CIHI - CoronaNet Taxonomy Map

0 Introduction

This document maps the taxonomy used by the Canadian Data Set of COVID-19 Interventions from the Candian Institute for Health Information (CIHI) to document government policies made in response to COVID-19 into the CoronaNet Research Project taxonomy. Each section maps the general area for which the taxonomy is mapped and each sub-section provides further detail as necessary. Following each explanation for how the mapping is conceptualized, there is R code for operationalizing this mapping. Please refer to the CIHI Data Dictionary, which they release as a separate sheet in their dataset accessible through their website and the CoronaNet Codebook for more information on their respective taxonomies.

Note that the code below is customized to adjust for errors and idiosyncrasies in the version of the CIHI dataset available asof August 12, 2021. You can access (i) this original version of the CIHI dataset, “covid-19-intervention-scan-data-tables-en.xlsx”, as well as (ii) the version which transforms this version of the CIHI dataset into the CoronaNet taxonomy, “cihi_coronanet_map.csv” (the rest of this document details how this transformation was implemented) from the CoronaNet pubic git repo.

1 Setup

To create replicate this taxonomy mapping exercise, users will need to load the following R packages and to read in the original CIHI data as follows:

library(readr)
library(dplyr)
library(magrittr)
library(tidyr)
library(readxl)
library(lubridate)
library(openxlsx)
library(tidyverse)
library(here)

cihi = read_excel("./data/collaboration/cihi/covid-19-intervention-scan-data-tables-en.xlsx", sheet = "Intervention scan", skip = 2)
cihi$`Date announced` <- convertToDate(cihi$`Date announced`)
cihi$`Date implemented` <- convertToDate(cihi$`Date implemented`)
cihi<- subset(cihi, cihi$`Entry ID` != "End of worksheet")

2 Map Creation

The following code creates a map to translate the CIHI data to the CoronaNet taxonomy. Where there is a straightforward one-to-one relationship between the two taxonomies, these are directly mapped in the below:

The CIHI Entry ID variable allows each unique observation to be identifiable. This is conceptually the same as CoronaNet’s record_id variable. However, to make it clear when a policy originates from CIHI and when it originates from CoronaNet, we encode this information into a new variable we name unique_id.
CIHI Date announced variable, which captures when a policy was implemented, is a direct match for CoronaNet’s date_announced variable.
CIHI Date implemented variable, which captures when a policy was implemented, is a direct match for CoronaNet’s date_start variable.
CIHI Intervention summary variable is a close approximation to CoronaNet’s description variable. The main difference is that (at least in theory), CoronaNet’s description variable must always contain certain information (the policy initiator, the type of policy, the date the policy started and if applicable: the geographic target of the policy, the demographic target of the policy and the end date of the policy) while there does not appear to be same amount of information consistently captured in the CIHI Comments variable. As such, it will likely be necessary to backcode for this information for observations in the CIHI dataset that are not in the CoronaNet dataset.

cihi_coronanet_map <- data.frame(unique_id = cihi$`Entry ID`,
                                `date_announced` = cihi$`Date announced`,
                                `date_start` = cihi$`Date implemented`,
                                `date_end` = NA,
                                `type` = NA,
                                `type_sub_cat` = NA,
                                `description` = cihi$`Intervention summary`,
                                `country` = "Canada", 
                                `enforcer` = NA,
                                `target_geog_level` = NA,
                                `init_country_level` = NA,
                                `cihi_category` = cihi$`Intervention category`,
                                `cihi_type` = cihi$`Intervention type`)

2.1 Link source

The Primary source (news release or specific resource) and Secondary source variables in the CIHI dataset captures the original source of information from which a policy is documented. While this is conceptually a direct mapping for CoronaNet’s link variable, the latter includes all sources into one field. As such, additional processing must be done to reformat how the sources are saved in the CIHI dataset, which the following code does.

# Clean colnames related to the sources.
if(grepl("Secondary", names(cihi)[9])){names(cihi)[9] = "Secondary source"}
if(grepl("Primary", names(cihi)[8])){names(cihi)[8] = "Primary source (news release or specific resource)"}
# Concatenate sources columns into the new column "link" by CIHI id.
link <- cihi[c("Entry ID", "Primary source (news release or specific resource)", "Secondary source")]
link$`Primary source (news release or specific resource)`<- str_remove(link$`Primary source (news release or specific resource)` ,"Not applicable")
link$link <- ifelse(link$`Secondary source`  == "Not applicable", 
                    link$`Primary source (news release or specific resource)`, 
                    paste(link$`Primary source (news release or specific resource)`, link$`Secondary source`, sep = ", "))
link <- link[ -c(2:3) ]

Following this, the object which incorporates the mapping of the relevant subset of the data, link, is incorporated into the main object which records this mapping, cihi_coronanet_map, using the unique_id variable to match the corresponding records.

