claims_db/phclaims/stage/tables/qa_stage.mcaid_claim_procedure.R
In PHSKC-APDE/claims_data: Query and analyze WA State Medicaid, Medicare, and APCD data
# This code QAs table claims.stage_mcaid_claim_procedure
#
# It is designed to be run as part of the master Medicaid script:
# https://github.com/PHSKC-APDE/claims_data/blob/main/claims_db/db_loader/mcaid/master_mcaid_analytic.R
#
# 2019-12
# Alastair Matheson (building on SQL from Philip Sylling)
#
# QA checks:
# 1) IDs are all found in the elig tables
# 2) Procedure codes are formatted appropriately
# 3) procedure_code_number falls in an acceptable range
# 4) Check there were as many or more procedure codes for each calendar year
### Function elements
# conn = database connection
# server = whether we are working in HHSAW or PHClaims
# config = the YAML config file. Can be either an object already loaded into
# R or a URL that should be used
# get_config = if a URL is supplied, set this to T so the YAML file is loaded
qa_stage_mcaid_claim_procedure_f <- function(conn = NULL,
server = c("hhsaw", "phclaims"),
config = NULL,
get_config = F) {
# Set up variables specific to the server
server <- match.arg(server)
if (get_config == T){
if (stringr::str_detect(config, "^http")) {
config <- yaml::yaml.load(getURL(config))
} else{
stop("A URL must be specified in config if using get_config = T")
}
}
from_schema <- config[[server]][["from_schema"]]
from_table <- config[[server]][["from_table"]]
to_schema <- config[[server]][["to_schema"]]
to_table <- config[[server]][["to_table"]]
final_schema <- config[[server]][["final_schema"]]
final_table <- ifelse(is.null(config[[server]][["final_table"]]), '',
config[[server]][["final_table"]])
ref_schema <- config[[server]][["ref_schema"]]
ref_table <- ifelse(is.null(config[[server]][["ref_table"]]), '',
config[[server]][["ref_table"]])
qa_schema <- config[[server]][["qa_schema"]]
qa_table <- ifelse(is.null(config[[server]][["qa_table"]]), '',
config[[server]][["qa_table"]])
message("Running QA on ", to_schema, ".", to_table)
#### PULL OUT VALUES NEEDED MULTIPLE TIMES ####
last_run <- as.POSIXct(odbc::dbGetQuery(
conn, glue::glue_sql("SELECT MAX (last_run) FROM {`to_schema`}.{`to_table`}",
.con = conn))[[1]])
#### Check all IDs are also found in the elig_demo and time_var tables ####
ids_demo_chk <- as.integer(DBI::dbGetQuery(
conn, glue::glue_sql("SELECT COUNT (DISTINCT a.id_mcaid) AS cnt_id
FROM {`to_schema`}.{`to_table`} AS a
LEFT JOIN {`final_schema`}.{DBI::SQL(final_table)}mcaid_elig_demo AS b
ON a.id_mcaid = b.id_mcaid
WHERE b.id_mcaid IS NULL",
.con = conn)))
ids_timevar_chk <- as.integer(DBI::dbGetQuery(
conn, glue::glue_sql("SELECT COUNT (DISTINCT a.id_mcaid) AS cnt_id
FROM {`to_schema`}.{`to_table`} AS a
LEFT JOIN {`final_schema`}.{DBI::SQL(final_table)}mcaid_elig_timevar AS b
ON a.id_mcaid = b.id_mcaid
WHERE b.id_mcaid IS NULL",
.con = conn)))
# Write findings to metadata
if (ids_demo_chk == 0 & ids_timevar_chk == 0) {
ids_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Distinct IDs compared to elig tables',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'There were the same number of IDs as in the final mcaid_elig_demo ",
"and mcaid_elig_timevar tables')",
.con = conn))
} else {
ids_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Distinct IDs compared to elig tables',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {ids_demo_chk} {DBI::SQL(ifelse(ids_demo_chk >= 0, 'more', 'fewer'))} ",
"IDs than in the final mcaid_elig_demo table and ",
