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closes #39
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@andrewallenbruce
andrewallenbruce committed Nov 6, 2023
1 parent e0f74df commit 87f232c
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Showing 2 changed files with 150 additions and 131 deletions.
2 changes: 2 additions & 0 deletions R/globals.R
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,7 @@ utils::globalVariables(c(
"identifier", # <open_ids>
"y", # <opt_out>
"y", # <order_refer>
"status", # <order_refer>
"distro", # <outpatient>
"y", # <outpatient>
"y", # <pending>
Expand Down Expand Up @@ -181,6 +182,7 @@ utils::globalVariables(c(
"set", # <quality_payment>
"val", # <quality_payment>
"score", # <quality_payment>
"status", # <quality_payment>
"y", # <reassignments>
"code", # <download_nucc_csv>
"section", # <download_nucc_csv>
Expand Down
279 changes: 148 additions & 131 deletions R/laboratories.R
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Original file line number Diff line number Diff line change
Expand Up @@ -151,16 +151,16 @@ laboratories <- function(name = NULL,
results <- tidyup(results, dtype = 'ymd', dt = '_dt', yn = '_sw') |>
combine(address, c('st_adr', 'addtnl_st_adr')) |>
combine(provider_name, c('fac_name', 'addtnl_fac_name')) |>
dplyr::mutate(pgm_trmntn_cd = termcd(pgm_trmntn_cd),
crtfctn_actn_type_cd = toa(crtfctn_actn_type_cd),
cmplnc_stus_cd = status(cmplnc_stus_cd),
rgn_cd = region(rgn_cd),
gnrl_cntl_type_cd = owner(gnrl_cntl_type_cd),
crtfct_type_cd = app(crtfct_type_cd),
gnrl_fac_type_cd = factype(gnrl_fac_type_cd),
current_clia_lab_clsfctn_cd = labclass(current_clia_lab_clsfctn_cd),
prvdr_ctgry_cd = labclass(prvdr_ctgry_cd),
prvdr_ctgry_sbtyp_cd = labclass(prvdr_ctgry_sbtyp_cd),
dplyr::mutate(pgm_trmntn_cd = fct_term(pgm_trmntn_cd),
crtfctn_actn_type_cd = fct_toa(crtfctn_actn_type_cd),
cmplnc_stus_cd = fct_stat(cmplnc_stus_cd),
rgn_cd = fct_region(rgn_cd),
gnrl_cntl_type_cd = fct_owner(gnrl_cntl_type_cd),
crtfct_type_cd = fct_app(crtfct_type_cd),
gnrl_fac_type_cd = fct_facility(gnrl_fac_type_cd),
current_clia_lab_clsfctn_cd = fct_lab(current_clia_lab_clsfctn_cd),
prvdr_ctgry_cd = fct_lab(prvdr_ctgry_cd),
prvdr_ctgry_sbtyp_cd = fct_lab(prvdr_ctgry_sbtyp_cd),
duration = duration_vec(trmntn_exprtn_dt),
expired = dplyr::if_else(duration < 0, TRUE, FALSE),
duration = NULL) |>
Expand Down Expand Up @@ -263,7 +263,7 @@ cols_lab <- function(df) {
cols <- c('provider_name',
'clia_number' = 'prvdr_num',
'certificate' = 'crtfct_type_cd',
# 'clia_medicare' = 'clia_mdcr_num',
'clia_medicare' = 'clia_mdcr_num',
# 'application' = 'aplctn_type_cd',
'effective_date' = 'crtfct_efctv_dt',
'expiration_date' = 'trmntn_exprtn_dt',
Expand All @@ -290,7 +290,7 @@ cols_lab <- function(df) {
'certification_date' = 'crtfctn_dt',
'mailed_date' = 'crtfct_mail_dt',

# 'region' = 'rgn_cd',
'region' = 'rgn_cd',
# 'state_region' = 'state_rgn_cd',
# 'fips_county' = 'fips_cnty_cd',
# 'fips_state' = 'fips_state_cd',
Expand Down Expand Up @@ -365,156 +365,173 @@ cols_lab <- function(df) {

#' @autoglobal
#' @noRd
toa <- function(x) {
cert <- function(x) {
dplyr::case_match(x,
"1" ~ "Initial",
"2" ~ "Recertification",
"3" ~ "Termination",
"4" ~ "Change of Ownership",
"5" ~ "Validation",
"8" ~ "Full Survey After Complaint",
.default = x)
"compliance" ~ "1",
"waiver" ~ "2",
"accreditation" ~ "3",
"ppm" ~ "4",
"registration" ~ "9",
.default = x)
}