# Join link data into CIHI mapping.
cihi_coronanet_map = left_join(cihi_coronanet_map, link, by = c('unique_id' = 'Entry ID'))

2.2 Province Level

The Jurisdiction variable in the CIHI dataset captures which subnational province a policy is applied to, if applicable. While this is conceptually a direct mapping for CoronaNet’s province variable, additional processing must be done to harmonize the province names, which the following code does.

province_name <- cihi %>%
      mutate(province = 
               recode(Jurisdiction,
                           'Alta.'= "Alberta",
                           'B.C.' = "British Columbia",
                           'Man.' = "Manitoba",
                           'N.B.' = "New Brunswick" ,
                           'N.L.' = "Newfoundland and Labrador",
                           'N.W.T.' = "Northwest Territories",
                           'N.S.' = "Nova Scotia",
                           'Nun.' = "Nunavut",
                           'Ont.' = "Ontario",
                           'P.E.I.' = "Prince Edward Island",
                           'Que.' =  "Quebec",
                           'Sask.' = "Saskatchewan" ,
                           "Y.T." = "Yukon")) %>%
      mutate(province = ifelse(Jurisdiction == 'Can.', NA, province)) %>%
      select(`Entry ID`, province)

Following this, the object which incorporates the mapping of the relevant subset of the data, province_name, is incorporated into the main object which records this mapping, cihi_coronanet_map, using the unique_id variable to match the corresponding records.

cihi_coronanet_map = left_join(cihi_coronanet_map, province_name, by = c('unique_id' = 'Entry ID'))

2.3 Initiating Geographic Level

The init_country_level variable in the CoronaNet taxonomy captures information as to which level of government a COVID-19 policy originates from, which the CIHI taxonomy does not directly document. In the following code, we assume that if a policy applies to a province, it is a Provincial level policy and if it applies to the entire country, it is a National level policy. Note however, it is possible that the central government applies a policy not to the entire country, but only to a limited number of provinces. In this case, this mapping will be incorrect and downstream manual harmonization will need to correct for this error.

# set init_country_level
cihi_coronanet_map = cihi_coronanet_map %>%
  mutate(init_country_level = 
           case_when(
              !is.na(province) ~ 'Provincial',
              TRUE ~ "National"
          )
        )

2.4 Target Geographic Level

The target_geog_level variable in the CoronaNet taxonomy captures information as to which level of government a COVID-19 policy applies to, which the CIHI taxonomy also captures in its Level variable. Additional processing must be done to harmonize the names of these levels, which the following code does.

# adjust 'level' to 'target_geog_level'
target_geog_level = cihi  %>%
  mutate(target_geog_level = 
           case_when(
              Level  == 'Federal' ~ 'National',
              Level  == 'Provincial/territorial' ~ 'Provincial',
              Level  == 'Regional' ~ 'Other (e.g., county)',
              TRUE ~ as.character(NA)
              )
         )

Following this, the object which incorporates the mapping of the relevant subset of the data, target_geog_level, is incorporated into the main object which records this mapping, cihi_coronanet_map, using the unique_id variable to match the corresponding records.

cihi_coronanet_map = left_join(cihi_coronanet_map, target_geog_level, by = c('unique_id' = 'Entry ID'))

2.5 End dates

The following code maps how CIHI captures end dates in its taxonomy into the CoronaNet taxonomy.

In the CIHI taxonomy, end dates are not captured in a separate variable field but is rather documented in its text field Intervention summary. Because CIHI systematized how it documented this information in its text field, it was possible to extract this information, which the following code does. Some additional code was added to account for situations in which end dates were not recorded for a given policy.

end_date = cihi %>% 
  mutate(
    date_end = sub(".*Effective until|.*Effective Until||.*Effectiveuntil|Effective date:", '',  `Intervention summary`),
  date_end = gsub("^:|\\(at minimum\\)|\\(southern Ontario\\)", '', `date_end`) %>% 
    str_trim,
  date_end = 
    case_when(
      !grepl("\\d", `Intervention summary`) & grepl("What: BC daycares remain open as an essential service" , `Intervention summary`) ~ as.character(NA),
      !grepl("\\d", `Intervention summary`) & grepl("What: Assessment centres have been established at lower jurisdictional levels. Not all areas have clearly designated centres" , `Intervention summary`) ~as.character(NA),
      !grepl("\\d", `Intervention summary`) & grepl("veryone crossing the bridge will be stopped to determine reason of travel into PEI" , `Intervention summary`) ~as.character(NA),
       grepl("campaign through social media and traditional media including newspapers and radio ads to raise " , `Intervention summary`) ~ as.character(NA),
      !grepl("\\d", `Intervention summary`) & grepl("Medical Society of Prince Edward Island\r\nWhat: Released virtual care billing codes for physicians " , `Intervention summary`) ~ as.character(NA),
      date_end == '' ~ as.character(NA),
      TRUE ~ date_end
    )
  ) %>%
  select(unique_id = `Entry ID`, date_end)

Following this, the object which incorporates the mapping of the relevant subset of the data, end_date, is incorporated into the main object which records this mapping, cihi_coronanet_map, using the unique_id variable to match the corresponding records.

cihi_coronanet_map = rows_update(cihi_coronanet_map, end_date, by = "unique_id")

2.6 Enforcers

The following code maps how CIHI captures information about the organizational body in charge of enforcing compliance with a particular policy or issuing recommendations for a particular policy.

