Data 110 Project #2 CMS Innovation Center Participants
Jennifer Paraboschi
December 1, 2019
#getwd()Centers for Medicare & Medicaid Services (CMS)
Center for Medicare and Medicaid Innovation (The Innovation Center) dataset
https://data.cms.gov/Special-Programs-Initiatives-Speed-Adoption-of-Bes/CMS-Innovation-Center-Model-Participants/x8pc-u7ta
An analysis of CMS Innovation Center’s Model Participants.
Medicare is a federal health insurance program primarily for people ages 65 and older, for younger people with disabilities, or for people with end stage renal disease (ESRD). Over 60 million people use Medicare each year, and Medicare spending accounted for 15% of total federal spending in 2018, amounting to $731 billion [^1]. The image below indicates Medicare’s portion of the federal budget for 2018.
Medicare2018.
CMS is the single largest payer for health care in the United States [^2] and the leadership of CMS takes this role in overall health care services seriously. CMS influences the use of best practices, prevention initiatives, treatment choices, overall harm-free care, and patient follow-up across providers and insurance payers because of its major role in the industry. The decisions at CMS impact each person’s health care experience, whether they are aware of this influence or even whether they utilize Medicare for their health insurance or not.
For part of my job, I support one of the CMS Innovation Center’s voluntary payment model tests called Bundled Payments for Care Improvement (BPCI) Advanced. The Innovation Center tests payment and care delivery models like this to evaluate incentives for improving quality care and lowering healthcare costs delivered to Medicare beneficiaries. In this project, I explore the participants (i.e., providers, hospitals) in Innovation Center models, especially participants in BPCI Advanced. For the BPCI models, the participants are acute care hospitals (ACHs) or physician group practices (PGPs). These participants choose which clinical episodes they want CMS to evaluate and pay them a bundled payment amount for. For example, a hospital may agree to participate in the congestive heart failure (CHF) clinical episode. This means that for a Medicare beneficiary who triggers a CHF episode at this ACH, CMS will pay the hospital a set dollar amount to care for that beneficiary within a 90-day window. If the hospital provides CHF care efficiently, reports on completing activities, provides services, with positive outcomes, they can do this for less cost than what CMS pays, thereby making a profit. If the hospital provides CHF care poorly, reports that they did not complete certain activities, did not provide services, and the beneficiary had negative outcomes, CMS reduces the payment so the hospital is penalized or loses money. This is a simplified explanation of a very complex payment system.
For my analysis, I begin by looking at the number of clinical episodes that participants select within each of the BPCI models.
Let’s begin.
[^1]: https://www.kff.org/medicare/issue-brief/the-facts-on-medicare-spending-and-financing/
[^2]: https://www.cms.gov/Medicare/Quality-Initiatives-Patient-Assessment-Instruments/QualityInitiativesGenInfo/Downloads/RoadmapOverview_OEA_1-16.pdf
Install packages and dataset.
Before importing the dataset into R, I did some cleaning in Excel.
- I deleted columns with all blanks.
- Phase 1
- MSA Name
- Map Display
- Phase 1
- I edited the record for Unique ID #7437 (Baptist Cancer Center - Tipton) to remove artifacts in the organization name.
- I renamed the dataset “CMSdata”.
I will use functions from the dplyr package like filter(), group_by(), and summarize() to manipulate the data.
