Omar AI project
Noura Elsayed
05/18/24
Record ID 312 being omitted because sex = NA
Read in Data
- Upload our data
Omarallergy<- as.data.frame(read.csv("AdultFoodAllergyCorr-ShellfishTrueAllergy_DATA_LABELS_2024-05-30_0822.csv"))
Omarallergy$Race..ethnicity..choice.otherRace. <- Omarallergy$Race..ethnicity..choice.other.
Omarallergy$Race..ethnicity..choice.other. <- NULL
##changing the variable names for ease
names(Omarallergy)<- gsub("Race..ethnicity..choice.", "", names(Omarallergy))
names(Omarallergy)<- gsub("shellfish.that.the.patient.reacted.to..or.suspected.reacted.to...choice.", "", names(Omarallergy))
Omarallergy[][Omarallergy[] == "Checked"] <- 1
Omarallergy[][Omarallergy[] == "Unchecked"] <- 0Descriptives of all variables
#describe(Omarallergy)First step, make race categories, categorize everyone as either white, black, or other
#Omit individuals who are not black or white
col_names <- colnames(Omarallergy)
duplicate_cols <- col_names[duplicated(col_names)]
Omarallergy <- mutate(Omarallergy, pdemrace = ifelse(White. == 1, "1", ifelse(Black.or.African.American. == 1, "2", ifelse(American.Indian.or.Alaska.Native. == 1, "3", ifelse(Asian. == 1, "3", ifelse(Native.Hawaiian.or.Other.Pacific.Islander. == 1, "3", ifelse(not.documented. == 1, "3",
ifelse(otherRace. == 1, "3",
ifelse(not.documented..1 == 1, 3, "")))))))))
table(Omarallergy$pdemrace) ##
## 1 2 3
## 93 102 12filtered_data <- Omarallergy %>%
filter(pdemrace != 3)
table(filtered_data$pdemrace) ##
## 1 2
## 93 102- 93 white, 102 black # Categories of allergy
sensitized : positive testing ORRRRRRRR serum IgE > 0 AND no symptoms symptomatic: negative testing + symptoms, allergic: positive testing + symptoms
# names(Omarallergy)
IgE_columns <- Omarallergy[, grepl("IgE", names(Omarallergy))]
IgE_columns <- IgE_columns[2:7]
psych::describe(Omarallergy)targe_colname <- c("clam.IgE", "crab.IgE", "lobster.IgE", "oyster.IgE", "scallops.IgE", "shrimp.IgE")
col_numbers <- which(colnames(Omarallergy) %in% targe_colname)
Omarallergy$result <- ifelse(Omarallergy[, col_numbers] > 0, 1, 0)
skintesting <- Omarallergy[, grepl(".skin.test.interpretation", names(Omarallergy))]
# names(skintesting)
col_numbers <- which(colnames(Omarallergy) %in% targe_colname)
write.csv(Omarallergy, 'omarai.csv')
Omarallergy <- read.csv('omarai.csv')
# names(Omarallergy)
columns_to_check <- c("result.clam.IgE", "result.crab.IgE", "result.lobster.IgE",
"result.oyster.IgE", "result.scallops.IgE", "result.shrimp.IgE")
Omarallergy$totalIGE <- rowSums(Omarallergy[, columns_to_check],na.rm = TRUE)
table(Omarallergy$totalIGE)##
## 0 1 2 3 4 5 6
## 105 30 15 27 8 7 15Omarallergy <- mutate(Omarallergy, IGEpos = ifelse(totalIGE >= 1, 1,0))
table(Omarallergy$IGEpos) ##
## 0 1
## 105 102skin testing
Omarallergy[][Omarallergy[] == "positive"] <- 1
Omarallergy[][Omarallergy[] == "negative"] <- 0
Omarallergy[][Omarallergy[] == "unable to interpret"] <- 0
targe_colname <- c("clam.skin.test.interpretation", "crab.skin.test.interpretation", "lobster.skin.test.interpretation", "oyster.skin.test.interpretation", "scallops.skin.test.interpretation", "shrimp.skin.test.interpretation")
Omarallergy$clam.skin.test.interpretation <- as.numeric(Omarallergy$clam.skin.test.interpretation)
Omarallergy$crab.skin.test.interpretation <- as.numeric(Omarallergy$crab.skin.test.interpretation)
Omarallergy$lobster.skin.test.interpretation <- as.numeric(Omarallergy$lobster.skin.test.interpretation)