In the CIHI taxonomy, information about enforcement is not captured in a separate variable field but is rather documented in its text field Intervention summary. Because CIHI systematized how it documented this information in its text field, it was possible to extract this information, which the following code does.

enforcer <- cihi %>%   
  mutate(
    enforcer = sub(".*Who:", '',  `Intervention summary`),
    enforcer = sub("What:.*$", '',  enforcer),
    enforcer = gsub("\\r|\\n", '',  enforcer) %>% 
  str_trim,) %>% 
  select(unique_id = `Entry ID`, enforcer)

Following this, the object which incorporates the mapping of the relevant subset of the data, enforcer, is incorporated into the main object which records this mapping, cihi_coronanet_map, using the unique_id variable to match the corresponding records.

cihi_coronanet_map = rows_update(cihi_coronanet_map, enforcer, by = "unique_id")

3 Policy Type

3.1 Case management:

3.1.1 Health Resources

The following code maps how CIHI captures health resources policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — assessment centres.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Resources and the type_sub_cat as Other Health Infrastructure.

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Case management" & cihi_coronanet_map$cihi_type == 'Case management — assessment centres',
                                  "Health Resources", cihi_coronanet_map$type)
cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Case management" & cihi_coronanet_map$cihi_type == 'Case management — assessment centres',
                                          "Other Health Infrastructure", cihi_coronanet_map$type_sub_cat)

3.1.2 Health Testing

The following code maps how CIHI captures health testing policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — online assessment or Case management — test criteria .
The CoronaNet taxonomy aims to capture such policies by coding thetype as Health Testing and the type_sub_cat as Other Health Testing.

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" &
  cihi_coronanet_map$cihi_type %in% 
      c('Case management — online assessment',                                                          'Case management — test criteria'), 
      "Health Testing", 
      cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(
    cihi_coronanet_map$cihi_category == "Case management" & 
    cihi_coronanet_map$cihi_type == 'Case management — online assessment', 
        "Other Health Testing", 
         cihi_coronanet_map$type_sub_cat)

3.1.3 Health Monitoring

The following code maps how CIHI captures health monitoring policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — contact tracing.
The CoronaNet taxonomy aims to capture such policies by coding thetype as Health Monitoring and the type_sub_cat as Who a person has come into contact with over time.

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" & 
  cihi_coronanet_map$cihi_type == 'Case management — contact tracing', 
  "Health Monitoring", 
  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(
    cihi_coronanet_map$cihi_category == "Case management" & 
    cihi_coronanet_map$cihi_type == 'Case management — contact tracing', 
    "Who a person has come into contact with over time", 
    cihi_coronanet_map$type_sub_cat)

3.1.4 Health Quarantine

The following code maps how CIHI captures quarantine policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — self-isolation.
The CoronaNet taxonomy aims to capture such policies by coding the type as Quarantine.

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" &
  cihi_coronanet_map$cihi_type == 'Case management — self-isolation', 
  "Quarantine", 
  cihi_coronanet_map$type)

3.1.5 Regulation of Schools

The following code maps how CIHI captures regulation of schools policies, e.g. testing of students and children, into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — education.
The CoronaNet taxonomy broadly aims to capture such policies by coding thetype as Closure and Regulation of Schools and the type_sub_cat as “Primary Schools (generally for children ages 10 and below), Secondary Schools (generally for children
ages 10 to 18), Higher education institutions (i.e. degree granting institutions)”. More detailed mapping capturing the testing aspect of such policies is in principal possible, but will be conducted downstream during manual data harmonization.

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" &
  cihi_coronanet_map$cihi_type == 'Case management — education', 
  "Closure and Regulation of Schools", 
  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" & 
  cihi_coronanet_map$cihi_type == 'Case management — education', 
  "Primary Schools (generally for children ages 10 and below), Secondary Schools (generally for 
  children ages 10 to 18), Higher education institutions (i.e. degree granting institutions)", 
  cihi_coronanet_map$type_sub_cat)

3.1.6 Public Awareness Measures

The following code maps how CIHI captures public awareness policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Case management and the cihi_type as Case management — outbreak definitions.
The CoronaNet taxonomy aims to capture such policies by coding thetype as Public Awareness Measures.

