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Report.tex
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Report.tex
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% Options for packages loaded elsewhere
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\title{Histopathology Research Template}
\author{true}
\date{2020-02-26}
\begin{document}
\maketitle
{
\setcounter{tocdepth}{5}
\tableofcontents
}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\([](https://doi.org/10.5281/zenodo.3635430)\)
\url{https://doi.org/10.5281/zenodo.3635430}
\url{https://osf.io/3tjfk/}
\href{https://sbalci.github.io/histopathology-template/}{Histopathology
Research Template 🔬}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{introduction}{%
\section{Introduction}\label{introduction}}
\begin{itemize}
\tightlist
\item
\textbf{State the marker of interest, the study objectives, and
hypotheses (Knijn, Simmer, and Nagtegaal 2015)}.\footnote{From Table
1: Proposed items for reporting histopathology studies.
Recommendations for reporting histopathology studies: a proposal
Virchows Arch (2015) 466:611--615 DOI 10.1007/s00428-015-1762-3
\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460276/}}
\end{itemize}
\hypertarget{materials-methods}{%
\section{Materials \& Methods}\label{materials-methods}}
\textbf{Describe Materials and Methods as highlighted in (Knijn, Simmer,
and Nagtegaal 2015)}.\footnote{From Table 1: Proposed items for
reporting histopathology studies. Recommendations for reporting
histopathology studies: a proposal Virchows Arch (2015) 466:611--615
DOI 10.1007/s00428-015-1762-3
\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460276/}}
\begin{itemize}
\item
Describe patient characteristics, and inclusion and exclusion criteria
\item
Describe treatment details
\item
Describe the type of material used
\item
Specify how expression of the biomarker was assessed
\item
Describe the number of independent (blinded) scorers and how they
scored
\item
State the method of case selection, study design, origin of the cases,
and time frame
\item
Describe the end of the follow-up period and median follow-up time
\item
Define all clinical endpoints examined
\item
Specify all applied statistical methods
\item
Describe how interactions with other clinical/pathological factors
were analyzed
\end{itemize}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{header-codes}{%
\subsection{Header Codes}\label{header-codes}}
\textbf{Codes for general settings.}\footnote{See
\href{https://github.com/sbalci/histopathology-template/blob/master/childRmd/_01header.Rmd}{\texttt{childRmd/\_01header.Rmd}}
file for other general settings}
\textbf{Setup global chunk settings}\footnote{Change
\texttt{echo\ =\ FALSE} to hide codes after knitting and Change
\texttt{cache\ =\ TRUE} to knit quickly. Change \texttt{error=TRUE} to
continue rendering while errors are present.}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\OperatorTok{::}\NormalTok{opts_chunk}\OperatorTok{$}\KeywordTok{set}\NormalTok{(}
\DataTypeTok{eval =} \OtherTok{TRUE}\NormalTok{,}
\DataTypeTok{echo =} \OtherTok{TRUE}\NormalTok{,}
\DataTypeTok{fig.path =}\NormalTok{ here}\OperatorTok{::}\KeywordTok{here}\NormalTok{(}\StringTok{"figs/"}\NormalTok{),}
\DataTypeTok{message =} \OtherTok{FALSE}\NormalTok{,}
\DataTypeTok{warning =} \OtherTok{FALSE}\NormalTok{,}
\DataTypeTok{error =} \OtherTok{TRUE}\NormalTok{,}
\DataTypeTok{cache =} \OtherTok{TRUE}\NormalTok{,}
\DataTypeTok{comment =} \OtherTok{NA}\NormalTok{,}
\DataTypeTok{tidy =} \OtherTok{TRUE}\NormalTok{,}
\DataTypeTok{fig.width =} \DecValTok{6}\NormalTok{,}
\DataTypeTok{fig.height =} \DecValTok{4}
\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(knitr)}
\NormalTok{hook_output =}\StringTok{ }\NormalTok{knit_hooks}\OperatorTok{$}\KeywordTok{get}\NormalTok{(}\StringTok{"output"}\NormalTok{)}
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\begin{Highlighting}[]
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\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# linewidth css}
\end{Highlighting}
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\textbf{Load Library}
see
\href{https://github.com/sbalci/histopathology-template/blob/master/R/loadLibrary.R}{\texttt{R/loadLibrary.R}}
for the libraries loaded.
