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n2015_4.Rmd
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n2015_4.Rmd
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---
title: "n2015_4"
output:
word_document: default
html_document:
df_print: paged
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(tidyverse);library(haven);library(survey);library(tableone);library(mosaic)
```
This is the R markdown notebook for analysis of the paper on aortic dissection trends using the NIS database.
year: 2015
period:q4
icd10
We need to replicate the same markdown document for the ICD-10 data here.
```{r read df into the notebook}
core <- read_csv("C:/Users/Salil/Desktop/NIS2015/nis2015core.csv") %>% tbl_df
hosp <- read_csv("C:/Users/Salil/Desktop/NIS2015/nis2015hospital.csv") %>% tbl_df
dx <- read_csv('C:/Users/Salil/Desktop/NIS2015/nis2015q4dx.csv') %>% tbl_df
names(core)
names(hosp)
names(dx) <- tolower(names(dx)) # convert all var to lowercase
dx %>% tbl_df
```
Will merge the df to keep only those with ICD 10 codes.
Start with hosp as they have the ones with ICD10 codes.
```{r}
df1 <- left_join(hosp, core, by = "hosp_nis")
df2 <- left_join(dx, df1, by = "key_nis")
n15.4 <- df2
names(n15.4) <- toupper(names(n15.4))
```
prior CABG V45.81 = Z95.1
```{r prior CABG}
pricabg <- as.character(c("Z951")) # prior MI
a <- pricabg
n15.4$pricabg <- with(n15.4, ifelse((I10_DX1 %in% a | I10_DX2 %in% a | I10_DX3 %in% a | I10_DX4 %in% a | I10_DX5 %in% a | I10_DX6 %in% a | I10_DX7 %in% a | I10_DX8 %in% a |I10_DX9 %in% a| I10_DX10 %in% a | I10_DX11 %in% a | I10_DX12 %in% a | I10_DX13 %in% a | I10_DX14 %in% a | I10_DX15 %in% a ), "yes","no"))
n15.4 %>% count(pricabg)
```
Remove patients with prior CABG.
```{r}
df3 <- n15.4 %>% filter(pricabg == "no")
```
saved df3 here... n2015_4.csv
```{r, echo = FALSE, tidy = TRUE, message = FALSE }
lita <- as.character(c("02100Z9"))
df3$lita <- with(df3,ifelse((I10_PR1 %in% lita | I10_PR2 %in% lita | I10_PR3 %in% lita | I10_PR4 %in% lita | I10_PR5 %in% lita),"yes","no"))
df3 %>% count(lita)
rita <- as.character(c("02100Z8"))
df3$rita <- with(df3,ifelse((I10_PR1 %in% rita | I10_PR2 %in% rita | I10_PR3 %in% rita | I10_PR4 %in% rita | I10_PR5 %in% rita),"yes","no"))
df3 %>% count(rita)
df3$bita <- with(df3, ifelse((lita == "yes" & rita == "yes"), "yes", "no"))
df3 %>% count(bita)
```
```{r, echo= TRUE, tidy = TRUE}
a <- as.character(c("021209W", "0210AW", "021249W","02124AW",
"021309W", "02130AW", "021349W","02134AW",
"021109F", "02110AF", "021149F","02114AF", "02100Z8", "02011Z9"))
df3$cabg <- with(df3, ifelse((I10_PR1 %in% a | I10_PR2 %in% a | I10_PR3 %in% a | I10_PR4 %in% a | I10_PR5 %in% a | I10_PR6 %in% a | I10_PR7 %in% a | I10_PR8 %in% a |I10_PR9 %in% a| I10_PR10 %in% a | I10_PR11 %in% a | I10_PR12 %in% a | I10_PR13 %in% a | I10_PR14 %in% a | I10_PR15 %in% a ), "yes","no"))
df3 %>% count(cabg)
```
```{r keep only CABG}
df4 <- df3 %>% filter(cabg == "yes")
dim(df4)
```
```{r identify patients with valve surgery also}
# open valve repair/replacement - ICD 10 codes
# aortic valve
avr <- as.character(c("02RF0JZ","02QF0ZZ","02RF07Z","02RF08Z","02F0KZ"))
# mitral valve repair - open approach
mvrepair <- as.character(c("027G0ZZ","02NG0ZZ","02QG0ZZ","02VG0ZZ"))
mvrep <- as.character(c("02RG0JZ","02RG07Z","02RG08Z","02RG0KZ"))
pvprep <- as.character(c("027H0DZ","027H0ZZ","02NH0ZZ","02RH0ZZ","02RH08Z","02RH0KZ","02RH0JZ"))
tvrep <- as.character(c("027J0ZZ","02NJ0ZZ","02QJ0ZZ"))
vs <- as.character(c("02RF0JZ","02QF0ZZ","02RF07Z","02RF08Z","02F0KZ",
"027G0ZZ","02NG0ZZ","02QG0ZZ","02VG0ZZ",
"02RG0JZ","02RG07Z","02RG08Z","02RG0KZ",
"027H0DZ","027H0ZZ","02NH0ZZ","02RH0ZZ","02RH08Z","02RH0KZ","02RH0JZ",
"027J0ZZ","02NJ0ZZ","02QJ0ZZ"))
a <- vs
df4$vs <- with(df4, ifelse((I10_PR1 %in% a | I10_PR2 %in% a | I10_PR3 %in% a | I10_PR4 %in% a | I10_PR5 %in% a | I10_PR6 %in% a | I10_PR7 %in% a | I10_PR8 %in% a |I10_PR9 %in% a| I10_PR10 %in% a | I10_PR11 %in% a | I10_PR12 %in% a | I10_PR13 %in% a | I10_PR14 %in% a | I10_PR15 %in% a ), "yes","no"))
df4 %>% count(vs)
```
Remove patients who have had concomitant valve surgery done.