#install.packages("tidyverse")
library(tidyverse)## -- Attaching packages ------------------------------------------------------------------------------- tidyverse 1.3.0 --## v ggplot2 3.2.1 v purrr 0.3.3
## v tibble 2.1.3 v dplyr 0.8.3
## v tidyr 1.0.0 v stringr 1.4.0
## v readr 1.3.1 v forcats 0.4.0## -- Conflicts ---------------------------------------------------------------------------------- tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()library(readr)
library(ggplot2)
allparticipants<-read_csv("CMSdata.csv") #this pulls my csv file from my working directory## Parsed with column specification:
## cols(
## `Name of Initiative` = col_character(),
## `Organization Name` = col_character(),
## Notes = col_character(),
## `Location 1` = col_character(),
## `Street Address` = col_character(),
## City = col_character(),
## State = col_character(),
## `State Based` = col_logical(),
## `Phase 2` = col_character(),
## Facebook = col_character(),
## Twitter = col_character(),
## Youtube = col_character(),
## Website = col_character(),
## Category = col_character(),
## `Unique ID` = col_double()
## )dim(allparticipants) #this gives the dimensions of the dataset which is the number of rows and columns## [1] 7886 15This dataset has 7,886 records with 15 variables.
summary(allparticipants) #get a summary of the dataset## Name of Initiative Organization Name Notes Location 1
## Length:7886 Length:7886 Length:7886 Length:7886
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
## Street Address City State State Based
## Length:7886 Length:7886 Length:7886 Mode :logical
## Class :character Class :character Class :character FALSE:315
## Mode :character Mode :character Mode :character TRUE :1
## NA's :7570
##
##
## Phase 2 Facebook Twitter Youtube
## Length:7886 Length:7886 Length:7886 Length:7886
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
## Website Category Unique ID
## Length:7886 Length:7886 Min. : 1
## Class :character Class :character 1st Qu.:1973
## Mode :character Mode :character Median :3970
## Mean :3976
## 3rd Qu.:5981
## Max. :7976The Notes column was a field of free text which had content for only a few of the initiatives. I cleaned up the Notes column using OpenRefine which is an open source application for data wrangling. I extracted the number of clinical episodes each participant selected in the BPCI initiatives into a separate column that I named “Number of Clinical Episodes”.
I used OpenRefine to:
- Filter to select BPCI Initiatives
- On Notes column - Edit column - Split column Notes into several columns
- By separator
- Separator :
- Guess cell Type - checked
- On Notes column - Edit column - Split column Notes into several columns
- On Notes 2 column - Edit column - Split column Notes 2 into several columns
- By separator
- Separator //
- By separator
- Delete Notes 3 column
- On Notes 2 column - Edit column - Split column Notes 2 several columns
- By separator
- Separator //
- By separator
- Delete Notes 2 column and Notes 2 2 column
- Rename the column “Number of Clinical Episodes”
- Rename the first column “Initiative”
- Remove the BPCI Initiatives filter
- Export the full dataset and name it as “CMSdata2”
Pull the refined dataset into R.
allparticipants <- read_csv("CMSdata2.csv")## Parsed with column specification:
## cols(
## Initiative = col_character(),
## `Organization Name` = col_character(),
## `Number of Clinical Episodes` = col_double(),
## `Location 1` = col_character(),
## `Street Address` = col_character(),
## City = col_character(),
## State = col_character(),
## `State Based` = col_logical(),
## `Phase 2` = col_logical(),
## Facebook = col_character(),
## Twitter = col_character(),
## Youtube = col_character(),
## Website = col_character(),
## Category = col_character(),
## `Unique ID` = col_double()
## )## Warning: 979 parsing failures.
## row col expected actual file
## 1889 Phase 2 1/0/T/F/TRUE/FALSE Major joint replacement of the lower extremity 'CMSdata2.csv'
## 1890 Phase 2 1/0/T/F/TRUE/FALSE Major joint replacement of the lower extremity 'CMSdata2.csv'
## 1891 Phase 2 1/0/T/F/TRUE/FALSE Major joint replacement of the lower extremity 'CMSdata2.csv'
## 1892 Phase 2 1/0/T/F/TRUE/FALSE Major bowel procedure 'CMSdata2.csv'
## 1893 Phase 2 1/0/T/F/TRUE/FALSE Chronic obstructive pulmonary disease, bronchitis, asthma 'CMSdata2.csv'
## .... ....... .................. ......................................................... ..............
## See problems(...) for more details.R is returning a warning note for 979 parsing failures in the column called “Phase 2”. These rows are the only records with values (strings) in this field. R is trying to read this column as a logical value. I will use the mutate command with as.character to convert these values to characters to dismiss this problem.