Omarallergy$oyster.skin.test.interpretation <- as.numeric(Omarallergy$oyster.skin.test.interpretation)
Omarallergy$scallops.skin.test.interpretation <- as.numeric(Omarallergy$scallops.skin.test.interpretation)
Omarallergy$shrimp.skin.test.interpretation <- as.numeric(Omarallergy$shrimp.skin.test.interpretation)
Omarallergy$totalskinpos <- rowSums(Omarallergy[, targe_colname],na.rm = TRUE)
Omarallergy <- mutate(Omarallergy, skinpos = ifelse(totalskinpos >= 1, 1,0))targe_colname <- c("skinpos","IGEpos")
Omarallergy$skinpos <- as.numeric(Omarallergy$skinpos)
Omarallergy$IGEpos <- as.numeric(Omarallergy$IGEpos)
Omarallergy$allergy <- NULL
Omarallergy$allergy<- rowSums(Omarallergy[, targe_colname],na.rm = TRUE)
table(Omarallergy$allergy)##
## 1 2
## 170 37# write.csv(Omarallergy, Omarallergy.csv)Difference in Age
library(ggpubr)
filtered_data$pdemrace <- as.factor(filtered_data$pdemrace)
anova(lm(age.in.years~ pdemrace, data=filtered_data))wilcox.test(age.in.years ~ pdemrace, data = filtered_data,
exact = FALSE, alternative = "two.sided")##
## Wilcoxon rank sum test with continuity correction
##
## data: age.in.years by pdemrace
## W = 5154.5, p-value = 0.2963
## alternative hypothesis: true location shift is not equal to 0filtered_data %>%
group_by(pdemrace) %>%
get_summary_stats(age.in.years, type = "mean_sd")ggboxplot(filtered_data, x = "pdemrace", y = "age.in.years",
color ="pdemrace", palette = c("#00AFBB", "#E7B800"),
order = c(1, 2),
ylab = "age(years)", xlab = "Race")
Difference in Age of onset
anova(lm(shellfish.age.of.allergy.onset ~ pdemrace, data=filtered_data))wilcox.test(shellfish.age.of.allergy.onset ~ pdemrace, data = filtered_data,
exact = FALSE, alternative = "two.sided")##
## Wilcoxon rank sum test with continuity correction
##
## data: shellfish.age.of.allergy.onset by pdemrace
## W = 1041.5, p-value = 0.2967
## alternative hypothesis: true location shift is not equal to 0filtered_data %>%
group_by(pdemrace) %>%
get_summary_stats(shellfish.age.of.allergy.onset, type = "mean_sd")ggboxplot(filtered_data, x = "pdemrace", y = "shellfish.age.of.allergy.onset",
color = "pdemrace", palette = c("#00AFBB", "#E7B800"),
order = c(1, 2),
ylab = "age of onset (years)", xlab = "Race")## Warning: Removed 97 rows containing non-finite outside the scale range
## (`stat_boxplot()`).
compare black and white patients on roach and mites, and symptoms, for eahc of the seven symtpoms, compare on sex, age, and age of onset of the allergy
Difference in sex
Omit individuals whose sex is not male or female
filtered_data$Sex <- dplyr::recode(filtered_data$Sex, female = "0", male = "1", na.action = "na.omit")
filtered_data$Sex <- as.factor(filtered_data$Sex)
table(filtered_data$Sex)##
## 0 1
## 131 64cont_table <- table(filtered_data$pdemrace, filtered_data$Sex)
chi_squared <- chisq.test(cont_table)
print(chi_squared) ##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table
## X-squared = 7.5132, df = 1, p-value = 0.006125Difference in roach
df1 = filtered_data %>%
count(pdemrace, rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
filtered_data$pdemrace <- as.factor(filtered_data$pdemrace)
filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite. <- as.factor(filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite.)
filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach. <- as.factor(filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.)
cont_table <- table(filtered_data$pdemrace, filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.)
