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eda.sthlp
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{smcl}
{* *! version 0.0.0 30OCT2015}{...}
{cmd:help eda}
{hline}
{marker edati}{p 2 2 2}{title:{hi:EDA}}{p_end}
{p 4 4 4}{hi:eda {hline 2}} A program for the automated generation of graphs and
tables used in Exploratory Data Analyses ({help eda##edarefs:Tukey (1977)}. {p_end}
{marker edasyntax}{p 2 2 2}{title:{hi:Syntax}}{p_end}
{p 4 4 4}{cmd:eda} [{opt varlist}] [{opt using}] {ifin} ,
{cmdab:o:utput(}{it:string}{opt )} {cmdab:r:oot(}{it:string}{opt )}
[{cmdab:id:vars(}{it:varlist}{opt )} {cmdab:str:ok}[({it:varlist})]
{cmdab:minn:size(}{it:integer}{opt )} {cmdab:min:cat(}{it:integer}{opt )}
{cmdab:max:cat(}{it:integer}{opt )} {cmdab:cat:vars(}{it:varlist}{opt )}
{cmdab:cont:vars(}{it:varlist}{opt )} {cmdab:auth:orname(}{it:string}{opt )}
{cmdab:repo:ortname(}{it:string}{opt )}
{cmd:scheme(}{it:string}{opt )} {cmd:keepgph}
{cmdab:grlabl:ength(}{it:integer}{opt )} {cmdab:miss:ing} {cmdab:perc:ent}
{cmdab:nobargr:aphs} {cmdab:bargra:phopts(}{it:string}{opt )}
{cmdab:nopiec:harts} {cmdab:piech:artopts(}{it:string}{opt )}
{cmdab:nohisto:grams} {cmdab:histog:ramopts(}{it:string}{opt )}
{cmdab:kdens:ity} {cmdab:kdenso:pts(}{it:string}{opt )}
{cmdab:fivenum:sum} {cmdab:fnso:pts(}{it:string}{opt )}
{cmdab:nodistro:plots} {cmdab:distrop:lotopts(}{it:string}{opt )}
{cmdab:noladder:plots} {cmdab:noscat:terplots}
{cmd:lfit}[({it:string})] {cmd:qfit}[({it:string})]
{cmd:lowess}[({it:string})] {cmd:fpfit}[({it:string})]
{cmd:lfitci}[({it:string})] {cmd:qfitci}[({it:string})]
{cmd:fpfitci}[({it:string})] {cmdab:nobox:plots} {cmd:nomosaic}
{cmdab:noheat:map} {cmdab:nobubble:plots} {cmdab:weight:type(}{it:int}{opt )}
{cmdab:comp:ile} {cmdab:pdfl:atex(}{it:string}{opt )}
]
{marker edadesc}{p 2 2 2}{title:{hi:Description}}{p_end}
{p 4 4 4}{cmd:eda} is a program used to automate the production of an exploratory
data analysis "report" of a data set. With minimal user intervention, the
program will use decision rules to classify variables as continuous vs categorical
and use these variable lists to generate appropriate visualizations and summary
statistics based on the properties of categorical and continuous variables. For
categorical variables, this means using bar graphs, pie charts, and mosaic plots
to show univariate and bivariate distributions - as well as one and twoway
tables of frequencies and percentages. For continuous data, the program creates
histograms (with options to overlay a kernel density plot and to include vertical
reference lines showing Tukey's five number summary), distribution plots (e.g.,
quantile/q-norm, chi-norm, p-norm, etc...), ladder of powers graphs, scatterplots
(with options to add fractional polynomial smoothers [with/without CI], quadratic
smoothers [with/without CI], linear smoothers [with/without CI], and lowess
smoothers [without CI]), weighted scatterplots (a.k.a., bubble plots), and a
heatmap to illustrate the Pearson correlations. Additionally, conditional
distributions are also illustrated via box plots and tables of conditional
descriptive statistics. All of the output is place into separate subdirectories
for graphs and tables and a single LaTeX source document is created to organize
all of the output in a single document.{p_end}
{p 4 4 4}This program has several dependencies which you can find {help eda##edadeps:here}.