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{source}\NormalTok{(}\DataTypeTok{file =}\NormalTok{ here}\OperatorTok{::}\KeywordTok{here}\NormalTok{(}\StringTok{"R"}\NormalTok{, }\StringTok{"loadLibrary.R"}\NormalTok{))}
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\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{generate-fake-data}{%
\subsection{Generate Fake Data}\label{generate-fake-data}}
\textbf{Codes for generating fake data}.\footnote{See
\href{https://github.com/sbalci/histopathology-template/blob/master/childRmd/_02fakeData.Rmd}{\texttt{childRmd/\_02fakeData.Rmd}}
file for other codes}
\textbf{Generate Fake Data}
This code generates a fake histopathological data. Some sources for fake
data generation here\footnote{Synthea The validity of synthetic clinical
data: a validation study of a leading synthetic data generator
(Synthea) using clinical quality measures. BMC Med Inform Decis Mak
19, 44 (2019) \url{doi:10.1186/s12911-019-0793-0}} , here\footnote{\url{https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-019-0793-0}}
, here\footnote{\href{https://synthetichealth.github.io/synthea/}{Synthetic
Patient Generation}} , here\footnote{\href{https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running}{Basic
Setup and Running}} , here\footnote{\href{http://www.mli.gmu.edu/index.php/research/ipdg/}{intelligent
patient data generator (iPDG)}} , here\footnote{\url{https://medium.com/free-code-camp/how-our-test-data-generator-makes-fake-data-look-real-ace01c5bde4a}}
, here\footnote{\url{https://forums.librehealth.io/t/demo-data-generation/203}}
, here\footnote{\url{https://mihin.org/services/patient-generator/}} ,
and here\footnote{lung, cancer, breast datası ile birleştir} .
\textbf{Use
\href{https://github.com/sbalci/histopathology-template/blob/master/R/gc_fake_data.R}{this
code} to generate fake clinicopathologic data}
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{source}\NormalTok{(}\DataTypeTok{file =}\NormalTok{ here}\OperatorTok{::}\KeywordTok{here}\NormalTok{(}\StringTok{"R"}\NormalTok{, }\StringTok{"gc_fake_data.R"}\NormalTok{))}
\end{Highlighting}
\end{Shaded}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{wakefield}\OperatorTok{::}\KeywordTok{table_heat}\NormalTok{(}\DataTypeTok{x =}\NormalTok{ fakedata, }\DataTypeTok{palette =} \StringTok{"Set1"}\NormalTok{, }\DataTypeTok{flip =} \OtherTok{TRUE}\NormalTok{, }\DataTypeTok{print =} \OtherTok{TRUE}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\includegraphics{/Users/serdarbalciold/histopathRprojects/histopathology-template/figs/plot fake data-1.pdf}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{import-data}{%
\subsection{Import Data}\label{import-data}}
\textbf{Codes for importing data.}\footnote{See
\href{https://github.com/sbalci/histopathology-template/blob/master/childRmd/_03importData.Rmd}{\texttt{childRmd/\_03importData.Rmd}}
file for other codes}
\textbf{Read the data}
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(readxl)}
\NormalTok{mydata <-}\StringTok{ }\NormalTok{readxl}\OperatorTok{::}\KeywordTok{read_excel}\NormalTok{(here}\OperatorTok{::}\KeywordTok{here}\NormalTok{(}\StringTok{"data"}\NormalTok{, }\StringTok{"mydata.xlsx"}\NormalTok{))}
\CommentTok{# View(mydata) # Use to view data after importing}
\end{Highlighting}
\end{Shaded}
Add code for import multiple data purrr reduce
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{study-population}{%
\subsection{Study Population}\label{study-population}}
\hypertarget{report-general-features}{%
\subsubsection{Report General Features}\label{report-general-features}}
\textbf{Codes for reporting general features.}\footnote{See
\href{https://github.com/sbalci/histopathology-template/blob/master/childRmd/_04briefSummary.Rmd}{\texttt{childRmd/\_04briefSummary.Rmd}}
file for other codes}
\textbf{Dataframe Report}
\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# Dataframe report}
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\OperatorTok{-}\KeywordTok{contains}\NormalTok{(}\StringTok{"Date"}\NormalTok{)) }\OperatorTok{%>%}\StringTok{ }\NormalTok{report}\OperatorTok{::}\KeywordTok{report}\NormalTok{(.)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
The data contains 250 observations of the following variables:
- ID: 250 entries: 001, n = 1; 002, n = 1; 003, n = 1 and 247 others (0 missing)
- Name: 249 entries: Aadan, n = 1; Aadhyan, n = 1; Abduljaleel, n = 1 and 246 others (1 missing)
- Sex: 2 entries: Male, n = 134; Female, n = 115 (1 missing)
- Age: Mean = 48.99, SD = 14.44, Median = , MAD = 19.27, range: [25, 73], Skewness = 0.03, Kurtosis = -1.28, 1 missing
- Race: 7 entries: White, n = 167; Hispanic, n = 36; Black, n = 23 and 4 others (1 missing)
- PreinvasiveComponent: 2 entries: Absent, n = 194; Present, n = 55 (1 missing)
