ZSFG Flu and Pneumovax Audit
Coco Donovan
2024-03-12
Instructions:
Graph the data to show compliance by unit, analyze your findings, and provide recommendations for improvement. (Important context: Target Compliance = 90%)
Key:
- Y = Yes
- N = No
- NA = Not Applicable
Loading Packages
library(readr)
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(tidyverse)## Warning: package 'ggplot2' was built under R version 4.3.1## Warning: package 'lubridate' was built under R version 4.3.1## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
## ✔ purrr 1.0.2## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(ggplot2)Loading Data
df = read_csv('ZSFG Flu and Pneumovax Audit.csv')## Rows: 274 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (8): Date, Unit, Flu Vaccine screening completed correctly., Flu Vaccine...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Columns:
print(colnames(df))## [1] "Date"
## [2] "Unit"
## [3] "Flu Vaccine screening completed correctly."
## [4] "Flu Vaccine Information Sheet (VIS) provided to the patient."
## [5] "Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR)."
## [6] "Pneumovax Vaccine screening completed correctly."
## [7] "Pneumovax Vaccine Information Sheet (VIS) provided to the patient."
## [8] "Documentation of Pneumovax vaccine administration is recorded on the Medication Administration Record (MAR)."Preliminary Inspection:
head(df)## # A tibble: 6 × 8
## Date Unit Flu Vaccine screening completed corre…¹ Flu Vaccine Informat…²
## <chr> <chr> <chr> <chr>
## 1 3/4/2018 B N <NA>
## 2 3/4/2018 B N <NA>
## 3 3/4/2018 B N <NA>
## 4 3/4/2018 B N <NA>
## 5 3/4/2018 B Y <NA>
## 6 2/28/2018 C Y Y
## # ℹ abbreviated names: ¹​`Flu Vaccine screening completed correctly.`,
## # ²​`Flu Vaccine Information Sheet (VIS) provided to the patient.`
## # ℹ 4 more variables:
## # `Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR).` <chr>,
## # `Pneumovax Vaccine screening completed correctly.` <chr>,
## # `Pneumovax Vaccine Information Sheet (VIS) provided to the patient.` <chr>,
## # `Documentation of Pneumovax vaccine administration is recorded on the Medication Administration Record (MAR).` <chr>Data Cleaning:
# converting the 'Y' and 'N' values to binary
df = df %>%
mutate_at(vars(3:8), ~ as.double(recode(., "N" = '0.0', 'Y' = '1.0')))Data Aggregation by Unit:
distinct_dates <- df %>%
group_by(Unit) %>%
summarise(distinct_dates = n_distinct(Date))
distinct_dates## # A tibble: 6 × 2
## Unit distinct_dates
## <chr> <int>
## 1 A 16
## 2 B 4
## 3 C 24
## 4 D 25
## 5 E 3
## 6 G 2average_rows_per_date <- df %>%
group_by(Unit, Date) %>%
summarise(rows_count = n()) %>%
group_by(Unit) %>%
summarise(average_patients_per_day = mean(rows_count))## `summarise()` has grouped output by 'Unit'. You can override using the
## `.groups` argument.average_rows_per_date## # A tibble: 6 × 2
## Unit average_patients_per_day
## <chr> <dbl>
## 1 A 3.25
## 2 B 2.5
## 3 C 3.67
## 4 D 4.56
## 5 E 2
## 6 G 2Data Aggregation by Unit:
df_by_unit = df %>%
select(-Date) %>%
group_by(Unit) %>%
summarise_all(
list(
Mean = ~ mean(., na.rm = TRUE),
NA_Count = ~ sum(is.na(.)),
Proportion_NA = ~ mean(is.na(.))