```{r remove valve patients}
df5 <- df4 %>% filter(vs == "no")
dim(df5)
```
```{r, ECHO = FALSE, tidy= TRUE}
hiv <- c("B20")
chrnlung <- c("J40",
"J410",
"J411",
"J418",
"J42",
"J430",
"J431",
"J432",
"J438",
"J439",
"J440",
"J441",
"J449",
"J4520",
"J4521",
"J4522",
"J4530",
"J4531",
"J4532",
"J4540",
"J4541",
"J4542",
"J4550",
"J4551",
"J4552",
"J45901",
"J45902",
"J45909",
"J45990",
"J45991",
"J45998",
"J470",
"J471",
"J479",
"J60",
"J61",
"J620",
"J628",
"J630",
"J631",
"J632",
"J633",
"J634",
"J635",
"J636",
"J64",
"J660",
"J661",
"J662",
"J668",
"J670",
"J671",
"J672",
"J673",
"J674",
"J675",
"J676",
"J677",
"J678",
"J679",
"J684")
dm <- c(
"E0800",
"E0801",
"E0810",
"E0811",
"E089",
"E0900",
"E0901",
"E0910",
"E0911",
"E099",
"E1010",
"E1011",
"E109",
"E1100",
"E1101",
"E1110",
"E1111",
"E119",
"E1300",
"E1301",
"E1310",
"E1311",
"E139",
"O24011",
"O24012",
"O24013",
"O24019",
"O2402",
"O2403",
"O24111",
"O24112",
"O24113",
"O24119",
"O2412",
"O2413",
"O24311",
"O24312",
"O24313",
"O24319",
"O2432",
"O2433",
"O24811",
"O24812",
"O24813",
"O24819",
"O2482",
"O2483",
"O24911",
"O24912",
"O24913",
"O24919",
"O2492",
"O2493")
dmcx <- c(
"E0821",
"E0822",
"E0829",
"E08311",
"E08319",
"E08321",
"E083211",
"E083212",
"E083213",
"E083219",
"E08329",
"E083291",
"E083292",
"E083293",
"E083299",
"E08331",
"E083311",
"E083312",
"E083313",
"E083319",
"E08339",
"E083391",
"E083392",
"E083393",
"E083399",
"E08341",
"E083411",
"E083412",
"E083413",
"E083419",
"E08349",
"E083491",
"E083492",
"E083493",
"E083499",
"E08351",
"E083511",
"E083512",
"E083513",
"E083519",
"E083521",
"E083522",
"E083523",
"E083529",
"E083531",
"E083532",
"E083533",
"E083539",
"E083541",
"E083542",
"E083543",
"E083549",
"E083551",
"E083552",
"E083553",
"E083559",
"E08359",
"E083591",
"E083592",
"E083593",
"E083599",
"E0836",
"E0837X1",
"E0837X2",
"E0837X3",
"E0837X9",
"E0839",
"E0840",
"E0841",
"E0842",
"E0843",
"E0844",
"E0849",
"E0851",
"E0852",
"E0859",
"E08610",
"E08618",
"E08620",
"E08621",
"E08622",
"E08628",
"E08630",
"E08638",
"E08641",
"E08649",
"E0865",
"E0869",
"E088",
"E0921",
"E0922",
"E0929",
"E09311",
"E09319",
"E09321",
"E093211",
"E093212",
"E093213",
"E093219",
"E09329",
"E093291",
"E093292",
"E093293",
"E093299",
"E09331",
"E093311",
"E093312",
"E093313",
"E093319",
"E09339",
"E093391",
"E093392",
"E093393",
"E093399",
"E09341",
"E093411",
"E093412",
"E093413",
"E093419",
"E09349",
"E093491",
"E093492",
"E093493",
"E093499",
"E09351",
"E093511",
"E093512",
"E093513",
"E093519",
"E093521",
"E093522",
"E093523",
"E093529",
"E093531",
"E093532",
"E093533",
"E093539",
"E093541",
"E093542",
"E093543",
"E093549",
"E093551",
"E093552",
"E093553",
"E093559",
"E09359",