- LVI: 2 entries: Absent, n = 166; Present, n = 84 (0 missing)
- PNI: 2 entries: Absent, n = 165; Present, n = 84 (1 missing)
- Death: 2 levels: FALSE (n = 69, 27.60%); TRUE (n = 180, 72.00%) and missing (n = 1, 0.40%)
- Group: 2 entries: Treatment, n = 129; Control, n = 120 (1 missing)
- Grade: 3 entries: 3, n = 110; 2, n = 79; 1, n = 60 (1 missing)
- TStage: 4 entries: 4, n = 117; 2, n = 58; 3, n = 53 and 1 other (1 missing)
- AntiX_intensity: Mean = 2.42, SD = 0.64, Median = , MAD = 0.00, range: [1, 3], Skewness = -0.67, Kurtosis = -0.57, 1 missing
- AntiY_intensity: Mean = 2.07, SD = 0.77, Median = , MAD = 1.48, range: [1, 3], Skewness = -0.12, Kurtosis = -1.29, 1 missing
- LymphNodeMetastasis: 2 entries: Absent, n = 155; Present, n = 94 (1 missing)
- Valid: 2 levels: FALSE (n = 135, 54.00%); TRUE (n = 114, 45.60%) and missing (n = 1, 0.40%)
- Smoker: 2 levels: FALSE (n = 132, 52.80%); TRUE (n = 117, 46.80%) and missing (n = 1, 0.40%)
- Grade_Level: 3 entries: high, n = 103; moderate, n = 78; low, n = 68 (1 missing)
- DeathTime: 2 entries: Within1Year, n = 148; MoreThan1Year, n = 102 (0 missing)
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{explore}\OperatorTok{::}\KeywordTok{describe_tbl}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
250 observations with 21 variables
18 variables containing missings (NA)
0 variables with no variance
\end{verbatim}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{ethics-and-irb}{%
\subsection{Ethics and IRB}\label{ethics-and-irb}}
\hypertarget{always-respect-patient-privacy}{%
\subsubsection{Always Respect Patient
Privacy}\label{always-respect-patient-privacy}}
\textbf{Always Respect Patient Privacy}\\
- Health Information Privacy\footnote{\url{https://www.hhs.gov/hipaa/index.html}}~\\
- Kişisel Verilerin Korunması\footnote{\href{https://barandogan.av.tr/blog/ceza-hukuku/kisisel-verilerin-ele-gecirilmesi-yayilmasi-baskasina-verilmesi-sucu.html}{Kişisel
verilerin kaydedilmesi ve kişisel verileri hukuka aykırı olarak verme
veya ele geçirme Türk Ceza Kanunu'nun 135. ve 136. maddesi kapsamında
bizim hukuk sistemimizde suç olarak tanımlanmıştır. Kişisel verilerin
kaydedilmesi suçunun cezası 1 ila 3 yıl hapis cezasıdır. Suçun
nitelikli hali ise, kamu görevlisi tarafından görevin verdiği yetkinin
kötüye kullanılarak veya belirli bir meslek veya sanatın sağladığı
kolaylıktan yararlanılarak işlenmesidir ki bu durumda suçun cezası 1.5
ile 4.5 yıl hapis cezası olacaktır.}}
\noindent
\colorbox{yellow}{
\parbox{\dimexpr\linewidth-2\fboxsep}{
**Always Respect Patient Privacy**
- Health Information Privacy^[https://www.hhs.gov/hipaa/index.html]
- Kişisel Verilerin Korunması^[[Kişisel verilerin kaydedilmesi ve kişisel verileri hukuka aykırı olarak verme veya ele geçirme Türk Ceza Kanunu'nun 135. ve 136. maddesi kapsamında bizim hukuk sistemimizde suç olarak tanımlanmıştır. Kişisel verilerin kaydedilmesi suçunun cezası 1 ila 3 yıl hapis cezasıdır. Suçun nitelikli hali ise, kamu görevlisi tarafından görevin verdiği yetkinin kötüye kullanılarak veya belirli bir meslek veya sanatın sağladığı kolaylıktan yararlanılarak işlenmesidir ki bu durumda suçun cezası 1.5 ile 4.5 yıl hapis cezası olacaktır.](https://barandogan.av.tr/blog/ceza-hukuku/kisisel-verilerin-ele-gecirilmesi-yayilmasi-baskasina-verilmesi-sucu.html)]
}
}
\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center}
\hypertarget{define-variable-types}{%
\subsection{Define Variable Types}\label{define-variable-types}}
\textbf{Codes for defining variable types}.\footnote{See
\href{https://github.com/sbalci/histopathology-template/blob/master/childRmd/_06variableTypes.Rmd}{\texttt{childRmd/\_06variableTypes.Rmd}}
file for other codes}
\textbf{print column names as vector}
\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{dput}\NormalTok{(}\KeywordTok{names}\NormalTok{(mydata))}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
c("ID", "Name", "Sex", "Age", "Race", "PreinvasiveComponent",
"LVI", "PNI", "LastFollowUpDate", "Death", "Group", "Grade",
"TStage", "AntiX_intensity", "AntiY_intensity", "LymphNodeMetastasis",
"Valid", "Smoker", "Grade_Level", "SurgeryDate", "DeathTime")
\end{verbatim}
\hypertarget{find-key-columns}{%
\subsubsection{Find Key Columns}\label{find-key-columns}}
\hypertarget{find-id-and-key-columns-to-exclude-from-analysis}{%
\paragraph{Find ID and key columns to exclude from
analysis}\label{find-id-and-key-columns-to-exclude-from-analysis}}
\begin{verbatim}
vctrs::vec_assert()
dplyr::all_equal()
arsenal::compare()
visdat::vis_compare()
\end{verbatim}
See the code as function in
\href{https://github.com/sbalci/histopathology-template/blob/master/R/find_key.R}{\texttt{R/find\_key.R}}.