allparticipants <- allparticipants %>%
mutate_if(is.logical, as.character) #this changes all the columns/fields in the dataframe from logical (if applicable) to character which meets my needs for this dataset.Make all headings (column names) lowercase. Remove the spaces between words in the headings. Then look at the data with head command.
names(allparticipants) <- tolower(names(allparticipants)) #makes the column headings lowercase
names(allparticipants) <- gsub(" ","",names(allparticipants)) #removes the space in the headings, if applicable.
head(allparticipants)## # A tibble: 6 x 15
## initiative organizationname numberofclinica~ location1 streetaddress city
## <chr> <chr> <dbl> <chr> <chr> <chr>
## 1 Comprehen~ Brown Medicine ~ NA 375 Wamp~ 375 Wampanoa~ East~
## 2 Comprehen~ Brown Medicine ~ NA 375 Wamp~ 375 Wampanoa~ East~
## 3 Comprehen~ Brown Medicine ~ NA 375 Wamp~ 375 Wampanoa~ East~
## 4 Comprehen~ Brown Medicine ~ NA 909 Nort~ 909 North Ma~ Prov~
## 5 Comprehen~ Coastal Medical~ NA 11445 Wa~ 11445 Wampan~ East~
## 6 Comprehen~ LPG Primary Car~ NA 50 Memor~ 50 Memorial ~ Newp~
## # ... with 9 more variables: state <chr>, statebased <chr>, phase2 <chr>,
## # facebook <chr>, twitter <chr>, youtube <chr>, website <chr>,
## # category <chr>, uniqueid <dbl>Look at the summary of the dataset again.
summary(allparticipants)## initiative organizationname numberofclinicalepisodes
## Length:7886 Length:7886 Min. : 1.000
## Class :character Class :character 1st Qu.: 2.000
## Mode :character Mode :character Median : 4.000
## Mean : 7.023
## 3rd Qu.: 9.000
## Max. :47.000
## NA's :5612
## location1 streetaddress city state
## Length:7886 Length:7886 Length:7886 Length:7886
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## statebased phase2 facebook twitter
## Length:7886 Length:7886 Length:7886 Length:7886
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## youtube website category uniqueid
## Length:7886 Length:7886 Length:7886 Min. : 1
## Class :character Class :character Class :character 1st Qu.:1973
## Mode :character Mode :character Mode :character Median :3970
## Mean :3976
## 3rd Qu.:5981
## Max. :7976
## Now I have a quantitative variable for the number of clinical episodes column.
Group the dataframe by multiple columns with mean number of clinical episodes.
I want to see the mean number of clinical episodes for each of the BPCI models.
#this chunk says to group the df by the initiative column then
#take the variable called numberofclinicalepisodes and apply the function mean and remove the nas when calculating
#then I filtered out the nas so that I only had the initiatives with clinical episodes selected.
#I assigned that summarization to something called bpcimodels.
bpcimodels <- summarise_at(group_by(allparticipants, initiative),vars(numberofclinicalepisodes),funs(mean(.,na.rm=TRUE))) %>%
filter(!is.na(numberofclinicalepisodes)) ## Warning: funs() is soft deprecated as of dplyr 0.8.0
## Please use a list of either functions or lambdas:
##
## # Simple named list:
## list(mean = mean, median = median)
##
## # Auto named with `tibble::lst()`:
## tibble::lst(mean, median)
##
## # Using lambdas
## list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
## This warning is displayed once per session.#filter here says to take all rows that do not have an 'na' value in the numberofclinicalepisodes variable.