chi_squared <- chisq.test(cont_table)
print(chi_squared)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table
## X-squared = 4.9651e-05, df = 1, p-value = 0.9944df1 = filtered_data %>%
count(pdemrace, rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach.))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
## Difference in mites
cont_table <- table(filtered_data$pdemrace, filtered_data$rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite.)
chisq.test(cont_table)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table
## X-squared = 1.3362, df = 1, p-value = 0.2477fisher_result <- fisher.test(cont_table)
df1 = filtered_data %>%
count(pdemrace, rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite.) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite.))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
Difference in Symptoms
symptoms <- Omarallergy[, grepl("symptoms", names(Omarallergy))]
targetcolnames <- names(symptoms)
for (var in targetcolnames) {
cat(sprintf("Chi-square test between %s and pdemrace:\n", var))
contingency_table <- table(filtered_data[[var]], filtered_data$pdemrace)
chi_square_result <- chisq.test(contingency_table)
print(chi_square_result)
cat("\n")
}## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema.. and pdemrace:
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 3.4153, df = 1, p-value = 0.06459
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea.. and pdemrace:
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 0.46889, df = 1, p-value = 0.4935
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.Respiratory..wheezing..stridor..voice.change..or.shortness.of.breath.. and pdemrace:
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 0.37954, df = 1, p-value = 0.5378
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.Cardiovascular..hypotension..syncope..lightheartedness.. and pdemrace:## Warning in chisq.test(contingency_table): Chi-squared approximation may be
## incorrect##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 0.020142, df = 1, p-value = 0.8871
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.Neurologic..headache..parasthesias.. and pdemrace:## Warning in chisq.test(contingency_table): Chi-squared approximation may be
## incorrect##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 1.8505, df = 1, p-value = 0.1737
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.Other. and pdemrace:
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: contingency_table
## X-squared = 2.2621, df = 1, p-value = 0.1326
##
##
## Chi-square test between shellfish.symptoms.with.any.prior.reaction..choice.not.documented. and pdemrace:
##
## Chi-squared test for given probabilities
##
## data: contingency_table
## X-squared = 0.41538, df = 1, p-value = 0.5192# Assuming targetcolnames contains the names of variables you want to iterate over
filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema.. <- as.factor(filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema..)
df1 = filtered_data %>%
count(pdemrace, shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema..) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema..))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea.. <- as.factor(filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea..)
df1 = filtered_data %>%
count(pdemrace, shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea..) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea..))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.Respiratory..wheezing..stridor..voice.change..or.shortness.of.breath.. <- as.factor(filtered_data$shellfish.symptoms.with.any.prior.reaction..choice.Respiratory..wheezing..stridor..voice.change..or.shortness.of.breath..)
df1 = filtered_data %>%
count(pdemrace, shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea..) %>%
group_by(pdemrace) %>%
mutate(prop=prop.table(n))
df1ggplot(df1, aes(pdemrace, prop, fill = shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea..))+
geom_col() +
geom_text(aes(label = scales::percent(prop)),
position = position_stack(vjust = 0.5)) +
scale_y_continuous(labels = scales::percent)
##medical comorbidities
names(Omarallergy)## [1] "X"
