Information for downloading, cleaning and processing COVID-19 region level 1 and 2 data for Lithuania.
The Official Statistics Portal (OSP) provides many data series in their table.
The full range of these vectors can be returned by setting
all_osp_fields to TRUE.
The following describes the data provided by the OSP.
| field | description |
date |
the reporting day during which the events occurred or at the end of which the accounting was performed |
municipality_code * |
code of the municipality assigned to persons |
municipality_name + |
the name of the municipality assigned to the persons |
population |
population size according to the data of the beginning of 2021, according to the declared place of residence |
ab_pos_day |
Number of positive antibody test responses, days |
ab_neg_day |
Number of negative antibody test responses, days |
ab_tot_day |
Number of antibody tests, daily |
ab_prc_day |
Percentage of positive antibody test responses per day |
ag_pos_day |
Number of positive antigen test responses, daily |
ag_neg_day |
Number of negative antigen test responses, daily |
ag_tot_day |
Number of antigen tests, daily |
ag_prc_day |
Percentage of positive responses to antigen tests per day |
pcr_pos_day |
number of positive PCR test responses, daily |
pcr_neg_day |
Number of PCR test negative responses, daily |
pcr_tot_day |
number of PCR tests per day |
pcr_prc_day |
Percentage of positive PCR test responses per day |
dgn_pos_day |
Number of positive answers to diagnostic tests / tests, days |
dgn_neg_day |
Number of negative answers to diagnostic tests / tests, days |
dgn_prc_day |
Number of diagnostic examinations / tests, days |
dgn_tot_day |
Percentage of positive answers to diagnostic tests / tests per day |
dgn_tot_day_gmp |
Number of diagnostic examinations / tests of samples collected at mobile points, days |
daily_deaths_def1 |
The number of new deaths per day according to the (narrowest) COVID death definition No. 1. # |
daily_deaths_def2 |
Number of new deaths per day according to COVID death definition No. 2. # |
daily_deaths_def3 |
Number of new deaths per day according to COVID death definition No. 3. # |
daily_deaths_all |
Daily deaths in Lithuania (by date of death) |
incidence + |
Number of new COVID cases per day (laboratory or physician confirmed) |
cumulative_totals + |
Total number of COVID cases (laboratory or physician confirmed) |
active_de_jure |
Declared number of people with COVID |
active_sttstcl |
Statistical number of people with COVID |
dead_cases |
The number of dead persons who were ever diagnosed with COVID |
recovered_de_jure |
Declared number of recovered live persons |
recovered_sttstcl |
Statistical number of recovered live persons |
map_colors $ |
The map colour-coding for the municipality, based on averages of test positivity and incidence per capita |
* The municipality_code is discarded since it does not correspond
to ISO-3166:2 codes used elsewhere in the package.
+ These fields are renamed but returned unmodified.
# Lithuania offers counts according to three
different definitions of whether a death is attributable to COVID-19.
$ This field is not recalculated for counties and is deleted.
Beginning in February 2021 the OSP publishes death counts according to three different criteria, from most to least strictly attributed to COVID-19.
of Number of deaths with COVID-19 (coronavirus infection) as
the leading cause of death. The indicator is calculated by summing
all registered records of medical form E106 (unique persons), in which
the main cause of death is IPC disease codes U07.1 or U07.2. Deaths
due to external causes are not included (ICD disease codes are V00-Y36,
or Y85-Y87, or Y89, or S00-T79, or T89-T98).
with Number of deaths with COVID-19 (coronavirus infection) of
any cause of death.
The indicator is calculated by summing all registered records of the
medical form E106 (unique persons), in which the ICD disease codes
U07.1, U07.2, U07.3, U07.4, U07.5 are indicated as the main, direct,
intermediate cause of death or other important pathological condition,
or identified as related to COVID-19 disease (coronavirus infection).
Deaths due to external causes are not included (ICD disease codes
are V00-Y36, or Y85-Y87, or Y89, or S00-T79, or T89-T98).
after Number of deaths from any cause of COVID-19 or COVID-19
deaths due to non-external causes within 28 days.
The indicator is calculated by summing all registered records of the
medical form E106 (unique persons), in which the ICD disease codes
U07.1, U07.2, U07.3, U07.4, U07 are indicated as the main, direct,
intermediate cause of death or other important pathological condition,
or identified as related to COVID-19 disease (coronavirus infection)
and all records of medical form E106 (unique individuals) where the
person died within the last 28 days after receiving a positive
diagnostic response to the SARS-CoV-2 test or had an entry in medical
form E025 with ICD disease code U07.2 or U07.1. Deaths due to external
causes are not included (ICD disease codes are V00-Y36, or Y85-Y87, or
Y89, or S00-T79, or T89-T98).
The number of deaths reported in the last day is preliminary and increases by about 20-40% in a few days. Such a "delay" in the data is natural: for example, for those who died last night, a death certificate is likely to be issued as soon as this report is published this morning.
Beginning in February 2021 the OSP makes statistical estimates of the number of recovered and active cases, since review of the data showed that some cases individuals still considered as active cases had recovered, but not documented or registered as such.
These are listed as by the OSP as active_de_jure and
recovered_de_jure (officially still considered sick),
and active_sttstcl and recovered_sttstcl (an estimate of how
many of these are still ill).
covidregionaldata::DataClass -> Lithuania
originname of origin to fetch data for
supported_levelsA list of supported levels.
supported_region_namesA list of region names in order of level.
supported_region_codesA list of region codes in order of level.
common_data_urlsList of named links to raw data that are common across levels.
source_data_colsexisting columns within the raw data
source_textPlain text description of the source of the data
source_urlWebsite address for explanation/introduction of the data
death_definitionwhich criteria of deaths attributed to COVID to use
recovered_definitionwhether to use the official counts of recovered cases or the statistical estimates provided by OSP
all_osp_fieldswhether to return all the data vectors provided by OSP
national_datawhether to return data rows for national results
set_region_codes()Set up a table of region codes for clean data
Lithuania$set_region_codes()
clean_common()Common data cleaning for both levels
Lithuania$clean_common()
clean_level_1()Lithuania Specific County Level Data Cleaning
Aggregates data to the level 1 (county) regional level. Data is provided by the source at the level 2 (municipality) regional level.
Lithuania$clean_level_1()
new()Initialize the country
Lithuania$new( death_definition = "of", recovered_definition = "official", all_osp_fields = FALSE, national_data = FALSE, ... )
death_definitionA character string. Determines which criteria
for attributing deaths to COVID is used. Should be "of",
"with", or "after". Can also be "daily_deaths_def1",
"daily_deaths_def2", or "daily_deaths_def3". (Defaults
to "of", the strictest definition.)
recovered_definitionA character string. Determines whether
the count of officially-recovered (de jure) cases is used, or
the statistical estimate provided by OSP. Should be "official"
or "statistical". (Defaults to "official".)
all_osp_fieldsA logical scalar. Should all the meaningful
data fields from the OSP source be returned? (Defaults FALSE)
national_dataA logical scalar. Should national values be
returned? (Defaults FALSE)
...Parameters passed to DataClass() initalize
clone()The objects of this class are cloneable with this method.
Lithuania$clone(deep = FALSE)
deepWhether to make a deep clone.
Subnational data sources
Belgium,
Brazil,
Canada,
Colombia,
Covid19DataHub,
Cuba,
Estonia,
France,
Germany,
Google,
India,
Italy,
JHU,
Mexico,
Netherlands,
SouthAfrica,
Switzerland,
UK,
USA
# NOT RUN {
region <- Lithuania$new(verbose = TRUE, steps = TRUE, get = TRUE)
# }
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