Figure 1: County

kable(table_data, format = "html", booktabs = T,
col.names = c("", "New Infection", "Severe Infection"),
caption = 
  "Cumulative Incidence Rate of Infectious Respiratory Disease in California by County in 2023",
digits = 2) %>%
  pack_rows("County", 1,58) %>%
  kable_styling(full_width = F) %>%
  kable_styling(position = "center") %>%
  kable_styling(font_size = 10) %>%
  column_spec(2, color = case_when(
    table_data$risk_new_infection >15 ~ "red",
    table_data$risk_new_infection <15 & table_data$risk_new_infection > 10 ~ "orange",
    T ~ "black")) %>%
  column_spec(2, bold = if_else(
    table_data$risk_new_infection >15, T, F)) %>%
  column_spec(3, color = if_else(table_data$risk_severe_infection > 0.5, "red", "black"))%>%
  column_spec(3, bold = if_else(table_data$risk_severe_infection > 0.5, T, F)) %>%
  column_spec(1, bold = case_when(
    table_data$risk_new_infection >15 ~T,
    TRUE ~F)) %>%
  add_header_above(c(" " = 1, "Cumulative Incidence (%)" = 2)) %>%
  footnote(general=
    "Case data was from the California Department of Public Health. Population denominators were retrieved based on demographic category and county in California for 2023.",
    general_title="Data Sources", 
    title_format=c("italic")
           )
Cumulative Incidence Rate of Infectious Respiratory Disease in California by County in 2023
Cumulative Incidence (%)
New Infection Severe Infection
County
Alameda 9.00 0.25
Alpine 10.99 0.34
Amador 8.80 0.35
Butte 10.12 0.33
Calaveras 10.48 0.45
Colusa 21.12 0.62
Contra Costa 8.99 0.28
Del Norte 10.36 0.31
El Dorado 10.10 0.38
Fresno 8.49 0.22
Glenn 9.05 0.30
Humboldt 9.51 0.31
Imperial 43.77 1.09
Inyo 26.89 1.11
Kern 24.19 0.56
Kings 22.84 0.53
Lake 10.42 0.40
Lassen 10.54 0.36
Los Angeles 9.02 0.26
Madera 10.69 0.28
Marin 9.55 0.36
Mariposa 11.27 0.46
Mendocino 10.18 0.38
Merced 22.62 0.54
Modoc 11.97 0.43
Mono 9.37 0.31
Monterey 10.11 0.30
Napa 9.42 0.30
Nevada 9.84 0.40
Orange 8.83 0.26
Placer 8.93 0.29
Plumas 12.76 0.50
Riverside 8.91 0.26
Sacramento 19.43 0.53
San Benito 8.13 0.25
San Bernardino 22.48 0.55
San Diego 8.71 0.25
San Francisco 10.04 0.28
San Joaquin 19.15 0.49
San Luis Obispo 12.59 0.45
San Mateo 9.08 0.29
Santa Barbara 9.07 0.26
Santa Clara 9.05 0.26
Santa Cruz 10.01 0.32
Shasta 9.06 0.33
Sierra 12.82 0.67
Siskiyou 11.04 0.44
Solano 18.88 0.55
Sonoma 9.65 0.34
Stanislaus 19.95 0.53
Sutter 19.15 0.53
Tehama 19.55 0.63
Trinity 7.83 0.33
Tulare 23.69 0.56
Tuolumne 10.20 0.39
Ventura 9.01 0.27
Yolo 10.20 0.26
Yuba 17.31 0.44
Data Sources
Case data was from the California Department of Public Health. Population denominators were retrieved based on demographic category and county in California for 2023.

Counties with a cumulative incidence rate of new infections larger than 17% were Colusa, Imperial, Inyo, Kern, Kings, Merced, Sacramento, San Bernardino, San Joaquin, Solano, Stanislaus, Sutter, Tehama, Tulare, and Yuba, with Imperial County having the highest cumulative incidence at 44.77%. This suggests that rural counties were more negatively impacted by the respiratory outbreak compared to urban counties, such as San Diego, San Mateo and Alameda county.

Figure 2: Age

ggplot(age_data, aes(x = category, y = prevalence_new_infection)) + 
  geom_col(fill = "darkorange", alpha = 0.7) +
  geom_text(aes(label = round(prevalence_new_infection, 1)), 
            vjust = -0.5, 
            size = 3.5) +
  theme_classic() +
  labs(
    title = "Cumulative Incidence of Respiratory Infections by Age in California, 2023",
    x = "Age Category",
    y = "Cumulative Incidence of New Infections (%)"
  )

The cumulative incidence rate of respiratory infections in California is highest among individuals aged 65 and older (19.1%) and lowest among those aged 0–17 (4.1%), demonstrating an upward trend with increasing age.

Figure 3: Race/ethnicity

ggplot(race_data, aes(x = reorder(category, -prevalence_new_infection), y = prevalence_new_infection)) + 
  geom_col(fill = "cyan3", alpha = 0.7) +
  geom_text(aes(label = round(prevalence_new_infection, 1)), 
            vjust = 0.5,
            hjust = 1.1,
            size = 3.5) +
  coord_flip() +
  theme_classic() +
  labs(
    title = "Cumulative Incidence of Respiratory Infections 
    by Race/Ethnicity in California, 2023",
    x = "Race/Ethnicity",
    y = "Cumulative Incidence of New Infections (%)"
  ) +
  scale_x_discrete(labels= race_eth_labels)

The cumulative incidence rate of respiratory infections in California is highest among non-Hispanic American Indian/Alaska Native individuals (14%) followed by non-Hispanic White individuals (12.8%) and non-Hispanic Black individuals (12.3%), while it was lowest among non-Hispanic multiracial individuals (7.2%) and non-Hispanic Asian individuals (8.7%). These rates indicate that there are disparities for American Indian/Alaska Native, White, and Black individuals, suggesting that there are underlying factors contributing to differences.