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Case management" &
  cihi_coronanet_map$cihi_type == 'Case management — outbreak definitions',
  "Public Awareness Measures", 
  cihi_coronanet_map$type)

3.2 Closures/openings:

3.2.1 Closure and Regulation of Schools - daycares

The following code maps how CIHI captures closure and regulation of day care policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Closures/openings and the cihi_type as Closures/openings — daycares
The CoronaNet taxonomy aims to capture such policies by coding the type as Closure and Regulation of Schools and the type_sub_cat as Preschool or childcare facilities (generally for children ages 5 and below).

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" & 
    cihi_coronanet_map$cihi_type == 'Closures/openings — daycares', 
  "Closure and Regulation of Schools", 
  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" & 
  cihi_coronanet_map$cihi_type == 'Closures/openings — daycares', 
  "Preschool or childcare facilities (generally for children ages 5 and below)", 
  cihi_coronanet_map$type_sub_cat)

3.2.2 Closure and Regulation of Schools - all schools

The following code maps how CIHI captures general closure and regulation of schools policies into CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Closures/openings and the cihi_type as or Closures/openings — education.
The CoronaNet taxonomy aims to capture such policies by coding the type as Closure and Regulation of Schools and the type_sub_cat as Primary Schools (generally for children ages 10 and below), Secondary Schools (generally for children
ages 10 to 18), Higher education institutions (i.e. degree granting institutions).

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" & 
  cihi_coronanet_map$cihi_type == 'Closures/openings — education', "
  Closure and Regulation of Schools", cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" &
  cihi_coronanet_map$cihi_type == 'Closures/openings — education',
  "Primary Schools (generally for children ages 10 and below), Secondary Schools (generally for children ages 10 to 18), Higher education institutions (i.e. degree granting institutions)", cihi_coronanet_map$type_sub_cat)

3.2.3 Health services

The following code maps how CIHI captures closing and openings of health services can be mapped into the CoronaNet taxonomy despite the fact that it cannot be directly done.

On manual inspection of the policies coded with the value of Closures/openings for the variable cihi_category and Closures/openings — health services for the variable cihi_type, we found that they could be mapped as either Health Resources or Restriction and Regulation of Businesses in the CoronaNet type variable.
Because there was no systematic way to map such policies in a one to one manner, we (i) appended the phrase “-health_res” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI and (ii) mapped such policies as Health Resources or Restriction and Regulation of Businesses in the CoronaNet type variable to provide guidance to researchers manually harmonizing this data later downstream.

cihi_coronanet_map$unique_id <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" &
  cihi_coronanet_map$cihi_type == 'Closures/openings — health services', 
  paste0(cihi_coronanet_map$unique_id, "-health_res"), 
  cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Closures/openings" &
    cihi_coronanet_map$cihi_type == 'Closures/openings — health services',
    "Health Resources or Restriction and Regulation of Businesses", cihi_coronanet_map$type)

3.2.4 Recreation; non-essential services

The following code maps how CIHI closing and openings of recreation and non-essential services policies can be mapped into the CoronaNet taxonomy despite the fact that it cannot be directly done.

On manual inspection of the policies coded with (a) the value of Closures/openings for the variable cihi_category and Closures/openings — recreation for the variable cihi_type as well as (b) the value of Closures/openings for the variable cihi_category and Closures/openings — — non-essential services for the variable cihi_type , we found that they could be mapped as either Restriction and Regulation of Businesses, Restriction and Regulation of Government Services, or Restrictions of Mass Gatherings in the CoronaNet type variable.
Because there was no systematic way to map such policies in a one to one manner, we (i) appended the phrase “-business” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI and (ii) mapped such policies as Restriction and Regulation of Businesses or Restriction and Regulation of Government Services or Restrictions of Mass Gatherings in the CoronaNet type variable to provide guidance to researchers manually harmonizing this data later downstream.

cihi_coronanet_map$unique_id <- ifelse(
  cihi_coronanet_map$cihi_type == "Closures/openings — recreation"  |
  cihi_coronanet_map$cihi_type == "Closures/openings — non-essential services", paste0(cihi_coronanet_map$unique_id, "-business"), cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_type == "Closures/openings — recreation"  | 
  cihi_coronanet_map$cihi_type == "Closures/openings — non-essential services",
  "Restriction and Regulation of Businesses or Restriction and Regulation of Government Services 
  or Restrictions of Mass Gatherings", 
  cihi_coronanet_map$type)

3.3 Distancing:

3.3.1 Gatherings

The following code maps how CIHI restrictions on gathering policies can be mapped into the CoronaNet taxonomy despite the fact that it cannot be directly done.