"E093591",
"E093592",
"E093593",
"E093599",
"E0936",
"E0937X1",
"E0937X2",
"E0937X3",
"E0937X9",
"E0939",
"E0940",
"E0941",
"E0942",
"E0943",
"E0944",
"E0949",
"E0951",
"E0952",
"E0959",
"E09610",
"E09618",
"E09620",
"E09621",
"E09622",
"E09628",
"E09630",
"E09638",
"E09641",
"E09649",
"E0965",
"E0969",
"E098",
"E1021",
"E1022",
"E1029",
"E10311",
"E10319",
"E10321",
"E103211",
"E103212",
"E103213",
"E103219",
"E10329",
"E103291",
"E103292",
"E103293",
"E103299",
"E10331",
"E103311",
"E103312",
"E103313",
"E103319",
"E10339",
"E103391",
"E103392",
"E103393",
"E103399",
"E10341",
"E103411",
"E103412",
"E103413",
"E103419",
"E10349",
"E103491",
"E103492",
"E103493",
"E103499",
"E10351",
"E103511",
"E103512",
"E103513",
"E103519",
"E103521",
"E103522",
"E103523",
"E103529",
"E103531",
"E103532",
"E103533",
"E103539",
"E103541",
"E103542",
"E103543",
"E103549",
"E103551",
"E103552",
"E103553",
"E103559",
"E10359",
"E103591",
"E103592",
"E103593",
"E103599",
"E1036",
"E1037X1",
"E1037X2",
"E1037X3",
"E1037X9",
"E1039",
"E1040",
"E1041",
"E1042",
"E1043",
"E1044",
"E1049",
"E1051",
"E1052",
"E1059",
"E10610",
"E10618",
"E10620",
"E10621",
"E10622",
"E10628",
"E10630",
"E10638",
"E10641",
"E10649",
"E1065",
"E1069",
"E108",
"E1121",
"E1122",
"E1129",
"E11311",
"E11319",
"E11321",
"E113211",
"E113212",
"E113213",
"E113219",
"E11329",
"E113291",
"E113292",
"E113293",
"E113299",
"E11331",
"E113311",
"E113312",
"E113313",
"E113319",
"E11339",
"E113391",
"E113392",
"E113393",
"E113399",
"E11341",
"E113411",
"E113412",
"E113413",
"E113419",
"E11349",
"E113491",
"E113492",
"E113493",
"E113499",
"E11351",
"E113511",
"E113512",
"E113513",
"E113519",
"E113521",
"E113522",
"E113523",
"E113529",
"E113531",
"E113532",
"E113533",
"E113539",
"E113541",
"E113542",
"E113543",
"E113549",
"E113551",
"E113552",
"E113553",
"E113559",
"E11359",
"E113591",
"E113592",
"E113593",
"E113599",
"E1136",
"E1137X1",
"E1137X2",
"E1137X3",
"E1137X9",
"E1139",
"E1140",
"E1141",
"E1142",
"E1143",
"E1144",
"E1149",
"E1151",
"E1152",
"E1159",
"E11610",
"E11618",
"E11620",
"E11621",
"E11622",
"E11628",
"E11630",
"E11638",
"E11641",
"E11649",
"E1165",
"E1169",
"E118",
"E1321",
"E1322",
"E1329",
"E13311",
"E13319",
"E13321",
"E133211",
"E133212",
"E133213",
"E133219",
"E13329",
"E133291",
"E133292",
"E133293",
"E133299",
"E13331",
"E133311",
"E133312",
"E133313",
"E133319",
"E13339",
"E133391",
"E133392",
"E133393",
"E133399",
"E13341",
"E133411",
"E133412",
"E133413",
"E133419",
"E13349",
"E133491",
"E133492",
"E133493",
"E133499",
"E13351",
"E133511",
"E133512",
"E133513",
"E133519",
"E133521",
"E133522",
"E133523",
"E133529",
"E133531",
"E133532",
"E133533",
"E133539",
"E133541",
"E133542",
"E133543",