"{ids_timevar_chk} {DBI::SQL(ifelse(ids_timevar_chk >= 0, 'more', 'fewer'))} ",
"IDs than in the final mcaid_elig_timevar table')",
.con = conn))
}
#### Check format of procedure codes ####
procedure_format_chk <- as.integer(DBI::dbGetQuery(
conn = conn, glue::glue_sql("WITH CTE AS
(SELECT
CASE WHEN LEN([procedure_code]) = 5 AND ISNUMERIC([procedure_code]) = 1 THEN 'CPT Category I'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) = 'F' THEN 'CPT Category II'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) = 'T' THEN 'CPT Category III'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) IN ('M', 'U') THEN 'CPT Other'
WHEN LEN([procedure_code]) = 5 AND
SUBSTRING([procedure_code], 1, 1) LIKE '[A-Z]' AND
ISNUMERIC(SUBSTRING([procedure_code], 2, 4)) = 1 THEN 'HCPCS'
WHEN LEN([procedure_code]) IN (3, 4) AND
ISNUMERIC([procedure_code]) = 1 THEN 'ICD-9-PCS'
WHEN LEN([procedure_code]) = 7 THEN 'ICD-10-PCS'
ELSE 'UNKNOWN' END AS [code_system]
,*
FROM {`to_schema`}.{`to_table`}
)
SELECT COUNT(DISTINCT [procedure_code])
FROM CTE
WHERE [code_system] = 'UNKNOWN';",
.con = conn)))
# Write findings to metadata
if (procedure_format_chk < 50) {
procedure_format_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Format of procedure codes',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_format_chk} distinct procedure codes with an unknown format (<50 ok)')",
.con = conn))
} else {
procedure_format_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Format of procedure codes',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_format_chk} distinct procedure codes with an unknown format')",
.con = conn))
}
#### Check that procedure_code_number in ('01':'12','line') ####
procedure_num_chk <- as.integer(
DBI::dbGetQuery(conn,
glue::glue_sql("SELECT count([procedure_code_number])
FROM {`to_schema`}.{`to_table`}
where [procedure_code_number] not in
('01','02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', 'line')",
.con = conn)))
# Write findings to metadata
if (procedure_num_chk == 0) {
procedure_num_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'procedure_code_number = 01-12 or line',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'All procedure_code_number values were 01:12 or line')",
.con = conn))
} else {
procedure_num_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'procedure_code_number = 01-12 or line',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_num_chk} procedure_code_number values not 01 through 12 or line')",
.con = conn))
}
#### Compare number of procedure codes in current vs. prior analytic tables ####
if (DBI::dbExistsTable(conn,
DBI::Id(schema = final_schema, table = paste0(final_table, "mcaid_claim_procedure")))) {
num_procedure_current <- DBI::dbGetQuery(
conn, glue::glue_sql("SELECT YEAR(first_service_date) AS claim_year, COUNT(*) AS current_num_procedure
FROM {`final_schema`}.{DBI::SQL(final_table)}mcaid_claim_procedure
GROUP BY YEAR(first_service_date) ORDER BY YEAR(first_service_date)",
.con = conn))
num_procedure_new <- DBI::dbGetQuery(
conn, glue::glue_sql("SELECT YEAR(first_service_date) AS claim_year, COUNT(*) AS new_num_procedure
FROM {`to_schema`}.{`to_table`}
GROUP BY YEAR(first_service_date) ORDER by YEAR(first_service_date)", .con = conn))
num_procedure_overall <- left_join(num_procedure_new, num_procedure_current, by = "claim_year") %>%
mutate_at(vars(new_num_procedure, current_num_procedure), list(~ replace_na(., 0))) %>%
mutate(pct_change = round((new_num_procedure - current_num_procedure) / current_num_procedure * 100, 4))