)
)
df_n_unit = df %>%
group_by(Unit) %>%
summarise(Observations = n())
df_by_unit <- left_join(df_by_unit, df_n_unit, by = "Unit")
# Print the joined dataframe
df_by_unit## # A tibble: 6 × 20
## Unit Flu Vaccine screening co…¹ Flu Vaccine Informat…² Documentation of Flu…³
## <chr> <dbl> <dbl> <dbl>
## 1 A 0.980 0.882 0.9
## 2 B 0.6 1 0.333
## 3 C 0.586 0.923 0.571
## 4 D 1 0.905 0.571
## 5 E 1 1 1
## 6 G 1 1 1
## # ℹ abbreviated names: ¹​`Flu Vaccine screening completed correctly._Mean`,
## # ²​`Flu Vaccine Information Sheet (VIS) provided to the patient._Mean`,
## # ³​`Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR)._Mean`
## # ℹ 16 more variables:
## # `Pneumovax Vaccine screening completed correctly._Mean` <dbl>,
## # `Pneumovax Vaccine Information Sheet (VIS) provided to the patient._Mean` <dbl>,
## # `Documentation of Pneumovax vaccine administration is recorded on the Medication Administration Record (MAR)._Mean` <dbl>, …Summary: Flu Vaccine screening completed correctly
df1 <- df_by_unit %>%
select(Unit,
Observations,
`Flu Vaccine screening completed correctly._Mean`,
`Flu Vaccine screening completed correctly._NA_Count`,
`Flu Vaccine screening completed correctly._Proportion_NA`)
colnames(df1) = c('Unit','Observations','Mean','n_na','proportion_na')
df1$color <- ifelse(df1$Mean < 0.9, "red", "grey")
df1## # A tibble: 6 × 6
## Unit Observations Mean n_na proportion_na color
## <chr> <int> <dbl> <int> <dbl> <chr>
## 1 A 52 0.980 3 0.0577 grey
## 2 B 10 0.6 0 0 red
## 3 C 88 0.586 1 0.0114 red
## 4 D 114 1 1 0.00877 grey
## 5 E 6 1 0 0 grey
## 6 G 4 1 0 0 greyPlotting df1:
ggplot(df1, aes(x = Unit, y = round(Mean * 100, 2), fill = color)) +
geom_bar(stat = "identity") +
geom_text(aes(label = paste0(round(Mean * 100, 2), "%"), fontface = "bold"), vjust = -0.5, size = 3, color = "black") + # Add numerical values with percent signs
scale_fill_identity() +
geom_hline(yintercept = 90, linetype = "dotted") +
geom_text(aes(x = Inf, y = 90, label = "Compliance Target"), hjust = 1, vjust = -0.5, color = "black") + # Add "Compliance Target" text
labs(x = "Unit", y = "Completion (%)", title = "Patients with Flu Vaccine Screening Completed Correctly by Unit") + # Modify the title
theme_minimal() +
theme(legend.position = "right") +
guides(fill = guide_legend(title = "Color"))
Summary: Flu Vaccine Information Sheet (VIS) provided to the patient
df2 <- df_by_unit %>%
select(Unit,
Observations,
`Flu Vaccine Information Sheet (VIS) provided to the patient._Mean`,
`Flu Vaccine Information Sheet (VIS) provided to the patient._NA_Count`,
`Flu Vaccine Information Sheet (VIS) provided to the patient._Proportion_NA`)
colnames(df2) = c('Unit','Observations','Mean','n_na','proportion_na')
df2$color <- ifelse(df2$Mean < 0.9, "red", "grey")
df2## # A tibble: 6 × 6
## Unit Observations Mean n_na proportion_na color
## <chr> <int> <dbl> <int> <dbl> <chr>
## 1 A 52 0.882 35 0.673 red
## 2 B 10 1 7 0.7 grey
## 3 C 88 0.923 49 0.557 grey
## 4 D 114 0.905 72 0.632 grey
## 5 E 6 1 4 0.667 grey
## 6 G 4 1 0 0 greyPlotting df2:
ggplot(df2, aes(x = Unit, y = round(Mean * 100, 2), fill = color)) +
geom_bar(stat = "identity") +
geom_text(aes(label = paste0(round(Mean * 100, 2), "%"), fontface = "bold"), vjust = -0.5, size = 3, color = "black") + # Add numerical values with percent signs
scale_fill_identity() +
geom_hline(yintercept = 90, linetype = "dotted") +
geom_text(aes(x = Inf, y = 90, label = "Compliance Target"), hjust = 1, vjust = -0.5, color = "black") + # Add "Compliance Target" text
labs(x = "Unit", y = "Completion (%)", title = "Flu Vaccine Information Sheet (VIS) Provided to the Patient by Unit") + # Modify the title
theme_minimal() +
theme(legend.position = "right") +
guides(fill = guide_legend(title = "Color"))
Summary: Documentation of Flu vaccine administration is recorded
# Documentation of Flu vaccine administration is recorded
df3 <- df_by_unit %>%
select(Unit,
Observations,
`Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR)._Mean`,
`Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR)._NA_Count`,
`Documentation of Flu vaccine administration is recorded on the Medication Administration Record (MAR)._Proportion_NA` )