"E133549",
"E133551",
"E133552",
"E133553",
"E133559",
"E13359",
"E133591",
"E133592",
"E133593",
"E133599",
"E1336",
"E1337X1",
"E1337X2",
"E1337X3",
"E1337X9",
"E1339",
"E1340",
"E1341",
"E1342",
"E1343",
"E1344",
"E1349",
"E1351",
"E1352",
"E1359",
"E13610",
"E13618",
"E13620",
"E13621",
"E13622",
"E13628",
"E13630",
"E13638",
"E13641",
"E13649",
"E1365",
"E1369",
"E138",
"P702")
hhrwchf <- c("I130")
hhrwhrf <- c("I132")
hhrwohrf <- c("I1310")
hhrwrf <- c("I1311")
hrenworf <- c("I129","I150","I151")
htn <- c(
"I10",
"O10011",
"O10012",
"O10013",
"O10019",
"O1002",
"O1003",
"O10911",
"O10912",
"O10913",
"O10919",
"O1092",
"O1093")
htncx <- c("I160",
"I161",
"I169",
"I674")
htnpreg <- c( "O10111",
"O10112",
"O10113",
"O10119",
"O1012",
"O1013",
"O10211",
"O10212",
"O10213",
"O10219",
"O1022",
"O1023",
"O10311",
"O10312",
"O10313",
"O10319",
"O1032",
"O1033",
"O10411",
"O10412",
"O10413",
"O10419",
"O1042",
"O1043",
"O111",
"O112",
"O113",
"O114",
"O115",
"O119")
htnwchf <- c("I110")
htnwochf <- c("I119","I152","I158","I159")
hypo <- c(
"E000",
"E001",
"E002",
"E009",
"E018",
"E02",
"E030",
"E031",
"E032",
"E033",
"E038",
"E039",
"E890")
liver <- c(
"B180",
"B181",
"B182",
"I8500",
"I8501",
"I8510",
"I8511",
"K700",
"K702",
"K7030",
"K7031",
"K7040",
"K7041",
"K709",
"K7210",
"K7211",
"K7290",
"K7291",
"K730",
"K731",
"K732",
"K738",
"K739",
"K740",
"K741",
"K742",
"K743",
"K744",
"K745",
"K7460",
"K7469",
"K754",
"K7581",
"K760",
"K766",
"K7689",
"K769",
"Z944")
lymph <- c("C8100",
"C8101",
"C8102",
"C8103",
"C8104",
"C8105",
"C8106",
"C8107",
"C8108",
"C8109",
"C8110",
"C8111",
"C8112",
"C8113",
"C8114",
"C8115",
"C8116",
"C8117",
"C8118",
"C8119",
"C8120",
"C8121",
"C8122",
"C8123",
"C8124",
"C8125",
"C8126",
"C8127",
"C8128",
"C8129",
"C8130",
"C8131",
"C8132",
"C8133",
"C8134",
"C8135",
"C8136",
"C8137",
"C8138",
"C8139",
"C8140",
"C8141",
"C8142",
"C8143",
"C8144",
"C8145",
"C8146",
"C8147",
"C8148",
"C8149",
"C8170",
"C8171",
"C8172",
"C8173",
"C8174",
"C8175",
"C8176",
"C8177",
"C8178",
"C8179",
"C8190",
"C8191",
"C8192",
"C8193",
"C8194",
"C8195",
"C8196",
"C8197",
"C8198",
"C8199",
"C8200",
"C8201",
"C8202",
"C8203",
"C8204",
"C8205",
"C8206",
"C8207",
"C8208",
"C8209",
"C8210",
"C8211",
"C8212",
"C8213",
"C8214",
"C8215",
"C8216",
"C8217",
"C8218",
"C8219",
"C8220",
"C8221",
"C8222",
"C8223",
"C8224",
"C8225",
"C8226",
"C8227",
"C8228",
"C8229",
"C8230",
"C8231",
"C8232",
"C8233",
"C8234",
"C8235",
"C8236",
"C8237",
"C8238",
"C8239",
"C8240",
"C8241",
"C8242",
"C8243",
"C8244",
"C8245",
"C8246",
"C8247",
"C8248",
"C8249",
"C8250",
"C8251",
"C8252",
"C8253",
"C8254",
"C8255",
"C8256",
"C8257",
"C8258",
"C8259",
"C8260",
"C8261",
"C8262",