# Write findings to metadata
if (max(num_procedure_overall$pct_change, na.rm = T) > 0 &
min(num_procedure_overall$pct_change, na.rm = T) >= 0) {
num_procedure_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'The following years had more procedures than in the final schema table: ",
"{DBI::SQL(glue::glue_collapse(
glue::glue_data(data.frame(year = num_procedure_overall$claim_year[num_procedure_overall$pct_change > 0],
pct = round(abs(num_procedure_overall$pct_change[num_procedure_overall$pct_change > 0]), 2)),
'{year} ({pct}% more)'), sep = ', ', last = ' and '))}')",
.con = conn))
} else if (min(num_procedure_overall$pct_change, na.rm = T) + max(num_procedure_overall$pct_change, na.rm = T) == 0) {
num_procedure_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'No change in the number of procedures compared to final schema table')",
.con = conn))
} else if (min(num_procedure_overall$pct_change, na.rm = T) < 0) {
num_procedure_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'The following years had fewer procedures than in the final schema table: ",
"{DBI::SQL(glue::glue_collapse(
glue::glue_data(data.frame(year = num_procedure_overall$claim_year[num_procedure_overall$pct_change < 0],
pct = round(abs(num_procedure_overall$pct_change[num_procedure_overall$pct_change < 0]), 2)),
'{year} ({pct}% fewer)'), sep = ', ', last = ' and '))}')",
.con = conn))
}
} else {
num_procedure_fail <- 0
}
#### SUM UP FAILURES ####
fail_tot <- sum(ids_fail, procedure_format_fail, procedure_num_fail, num_procedure_fail)
return(fail_tot)
}
PHSKC-APDE/claims_data documentation built on May 2, 2024, 8:16 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# This code QAs table claims.stage_mcaid_claim_procedure
#
# It is designed to be run as part of the master Medicaid script:
# https://github.com/PHSKC-APDE/claims_data/blob/main/claims_db/db_loader/mcaid/master_mcaid_analytic.R
#
# 2019-12
# Alastair Matheson (building on SQL from Philip Sylling)
#
# QA checks:
# 1) IDs are all found in the elig tables
# 2) Procedure codes are formatted appropriately
# 3) procedure_code_number falls in an acceptable range
# 4) Check there were as many or more procedure codes for each calendar year
### Function elements
# conn = database connection
# server = whether we are working in HHSAW or PHClaims
# config = the YAML config file. Can be either an object already loaded into
# R or a URL that should be used
# get_config = if a URL is supplied, set this to T so the YAML file is loaded
qa_stage_mcaid_claim_procedure_f <- function(conn = NULL,
server = c("hhsaw", "phclaims"),
config = NULL,
get_config = F) {
# Set up variables specific to the server
server <- match.arg(server)
if (get_config == T){
if (stringr::str_detect(config, "^http")) {
config <- yaml::yaml.load(getURL(config))
} else{
stop("A URL must be specified in config if using get_config = T")
}
}
from_schema <- config[[server]][["from_schema"]]
from_table <- config[[server]][["from_table"]]
to_schema <- config[[server]][["to_schema"]]
to_table <- config[[server]][["to_table"]]
final_schema <- config[[server]][["final_schema"]]
final_table <- ifelse(is.null(config[[server]][["final_table"]]), '',
config[[server]][["final_table"]])
ref_schema <- config[[server]][["ref_schema"]]
ref_table <- ifelse(is.null(config[[server]][["ref_table"]]), '',
config[[server]][["ref_table"]])
qa_schema <- config[[server]][["qa_schema"]]
qa_table <- ifelse(is.null(config[[server]][["qa_table"]]), '',
config[[server]][["qa_table"]])
message("Running QA on ", to_schema, ".", to_table)