#that leaves me with the 4 BPCI models with their mean number of clinical episodes selected.
bpcimodels #this displays the df in a tibble## # A tibble: 4 x 2
## initiative numberofclinicalepisodes
## <chr> <dbl>
## 1 BPCI Advanced 5.95
## 2 BPCI Initiative: Model 2 5.43
## 3 BPCI Initiative: Model 3 10.5
## 4 BPCI Initiative: Model 4 6.5Let’s try a plot.
I’ll look at the average number of clinical episodes that participants chose within each iteration of the BPCI models.
#install.packages("plotly")
#install.packages("ggthemes")
library(plotly)##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layoutlibrary(ggthemes)
bpciepisodes <- bpcimodels %>% #this uses the small dataframe of just the bpci models
ggplot(aes(x=initiative, y=numberofclinicalepisodes,fill=initiative)) +
geom_bar(stat="identity") +
theme_stata() +
labs(x="Initiative", y="Average Number of Clinical Episodes Chosen", title="Average Number of Clinical Episodes within each Initiative")
ggplotly(bpciepisodes) #using ggplotly makes the labels appear when you hover####This plot is a good start. The axis labels are overcrowded and the hovering labels are repetitive. The legend label needs fixed, too.
###Let’s try a plot that nudges the axis labels.
#install.packages("plotly")
#install.packages("ggthemes")
#install.packages("ggrepel")
library(plotly)
library(ggthemes)
library(ggrepel)
bpciepisodes <- bpcimodels %>% #this uses the small dataframe of just the bpci models
ggplot(aes(x=initiative, y=numberofclinicalepisodes, fill=initiative, label=initiative)) +
geom_text_repel(nudge_x = 0.005) +
geom_bar(stat="identity") +
theme_stata() +
labs(x="Initiative", y="Average Number of Clinical Episodes Chosen", title="Average Number of Clinical Episodes within each Initiative")
ggplotly(bpciepisodes) #using ggplotly makes the labels appear when you hover## Warning in geom2trace.default(dots[[1L]][[4L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[4L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[4L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[4L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issuesSo this version fixes the axis labels but the legend is not viewable.
I want to plot the mean of the number of clinical episodes.
First I will get some statistics on the variation.
#install.packages("rcompanion") # this has the groupwiseMean command which I use to get the statistics across all the BPCI participants' selection of clinical episodes.
library(rcompanion)
bpciparticipants <- allparticipants %>%
filter(!is.na(numberofclinicalepisodes))
Sum <- groupwiseMean(data=bpciparticipants, var="numberofclinicalepisodes", group="initiative",conf=0.95,digits=3)
Sum## initiative n Mean Conf.level Trad.lower Trad.upper
## 1 BPCI Advanced 1295 5.95 0.95 5.63 6.27
## 2 BPCI Initiative: Model 2 402 5.43 0.95 4.83 6.03
## 3 BPCI Initiative: Model 3 575 10.50 0.95 9.65 11.40
## 4 BPCI Initiative: Model 4 2 6.50 0.95 -63.40 76.40summary(Sum)## initiative n Mean Conf.level
## Length:4 Min. : 2.0 Min. : 5.430 Min. :0.95
## Class :character 1st Qu.: 302.0 1st Qu.: 5.820 1st Qu.:0.95
## Mode :character Median : 488.5 Median : 6.225 Median :0.95
## Mean : 568.5 Mean : 7.095 Mean :0.95
## 3rd Qu.: 755.0 3rd Qu.: 7.500 3rd Qu.:0.95
## Max. :1295.0 Max. :10.500 Max. :0.95
## Trad.lower Trad.upper
## Min. :-63.400 Min. : 6.030
## 1st Qu.:-12.227 1st Qu.: 6.210
## Median : 5.230 Median : 8.835
## Mean :-10.822 Mean :25.025
## 3rd Qu.: 6.635 3rd Qu.:27.650
## Max. : 9.650 Max. :76.400So this gives the mean of the number of clinical episodes with the quartiles.
Plotting the Means with a deviation.
A standard error is for a sample and standard deviation is for an entire population. I have the whole population of participants in the models so I can plot the standard error calculated above.
