Add any other context or screenshots about the data request here.

Please consider a pull request in addition to or in place of this feature request.