On manual inspection of the policies coded with the value of Distancing for the variable cihi_category and Distancing — gatherings for the variable cihi_type, we found that they could be mapped as either Restrictions of Mass Gathering or Social Distancing in the CoronaNet type variable.
Because there was no systematic way to map such policies in a one to one manner, we (i) appended the phrase “-mass_gatherings” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI and (ii) mapped such policies as Restrictions of Mass Gathering or Social Distancing in the CoronaNet type variable to provide guidance to researchers manually harmonizing this data later downstream.

cihi_coronanet_map$unique_id <- ifelse(cihi_coronanet_map$cihi_category == "Distancing" 
                                       & cihi_coronanet_map$cihi_type == 'Distancing — gatherings', 
                                       paste0(cihi_coronanet_map$unique_id, "-mass_gatherings"), 
                                       cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Distancing" &
                                    cihi_coronanet_map$cihi_type == 'Distancing — gatherings', 
                                  "Restrictions of Mass Gatherings or Social Distancing", 
                                  cihi_coronanet_map$type)

3.3.2 Other distancing types

The following code maps how CIHI other distancing types can be mapped into the CoronaNet taxonomy despite the fact that it cannot be directly done.

On manual inspection of the policies coded with the value of Distancing for the variable cihi_category and Distancing — other for the variable cihi_type, we found that they could be mapped as either Curfew, Other Policy Not Listed Above, New Task Force, Bureau or Administrative Configuration or Lockdown.
We found that it was largely possible to make use of regular expressions to categorize this data as either Curfew, Other Policy Not Listed Above, New Task Force, Bureau or Administrative Configuration or Lockdown. Based on keywords in the textual description of these policies, which we identifid based on manual inspection of the CIHI data, we customized the code to sort these policies into different values in CoronaNet’s type variable, with Lockdown being the default option when no other keyword was found. While this does not provide a perfect mapping of these policies, it is sufficient for a large proportion of the data; downstream manual harmonization will correct for any mis-mappings.
To aid with downstream manual harmonization, we appended the phrase “-soc_dist” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI.

# Other distancing
cihi_coronanet_map$unique_id <- ifelse(cihi_coronanet_map$cihi_category == "Distancing" & 
                                         cihi_coronanet_map$cihi_type == "Distancing — other", 
                                       paste0(cihi_coronanet_map$unique_id, "-soc_dist"), cihi_coronanet_map$unique_id)

cihi_coronanet_map = cihi_coronanet_map %>%
  mutate(
    type = case_when(
      cihi_coronanet_map$cihi_category == "Distancing" &
        cihi_coronanet_map$cihi_type == "Distancing — other" &
        grepl("curfew", description) ~ "Curfew",
      
      cihi_coronanet_map$cihi_category == "Distancing" &
        cihi_coronanet_map$cihi_type == "Distancing — other"  &
        grepl("\\$", description) ~ 
        "Other Policy Not Listed Above",
      
      cihi_coronanet_map$cihi_category == "Distancing" &
        cihi_coronanet_map$cihi_type == "Distancing — other"  & 
        grepl("task force", description) ~ 
        "New Task Force, Bureau or Administrative Configuration",
      
      cihi_coronanet_map$cihi_category == "Distancing" &
        cihi_coronanet_map$cihi_type == 
        "Distancing — other" ~ "Lockdown",
      
      TRUE ~ type
    )
  )

3.3.3 Work from Home

The following code maps how CIHI work from home policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Distancing and the cihi_type as Distancing — work from home
The CoronaNet taxonomy aims to capture such policies by coding the type as Restriction and Regulation of Businesses. More detailed mapping of such policies is in principal possible, but will be conducted downstream during manual data harmonization.

#Distancing — work from home: 
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Distancing" 
                                  & cihi_coronanet_map$cihi_type == 'Distancing — work from home', 
                                  "Restriction and Regulation of Businesses",
                                  cihi_coronanet_map$type)

3.4 Financial and Economic

3.4.1 Financial and economic assistance

The following code maps how CIHI’s financial and economic assistance policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Financial and economic and the cihi_type as Financial and economic — assistance
The CoronaNet taxonomy does not systematically capture such policies but to the extent it records them nevertheless, they are documented in its type as Other Policy Not Listed Above (econ).

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Financial and economic" 
                                  & cihi_coronanet_map$cihi_type == 'Financial and economic — assistance', 
                                  "Other Policy Not Listed Above (econ)", 
                                  cihi_coronanet_map$type)

3.4.2 Financial and economic research and development

The following code maps how CIHI’s financial and economic research and development policies can be mapped into the CoronaNet taxonomy, despite the fact that it cannot be directly done.

