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\title{Open Case Studies: Mental Health of American Youth}
\author{}
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\begin{document}
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{
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\hypertarget{section}{%
\paragraph{}\label{section}}
\begin{center}\includegraphics[width=800 px]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/mainplot} \end{center}
\hypertarget{section-1}{%
\paragraph{}\label{section-1}}
\hypertarget{section-2}{%
\paragraph{}\label{section-2}}
\textbf{Disclaimer}: The purpose of the
\href{https://opencasestudies.github.io}{Open Case Studies} project is
\textbf{to demonstrate the use of various data science methods, tools,
and software in the context of messy, real-world data}. A given case
study does not cover all aspects of the research process, is not
claiming to be the most appropriate way to analyze a given data set, and
should not be used in the context of making policy decisions without
external consultation from scientific experts.
\hypertarget{section-3}{%
\paragraph{}\label{section-3}}
\hypertarget{section-4}{%
\paragraph{}\label{section-4}}
This work is licensed under the Creative Commons
Attribution-NonCommercial 3.0
\href{https://creativecommons.org/licenses/by-nc/3.0/us/}{(CC BY-NC
3.0)} United States License.
\hypertarget{section-5}{%
\paragraph{}\label{section-5}}
\hypertarget{section-6}{%
\paragraph{}\label{section-6}}
To cite this case study please use:
Wright, Carrie and Ontiveros, Michael and Jager, Leah and Taub, Margaret
and Hicks, Stephanie C. (2020).
\url{https://github.com/opencasestudies/ocs-bp-youth-mental-health}.
Mental Health of American Youth.
\hypertarget{section-7}{%
\paragraph{}\label{section-7}}
\hypertarget{section-8}{%
\paragraph{}\label{section-8}}
\textbf{Please be advised that the material in this case study describes
and discusses rates of suicide, as well as rates and symptoms of
depression.}
According to the
\href{https://www.nimh.nih.gov/health/publications/teen-depression/index.shtml}{National
Institute of Mental Health (NIMH)}:
If you are in crisis and need help, call this toll-free number for the
\textbf{National Suicide Prevention Lifeline (NSPL)}, available 24 hours
a day, every day: \textbf{1-800-273-TALK (8255)}. The service is
available to everyone. The deaf and hard of hearing can contact the
Lifeline via TTY at 1-800-799-4889. All calls are confidential. You can
also visit the Lifeline's website at
\url{www.suicidepreventionlifeline.org}.
The \textbf{Crisis Text Line} is another free, confidential resource
available 24 hours a day, seven days a week. Text ``HOME'' to
\textbf{741741} and a trained crisis counselor will respond to you with
support and information over text message. Visit
\url{www.crisistextline.org}.
Also see \href{https://www.mhanational.org/depression-teens-0}{here} for
more information about how to recognize and help youths experiencing
symptoms of depression.
\hypertarget{section-9}{%
\paragraph{}\label{section-9}}
To access the GitHub repository for this case study see here:
\url{https://github.com//opencasestudies/ocs-bp-youth-mental-health}.\\
This case study is part of a series of public health case studies for
the \href{https://americanhealth.jhu.edu/open-case-studies}{Bloomberg
American Health Initiative}.
\hypertarget{motivation}{%
\subsection{\texorpdfstring{\textbf{Motivation}}{Motivation}}\label{motivation}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
Rates of depression appear to have been increasing among American youths
since around 2010 according to a recent
\href{https://content.apa.org/record/2019-12578-001}{report}. A
\href{https://pubmed.ncbi.nlm.nih.gov/24285382/}{recent study} also
shows that youths appear to be seeking more care from mental health
services.