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{keycolumns <-}\StringTok{ }\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\KeywordTok{sapply}\NormalTok{(., }\DataTypeTok{FUN =}\NormalTok{ dataMaid}\OperatorTok{::}\NormalTok{isKey) }\OperatorTok{%>%}\StringTok{ }\NormalTok{tibble}\OperatorTok{::}\KeywordTok{as_tibble}\NormalTok{() }\OperatorTok{%>%}\StringTok{ }
\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\KeywordTok{which}\NormalTok{(.[}\DecValTok{1}\NormalTok{, ] }\OperatorTok{==}\StringTok{ }\OtherTok{TRUE}\NormalTok{)) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{names}\NormalTok{()}
\NormalTok{keycolumns}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "ID" "Name"
\end{verbatim}
\hypertarget{variable-types}{%
\subsubsection{Variable Types}\label{variable-types}}
\textbf{Get variable types}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\OperatorTok{-}\NormalTok{keycolumns) }\OperatorTok{%>%}\StringTok{ }\NormalTok{inspectdf}\OperatorTok{::}\KeywordTok{inspect_types}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
# A tibble: 4 x 4
type cnt pcnt col_name
<chr> <int> <dbl> <list>
1 character 11 57.9 <chr [11]>
2 logical 3 15.8 <chr [3]>
3 numeric 3 15.8 <chr [3]>
4 POSIXct POSIXt 2 10.5 <chr [2]>
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\OperatorTok{-}\NormalTok{keycolumns, }\OperatorTok{-}\KeywordTok{contains}\NormalTok{(}\StringTok{"Date"}\NormalTok{)) }\OperatorTok{%>%}\StringTok{ }\NormalTok{describer}\OperatorTok{::}\KeywordTok{describe}\NormalTok{() }\OperatorTok{%>%}\StringTok{ }
\StringTok{ }\NormalTok{knitr}\OperatorTok{::}\KeywordTok{kable}\NormalTok{(}\DataTypeTok{format =} \StringTok{"markdown"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable}[]{@{}lllrrrlrrrl@{}}
\toprule
\begin{minipage}[b]{0.10\columnwidth}\raggedright
.column\_name\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright
.column\_class\strut
\end{minipage} & \begin{minipage}[b]{0.06\columnwidth}\raggedright
.column\_type\strut
\end{minipage} & \begin{minipage}[b]{0.08\columnwidth}\raggedleft
.count\_elements\strut
\end{minipage} & \begin{minipage}[b]{0.06\columnwidth}\raggedleft
.mean\_value\strut
\end{minipage} & \begin{minipage}[b]{0.05\columnwidth}\raggedleft
.sd\_value\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright
.q0\_value\strut
\end{minipage} & \begin{minipage}[b]{0.05\columnwidth}\raggedleft
.q25\_value\strut
\end{minipage} & \begin{minipage}[b]{0.05\columnwidth}\raggedleft
.q50\_value\strut
\end{minipage} & \begin{minipage}[b]{0.05\columnwidth}\raggedleft
.q75\_value\strut
\end{minipage} & \begin{minipage}[b]{0.06\columnwidth}\raggedright
.q100\_value\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Sex\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Female\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Male\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Age\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
numeric\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
double\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
48.991968\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
14.4417607\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
25\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
36\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
50\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
62\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
73\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Race\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Asian\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
White\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
PreinvasiveComponent\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Absent\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Present\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
LVI\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Absent\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Present\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
PNI\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Absent\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Present\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Death\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
FALSE\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
TRUE\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Group\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Control\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Treatment\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Grade\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
1\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
3\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
TStage\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
1\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
4\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