#### PULL OUT VALUES NEEDED MULTIPLE TIMES ####
last_run <- as.POSIXct(odbc::dbGetQuery(
conn, glue::glue_sql("SELECT MAX (last_run) FROM {`to_schema`}.{`to_table`}",
.con = conn))[[1]])
#### Check all IDs are also found in the elig_demo and time_var tables ####
ids_demo_chk <- as.integer(DBI::dbGetQuery(
conn, glue::glue_sql("SELECT COUNT (DISTINCT a.id_mcaid) AS cnt_id
FROM {`to_schema`}.{`to_table`} AS a
LEFT JOIN {`final_schema`}.{DBI::SQL(final_table)}mcaid_elig_demo AS b
ON a.id_mcaid = b.id_mcaid
WHERE b.id_mcaid IS NULL",
.con = conn)))
ids_timevar_chk <- as.integer(DBI::dbGetQuery(
conn, glue::glue_sql("SELECT COUNT (DISTINCT a.id_mcaid) AS cnt_id
FROM {`to_schema`}.{`to_table`} AS a
LEFT JOIN {`final_schema`}.{DBI::SQL(final_table)}mcaid_elig_timevar AS b
ON a.id_mcaid = b.id_mcaid
WHERE b.id_mcaid IS NULL",
.con = conn)))
# Write findings to metadata
if (ids_demo_chk == 0 & ids_timevar_chk == 0) {
ids_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Distinct IDs compared to elig tables',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'There were the same number of IDs as in the final mcaid_elig_demo ",
"and mcaid_elig_timevar tables')",
.con = conn))
} else {
ids_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Distinct IDs compared to elig tables',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {ids_demo_chk} {DBI::SQL(ifelse(ids_demo_chk >= 0, 'more', 'fewer'))} ",
"IDs than in the final mcaid_elig_demo table and ",
"{ids_timevar_chk} {DBI::SQL(ifelse(ids_timevar_chk >= 0, 'more', 'fewer'))} ",
"IDs than in the final mcaid_elig_timevar table')",
.con = conn))
}
#### Check format of procedure codes ####
procedure_format_chk <- as.integer(DBI::dbGetQuery(
conn = conn, glue::glue_sql("WITH CTE AS
(SELECT
CASE WHEN LEN([procedure_code]) = 5 AND ISNUMERIC([procedure_code]) = 1 THEN 'CPT Category I'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) = 'F' THEN 'CPT Category II'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) = 'T' THEN 'CPT Category III'
WHEN LEN([procedure_code]) = 5 AND
ISNUMERIC(SUBSTRING([procedure_code], 1, 4)) = 1 AND
SUBSTRING([procedure_code], 5, 1) IN ('M', 'U') THEN 'CPT Other'
WHEN LEN([procedure_code]) = 5 AND
SUBSTRING([procedure_code], 1, 1) LIKE '[A-Z]' AND
ISNUMERIC(SUBSTRING([procedure_code], 2, 4)) = 1 THEN 'HCPCS'
WHEN LEN([procedure_code]) IN (3, 4) AND
ISNUMERIC([procedure_code]) = 1 THEN 'ICD-9-PCS'
WHEN LEN([procedure_code]) = 7 THEN 'ICD-10-PCS'
ELSE 'UNKNOWN' END AS [code_system]
,*
FROM {`to_schema`}.{`to_table`}
)
SELECT COUNT(DISTINCT [procedure_code])
FROM CTE
WHERE [code_system] = 'UNKNOWN';",
.con = conn)))
# Write findings to metadata
if (procedure_format_chk < 50) {
procedure_format_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Format of procedure codes',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_format_chk} distinct procedure codes with an unknown format (<50 ok)')",
.con = conn))
} else {
procedure_format_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Format of procedure codes',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_format_chk} distinct procedure codes with an unknown format')",
.con = conn))
}
#### Check that procedure_code_number in ('01':'12','line') ####
procedure_num_chk <- as.integer(
DBI::dbGetQuery(conn,
glue::glue_sql("SELECT count([procedure_code_number])
FROM {`to_schema`}.{`to_table`}
where [procedure_code_number] not in
('01','02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', 'line')",
.con = conn)))