This case study will explore how rates of major depressive episodes have
changed since the early 2000s and across different youth subgroups (age,
gender, ethnicity). We also will explore how rates of treatment for
depression of youths have changed over time.
\begin{center}\includegraphics[width=0.4\linewidth]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/k-mitch-hodge-IqSaG9zv2e0-unsplash} \end{center}
{Photo by K. Mitch Hodge on Unsplash}
The major symptoms of a major depressive episode include:
\textbf{S}leep disorder (increased or decreased)\\
\textbf{I}nterest deficit (anhedonia)\\
\textbf{G}uilt (worthlessness, hopelessness, regret)\\
\textbf{E}nergy deficit\\
\textbf{C}oncentration deficit\\
\textbf{A}ppetite disorder (increased or decreased)\\
\textbf{P}sychomotor retardation or agitation\\
\textbf{S}uicidality
\hypertarget{source}{%
\subparagraph{\texorpdfstring{\href{https://www.icsi.org/guideline/depression/diagnose-and-characterize-major-depression-persistent-depressive-disorder-with-clinical-interview/}{{[}source{]}}}{{[}source{]}}}\label{source}}
\begin{center}\includegraphics[width=0.8\linewidth]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/depression-symptoms-and-treatment-768x768} \end{center}
\hypertarget{source-1}{%
\subparagraph{\texorpdfstring{\href{https://newmilfordcounselingcenter.com/depression-2/}{{[}source{]}}}{{[}source{]}}}\label{source-1}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
Click here to see the diagnostic requirements for a major depressive
episode (MSE) according to the
\href{https://en.wikipedia.org/wiki/DSM-5}{DSM 5}.
A. Five or more of the following symptoms have been present and
documented during the same two-week period and represent a change from
previous functioning; at least one of the symptoms is either (1)
depressed mood or (2) loss of interest or pleasure.
\textbf{Note}: Do not include symptoms that are clearly attributable to
another medical condition.
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\item
Depressed mood most of the day, nearly every day, as indicated by
either subjective report (e.g., feels sad, empty, hopeless) or
observation made by others (e.g., appears tearful)
\item
Markedly diminished interest or pleasure in all, or almost all,
activities most of the day, nearly every day (as indicated by either
subjective account or observation)
\item
Significant weight loss when not dieting or weight gain (e.g., a
change of more than 5\% of body weight in a month), or decrease or
increase in appetite nearly every day
\item
Insomnia or hypersomnia nearly every day
\item
Psychomotor agitation or retardation nearly every day (observable by
others, not merely subjective feelings of restlessness or being slowed
down)
\item
Fatigue or loss of energy nearly every day
\item
Feelings of worthlessness or excessive or inappropriate guilt (which
may be delusional) nearly every day (not merely self-reproach or guilt
about being sick)
\item
Diminished ability to think or concentrate, or indecisiveness, nearly
every day (either by subjective account or as observed by others)
\item
Recurrent thoughts of death (not just fear of dying), recurrent
suicidal ideation without a specific plan, or a suicide attempt or a
specific plan for committing suicide
\end{enumerate}
B. The symptoms do not meet criteria for a mixed episode.
C. The episode is not attributable to the physiological effects of a
substance or to another medical condition.
\textbf{Note}: Criteria A-C represent a major depressive episode.
\textbf{Note}: Responses to a significant loss (e.g., bereavement,
financial ruin, losses from a natural disaster, a serious medical
illness or disability) may include feelings of intense sadness,
rumination about the loss, insomnia, poor appetite and weight loss noted
in Criterion A, which may resemble a depressive episode. Although such
symptoms may be understandable or considered appropriate to the loss,
the presence of a major depressive episode in addition to the normal
response to a significant loss should also be carefully considered. This
decision inevitably requires the exercise of clinical judgment based on
the individual's history of and the cultural norms for the expression of
distress in the context of loss.
D. The occurrence of the major depressive episode is not better
explained by schizoaffective disorder, schizophrenia, schizophreniform
disorder, delusional disorder, or other specified and unspecified
schizophrenia spectrum and other psychotic disorders.
