General framework for loading and tidying data.
LoadData(
functionNames = NULL,
custom = FALSE,
filepath = NULL,
interactiveMode = interactive(),
tidy = TRUE,
DaysOld = 30,
minimumpercapitaactivecases = 0,
RiskEval = NULL,
dropNACountry = TRUE,
dropNAall = FALSE,
verbose = TRUE
)Name(s) of function representing that for loading data - options are in countrylist. Use NULL to attempt to download all available datasets.
If TRUE, allows for use with functions not listed in object countrylist (experimental usage).
Optionally, provide a filepath to save an error csv file to.
Set whether the session is being run interactively. If not and no googledrive oauth token is found, avoid data requiring googledrive auth token.
If TRUE, then perform tidying according to other parameters. If FALSE, then do nothing. (passed to tidy_Data).
Set any pInf data more than this days old to NA.(passed to tidy_Data).
Set any pInf data less than this to NA.(passed to tidy_Data).
Set pInf to NA when risk is below RiskEval$minimumRisk (%) using RiskEval$ascertainmentbias and a maximum group size, RiskEval$maximumN (Note: this setting overwrites minimumpercapitaactivecases). (passed to tidy_Data).
If TRUE, remove rows for countries whose pInf estimates all return NA.(passed to tidy_Data).
If TRUE, remove rows for any region whose pInf estimates all return NA. (passed to tidy_Data).
If TRUE, reports on loading progress and returns warnings/errors to console.
A simple feature returning the date of most recent data (DateReport), a unique region code (geoid), the region name (RegionName) and country name (Country), the number of active cases per capita (pInf) and the regions geometry (geometry).
LoadData("LoadUS")
#> LoadUS
#> Simple feature collection with 3216 features and 5 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: -178.8706 ymin: 17.91523 xmax: 179.7739 ymax: 71.29585
#> Geodetic CRS: WGS 84
#> # A tibble: 3,216 × 6
#> DateReport geoid RegionN…¹ Country pInf geometry
#> * <chr> <chr> <chr> <chr> <dbl> <MULTIPOLYGON [°]>
#> 1 2023-01-22 USA840_AL_1001 Autauga,… United… 0.00235 (((-86.90674 32.53698, -…
#> 2 2023-01-22 USA840_AL_1003 Baldwin,… United… 0.00186 (((-87.92538 30.64889, -…
#> 3 2023-01-22 USA840_AL_1005 Barbour,… United… 0.00399 (((-85.66363 31.78236, -…
#> 4 2023-01-22 USA840_AL_1007 Bibb, Al… United… 0.00258 (((-87.4212 32.87451, -8…
#> 5 2023-01-22 USA840_AL_1009 Blount, … United… 0.00220 (((-86.95366 33.8153, -8…
#> 6 2023-01-22 USA840_AL_1011 Bullock,… United… 0.00212 (((-85.99916 32.25054, -…
#> 7 2023-01-22 USA840_AL_1013 Butler, … United… 0.00250 (((-86.90894 31.96167, -…
#> 8 2023-01-22 USA840_AL_1015 Calhoun,… United… 0.00302 (((-86.04399 33.7636, -8…
#> 9 2023-01-22 USA840_AL_1017 Chambers… United… 0.00303 (((-85.59315 32.72853, -…
#> 10 2023-01-22 USA840_AL_1019 Cherokee… United… 0.00248 (((-85.57679 34.48444, -…
#> # … with 3,206 more rows, and abbreviated variable name ¹RegionName
LoadData("LoadUS", dropNAall = TRUE)
#> LoadUS
#> Simple feature collection with 3150 features and 5 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: -178.8706 ymin: 17.91523 xmax: 179.7739 ymax: 71.29585
#> Geodetic CRS: WGS 84
#> # A tibble: 3,150 × 6
#> DateReport geoid RegionN…¹ Country pInf geometry
#> <chr> <chr> <chr> <chr> <dbl> <MULTIPOLYGON [°]>
#> 1 2023-01-22 USA840_AL_1001 Autauga,… United… 0.00235 (((-86.90674 32.53698, -…
#> 2 2023-01-22 USA840_AL_1003 Baldwin,… United… 0.00186 (((-87.92538 30.64889, -…