AntiX\_intensity\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
numeric\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
double\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
2.421687\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
0.6435878\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
1\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
2\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
3\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
3\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
3\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
AntiY\_intensity\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
numeric\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
double\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
2.068273\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
0.7668520\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
1\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
1\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
2\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
3\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
3\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
LymphNodeMetastasis\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
Absent\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Present\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Valid\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
FALSE\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
TRUE\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Smoker\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
logical\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
FALSE\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
TRUE\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
Grade\_Level\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
high\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
moderate\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.10\columnwidth}\raggedright
DeathTime\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
character\strut
\end{minipage} & \begin{minipage}[t]{0.08\columnwidth}\raggedleft
250\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright
MoreThan1Year\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.05\columnwidth}\raggedleft
NA\strut
\end{minipage} & \begin{minipage}[t]{0.06\columnwidth}\raggedright
Within1Year\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\textbf{Plot variable types}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\OperatorTok{-}\NormalTok{keycolumns) }\OperatorTok{%>%}\StringTok{ }\NormalTok{inspectdf}\OperatorTok{::}\KeywordTok{inspect_types}\NormalTok{() }\OperatorTok{%>%}\StringTok{ }\NormalTok{inspectdf}\OperatorTok{::}\KeywordTok{show_plot}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\includegraphics{/Users/serdarbalciold/histopathRprojects/histopathology-template/figs/variable type plot inspectdf-1.pdf}
\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# https://github.com/ropensci/visdat}
\CommentTok{# http://visdat.njtierney.com/articles/using_visdat.html}
\CommentTok{# https://cran.r-project.org/web/packages/visdat/index.html}
\CommentTok{# http://visdat.njtierney.com/}
\CommentTok{# visdat::vis_guess(mydata)}
\NormalTok{visdat}\OperatorTok{::}\KeywordTok{vis_dat}\NormalTok{(mydata)}
\end{Highlighting}
\end{Shaded}
\includegraphics{/Users/serdarbalciold/histopathRprojects/histopathology-template/figs/variable type plot visdat-1.pdf}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{explore}\OperatorTok{::}\KeywordTok{explore_tbl}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\includegraphics{/Users/serdarbalciold/histopathRprojects/histopathology-template/figs/variable type plot explore-1.pdf}
\hypertarget{define-variable-types-1}{%
\subsubsection{Define Variable Types}\label{define-variable-types-1}}
\hypertarget{find-character-variables}{%
\paragraph{\texorpdfstring{Find \texttt{character}
variables}{Find character variables}}\label{find-character-variables}}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{characterVariables <-}\StringTok{ }\NormalTok{mydata }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(}\OperatorTok{-}\NormalTok{keycolumns) }\OperatorTok{%>%}\StringTok{ }\NormalTok{inspectdf}\OperatorTok{::}\KeywordTok{inspect_types}\NormalTok{() }\OperatorTok{%>%}\StringTok{ }
\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{filter}\NormalTok{(type }\OperatorTok{==}\StringTok{ "character"}\NormalTok{) }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{select}\NormalTok{(col_name) }\OperatorTok{%>%}\StringTok{ }\NormalTok{dplyr}\OperatorTok{::}\KeywordTok{pull}\NormalTok{() }\OperatorTok{%>%}\StringTok{ }
\StringTok{ }\KeywordTok{unlist}\NormalTok{()}
\NormalTok{characterVariables}
\end{Highlighting}