E. There has never been a manic episode or a hypomanic episode.
Note: This exclusion does not apply if all of the manic-like or
hypomanic-like episodes are substance-induced or are attributable to the
physiological effects of another medical condition.
\hypertarget{source-2}{%
\paragraph{\texorpdfstring{\href{https://www.icsi.org/guideline/depression/diagnose-and-characterize-major-depression-persistent-depressive-disorder-with-clinical-interview/}{{[}source{]}}}{{[}source{]}}}\label{source-2}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
This case study is motivated by the following two articles:
\hypertarget{section-10}{%
\paragraph{}\label{section-10}}
Twenge JM, Cooper AB, Joiner TE, Duffy ME, Binau SG. Age, period, and
cohort trends in mood disorder indicators and suicide-related outcomes
in a nationally representative dataset, 2005-2017. \emph{J Abnorm
Psychol}.128,3 (2019):185-199. \url{doi:10.1037/abn0000410}
Olfson, M., Blanco, C., Wang, S., Laje, G. \& Correll, C. U. National
Trends in the Mental Health Care of Children, Adolescents, and Adults by
Office-Based Physicians. \emph{JAMA Psychiatry}. 71, 81 (2014):81-90.
doi: 10.1001/jamapsychiatry.2013.3074.
\hypertarget{section-11}{%
\paragraph{}\label{section-11}}
The main findings of the first
\href{https://content.apa.org/record/2019-12578-001}{article} are:
\begin{quote}
Rates of major depressive episode in the last year increased 52\%
2005--2017 (from 8.7\% to 13.2\%) among adolescents aged 12 to 17 and
63\% 2009--2017 (from 8.1\% to 13.2\%) among young adults 18--25.
\end{quote}
\begin{quote}
Serious psychological distress in the last month and suicide-related
outcomes (suicidal ideation, plans, attempts, and deaths by suicide) in
the last year also increased among young adults 18--25 from 2008--2017
(with a 71\% increase in serious psychological distress), with less
consistent and weaker increases among adults ages 26 and over.
\end{quote}
\begin{quote}
Cultural trends contributing to an increase in mood disorders and
suicidal thoughts and behaviors since the mid-2000s, including the rise
of electronic communication and digital media and declines in sleep
duration, may have had a larger impact on younger people, creating a
cohort effect.
\end{quote}
While the main findings of the second
\href{https://pubmed.ncbi.nlm.nih.gov/24285382/}{article} are:
\begin{quote}
Compared with adult mental health care, the mental health care of young
people has increased more rapidly\ldots{}
\end{quote}
This means that the number of youths receiving mental health care has
increased faster than the number of adults receiving mental health care.
\begin{quote}
Between 1995-1998 and 2007-2010, visits resulting in mental disorder
diagnoses \ldots{} increased significantly faster for youths (from 7.78
to 15.30 visits) than for adults (from 23.23 to 28.48 visits)
(interaction: P \textless{} .001).
\end{quote}
\begin{quote}
Psychiatrist visits also increased significantly faster for youths (from
2.86 to 5.71 visits).
\end{quote}
\textbf{Summary}: While depression appears to be on the rise for youths,
youths also appear to be seeking more mental health care.
In this case study, we will be using data from the
\href{https://nsduhweb.rti.org/respweb/homepage.cfm}{National Survey on
Drug Use and Health (NSDUH)} related to treatment and major depressive
episode (MDE) rate to explore how trends in mental health have changed
over time and how different groups compare.
This data was also used in the first referenced article.
\hypertarget{main-questions}{%
\subsection{\texorpdfstring{\textbf{Main
Questions}}{Main Questions}}\label{main-questions}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{section-12}{%
\paragraph{}\label{section-12}}
Our main questions:
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\tightlist
\item
How have depression rates in American youth changed since 2004,
according to the NSDUH data? How have rates differed between different
youth subgroups (age, gender, ethnicity)?
\item
Do mental health services appear to be reaching more youths? Again,
how have rates differed between different youth subgroups (age,
gender, ethnicity)?