If these programs are not available, the program will ask if you would like to
install them. If any response is no, the program will exit and not continue to
run. If the answer is yes to all, it will install each of the dependencies
sequentially. {p_end}
{p 4 4 4}The help file is divided into several segments that hopefully will make
it easier for you to find information quickly about the options you need/want to
use. {help eda##edaexplain:Required Arguments} contains information about
parameters that must always have a value for the program to run. {help eda##edaopts:Optional Arguments}
is the start of the section of the help file listing all of the optional parameters.
{help eda##classify:Variable Classification} contains arguments related to the way
the program classifies variables as categorical/continuous. {help eda##edaglobals:Global Options}
contains information about options that affect the resulting LaTeX document or the
production of graphs on a global scale (e.g., everything the program does).
{help eda##edacatdist:Univariate Graphs - Categorical Variables} contains information
about the options available for the control/rendering of bar graphs/pie charts.
{help eda##edacontdist:Univariate Graphs - Continuous Variables} contains information
about the options available for the control/rendering of histograms, ladder of powers
graphs, and distribution quality graphs. {help eda##edascatter:Bivariate Graphs - Continuous Variables} contains
information about the production/rendering of scatterplots and the associated smoothers available for
scatterplots. {help eda##edaboxp:Bivariate Graphs - Conditional Distributions} contains the option
used to control the production of box plots. {help eda##edamos:Bivariate Graphs - Categorical Variables}
contains information used to control the production of mosaic - or {help eda##edadeps:spineplots}.
{help eda##edamvcont:Multivariate Graphs - Continuous Variables} contains information used to
control options related to bubble plots and heatmaps. {help eda##edatex:LaTeX Options} contains
information about the options used to automatically compile the LaTeX source code and/or
method to specify the path to the LaTeX binary when creating the compilation script. {p_end}
{marker edaexplain}{p 2 2 2}{title:{hi:Required Arguments}}{p_end}{break}
{p 4 4 8}The following options are required for the program to run and must be
supplied by the end user. {p_end}{break}
{p 4 4 8}{cmdab:o:utput} is used to supply the program with the name stub to use
for the LaTeX source code file. {it:Note: Do not include the file extension in this argument.}
For example, o("eda-report") is a suitable value, but o("eda-report.tex") is not.
The program appends the file extension to this name in the background.{p_end}
{p 4 4 8}{cmdab:r:oot} is used to tell the program where to store the output and
create two subdirectories (graphs and tables). If the directory passed to this
argument does not already exist it will be created. If the directory exists,
the user will be prompted with a series of questions asking if the user wants to
delete individual files in the directory; if the directory is empty, the user
will be asked if they would like to delete the directory and rebuild it.{p_end}
{marker edaopts}{dlgtab 4 8:Optional Arguments}{break}
{p 4 4 8}These arguments mark the start of the optional arguments that allow the
user to control what output they would like and provide user defined methods for
variable classification. {p_end}
{p 8 8 8}{cmdab:id:vars} is an optional argument that takes a variable list
containing variables that should be excluded from graphs. For example, if the
data set includes a numeric patient ID, this option would prevent that variable
from being included in subsequent graphs/tables since the variable is nominal and
not intervallic/ratio scale in nature.{p_end}
{p 8 8 8}{cmdab:str:ok} is an optional argument used to allow string formatted
variables to be included in the program. Without a variable list, this argument
will use all string variables and with a variable list will only use the variables
supplied by the end user.{p_end}
{marker edaclassify}{dlgtab 8 8:Variable Classification}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}These options allow the user to control how variables are classified
as categorical vs continuous and the minimum number of non-missing values
required for a variable to be included in subsequent analysis. For variable
classification there are three methods available: User provided variable lists,
user defined criteria, or the program defaults. The program defaults to defining
a variable as categorical if it has two to nine distinct values and a variable is
classified as continuous if it has 10 or more distinct values. Since there are
heirarchical units that may have > 9 values, the user can also tell the program
how to classify the variables in the dataset manually by passing variable lists
to the catvar and contvar options. {p_end}{break}
{p 14 14 14}{cmdab:minn:size} is an option used to specify the minnimum number
of non-missing observations that must be present for a variable to be classified.