On manual inspection of the policies coded with the value of Financial and economic for the variable cihi_category and Financial and economic — research and development for the variable cihi_type, we found that they could be mapped as either Health Resources or Other Policy Not Listed Above in the CoronaNet type variable.
Because there was no systematic way to map such policies in a one to one manner, we (i) appended the phrase “-health_res” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI and (ii) mapped such policies as Health Resources or Other Policy Not Listed Above in the CoronaNet type variable to provide guidance to researchers manually harmonizing this data later downstream.

cihi_coronanet_map$unique_id <- ifelse(cihi_coronanet_map$cihi_category == "Financial and economic" &
                                         cihi_coronanet_map$cihi_type == 'Financial and economic — research and development',
                                       paste0(cihi_coronanet_map$unique_id, "-health_res"), 
                                       cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Financial and economic" &
                                  cihi_coronanet_map$cihi_type == 'Financial and economic — research and development',
                                  "Health Resources or Other Policy Not Listed Above", 
                                  cihi_coronanet_map$type )

3.5 Health services:

3.5.1 Resumed and delayed medical procedures

The following code maps how CIHI’s resumed and delayed medical medical procedures policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health services and the cihi_type as Health services — resumed medical procedures or Health services — delayed medical procedures respectively.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Resources and type_sub_cat Other Health Infrastructure. Any mis-mappings of such policies will be corrected downstream during manual data harmonization. Additionally, more detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                    cihi_coronanet_map$cihi_type %in% c( 'Health services — resumed medical procedures',
                                                                         'Health services — delayed medical procedures',
                                                                         
                                                                         ), 
                                  "Health Resources", 
                                  cihi_coronanet_map$type)


cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                            cihi_coronanet_map$cihi_type %in% c( 'Health services — resumed medical procedures',
                                                                                 'Health services — delayed medical procedures')
                                          "Other Health Infrastructure", 
                                          cihi_coronanet_map$type_sub_cat)

3.5.2 Health services — equipment

The following code maps how CIHI’s health equipment policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health services and the cihi_type as Health services — equipment.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Resources and type_sub_cat Unspecified Health Materials. More detailed mapping of such policies is in principal possible, but will be conducted downstream during manual data harmonization.

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                    cihi_coronanet_map$cihi_type == 'Health services — equipment',
                                  "Health Resources", 
                                  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                            cihi_coronanet_map$cihi_type == 'Health services — equipment', 
                                          "Unspecified Health Materials", 
                                          cihi_coronanet_map$type_sub_cat)

3.5.3 Health services — other

The following code maps how CIHI’s health equipment policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health services and the cihi_type as Health services — other.
Manual inspection of the data suggests that the best match for such policies is to map them in the CoronaNet taxonomy as follows: type as Health Resources and type_sub_cat Health Insurance. Any mis-mappings of such policies will be corrected downstream during manual data harmonization.

#Health services — other:
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                    cihi_coronanet_map$cihi_type == 'Health services — other',
                                  "Health Resources", 
                                  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                            cihi_coronanet_map$cihi_type == 'Health services — other',
                                          "Health Insurance", 
                                          cihi_coronanet_map$type_sub_cat)

3.5.4 Health services — telemedicine

The following code maps how CIHI’s telemedicine policies can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health services and the cihi_type as Health services — telemedicine/virtual care.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Resources and type_sub_cat Unspecified Health Materials. Any mis-mappings of such policies will be corrected downstream during manual data harmonization. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Health services — telemedicine/virtual care
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health services" &
                                    cihi_coronanet_map$cihi_type == 'Health services — telemedicine/virtual care',
                                  "Health Resources", 
                                  cihi_coronanet_map$type)

cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Health services" & 
                                            cihi_coronanet_map$cihi_type == 'Health services — telemedicine/virtual care', 
                                          "Other Health Infrastructure", 
                                          cihi_coronanet_map$type_sub_cat)

3.5.5 Health services — vistors

The following code maps how the policies CIHI documents as being about vistors to those in need of health services can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health services and the cihi_type as Health services — visitors
The CoronaNet taxonomy aims to capture such policies by coding the type as Social Distancing. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Health services — visitors:
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health services" & 
                                    cihi_coronanet_map$cihi_type == 'Health services — visitors', 
                                  "Social Distancing", 
                                  cihi_coronanet_map$type)

3.6 Health Workforce:

3.6.1 Change in practice and supply management

The following code maps how the policies CIHI documents as being about the change in practice and supply management in the health workforce can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health workforce and the cihi_type as Health workforce — change in practice or Health workforce — supply management.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Resources. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health workforce" & 
                                    cihi_coronanet_map$cihi_type %in% c( 'Health workforce — change in practice',
                                                                         'Health workforce — supply management'),
                                  "Health Resources",
                                  cihi_coronanet_map$type)

3.6.2 Licence reinstatement/reclassification

The following code maps how the policies CIHI documents as being about the licence reinstatement or reclassification in the health workforce can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health workforce and the cihi_type as Health workforce — licence reinstatement/reclassification.
The CoronaNet taxonomy aims to capture such policies by coding the type as Restriction and Regulation of Government Services. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Health workforce — licence reinstatement/reclassification
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health workforce" & 
                                    cihi_coronanet_map$cihi_type == 'Health workforce — licence reinstatement/reclassification',
                                  "Restriction and Regulation of Government Services", 
                                  cihi_coronanet_map$type)