\end{enumerate}
\hypertarget{section-13}{%
\paragraph{}\label{section-13}}
\hypertarget{learning-objectives}{%
\subsection{\texorpdfstring{\textbf{Learning
Objectives}}{Learning Objectives}}\label{learning-objectives}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
The skills, methods, and concepts that students will be familiar with by
the end of this case study are:
\textbf{Data Science Learning Objectives:}
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\tightlist
\item
Scrape data directly from a website (\texttt{rvest})\\
\item
Subset and filter data (\texttt{dplyr})\\
\item
Write functions to wrangle data repetitively\\
\item
Work with character strings (\texttt{stringr})\\
\item
Reshape data into different formats (\texttt{tidyr})\\
\item
Data visualizations (\texttt{ggplot2}) with labels
(\texttt{directlabels}) and facets for different groups\\
\item
Combine multiple plots (\texttt{cowplot})\\
\item
Optional: Create an animated gif (\texttt{magick})
\end{enumerate}
\textbf{Statistical Learning Objectives:}
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\tightlist
\item
Discuss the impact of self-reporting bias on survey responses\\
\item
Define and create a contingency table\\
\item
Implementation of a chi-squared test for independence\\
\item
Interpretation of a chi-squared test for independence
\end{enumerate}
In this case study, we will especially focus on using packages and
functions from the
\href{https://www.tidyverse.org/}{\texttt{Tidyverse}}, such as
\href{https://github.com/tidyverse/rvest}{\texttt{rvest}}. The tidyverse
is a library of packages created by RStudio. While some students may be
familiar with previous R programming packages, these packages make data
science in R more legible and intuitive.
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
We will begin by loading the packages that we will need:
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(here)}
\KeywordTok{library}\NormalTok{(rvest)}
\KeywordTok{library}\NormalTok{(dplyr)}
\KeywordTok{library}\NormalTok{(magrittr)}
\KeywordTok{library}\NormalTok{(stringr)}
\KeywordTok{library}\NormalTok{(tidyr)}
\KeywordTok{library}\NormalTok{(tibble)}
\KeywordTok{library}\NormalTok{(purrr)}
\KeywordTok{library}\NormalTok{(ggplot2)}
\KeywordTok{library}\NormalTok{(directlabels)}
\KeywordTok{library}\NormalTok{(scales)}
\KeywordTok{library}\NormalTok{(forcats)}
\KeywordTok{library}\NormalTok{(ggthemes)}
\KeywordTok{library}\NormalTok{(cowplot)}
\end{Highlighting}
\end{Shaded}
\textbf{Packages used in this case study:}
\begin{longtable}[]{@{}ll@{}}
\toprule
\begin{minipage}[b]{0.41\columnwidth}\raggedright
Package\strut
\end{minipage} & \begin{minipage}[b]{0.53\columnwidth}\raggedright
Use in this case study\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://github.com/jennybc/here_here}{here}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to easily load and save data\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://github.com/tidyverse/rvest}{rvest}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to scrape web pages\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://dplyr.tidyverse.org/}{dplyr}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to subset and filter the data for specific groups, to replace specific
values with \texttt{NA}, rename variables, and perform functions on
multiple variables\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://magrittr.tidyverse.org/}{magrittr}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to use and reassign data objects using the \%\textless\textgreater\%pipe
operator\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://stringr.tidyverse.org/}{stringr}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to manipulate strings\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://tidyr.tidyverse.org/}{tidyr}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to change the shape or format of tibbles to wide and long\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://tibble.tidyverse.org/}{tibble}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to create tibbles and convert values of a column to row names\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://purrr.tidyverse.org/}{purrr}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to apply a function to each column of a tibble or each tibble in a
list\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://ggplot2.tidyverse.org/}{ggplot2}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to create plots\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{http://directlabels.r-forge.r-project.org/docs/index.html}{directlabels}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to add labels directly to lines in plots\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://cran.r-project.org/web/packages/scales/scales.pdf}{scales}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to get the current linetype options\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://forcats.tidyverse.org/}{forcats}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to reorder factor for plot\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://cran.r-project.org/web/packages/ggthemes/ggthemes.pdf}{ggthemes}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to create a plot to see what the different linetypes look like\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.41\columnwidth}\raggedright
\href{https://cran.r-project.org/web/packages/cowplot/vignettes/introduction.html}{cowplot}\strut
\end{minipage} & \begin{minipage}[t]{0.53\columnwidth}\raggedright
to combine plots together\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
The first time we use a function, we will use the \texttt{::} to
indicate which package we are using. Unless we have overlapping function
names, this is not necessary, but we will include it here to be
informative about where the functions we will use come from.