For example, if a given variable is missing for all but 10 observations, setting
this parameter to a value of 20 would exclude it from all subsequent output. {p_end}
{p 14 14 14}{cmdab:min:cat} is an option to set the lower threshold of unique values
for a variable to be classified as categorical. This value defaults to 2. {p_end}
{p 14 14 14}{cmdab:max:cat} is an option to set the upper threshold of unique values
for a variable to be classified as categorical. This value defaults to 9. {p_end}
{p 14 14 14}{cmdab:cat:vars} is an option to define variables to be treated as
categorical by the program. If an argument is passed to this and the contvars
parameter it will override the mincat and maxcat parameters. {p_end}
{p 14 14 14}{cmdab:cont:vars} is an option to define variables to be treated as
continuous by the program. If an argument is passed to this and the catvars
parameter it will override the mincat and maxcat parameters. {p_end}
{marker edaglobals}{dlgtab 8 8:Global Options}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}These options affect the performance and/or aesthetics of {hi:all}
graphs. The program was designed specifically to leverage the power/flexibility
provided by {stata `"net desc brewscheme, from("http://www.paces-consulting.org/stata")"': brewscheme}.
{search brewscheme} provides a flexible interface to help users define customized
scheme files with a series of aesthetic adjustments from the default Stata
graphics/schemes. Although not using a scheme will still result in consistent
graph aesthetics (due to the use of default schemes), this is the easiest possible
way to control the aesthetics of the graphs created by this program. {p_end}{break}
{p 14 14 14}{cmdab:auth:orname} is an optional argument used to pass an author
name to the LaTeX file Title Page. If no value is specified the program will
use the value returned in the macro c(username).{p_end}
{p 14 14 14}{cmdab:repo:rtname} is an optional argument used to pass a subtitle
to the LaTeX file Title page. If no value is specified the program will use the
name of the file currently loaded in memory while the program is being executed. {p_end}
{p 14 14 14}{cmd:scheme} is an option used to pass a scheme argument to all of
the underlying graph commands. I strongly recommend using {search brewscheme}
to define a customized scheme file that meets your unique aesthetic and/or
visual needs and passing that schemefile to this parameter.{p_end}
{p 14 14 14}{cmd:keepgph} is an optional argument used to save the graphs as
Stata GPH files. If this is not specified, the graphs are only saved as PDF
files.{p_end}
{p 14 14 14}{cmdab:grlabl:ength} is an optional argument used to define how long
a variable label should be before it is split into multiple lines when used in
graphs. The program stores strings used for the titles temporarily in the
variable characteristics. If no value is passed, the program will insert line
breaks at 50 characters. This is done to help keep titles within the graph
region and to provide some consistency in the formatting of the titles. {p_end}
{marker edacatdist}{dlgtab 8 8:Univariate Graphs - Categorical Variables}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:miss:ing} is a parameter passed to the bar, boxplot, pie chart,
and mosaic plots to include missing values as categories. It is also used when
identifying the number of distinct values a variable may take.{p_end}
{p 14 14 14}{cmdab:perc:ent} is used to specify whether bar graphs and pie charts
should display counts or percentages. If the option is selected both graph types
will display percentages. Otherwise the graphs will display frequencies. {p_end}
{p 14 14 14}{cmdab:nobargr:aphs} is an option used to suppress the production of
bar graphs for categorical variables by {help eda}. {p_end}
{p 14 14 14}{cmdab:bargra:phopts} is an option to provide additional user options
to the underlying bar graph commands. The scheme, missing, legend, title, notes,
over, and asyvar options are already specified and cannot be modified with this
option. The most useful way the option could be used is to set the display of
bar labels and/or to format/render the values displayed differently. {p_end}
{p 14 14 14}{cmdab:nopiec:harts} is an option used to suppress the production of
pie charts for categorical variables by {help eda}. {p_end}
{p 14 14 14}{cmdab:piech:artopts} is used to pass aesthetic options to the
{help graph_pie:pie chart} graph command.{p_end}
{marker edacontdist}{dlgtab 8 8:Univariate Graphs - Continuous Variables}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:nohisto:grams} is an option used to suppress the production
of histograms for continuous variables by {help eda}. {p_end}
{p 14 14 14}{cmdab:histog:ramopts} is used to pass optional arguments to the
graph command creating the histograms. {p_end}
{p 14 14 14}{cmdab:kdens:ity} is an option used to request a kernel density plot
be overlaid on the histogram. {p_end}
{p 14 14 14}{cmdab:kdenso:pts} is an option used to pass arguments to
{help kdensity:kdensity} that control the rendering of the kernel density
estimates overlaid on the histogram.{p_end}
{p 14 14 14}{cmdab:fivenum:sum} is an option used to add reference lines to the
histogram that show Tukey's Five Number Summary in the background of the graph.{p_end}
{p 14 14 14}{cmdab:fnso:pts} is an option to pass arguments to the
{help added_line_options:xline} arguments used to draw the locations of the five
number summary with the histograms. {p_end}
{p 14 14 14}{cmdab:nodistro:plots} is an option used to suppress the production
of distribution quality/assumption plots for continuous variables by {help eda}.