#' @autoglobal
#' @noRd
app <- function(x) {
dplyr::case_match(x,
"1" ~ "Compliance",
"2" ~ "Waiver",
"3" ~ "Accreditation",
"4" ~ "PPM",
"9" ~ "Registration",
.default = x)
fct_toa <- function(x) {
factor(x,
levels = c("1", "2", "3", "4", "5", "8"),
labels = c("Initial",
"Recertification",
"Termination",
"Change of Ownership",
"Validation",
"Full Survey After Complaint"),
ordered = TRUE)
}

#' @autoglobal
#' @noRd
cert <- function(x) {
dplyr::case_match(x,
"compliance" ~ "1",
"waiver" ~ "2",
"accreditation" ~ "3",
"ppm" ~ "4",
"registration" ~ "9",
.default = x)
fct_app <- function(x) {
factor(x,
levels = c("1", "2", "3", "4", "9"),
labels = c("Compliance",
"Waiver",
"Accreditation",
"PPM",
"Registration"),
ordered = TRUE)
}

#' @autoglobal
#' @noRd
status <- function(x) {
dplyr::case_match(x,
"A" ~ "In Compliance",
"B" ~ "Not In Compliance",
.default = x)
fct_stat <- function(x) {
factor(x,
levels = c("A", "B"),
labels = c("In Compliance",
"Not In Compliance"),
ordered = TRUE)
}

#' @autoglobal
#' @noRd
region <- function(x) {
dplyr::case_match(x,
"01" ~ "Boston",
"02" ~ "New York",
"03" ~ "Philadelphia",
"04" ~ "Atlanta",
"05" ~ "Chicago",
"06" ~ "Dallas",
"07" ~ "Kansas City",
"08" ~ "Denver",
"09" ~ "San Francisco",
"10" ~ "Seattle",
.default = x)
fct_region <- function(x) {
factor(x,
levels = c('01', '02', '03', '04', '05',
'06', '07', '08', '09', '10'),
labels = c('Boston',
'New York',
'Philadelphia',
'Atlanta',
'Chicago',
'Dallas',
'Kansas City',
'Denver',
'San Francisco',
'Seattle'))
}

#' @autoglobal
#' @noRd
owner <- function(x) {
dplyr::case_match(x,
"01" ~ "Religious Affiliation",
"02" ~ "Private",
"03" ~ "Other",
"04" ~ "Proprietary",
"05" ~ "Govt: City",
"06" ~ "Govt: County",
"07" ~ "Govt: State",
"08" ~ "Govt: Federal",
"09" ~ "Govt: Other",
"10" ~ "Unknown",
.default = x)
fct_owner <- function(x) {
factor(x,
levels = c('01', '02', '03', '04', '05',
'06', '07', '08', '09', '10'),
labels = c('Religious Affiliation',
'Private',
'Other',
'Proprietary',
'Govt: City',
'Govt: County',
'Govt: State',
'Govt: Federal',
'Govt: Other',
'Unknown'))
}

#' @autoglobal
#' @noRd
factype <- function(x) {
dplyr::case_match(x,
"01" ~ "Ambulance",
"02" ~ "Ambulatory Surgical Center",
"03" ~ "Ancillary Test Site",
"04" ~ "Assisted Living Facility",
"05" ~ "Blood Banks",
"06" ~ "Community Clinic",
"07" ~ "Comprehensive Outpatient Rehab",
"08" ~ "End-Stage Renal Disease Dialysis",
"09" ~ "Federally Qualified Health Center",
"10" ~ "Health Fair",
"11" ~ "Health Maintenance Organization",
"12" ~ "Home Health Agency",
"13" ~ "Hospice",
"14" ~ "Hospital",
"15" ~ "Independent",
"16" ~ "Industrial",
"17" ~ "Insurance",
"18" ~ "Intermediate Care Facility/Individuals with Intellectual Disabilities",
"19" ~ "Mobile Lab",
"20" ~ "Pharmacy",
"21" ~ "Physician Office",
"22" ~ "Other Practitioner",
"23" ~ "Prison",
"24" ~ "Public Health Laboratory",
"25" ~ "Rural Health Clinic",
"26" ~ "School/Student Health Service",
"27" ~ "Skilled Nursing Facility",
"28" ~ "Tissue Bank/Repositories",
"29" ~ "Other",
.default = x)
fct_lab <- function(x) {
factor(x,
levels = c("00", "22", "01", "05", "10"),
labels = c("CLIA Lab",
"CLIA Lab",
"CLIA88 Lab",
"CLIA Exempt Lab",
"CLIA VA Lab"))
}