\hypertarget{context}{%
\subsection{\texorpdfstring{\textbf{Context}}{Context}}\label{context}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
To motivate the examination of the mental health of American youths, we
begin by exploring the rate of suicide in the United States (US).
According to the CDC the rate of suicide has increased for both genders.
\hypertarget{source-3}{%
\subparagraph{\texorpdfstring{\href{https://www.cdc.gov/nchs/products/databriefs/db309.htm}{{[}source{]}}}{{[}source{]}}}\label{source-3}}
While suicide does appear to be increasing among youths it also appears
to be increasing among most age groups in the US over the past decade
and a half for both females and males:
\includegraphics[width=0.5\linewidth]{https://www.cdc.gov/nchs/images/databriefs/301-350/db309_fig2}
\includegraphics[width=0.5\linewidth]{https://www.cdc.gov/nchs/images/databriefs/301-350/db309_fig3}
\hypertarget{source-4}{%
\subparagraph{\texorpdfstring{\href{https://www.cdc.gov/nchs/products/databriefs/db309.htm}{{[}source{]}}}{{[}source{]}}}\label{source-4}}
According to the
\href{https://www.cdc.gov/nchs/products/databriefs/db309.htm}{CDC}:
\begin{quote}
Since 2008, suicide has ranked as the 10th leading cause of death for
\textbf{all ages} in the United States.
\end{quote}
\begin{center}\includegraphics[width=800px]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/mortality} \end{center}
\hypertarget{source-5}{%
\subparagraph{\texorpdfstring{\href{https://www.cdc.gov/nchs/data/databriefs/db293.pdf}{{[}source{]}}}{{[}source{]}}}\label{source-5}}
Furthermore, according to the
\href{https://www.cdc.gov/nchs/products/databriefs/db309.htm}{CDC}:
\begin{quote}
In 2016, suicide became the \textbf{second leading cause of death} among
youths.
\end{quote}
\textbf{So although suicide is on the rise for most age groups, suicide
is one of the top \emph{two} contributors to death for youths.}
Thus, this warrants further examination of the mental health of American
youths.
\begin{center}\includegraphics[width=800px]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/mortality_age} \end{center}
\hypertarget{source-6}{%
\subparagraph{\texorpdfstring{\href{https://www.cdc.gov/nchs/data/nvsr/nvsr68/nvsr68_06-508.pdf}{{[}source{]}}}{{[}source{]}}}\label{source-6}}
Historically, suicide rates were much higher before 1950, however, we
are seeing an increase in the last 20 years.
\begin{center}\includegraphics[width=800px]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/suicide} \end{center}
\hypertarget{source-7}{%
\subparagraph{\texorpdfstring{\href{https://time.com/5609124/us-suicide-rate-increase/}{{[}source{]}}}{{[}source{]}}}\label{source-7}}
Besides the US,
\href{https://academic.oup.com/ije/article/48/5/1650/5366210}{other
countries} are also experiencing increased rates of depression in
youths.
See
\href{https://apps.who.int/iris/bitstream/handle/10665/254610/WHO-MSD-MER-2017.2-eng.pdf;jsessionid=E44360055DD83EAC472AA40C2853DBFA?sequence=1}{this
report} from the World Health Organization (WHO) about rates of
depression in other countries.