3.6.3 Safety guidelines

The following code maps how the policies CIHI documents as being about safety guidelines in the health workforce can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Health workforce and the cihi_type as Health workforce — safety guidelines.
The CoronaNet taxonomy aims to capture such policies by coding the type as Public Awareness Measures. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Health workforce — safety guidelines:
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Health workforce" & 
                                    cihi_coronanet_map$cihi_type == 'Health workforce — safety guidelines', 
                                  "Public Awareness Measures", 
                                  cihi_coronanet_map$type)

3.7 Public information

3.7.1 Launch of web page/resource

The following code maps how the policies CIHI documents as being about the launch of web page/resource can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Public information and the cihi_type as Public information — launch of web page/resource.
The CoronaNet taxonomy aims to capture such policies by coding the type as Public Awareness Measures and type_sub_cat as Disseminating information related to COVID-19 to the public that is reliable and factually accurate . More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Public information — launch of web page/resource:
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Public information" &
                                    cihi_coronanet_map$cihi_type == 'Public information — launch of web page/resource', 
                                  "Public Awareness Measures",
                                  cihi_coronanet_map$type)


cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Public information" &
                                            cihi_coronanet_map$cihi_type == 'Public information — launch of web page/resource', 
                                          "Disseminating information related to COVID-19 to the public that is reliable and factually accurate", cihi_coronanet_map$type_sub_cat)

3.7.2 Projections

The following code maps how the policies CIHI documents as being about the projections of public information can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Public information and the cihi_type as Public information — projectionse.
The CoronaNet taxonomy aims to capture such policies by coding the type as Public Awareness Measures. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Public information — launch of web page/resource:
 

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Public information" &
                                    cihi_coronanet_map$cihi_type == 'Public information — projections',
                                  "Public Awareness Measures",
                                  cihi_coronanet_map$type)

3.7.3 Masks

The following code maps how the policies CIHI documents as being about masks can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Public information and the cihi_type as Public information — masks.
The CoronaNet taxonomy aims to capture such policies by coding the type as Social Distancing. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#Public information — masks:
cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Public information" &
  cihi_coronanet_map$cihi_type == 'Public information — masks', 
  "Social Distancing", 
  cihi_coronanet_map$type)

3.7.4 Pandemic response plans

The following code maps how the policies CIHI documents as being about pandemic response plans can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Public information and the cihi_type as Public information — pandemic response plans.
On manual inspection of these policies, we found that the best match for them would be as Restriction and Regulation of Businesses in the CoronaNet type variable. Any mis-mappings of such policies will be corrected downstream during manual data harmonization. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$unique_id <- ifelse(
  cihi_coronanet_map$cihi_category == "Public information" &
    cihi_coronanet_map$cihi_type == "Public information — pandemic response plans",
  paste0(cihi_coronanet_map$unique_id, "-business") , 
  cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(
  cihi_coronanet_map$cihi_category == "Public information" &
  cihi_coronanet_map$cihi_type == "Public information — pandemic response plans",
  "Restriction and Regulation of Businesses",
  cihi_coronanet_map$type)

3.7.5 Phase and alert level changes

The following code maps how the policies CIHI documents as being about phase and alert level changes can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Public information and the cihi_type as Public information — phase and alert level changes.
The CoronaNet taxonomy aims to capture such policies by coding the type as Health Monitoring. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$type <- 
  ifelse(cihi_coronanet_map$cihi_category == "Public information" &
           cihi_coronanet_map$cihi_type == 'Public information — phase and alert level changes', 
         "Health Monitoring", 
         cihi_coronanet_map$type)

3.8 State of emergency

The following code maps how the policies CIHI documents as being about states of emergency can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as State of emergency and the cihi_type as State of emergency.
The CoronaNet taxonomy aims to capture such policies by coding the type as Declaration of Emergency.

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "State of emergency" &
                                    cihi_coronanet_map$cihi_type == 'State of emergency', 
                                  "Declaration of Emergency", 
                                  cihi_coronanet_map$type)

3.9 Travel

3.9.1 Travel restrictions

The following code maps how CIHI policies which seek to capture travel restrictions can be mapped into the CoronaNet taxonomy despite the fact that it cannot be directly done.

On manual inspection of the policies coded with the value of Travel for the variable cihi_category and Travel — restrictions for the variable cihi_type, we found that they could be mapped as either External Border Restrictions or Internal Border Restrictions in the CoronaNet type variable.
Because there was no systematic way to map such policies in a one to one manner, we (i) appended the phrase “-externalPborder” to the unique_id to provide additional information to those manually harmonizing this data downstream as to how such policies were originally coded in CIHI and (ii) mapped such policies as External Border Restrictions or Internal Border Restrictions in the CoronaNet type variable to provide guidance to researchers manually harmonizing this data later downstream.

cihi_coronanet_map$unique_id <- ifelse(cihi_coronanet_map$cihi_category == "Travel" &
                                         cihi_coronanet_map$cihi_type == 'Travel — restrictions',
                                       paste0(cihi_coronanet_map$unique_id, "-external_border"),
                                       cihi_coronanet_map$unique_id)

cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Travel" &
                                    cihi_coronanet_map$cihi_type == 'Travel — restrictions', 
                                  "External Border Restrictions or Internal Border Restrictions", 
                                  cihi_coronanet_map$type)

3.9.2 Travel restrictions

The following code maps how the policies CIHI documents as being about self-isolation can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Travel and the cihi_type as Travel — self-isolation.
The CoronaNet taxonomy aims to capture such policies by coding the type as Quarantine.