## [2] "Record.ID"
## [3] "age.in.years"
## [4] "Sex"
## [5] "White."
## [6] "Black.or.African.American."
## [7] "American.Indian.or.Alaska.Native."
## [8] "Asian."
## [9] "Native.Hawaiian.or.Other.Pacific.Islander."
## [10] "not.documented."
## [11] "not.documented..1"
## [12] "clam."
## [13] "crab."
## [14] "lobster."
## [15] "oyster."
## [16] "scallops."
## [17] "shrimp."
## [18] "unknown."
## [19] "other."
## [20] "name.of.other.shellfish.reacted.to.and.serum.IgE.level..name..0.00."
## [21] "clam.IgE"
## [22] "clam.skin.test.wheal.size.average"
## [23] "clam.skin.test.interpretation"
## [24] "crab.IgE"
## [25] "crab.skin.test.wheal.size.average"
## [26] "crab.skin.test.interpretation"
## [27] "lobster.IgE"
## [28] "lobster.skin.test.wheal.size.average"
## [29] "lobster.skin.test.interpretation"
## [30] "oyster.IgE"
## [31] "oyster.skin.test.wheal.size.average"
## [32] "oyster.skin.test.interpretation"
## [33] "scallops.IgE"
## [34] "scallops.skin.test.wheal.size.average"
## [35] "scallops.skin.test.interpretation"
## [36] "shrimp.IgE"
## [37] "shrimp.skin.prick.test.wheal.size.average"
## [38] "shrimp.skin.test.interpretation"
## [39] "shellfish.symptoms.with.any.prior.reaction..choice.Skin..hives.or.angioedema.."
## [40] "shellfish.symptoms.with.any.prior.reaction..choice.GI..nausea..vomiting..or.diarrhea.."
## [41] "shellfish.symptoms.with.any.prior.reaction..choice.Respiratory..wheezing..stridor..voice.change..or.shortness.of.breath.."
## [42] "shellfish.symptoms.with.any.prior.reaction..choice.Cardiovascular..hypotension..syncope..lightheartedness.."
## [43] "shellfish.symptoms.with.any.prior.reaction..choice.Neurologic..headache..parasthesias.."
## [44] "shellfish.symptoms.with.any.prior.reaction..choice.Other."
## [45] "shellfish.symptoms.with.any.prior.reaction..choice.not.documented."
## [46] "shellfish.other.symptom.description"
## [47] "shellfish.severity.of.any.prior.reaction..choice.no.treatment.or.antihistamine.only."
## [48] "shellfish.severity.of.any.prior.reaction..choice.presented.to.ED.and..or.epinephrine.use."
## [49] "shellfish.severity.of.any.prior.reaction..choice.not.documented."
## [50] "shellfish.age.of.allergy.onset"
## [51] "shellfish.clinical.course"
## [52] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.allergic.rhinitis."
## [53] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.asthma."
## [54] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.eczema."
## [55] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.contact.dermatitis."
## [56] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.oral.allergy.syndrome."
## [57] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.anxiety."
## [58] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.other.psychological.diagnosis..depression..bipolar..schizophrenia..etc.."
## [59] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.cardiac..hypertension..coronary.artery.dz..etc.."
## [60] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.gastrointestinal."
## [61] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.alpha.gal.allergy."
## [62] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.other.food.allergy."
## [63] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.drug.allergy."
## [64] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.stinging.insect.allergy..hymenoptera.."
## [65] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.none.of.the.above."
## [66] "medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.not.documented."
## [67] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.allergic.rhinitis."
## [68] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.asthma."
## [69] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.eczema."
## [70] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.contact.dermatitis."
## [71] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.oral.allergy.syndrome."
## [72] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.anxiety."
## [73] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.other.psychological.diagnosis..depression..bipolar..schizophrenia..etc.."
## [74] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.cardiac..hypertension..coronary.artery.dz..etc.."
## [75] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.gastrointestinal."
## [76] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.alpha.gal.allergy."
## [77] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.other.food.allergy."
## [78] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.drug.allergy."
## [79] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.stinging.insect.allergy..hymenoptera.."
## [80] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.none.of.the.above."
## [81] "medical.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.not.documented."
## [82] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.birch."
## [83] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.other.trees."
## [84] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.grass."
## [85] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.weeds."
## [86] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite."
## [87] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.mold."
## [88] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.no.testing.performed..information.not.available."
## [89] "rhinitis.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach."
## [90] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.birch."
## [91] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.other.trees."
## [92] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.grass."
## [93] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.weeds."
## [94] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.dust.mite."
## [95] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.mold."
## [96] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.no.testing.performed..information.not.available."
## [97] "oral.allergy.syndrome.specific.sensitization..skin.test.or.serum.IgE...choice.cockroach."
## [98] "gastrointestinal.comorbidities..choice.IBD..crohns..ulcerative.colitis.."
## [99] "gastrointestinal.comorbidities..choice.irritable.bowel.syndrome."
## [100] "gastrointestinal.comorbidities..choice.GERD."
## [101] "gastrointestinal.comorbidities..choice.eosinophilic.gastrointestinal.disorders..ie..EoE.."
## [102] "gastrointestinal.comorbidities..choice.Hx.of.abdominal.surgery."
## [103] "gastrointestinal.comorbidities..choice.another.GI.diagnosis.not.otherwise.specified."
## [104] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.IBD..crohns..ulcerative.colitis.."
## [105] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.irritable.bowel.syndrome."
## [106] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.GERD."
## [107] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.eosinophilic.gastrointestinal.disorders..ie..EoE.."
## [108] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.Hx.of.abdominal.surgery."
## [109] "gastrointestinal.comorbidities.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.comorbidities.question...choice.another.GI.diagnosis.not.otherwise.specified."