See \href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330161/}{here}
for an interesting discussion about what may be causing increased
depression rates.
\hypertarget{limitations}{%
\subsection{\texorpdfstring{\textbf{Limitations}}{Limitations}}\label{limitations}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
There are some important considerations regarding this data analysis to
keep in mind:
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\item
The data that we will use come from a survey and are therefore values
from a sample that estimate that of the true population. In our
statistical analysis we use these sample values as if they are
population estimates (because this is all we have access to). Thus,
our results are not necessarily indicative of population differences.
\item
Furthermore, the sampling mechanism utilized for the survey can
introduce
\href{https://en.wikipedia.org/wiki/Selection_bias?oldformat=true}{selection
bias} in cases where the the
\href{https://en.wikipedia.org/wiki/Sampling_(statistics)?oldformat=true}{sampling
methods do not produce a representative sample}.
\item
Data are collected from human participants; this presents the
\emph{potential} for information bias, as there is the
\emph{potential} that participants in the
\href{https://en.wikipedia.org/wiki/Sampling_frame?oldformat=true}{sampling
frame} may for a variety of reasons report inaccurate information.
\item
Data about certain group
\href{https://www.vox.com/the-highlight/2019/5/20/18542843/intersectionality-conservatism-law-race-gender-discrimination}{intersections}
(meaning for example individuals of a particular gender and ethnicity)
or particular groups in general such as specific ethnicities or gender
or sexual identity groups such as LGBTQIA+
(lesbian/gay/bisexual/transgender/queer and questioning) or non-binary
gender populations is unfortunately not available in the data used in
this analysis and in most research about this topic.
\end{enumerate}
Note: While
\href{https://www.who.int/genomics/gender/en/index1.html}{gender and
sex} are not actually binary, the data used in this analysis
unfortunately only contains information for groups of individuals who
self-reported as male or female. We also acknowledge that unfortunately
not all ethnicities or group intersections are represented in the data
either. More research should be devoted to collecting data about the
mental health of these groups.
\hypertarget{what-are-the-data}{%
\subsection{\texorpdfstring{\textbf{What are the
data?}}{What are the data?}}\label{what-are-the-data}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
We will be using data from the
\href{https://nsduhweb.rti.org/respweb/homepage.cfm}{National Survey on
Drug Use and Health (NSDUH)} which is directed by the
\href{https://www.samhsa.gov/}{Substance Abuse and Mental Health
Services Administration (SAMHSA)}, an agency in the
\href{https://www.hhs.gov/}{U.S. Department of Health and Human Services
(DHHS)}.
This survey started in 1971 and is conducted annually in all 50 states
and the District of Columbia. Approximately 70,000 people (ages 12 and
up) are interviewed each year about health-related issues. Only
civilian, non-institutionalized individuals are included. Households are
randomly selected and then a professional interviewer visits the
addresses and asks one or two of the residents to interview. The
interviewer brings a laptop with them that the participants use to fill
out the survey, which typically takes an hour to complete. If a
participant chooses to participate they receive \$30 in cash. All
collected information is confidential and is used for disease
surveillance and to guide public policy particularly focused on drug and
alcohol use as well as mental health. See
\href{https://nsduhweb.rti.org/respweb/about_nsduh.html}{here} for more
details about the survey.
The data are made available publicly online on the
\href{https://datafiles.samhsa.gov/}{Substance Abuse \& Mental Health
Data Archive}.
\begin{center}\includegraphics[width=1\linewidth]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/nsudh_screenshot_webpage} \end{center}
On the
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHDetailedTabs2018R2/NSDUHDetTabsSect11pe2018.htm}{website}
with the survey data, you can see that the results are displayed in many
tables. Importantly, there is no obvious way to download the data
directly from this particular website.
\begin{center}\includegraphics[width=1\linewidth]{/Users/carriewright/Documents/GitHub/ocs-youth-mental-health-case-study/img/website_overview} \end{center}
If you click on the TOC button on the far left upper corner, you will be
directed to another
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHDetailedTabs2018R2/NSDUHDetailedTabsTOC2018.htm\#toc}{website},
where a large
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHDetailedTabs2018R2/NSDUHDetailedTabs2018.pdf}{pdf
document} containing all of the results can be downloaded.