Sum %>% ggplot(aes(x=initiative, y=Mean,fill=initiative)) +
geom_bar(stat="identity") +
geom_errorbar(aes(ymin=Trad.lower, ymax=Trad.upper,width=0.15))
I need to remove BPCI Initiative: Model 4 since it is skewing everything.
#install.packages(data.table) # I tried an outlier.replace version first which did not work well for me.
library(data.table)##
## Attaching package: 'data.table'## The following objects are masked from 'package:dplyr':
##
## between, first, last## The following object is masked from 'package:purrr':
##
## transpose#Sum %>% outlier.replace(Sum,"numberofclinicalepisodes", which(numberofclinicalepisodes < 3), newValue=NA)
#Sum %>% filter(!is.na(numberofclinicalepisodes))
statson3models <- Sum %>% filter(n >= 3) %>% #this filters out model #4 so the plot is easier to read
ggplot(aes(x=initiative, y=Mean)) +
geom_bar(stat="identity", aes(fill=initiative)) +
geom_errorbar(aes(ymin=Trad.lower, ymax=Trad.upper,width=0.15))
ggplotly(statson3models)I realized after doing this analysis that this is not really meaningful, statistically. However, the standard error can be calculated for a sample but I have a record of the whole population. A standard deviation can be calculated for the whole population. I am really not sure what the ‘error bar’ in this case would even mean.
Instead, I will move on to a box and whisker plot and look at some outliers.
This will make a boxplot of the number of clinical episodes selected.
boxyplot1 <- allparticipants %>%
ggplot() +
geom_boxplot(aes(y=numberofclinicalepisodes, fill=initiative), notch=TRUE) #the notch puts indents at the mean.
boxyplot1## Warning: Removed 5612 rows containing non-finite values (stat_boxplot).## notch went outside hinges. Try setting notch=FALSE.
This plot is a good start to look at outliers. The “notch” feature does not add helpful information for this plot so I will remove it.
I will also try changing the color of the outlier(s).
boxyplot2 <- allparticipants %>%
ggplot() +
geom_boxplot(aes(y=numberofclinicalepisodes, fill=initiative), outlier.colour="red", outlier.shape=6, outlier.size=2) #these set the color, shape, and size of the indicator for each outlier
boxyplot2## Warning: Removed 5612 rows containing non-finite values (stat_boxplot).
This looks like a lot of outliers.
I also want to change the order of the models to reflect the chronological order they were implemented.
allparticipants$initiative <- factor(allparticipants$initiative, levels=c("BPCI Initiative: Model 2", "BPCI Initiative: Model 3", "BPCI Initiative: Model 4", "BPCI Advanced")) #this lists them in the correct order
boxyplot3 <- allparticipants %>%
ggplot() +
geom_boxplot(aes(y=numberofclinicalepisodes, fill=initiative), outlier.colour="red", outlier.shape=6, outlier.size=2) +
labs(fill="") #this removes the label for the legend
boxyplot3## Warning: Removed 5612 rows containing non-finite values (stat_boxplot).
I will focus in on Model 3 which has the highest number of clinical episodes chosen and identify the top 2 number of clinical episodes.
boxyplot4 <- allparticipants %>%
filter(initiative == "BPCI Initiative: Model 3") %>% #this filter chooses only Model 3
ggplot() +
geom_boxplot(aes(y=numberofclinicalepisodes, fill=initiative), outlier.colour="red", outlier.shape=6, outlier.size=2) +
labs(fill="") #this removes the label for the legend
ggplotly(boxyplot4)The highest number of clinical episodes selected were 47 and 45 episodes within BPCI Model 3.
The early BPCI models (Models 2-4) which began in 2013 included up to 48 clinical episodes while the most recent iteration (BPCI Advanced) has 31 clinical episodes. These included inpatient episodes for things like congestive heart failure, major joint replacement of the lower extremity, pacemaker, and stroke and outpatient episodes for percutaneous coronary intervention, cardiac defibrillator, and back & neck spinal fusion.