## [110] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.proton.pump.inhibitor."
## [111] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.beta.blocker."
## [112] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.ACE.ARB."
## [113] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.NSAID..prescribed.or.documented.in.note.."
## [114] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.sulfasalazine..azulfidine..or.mesalamine..5.ASA.."
## [115] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.immune.modulator..immune.suppressant..biologic..cyclophsophamide..MMF..calcineurin.inhibitor..mTOR.inhibitor..methotrexate..azathioprene.."
## [116] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.daily.oral.steroid."
## [117] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.none.of.the.above."
## [118] "medications.prescribed.at.time.of.food.allergy.diagnosis..choice.not.documented."
## [119] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.proton.pump.inhibitor."
## [120] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.beta.blocker."
## [121] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.ACE.ARB."
## [122] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.NSAID..prescribed.or.documented.in.note.."
## [123] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.sulfasalazine..azulfidine..or.mesalamine..5.ASA.."
## [124] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.immune.modulator..immune.suppressant..biologic..cyclophsophamide..MMF..calcineurin.inhibitor..mTOR.inhibitor..methotrexate..azathioprene.."
## [125] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.daily.oral.steroid."
## [126] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.none.of.the.above."
## [127] "medications.documented.at.the.time.of.chart.review..PMHx.section...not.already.included.in.previous.medication.question...choice.not.documented."
## [128] "prescribed.epinephrine.at.time.of.food.allergy.diagnosis"
## [129] "history.of.repeated.tick.bites"
## [130] "works.in.food.service.or.other.occupational.food.handling..chef..catering..fast.food..butcher..fishmonger..etc.."
## [131] "Complete."
## [132] "otherRace."
## [133] "pdemrace"
## [134] "result.clam.IgE"
## [135] "result.crab.IgE"
## [136] "result.lobster.IgE"
## [137] "result.oyster.IgE"
## [138] "result.scallops.IgE"
## [139] "result.shrimp.IgE"
## [140] "totalIGE"
## [141] "IGEpos"
## [142] "totalskinpos"
## [143] "skinpos"
## [144] "allergy"diff in med comorbidities
- contact derm
- eczema
- atopic, allergic rhininitis, asthma, eczema, contact derm, and OAS
cont_table_medcomorbidAR <- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.allergic.rhinitis)
chisq.test(cont_table_medcomorbidAR)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidAR
## X-squared = 0.75331, df = 1, p-value = 0.3854fisher_result <- fisher.test(cont_table_medcomorbidAR)
cont_table_medcomorbidAAT<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.asthma)
chisq.test(cont_table_medcomorbidAAT)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidAAT
## X-squared = 2.3469, df = 1, p-value = 0.1255fisher_resultAT <- fisher.test(cont_table_medcomorbidAAT)
cont_table_medcomorbidEC<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.eczema)
chisq.test(cont_table_medcomorbidEC)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidEC
## X-squared = 2.9762e-31, df = 1, p-value = 1fisher_resultEC <- fisher.test(cont_table_medcomorbidEC)
cont_table_medcomorbidCD<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.contact.dermatitis)
chisq.test(cont_table_medcomorbidCD)## Warning in chisq.test(cont_table_medcomorbidCD): Chi-squared approximation may
## be incorrect##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidCD
## X-squared = 0.28098, df = 1, p-value = 0.5961fisher_resultEC <- fisher.test(cont_table_medcomorbidCD)
cont_table_medcomorbidOAS<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.oral.allergy.syndrome)
chisq.test(cont_table_medcomorbidOAS)## Warning in chisq.test(cont_table_medcomorbidOAS): Chi-squared approximation may
## be incorrect##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidOAS
## X-squared = 2.0076, df = 1, p-value = 0.1565fisher_resultOAS <- fisher.test(cont_table_medcomorbidOAS)
cont_table_medcomorbidANXS<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.anxiety)
chisq.test(cont_table_medcomorbidANXS)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidANXS
## X-squared = 0.80343, df = 1, p-value = 0.3701fisher_resultANX <- fisher.test(cont_table_medcomorbidANXS)
cont_table_medcomorbidPSY<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.other.psychological.diagnosis..depression..bipolar..schizophrenia..etc.)