# Write findings to metadata
if (procedure_num_chk == 0) {
procedure_num_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'procedure_code_number = 01-12 or line',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'All procedure_code_number values were 01:12 or line')",
.con = conn))
} else {
procedure_num_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'procedure_code_number = 01-12 or line',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'There were {procedure_num_chk} procedure_code_number values not 01 through 12 or line')",
.con = conn))
}
#### Compare number of procedure codes in current vs. prior analytic tables ####
if (DBI::dbExistsTable(conn,
DBI::Id(schema = final_schema, table = paste0(final_table, "mcaid_claim_procedure")))) {
num_procedure_current <- DBI::dbGetQuery(
conn, glue::glue_sql("SELECT YEAR(first_service_date) AS claim_year, COUNT(*) AS current_num_procedure
FROM {`final_schema`}.{DBI::SQL(final_table)}mcaid_claim_procedure
GROUP BY YEAR(first_service_date) ORDER BY YEAR(first_service_date)",
.con = conn))
num_procedure_new <- DBI::dbGetQuery(
conn, glue::glue_sql("SELECT YEAR(first_service_date) AS claim_year, COUNT(*) AS new_num_procedure
FROM {`to_schema`}.{`to_table`}
GROUP BY YEAR(first_service_date) ORDER by YEAR(first_service_date)", .con = conn))
num_procedure_overall <- left_join(num_procedure_new, num_procedure_current, by = "claim_year") %>%
mutate_at(vars(new_num_procedure, current_num_procedure), list(~ replace_na(., 0))) %>%
mutate(pct_change = round((new_num_procedure - current_num_procedure) / current_num_procedure * 100, 4))
# Write findings to metadata
if (max(num_procedure_overall$pct_change, na.rm = T) > 0 &
min(num_procedure_overall$pct_change, na.rm = T) >= 0) {
num_procedure_fail <- 0
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'PASS',
{format(Sys.time(), usetz = FALSE)},
'The following years had more procedures than in the final schema table: ",
"{DBI::SQL(glue::glue_collapse(
glue::glue_data(data.frame(year = num_procedure_overall$claim_year[num_procedure_overall$pct_change > 0],
pct = round(abs(num_procedure_overall$pct_change[num_procedure_overall$pct_change > 0]), 2)),
'{year} ({pct}% more)'), sep = ', ', last = ' and '))}')",
.con = conn))
} else if (min(num_procedure_overall$pct_change, na.rm = T) + max(num_procedure_overall$pct_change, na.rm = T) == 0) {
num_procedure_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'No change in the number of procedures compared to final schema table')",
.con = conn))
} else if (min(num_procedure_overall$pct_change, na.rm = T) < 0) {
num_procedure_fail <- 1
DBI::dbExecute(conn = conn,
glue::glue_sql("INSERT INTO {`qa_schema`}.{DBI::SQL(qa_table)}qa_mcaid
(last_run, table_name, qa_item, qa_result, qa_date, note)
VALUES ({format(last_run, usetz = FALSE)},
'{DBI::SQL(to_schema)}.{DBI::SQL(to_table)}',
'Change in number of procedures',
'FAIL',
{format(Sys.time(), usetz = FALSE)},
'The following years had fewer procedures than in the final schema table: ",
"{DBI::SQL(glue::glue_collapse(
glue::glue_data(data.frame(year = num_procedure_overall$claim_year[num_procedure_overall$pct_change < 0],
pct = round(abs(num_procedure_overall$pct_change[num_procedure_overall$pct_change < 0]), 2)),
'{year} ({pct}% fewer)'), sep = ', ', last = ' and '))}')",
.con = conn))
}
} else {
num_procedure_fail <- 0
}
#### SUM UP FAILURES ####
fail_tot <- sum(ids_fail, procedure_format_fail, procedure_num_fail, num_procedure_fail)
return(fail_tot)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.