#> 3 2023-01-22 USA840_AL_1005 Barbour,… United… 0.00399 (((-85.66363 31.78236, -…
#> 4 2023-01-22 USA840_AL_1007 Bibb, Al… United… 0.00258 (((-87.4212 32.87451, -8…
#> 5 2023-01-22 USA840_AL_1009 Blount, … United… 0.00220 (((-86.95366 33.8153, -8…
#> 6 2023-01-22 USA840_AL_1011 Bullock,… United… 0.00212 (((-85.99916 32.25054, -…
#> 7 2023-01-22 USA840_AL_1013 Butler, … United… 0.00250 (((-86.90894 31.96167, -…
#> 8 2023-01-22 USA840_AL_1015 Calhoun,… United… 0.00302 (((-86.04399 33.7636, -8…
#> 9 2023-01-22 USA840_AL_1017 Chambers… United… 0.00303 (((-85.59315 32.72853, -…
#> 10 2023-01-22 USA840_AL_1019 Cherokee… United… 0.00248 (((-85.57679 34.48444, -…
#> # … with 3,140 more rows, and abbreviated variable name ¹RegionName
LoadData("LoadNewZealand",tidy = FALSE)
#> LoadNewZealand
#> Simple feature collection with 20 features and 5 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: 166.4263 ymin: -47.28706 xmax: 178.5504 ymax: -34.41452
#> Geodetic CRS: WGS 84
#> First 10 features:
#> DateReport geoid RegionName Country
#> 1 2022-02-11 NZL554_00_01 Northland, New Zealand New Zealand
#> 2 2022-02-11 NZL554_00_02 Waitemata, New Zealand New Zealand
#> 3 2022-02-11 NZL554_00_03 Auckland, New Zealand New Zealand
#> 4 2022-02-11 NZL554_00_04 Counties Manukau, New Zealand New Zealand
#> 5 2022-02-11 NZL554_00_05 Waikato, New Zealand New Zealand
#> 6 2022-02-11 NZL554_00_06 Lakes, New Zealand New Zealand
#> 7 2022-02-11 NZL554_00_07 Bay of Plenty, New Zealand New Zealand
#> 8 2022-02-09 NZL554_00_08 Tairāwhiti, New Zealand New Zealand
#> 9 2022-02-11 NZL554_00_09 Taranaki, New Zealand New Zealand
#> 10 2022-02-11 NZL554_00_10 Hawke's Bay, New Zealand New Zealand
#> pInf geometry
#> 1 0.0006516145 MULTIPOLYGON (((174.5898 -3...
#> 2 0.0003427975 MULTIPOLYGON (((174.6544 -3...
#> 3 0.0009744380 MULTIPOLYGON (((174.8526 -3...
#> 4 0.0019931647 MULTIPOLYGON (((175.2833 -3...
#> 5 0.0008287895 MULTIPOLYGON (((175.8982 -3...
#> 6 0.0006621188 MULTIPOLYGON (((176.6242 -3...
#> 7 0.0005054653 MULTIPOLYGON (((178.0066 -3...
#> 8 0.0002821503 MULTIPOLYGON (((177.9118 -3...
#> 9 0.0000917319 MULTIPOLYGON (((174.5904 -3...
#> 10 0.0001921062 MULTIPOLYGON (((177.799 -38...
LoadData(c("LoadUS","LoadMalaysia"))
#> LoadUS
#> LoadMalaysia
#> Simple feature collection with 3232 features and 5 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: -178.8706 ymin: 0.8623942 xmax: 179.7739 ymax: 71.29585
#> Geodetic CRS: WGS 84
#> # A tibble: 3,232 × 6
#> DateReport geoid RegionN…¹ Country pInf geometry
#> * <chr> <chr> <chr> <chr> <dbl> <MULTIPOLYGON [°]>
#> 1 2023-01-22 USA840_AL_1001 Autauga,… United… 0.00235 (((-86.90674 32.53698, -…
#> 2 2023-01-22 USA840_AL_1003 Baldwin,… United… 0.00186 (((-87.92538 30.64889, -…
#> 3 2023-01-22 USA840_AL_1005 Barbour,… United… 0.00399 (((-85.66363 31.78236, -…
#> 4 2023-01-22 USA840_AL_1007 Bibb, Al… United… 0.00258 (((-87.4212 32.87451, -8…
#> 5 2023-01-22 USA840_AL_1009 Blount, … United… 0.00220 (((-86.95366 33.8153, -8…
#> 6 2023-01-22 USA840_AL_1011 Bullock,… United… 0.00212 (((-85.99916 32.25054, -…
#> 7 2023-01-22 USA840_AL_1013 Butler, … United… 0.00250 (((-86.90894 31.96167, -…
#> 8 2023-01-22 USA840_AL_1015 Calhoun,… United… 0.00302 (((-86.04399 33.7636, -8…
#> 9 2023-01-22 USA840_AL_1017 Chambers… United… 0.00303 (((-85.59315 32.72853, -…
#> 10 2023-01-22 USA840_AL_1019 Cherokee… United… 0.00248 (((-85.57679 34.48444, -…
#> # … with 3,222 more rows, and abbreviated variable name ¹RegionName
if (FALSE) {
LoadData()
}