chisq.test(cont_table_medcomorbidPSY)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidPSY
## X-squared = 7.2221, df = 1, p-value = 0.007201fisherpsyc <- fisher.test(cont_table_medcomorbidPSY)
cont_table_medcomorbidhypertension<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.cardiac..hypertension..coronary.artery.dz..etc.)
chisq.test(cont_table_medcomorbidhypertension)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_medcomorbidhypertension
## X-squared = 1.9437, df = 1, p-value = 0.1633fisherhypertension <- fisher.test(cont_table_medcomorbidhypertension)
cont_table_GI<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.gastrointestinal)
chisq.test(cont_table_GI)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_GI
## X-squared = 0.028037, df = 1, p-value = 0.867fisherGI <- fisher.test(cont_table_GI)
cont_table_alphagal<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.alpha.gal.allergy)
chisq.test(cont_table_alphagal)## Warning in chisq.test(cont_table_alphagal): Chi-squared approximation may be
## incorrect##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_alphagal
## X-squared = 2.5941, df = 1, p-value = 0.1073fisheralpha <- fisher.test(cont_table_alphagal)
cont_table_otherfoodallergy<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.other.food.allergy)
chisq.test(cont_table_otherfoodallergy)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_otherfoodallergy
## X-squared = 0.19538, df = 1, p-value = 0.6585fisherotherfoodllergy <- fisher.test(cont_table_otherfoodallergy)
cont_table_otherdrugallergy<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.drug.allergy)
chisq.test(cont_table_otherdrugallergy)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_otherdrugallergy
## X-squared = 4.0853, df = 1, p-value = 0.04326fisherotherdrugallergy <- fisher.test(cont_table_otherdrugallergy)
cont_table_insectallergy<- table(filtered_data$pdemrace, filtered_data$medical.comorbidities.at.the.time.of.food.allergy.diagnosis..choice.stinging.insect.allergy..hymenoptera.)
chisq.test(cont_table_insectallergy)##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: cont_table_insectallergy
## X-squared = 4.0889, df = 1, p-value = 0.04317fisherotherinsectallergy<- fisher.test(cont_table_insectallergy)#diff in medications at time of DX
shellfish.severity.of.any.prior.reaction..choice.no.treatment.or.antihistamine.only
shellfish.severity.of.any.prior.reaction..choice.presented.to.ED.and..or.epinephrine.use
shellfish.severity.of.any.prior.reaction..choice.not.documented
Omarallergy$shellfish.severity.of.any.prior.reaction..choice.no.treatment.or.antihistamine.only.## [1] 0 1 0 0 1 1 1 1 1 1 1 0 0 0 0 1 0 1 0 1 1 0 1 0 1 0 0 1 0 1 0 0 0 0 1 0 1
## [38] 0 1 0 0 0 0 1 1 1 0 0 0 1 0 0 0 0 1 0 0 1 0 0 1 0 1 1 0 1 0 1 0 0 0 0 0 0
## [75] 0 0 0 1 1 0 0 0 1 0 1 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 1 1 1 1 0 0 0 1 1 1
## [112] 1 0 0 0 0 1 1 1 0 0 1 1 0 0 1 1 0 1 0 1 0 1 0 0 1 0 1 1 1 1 0 0 0 0 0 0 0
## [149] 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0
## [186] 0 0 0 0 1 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 1Omarallergy$shellfish.severity.of.any.prior.reaction..choice.presented.to.ED.and..or.epinephrine.use.## [1] 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
## [38] 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 1 0 1 0 0 0
## [75] 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0
## [112] 0 0 0 1 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 1 0 0
## [149] 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [186] 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0#shellfish that patient is allergic to
##prescribed epinephrine at tm of dx