colnames(df3) = c('Unit','Observations','Mean','n_na','proportion_na')
df3$color <- ifelse(df3$Mean < 0.9, "red", "grey")
df3## # A tibble: 6 × 6
## Unit Observations Mean n_na proportion_na color
## <chr> <int> <dbl> <int> <dbl> <chr>
## 1 A 52 0.9 42 0.808 grey
## 2 B 10 0.333 7 0.7 red
## 3 C 88 0.571 53 0.602 red
## 4 D 114 0.571 86 0.754 red
## 5 E 6 1 5 0.833 grey
## 6 G 4 1 2 0.5 greyPlotting df3:
ggplot(df3, aes(x = Unit, y = round(Mean * 100, 2), fill = color)) +
geom_bar(stat = "identity") +
geom_text(aes(label = paste0(round(Mean * 100, 2), "%"), fontface = "bold"), vjust = -0.5, size = 3, color = "black") + # Add numerical values with percent signs
scale_fill_identity() +
geom_hline(yintercept = 90, linetype = "dotted") +
geom_text(aes(x = Inf, y = 90, label = "Compliance Target"), hjust = 1, vjust = -0.5, color = "black") + # Add "Compliance Target" text
labs(x = "Unit", y = "Completion (%)", title = "Documentation of Flu Vaccine Administration is Recorded by Unit") + # Modify the title
theme_minimal() +
theme(legend.position = "right") +
guides(fill = guide_legend(title = "Color"))
Summary: Pneumovax Vaccine screening completed correctly
# Pneumovax Vaccine screening completed correctly
df4 <- df_by_unit %>%
select(Unit,
Observations,
`Pneumovax Vaccine screening completed correctly._Mean`,
`Pneumovax Vaccine screening completed correctly._NA_Count`,
`Pneumovax Vaccine screening completed correctly._Proportion_NA`)
colnames(df4) = c('Unit','Observations','Mean','n_na','proportion_na')
df4$color <- ifelse(df4$Mean < 0.9, "red", "grey")
df4## # A tibble: 6 × 6
## Unit Observations Mean n_na proportion_na color
## <chr> <int> <dbl> <int> <dbl> <chr>
## 1 A 52 0.885 0 0 red
## 2 B 10 1 0 0 grey
## 3 C 88 0.849 2 0.0227 red
## 4 D 114 0.877 0 0 red
## 5 E 6 1 0 0 grey
## 6 G 4 1 0 0 greyPlotting df4:
ggplot(df4, aes(x = Unit, y = round(Mean * 100, 2), fill = color)) +
geom_bar(stat = "identity") +
geom_text(aes(label = paste0(round(Mean * 100, 2), "%"), fontface = "bold"), vjust = -0.5, size = 3, color = "black") + # Add numerical values with percent signs
scale_fill_identity() +
geom_hline(yintercept = 90, linetype = "dotted") +
geom_text(aes(x = Inf, y = 90, label = "Compliance Target"), hjust = 1, vjust = -0.5, color = "black") + # Add "Compliance Target" text
labs(x = "Unit", y = "Completion (%)", title = "Pneumovax Vaccine Screening Completed Correctly by Unit") + # Modify the title
theme_minimal() +
theme(legend.position = "right") +
guides(fill = guide_legend(title = "Color"))
Summary: Pneumovax Vaccine Information Sheet (VIS) provided to the patient
# Pneumovax Vaccine Information Sheet (VIS) provided to the patient
df5 <- df_by_unit %>%
select(`Unit`,
Observations,
`Pneumovax Vaccine Information Sheet (VIS) provided to the patient._Mean`,
`Pneumovax Vaccine Information Sheet (VIS) provided to the patient._NA_Count`,
`Pneumovax Vaccine Information Sheet (VIS) provided to the patient._Proportion_NA`)
colnames(df5) = c('Unit','Observations','Mean','n_na','proportion_na')
df5$color <- ifelse(df5$Mean < 0.9, "red", "grey")
df5## # A tibble: 6 × 6
## Unit Observations Mean n_na proportion_na color
## <chr> <int> <dbl> <int> <dbl> <chr>
## 1 A 52 0.818 41 0.788 red
## 2 B 10 1 7 0.7 grey
## 3 C 88 0.889 61 0.693 red
## 4 D 114 0.870 91 0.798 red
## 5 E 6 NaN 6 1 <NA>
## 6 G 4 1 3 0.75 greyPlotting df5:
ggplot(df5[df5$Unit != "E", ], aes(x = Unit, y = round(Mean * 100, 2), fill = color)) +
geom_bar(stat = "identity") +
geom_text(aes(label = paste0(round(Mean * 100, 2), "%"), fontface = "bold"), vjust = -0.5, size = 3, color = "black") + # Add numerical values with percent signs
scale_fill_identity() +
geom_hline(yintercept = 90, linetype = "dotted") +
geom_text(aes(x = Inf, y = 90, label = "Compliance Target"), hjust = 1, vjust = -0.5, color = "black") + # Add "Compliance Target" text
labs(x = "Unit", y = "Completion (%)", title = "Pneumovax Vaccine Information Sheet Provided to the Patient by Unit") + # Modify the title
theme_minimal() +
theme(legend.position = "right") +
guides(fill = guide_legend(title = "Color"))