We are interested in investigating how depression rates have changed and
how youths are interacting with mental health services. Thus, the
following tables are of interest to us:
\begin{longtable}[]{@{}ll@{}}
\toprule
\begin{minipage}[b]{0.18\columnwidth}\raggedright
Table\strut
\end{minipage} & \begin{minipage}[b]{0.76\columnwidth}\raggedright
Details\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.1A\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Settings Where Mental Health Services Were Received in Past Year among
Persons Aged 12 to 17: Numbers in Thousands, 2002-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.1B\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Settings Where Mental Health Services Were Received in Past Year among
Persons Aged 12 to 17: Percentages, 2002-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.2A\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Major Depressive Episode in Past Year among Persons Aged 12 to 17, by
Demographic Characteristics: Numbers in Thousands, 2004-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.2B\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Major Depressive Episode in Past Year among Persons Aged 12 to 17, by
Demographic Characteristics: Percentages, 2004-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.3A\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Major Depressive Episode with Severe Impairment in Past Year among
Persons Aged 12 to 17, by Demographic Characteristics: Numbers in
Thousands, 2006-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.3B\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Major Depressive Episode with Severe Impairment in Past Year among
Persons Aged 12 to 17, by Demographic Characteristics: Percentages,
2006-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.4A\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Receipt of Treatment for Depression in Past Year among Persons Aged 12
to 17 with Major Depressive Episode in Past Year, by Demographic
Characteristics: Numbers in Thousands, 2004-2018\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.18\columnwidth}\raggedright
Table 11.4B\strut
\end{minipage} & \begin{minipage}[t]{0.76\columnwidth}\raggedright
Receipt of Treatment for Depression in Past Year among Persons Aged 12
to 17 with Major Depressive Episode in Past Year, by Demographic
Characteristics: Percentages, 2004-2018\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
Our goal is to bring these data into R so we can explore them.
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
Click here for the NSDUH defines a major depressive episode (MDE)
According to the
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHNationalFindingsReport2018/NSDUHNationalFindingsReport2018.pdf}{NSDUH
2018 report}
\begin{quote}
Respondents were defined as having had an MDE in the past 12 months if
they had at least one period of 2 weeks or longer in the past year when
they experienced a depressed mood or loss of interest or pleasure in
daily activities, accompanied by problems with sleeping, eating, energy,
concentration, or self-worth. The MDE questions are based on diagnostic
criteria from DSM-5. Some of the wordings of the depression questions
for adolescents aged 12 to 17 and adults aged 18 or older differed
slightly to make the questions more developmentally appropriate for
adolescents.
\end{quote}
\begin{quote}
Adolescents were defined as having an MDE with severe impairment if
their depression caused severe problems with their ability to do chores
at home, do well at work or school, get along with their family, or have
a social life.
\end{quote}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{data-import}{%
\subsection{\texorpdfstring{\textbf{Data
Import}}{Data Import}}\label{data-import}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
Data are often made available online. Sometimes, the data we are
interested in is made available for download on a web page as a
delimited text file or an excel file. However, sometimes data are not
made available in this manner, such as the
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHDetailedTabs2018R2/NSDUHDetTabsSect11pe2018.htm}{NSDUH
survey data}.
How do we proceed in this scenario?
We can manually copy each cell of data; however, this process is often
inefficient, subject to error, and not reproducible. Say we wanted to
run an analysis next year on the next years data and it happens to be
formatted in the same way.