#' @autoglobal
#' @noRd
labclass <- function(x) {
dplyr::case_match(x,
c("00", "22") ~ "CLIA Lab",
"01" ~ "CLIA88 Lab",
"05" ~ "CLIA Exempt Lab",
"10" ~ "CLIA VA Lab",
.default = x)
fct_facility <- function(x) {
factor(x,
levels = c('01', '02', '03', '04', '05',
'06', '07', '08', '09', '10',
'11', '12', '13', '14', '15',
'16', '17', '18', '19', '20',
'21', '22', '23', '24', '25',
'26', '27', '28', '29'),
labels = c('Ambulance',
'Ambulatory Surgical Center',
'Ancillary Test Site',
'Assisted Living Facility',
'Blood Banks',
'Community Clinic',
'Comprehensive Outpatient Rehab',
'End-Stage Renal Disease Dialysis',
'Federally Qualified Health Center',
'Health Fair',
'Health Maintenance Organization',
'Home Health Agency',
'Hospice',
'Hospital',
'Independent',
'Industrial',
'Insurance',
'Intermediate Care Facility-Individuals with Intellectual Disabilities',
'Mobile Lab',
'Pharmacy',
'Physician Office',
'Other Practitioner',
'Prison',
'Public Health Laboratory',
'Rural Health Clinic',
'School-Student Health Service',
'Skilled Nursing Facility',
'Tissue Bank-Repositories',
'Other'),
ordered = TRUE)
}

#' @autoglobal
#' @noRd
termcd <- function(x) {
dplyr::case_match(x,
"00" ~ "Active Provider",
"01" ~ "Voluntary: Merger, Closure",
"02" ~ "Voluntary: Dissatisfaction with Reimbursement",
"03" ~ "Voluntary: Risk of Involuntary Termination",
"04" ~ "Voluntary: Other Reason for Withdrawal",
"05" ~ "Involuntary: Failure to Meet Health-Safety Req",
"06" ~ "Involuntary: Failure to Meet Agreement",
"07" ~ "Other: Provider Status Change",
"08" ~ "Nonpayment of Fees (CLIA Only)",
"09" ~ "Rev/Unsuccessful Participation in PT (CLIA Only)",
"10" ~ "Rev/Other Reason (CLIA Only)",
"11" ~ "Incomplete CLIA Application Information (CLIA Only)",
"12" ~ "No Longer Performing Tests (CLIA Only)",
"13" ~ "Multiple to Single Site Certificate (CLIA Only)",
"14" ~ "Shared Laboratory (CLIA Only)",
"15" ~ "Failure to Renew Waiver PPM Certificate (CLIA Only)",
"16" ~ "Duplicate CLIA Number (CLIA Only)",
"17" ~ "Mail Returned No Forward Address Cert Ended (CLIA Only)",
"20" ~ "Notification Bankruptcy (CLIA Only)",
"33" ~ "Accreditation Not Confirmed (CLIA Only)",
"80" ~ "Awaiting State Approval",
"99" ~ "OIG Action Do Not Activate (CLIA Only)",
.default = x)
fct_term <- function(x) {
factor(x,
levels = c('00', '01', '02', '03', '04',
'05', '06', '07', '08', '09',
'10', '11', '12', '13', '14',
'15', '16', '17', '20', '33',
'80', '99'),
labels = c('Active Provider',
'Voluntary: Merger, Closure',
'Voluntary: Dissatisfaction with Reimbursement',
'Voluntary: Risk of Involuntary Termination',
'Voluntary: Other Reason for Withdrawal',
'Involuntary: Failure to Meet Health-Safety Req',
'Involuntary: Failure to Meet Agreement',
'Other: Provider Status Change',
'Nonpayment of Fees (CLIA Only)',
'Rev/Unsuccessful Participation in PT (CLIA Only)',
'Rev/Other Reason (CLIA Only)',
'Incomplete CLIA Application Information (CLIA Only)',
'No Longer Performing Tests (CLIA Only)',
'Multiple to Single Site Certificate (CLIA Only)',
'Shared Laboratory (CLIA Only)',
'Failure to Renew Waiver PPM Certificate (CLIA Only)',
'Duplicate CLIA Number (CLIA Only)',
'Mail Returned No Forward Address Cert Ended (CLIA Only)',
'Notification Bankruptcy (CLIA Only)',
'Accreditation Not Confirmed (CLIA Only)',
'Awaiting State Approval',
'OIG Action Do Not Activate (CLIA Only)'),
ordered = TRUE)
}

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