From 5855d1479abe95a20167a90be24cda424574ab56 Mon Sep 17 00:00:00 2001 From: Robert A Overman Date: Sun, 12 May 2019 14:40:47 -0400 Subject: [PATCH 1/5] Add options to download 2017, and 2018 AHRQ lists fixes #142 --- R/parse-comorbid.R | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/R/parse-comorbid.R b/R/parse-comorbid.R index c0185faf..bc11d396 100644 --- a/R/parse-comorbid.R +++ b/R/parse-comorbid.R @@ -45,10 +45,13 @@ icd9_fetch_ahrq_sas <- function() { } icd10_fetch_ahrq_sas <- function(ver = "2016") { + if (!ver %in% c("2016","2017","2018")) { + stop(ver," not currently available") + } .download_to_data_raw( - url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_2016.txt"), - file_name = .get_versioned_raw_file_name("ahrq-comformat_icd10cm_2016.txt", - ver = "2016" + url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_",ver,".txt"), + file_name = .get_versioned_raw_file_name(paste0("ahrq-comformat_icd10cm_",ver,".txt"), + ver = ver ) ) } From 73a7188941bba7cf19797b1dc4f224c537e06077 Mon Sep 17 00:00:00 2001 From: Robert A Overman Date: Sun, 12 May 2019 14:56:05 -0400 Subject: [PATCH 2/5] Added ver into icd10_parse_ahrq_sas --- R/parse-comorbid.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/parse-comorbid.R b/R/parse-comorbid.R index bc11d396..1ee1ccdd 100644 --- a/R/parse-comorbid.R +++ b/R/parse-comorbid.R @@ -142,9 +142,9 @@ icd9_parse_ahrq_sas <- function(save_pkg_data = FALSE) { # This is in some ways simpler than that ICD-9 equivalent because I make no # attempt to find all the child codes. icd10_parse_ahrq_sas <- function(save_pkg_data = FALSE, - offline = TRUE) { + offline = TRUE, ver = "2016") { assert_flag(save_pkg_data) - ahrq_info <- icd10_fetch_ahrq_sas() + ahrq_info <- icd10_fetch_ahrq_sas(ver = ver) ahrq_sas_lines <- readLines(ahrq_info$file_path, warn = FALSE) icd10_map_ahrq <- sas_format_extract_rcomfmt(ahrq_sas_lines) unun <- function(x) unname(unlist(x)) From d3a77563f99f7536f7ce07cddc0e07ada55304f2 Mon Sep 17 00:00:00 2001 From: Robert A Overman Date: Sun, 12 May 2019 14:40:47 -0400 Subject: [PATCH 3/5] Add options to download 2017, and 2018 AHRQ lists, and fixes #142 Add options to download 2017, and 2018 AHRQ lists fixes #142 Added ver into icd10_parse_ahrq_sas --- R/parse-comorbid.R | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/R/parse-comorbid.R b/R/parse-comorbid.R index c0185faf..1ee1ccdd 100644 --- a/R/parse-comorbid.R +++ b/R/parse-comorbid.R @@ -45,10 +45,13 @@ icd9_fetch_ahrq_sas <- function() { } icd10_fetch_ahrq_sas <- function(ver = "2016") { + if (!ver %in% c("2016","2017","2018")) { + stop(ver," not currently available") + } .download_to_data_raw( - url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_2016.txt"), - file_name = .get_versioned_raw_file_name("ahrq-comformat_icd10cm_2016.txt", - ver = "2016" + url = paste0(.ahrq_url_base, "comorbidityicd10/comformat_icd10cm_",ver,".txt"), + file_name = .get_versioned_raw_file_name(paste0("ahrq-comformat_icd10cm_",ver,".txt"), + ver = ver ) ) } @@ -139,9 +142,9 @@ icd9_parse_ahrq_sas <- function(save_pkg_data = FALSE) { # This is in some ways simpler than that ICD-9 equivalent because I make no # attempt to find all the child codes. icd10_parse_ahrq_sas <- function(save_pkg_data = FALSE, - offline = TRUE) { + offline = TRUE, ver = "2016") { assert_flag(save_pkg_data) - ahrq_info <- icd10_fetch_ahrq_sas() + ahrq_info <- icd10_fetch_ahrq_sas(ver = ver) ahrq_sas_lines <- readLines(ahrq_info$file_path, warn = FALSE) icd10_map_ahrq <- sas_format_extract_rcomfmt(ahrq_sas_lines) unun <- function(x) unname(unlist(x)) From bbd5a35d8b6ea99c62c5a703d477a68059c18749 Mon Sep 17 00:00:00 2001 From: Robert A Overman Date: Tue, 14 May 2019 15:33:31 -0400 Subject: [PATCH 4/5] Changed the test to identical and ensuring it wasn't identical for 2016. 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zb^xt-Lq%@{U%$0fsY8uQ^cn;(BG*9yy<_uB5J{z8qmdqgav&KI~S2Bv_hoauxytBm8GgdfWPF8pjH%UI!5_(nd zWl9mcK{4p|sAq6T>M^AuCUd(1&BDu-kU6LRML>gg>jh%bi_@U2z0=oo95DR^pddB2 z9yRFQ8%>-Zn|p zogMe7+9ULn1Kfv&tdk0p3YONP#v78IniAe_o3oOA{?wi( zgRnIl+>|yC+#H;kThCtrcQ~ZWckphN)7>(hZ$7|G;?akMc2F60SEnoVhsE#&%I**{ zlQp$>W0mjhe&o3x-Cz;`%OHglz^$^e5f{Ly+7M{`3bkdH8w_^X`o^4v+(8^PZUuwF z&VDo&`z%=?(QEZq)NyBmk;Ee~s!;)Xc6W0_!F)D$1NO>iukqYNz}I&$_H;Kv>q)iztS>C?QK0J6JVYt_CDSzS(9izT`ov=%S7$1FYj-= z-StNxx;X?~Qv|ZkzZG+N@TXHS14qMedANCo9M{=$!AYr7<+hpLGl=G|8qR z;8UYn!M=Md$3ELZM;z1r9Kk2Yo&8yvn>0NtE*EE=du^Q@ zY*@4e{Mb7%h7}}h1^XW$4mMT=f|1H^=Ci Date: Tue, 14 May 2019 15:36:32 -0400 Subject: [PATCH 5/5] Updated to use version and for the version to be set to 2018 --- R/parse-comorbid.R | 8 ++++---- R/update.R | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/R/parse-comorbid.R b/R/parse-comorbid.R index 1ee1ccdd..288afd2f 100644 --- a/R/parse-comorbid.R +++ b/R/parse-comorbid.R @@ -44,7 +44,7 @@ icd9_fetch_ahrq_sas <- function() { ) } -icd10_fetch_ahrq_sas <- function(ver = "2016") { +icd10_fetch_ahrq_sas <- function(ver = "2018") { if (!ver %in% c("2016","2017","2018")) { stop(ver," not currently available") } @@ -141,10 +141,10 @@ icd9_parse_ahrq_sas <- function(save_pkg_data = FALSE) { # This is in some ways simpler than that ICD-9 equivalent because I make no # attempt to find all the child codes. -icd10_parse_ahrq_sas <- function(save_pkg_data = FALSE, - offline = TRUE, ver = "2016") { +icd10_parse_ahrq_sas <- function(version = "2018", save_pkg_data = FALSE, + offline = TRUE) { assert_flag(save_pkg_data) - ahrq_info <- icd10_fetch_ahrq_sas(ver = ver) + ahrq_info <- icd10_fetch_ahrq_sas(ver = version) ahrq_sas_lines <- readLines(ahrq_info$file_path, warn = FALSE) icd10_map_ahrq <- sas_format_extract_rcomfmt(ahrq_sas_lines) unun <- function(x) unname(unlist(x)) diff --git a/R/update.R b/R/update.R index 123c2f62..1849d4bf 100644 --- a/R/update.R +++ b/R/update.R @@ -39,7 +39,7 @@ icd9_generate_map_elix(save_pkg_data = TRUE) # ICD 10 .parse_icd10cm_all(save_pkg_data = TRUE) - icd10_parse_ahrq_sas(save_pkg_data = TRUE) + icd10_parse_ahrq_sas(version = "2018", save_pkg_data = TRUE) .parse_icd10cm_cc(save_pkg_data = TRUE) icd10_generate_map_quan_elix(save_pkg_data = TRUE) icd10_generate_map_quan_deyo(save_pkg_data = TRUE)