Alternatively, we could use \texttt{R} to scrape the data from the web!
Formally,
\href{https://en.wikipedia.org/wiki/Web_scraping?oldformat=true}{web
scraping} is the process of extracting data from a webpage. Let's learn
how to do this for our case study.
\hypertarget{basic-steps-of-web-scraping}{%
\subsubsection{\texorpdfstring{\textbf{Basic steps of web
scraping}}{Basic steps of web scraping}}\label{basic-steps-of-web-scraping}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
There are two main steps to web scraping:
\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\item
Identify \textbf{location} of data on the webpage that will be
scraped.
\item
Save the webpage \textbf{element} to an R \textbf{object}.
\end{enumerate}
We accomplish STEP 1 with our web browser.
We accomplish STEP 2 in the \texttt{R} programming environment.
The \textbf{location} of the data on the webpage that will be scraped
can be identified using a language called
\href{https://en.wikipedia.org/wiki/XPath}{XPath}, which is short for
XML Path Language. It is used to identify pieces (in this case called
\textbf{nodes}) of a document written in the
\href{https://en.wikipedia.org/wiki/XML}{XML} language.
\href{https://en.wikipedia.org/wiki/XML}{XML} which is short for
Extensible Markup Language is frequently used for documents on the
internet, similar to \href{https://en.wikipedia.org/wiki/HTML}{HTML}.
One of the
\href{https://techdifferences.com/difference-between-xml-and-html.html}{major
differences} between these two is that HTML does not provide structural
information, while XML does. This structural information can be used to
parse documents so that we can scrape only the data that we are
interested in from a website.
\hypertarget{section-14}{%
\paragraph{}\label{section-14}}
Additional resources for web scraping:
\begin{itemize}
\tightlist
\item
\href{https://rstudio-pubs-static.s3.amazonaws.com/266430_f3fd4660b2744751ab144aa130768a06.html}{Vignette}
\item
\href{http://blog.corynissen.com/2015/01/using-rvest-to-scrape-html-table.html}{Blog}
\item
\href{http://research.libd.org/rstatsclub/post/introduction-to-scraping-and-wranging-tables-from-research-articles/\#.Xw878ZNKhQJ}{Blog}
\item
\href{https://cran.r-project.org/web/packages/rvest/vignettes/selectorgadget.html}{Selectorgadget
Tool}
\end{itemize}
\hypertarget{section-15}{%
\paragraph{}\label{section-15}}
\hypertarget{the-rvest-package}{%
\subsubsection{\texorpdfstring{\textbf{The \texttt{rvest}
package}}{The rvest package}}\label{the-rvest-package}}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
In this case study, we will scrape data from the tables on the
\href{https://www.samhsa.gov/data/sites/default/files/cbhsq-reports/NSDUHDetailedTabs2018R2/NSDUHDetTabsSect11pe2018.htm}{NSDUH
survey} website.
Note that these data are available in a large PDF with all the results
by year if you wish to use the data from this particular source.
One option to import the data would be to import the PDF. However it is
not easy to find this PDF and it would be difficult and time consuming
to find our tables of interest and to extract our data of interest from
the pdf. However, if one wanted to do this, say if the tables were not
available online, they could use the \texttt{pdftools} package. See this
other \href{https://www.opencasestudies.org/ocs-bp-diet/}{case study}
and this other
\href{https://www.opencasestudies.org/ocs-bp-youth-disconnection/}{case
study} for two methods to work with PDFs.
Another option could be to copy and paste the data from the website to
another file that we would also need to import. But this would not be as
efficient or reproducible and might result in errors.
Alternatively, we will use the \texttt{rvest} package to
\href{https://en.wikipedia.org/wiki/Web_scraping?oldformat=true}{scrape}
the data directly from the tables on the website.
Assuming the data next year would be displayed in a similar manner, this
could allow us to simply modify our code based on the url for the data
next year to run the same analysis on the data easily.