#Travel — self-isolation: 
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Travel" & 
                                    cihi_coronanet_map$cihi_type == 'Travel — self-isolation', 
                                  "Quarantine", 
                                  cihi_coronanet_map$type)

3.10 Vaccine

The following code maps how the policies CIHI documents as being about vaccines can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Vaccine
The CoronaNet taxonomy aims to capture such policies by coding the type as COVID-19 Vaccines.

# policy type is the same 
cihi_coronanet_map$type <- ifelse(cihi_coronanet_map$cihi_category == "Vaccine",
                                  "COVID-19 Vaccines", 
                                  cihi_coronanet_map$type)

3.10.1 Implementation plans and frameworks; phase changes and milestones; population to be vaccinated

The following code maps how the policies CIHI documents as being about implementation plans and frameworks; phase changes and milestones; and population to be vaccinated can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Vaccine and the cihi_type as Vaccine — implementation plans and frameworks, Vaccine — phase changes and milestones, Vaccine — population to be vaccinated respectively.
The CoronaNet taxonomy aims to capture such policies by coding the type_sub_cat as Distribution (shipping, storage, administration) of COVID-19 vaccines. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

#sub_types
cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Vaccine" &
                                            cihi_coronanet_map$cihi_type %in% c(
                                              "Vaccine — implementation plans and frameworks",
                                              'Vaccine — phase changes and milestones',
                                              'Vaccine — population to be vaccinated')
                                          "Distribution (shipping, storage, administration) of COVID-19 vaccines",
                                          cihi_coronanet_map$type_sub_cat)

3.10.2 Regulatory approval

The following code maps how the policies CIHI documents as being about regulatory approval process for administering the COVID-19 vaccine can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Vaccine and the cihi_type as Vaccine — regulatory approval.
The CoronaNet taxonomy aims to capture such policies by coding the type_sub_cat as Regulatory approval process for administering the COVID-19 vaccine. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Vaccine" & 
                                            cihi_coronanet_map$cihi_type == 'Vaccine — regulatory approval', 
                                          "Regulatory approval process for administering the COVID-19 vaccine", 
                                          cihi_coronanet_map$type_sub_cat)

3.10.3 Purchasing and allocation

The following code maps how the policies CIHI documents as being about purchasing and allocation for COVID-19 vaccines can be mapped into the CoronaNet taxonomy.

The CIHI taxonomy aims to capture such policies by coding the cihi_category as Vaccine and the cihi_type as Vaccine — purchasing and allocation.
On manual inspection of these policies, we found that the best match for them would be as Purchase of COVID-19 vaccines or Distribution (shipping, storage, administration) of COVID-19 vaccines in the CoronaNet type_sub_cat variable. Any mis-mappings of such policies will be corrected downstream during manual data harmonization. More detailed mapping of such policies is in principal possible, but will also be conducted downstream during manual data harmonization.

cihi_coronanet_map$unique_id <- ifelse(cihi_coronanet_map$cihi_category == "Vaccine" & 
                                         cihi_coronanet_map$cihi_type == 'Vaccine — purchasing and allocation',
                                       paste0(cihi_coronanet_map$unique_id, "-vac_purchase"), 
                                       cihi_coronanet_map$unique_id)

cihi_coronanet_map$type_sub_cat <- ifelse(cihi_coronanet_map$cihi_category == "Vaccine" &
                                            cihi_coronanet_map$cihi_type == 'Vaccine — purchasing and allocation', 
                                          "Purchase of COVID-19 vaccines or Distribution (shipping, storage, administration) of COVID-19 vaccines",
                                          cihi_coronanet_map$type_sub_cat)

4 Final Map Adjustments

Before finally exporting the data, we remove the cihi_type and cihi_category variables from the dataset.

# excluding not needed columns
cihi_coronanet_map <- select(cihi_coronanet_map, - cihi_type, -cihi_category )

Finally, once all the variables that are possible to harmonize from the CIHI dataset to CoronaNet taxonomy have been identified, the results are exported in an .rds and .csv format, to be consolidated together with the other external databases to be harmonised. The final consolidated dataset is then processed for manual harmonisation into the CoronaNet Research Project dataset.

write.csv(cihi_coronanet_map ,"cihi_coronanet_map.csv")
saveRDS(cihi_coronanet_map ,"cihi_coronanet_map.rds")