{p_end}
{p 14 14 14}{cmdab:distrop:lotopts} is used to pass options for the rendering of
the chi squared probability and quantile plots. To pass the degrees of freedom
to both of these graphs you would use: distrop("df(3)" "df(2)") as an example.
The underlying program uses the first word of this argument for the Chi squared
quantiles plot and the second word is used for the Chi squared probability plots.
{p_end}
{p 14 14 14}{cmdab:noladder:plots} is an option used to suppress the production
of ladder of powers graphs for continuous variables by {help eda}. {p_end}
{marker edascatter}{dlgtab 8 8:Bivariate Graphs - Continuous Variables}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:noscat:terplots} is an option used to suppress the production
of scatterplots for all pairs of continuous variables by {help eda}. {p_end}
{p 14 14 14}{cmd:lfit} is an option to request a linear smoother be overlaid on
the scatterplot. Additional options to control the aesthetics for the linear
smoother can also be passed (see {help twoway_lfit:lfit} for additional
information). {p_end}
{p 14 14 14}{cmd:qfit} is an option to request a quadratic smoother be drawn with
the scatterplot. Additional options to control the aesthetics for the quadratic
smoother can also be passed (see {help twoway_qfit:qfit} for additional
information). {p_end}
{p 14 14 14}{cmd:lowess} is an option to request a lowess - or non-parametric
smoother - be drawn with the scatterplot. Additional options to control the
aesthetics for the lowess smoother can also be passed (see
{help twoway_lowess:lowess} for additional information). {it:Note: the lowess smoother is also called a "loess" smoother in some statistical packages.}{p_end}
{p 14 14 14}{cmd:fpfit} is an option to request a fractional polynomial smoother
be drawn with the scatterplot. Additional options to control the aesthetics for
the fractional polynomial smoother can also be passed (see
{help twoway_fpfit:fpfit} for additional information). {p_end}
{p 14 14 14}{cmd:lfitci} is an option to request a linear line of best fit
smoother with confidence intervals be drawn under the scatterplot. Additional
options to control the aesthetics for the linear smoother and confidence
intervals can also be passed (see {help twoway_lfitci:lfitci} for additional
information). {p_end}
{p 14 14 14}{cmd:qfitci} is an option to request a quadratic line of best fit
smoother with confidence intervals be drawn under the scatterplot. Additional
options to control the aesthetics for the quadratic smoother and confidence
intervals can also be passed (see {help twoway_qfitci:qfitci} for
additional information). {p_end}
{p 14 14 14}{cmd:fpfitci} is an option to request a fractional polynomial
smoother with confidence intervals be drawn under the scatterplot. Additional
options to control the aesthetics for the fractional polynomial smoother and
confidence intervals can also be passed (see {help twoway_fpfitci:fpfitci} for
additional information). {p_end}
{marker edaboxp}{dlgtab 8 8:Bivariate Graphs - Conditional Distributions}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:nobox:plots} is an option used to suppress the production
of box and whisker plots for each combination of continuous by categorical
variables by {help eda}. {p_end}
{marker edamos}{dlgtab 8 8:Bivariate Graphs - Categorical Variables}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmd:nomosaic} is an option used to suppress the production of
mosaic - or {help spineplot:spineplots} - for all pairs of categorical variables
by {help eda}. {p_end}
{marker edamvcont}{dlgtab 8 8:Multivariate Graphs - Continuous Variables}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:noheat:map} is an option used to suppress the production
of a heatmap used to illustrate pairwise correlations between all continuous
variables by {help eda}. {p_end}
{p 14 14 14}{cmdab:nobubble:plots} is an option used to suppress the production
of weighted scatterplots - or Bubble Plots - for all pairs of continuous
variables by {help eda}. {p_end}
{p 14 14 14}{cmdab:weight:type} is an optional parameter used to specify a method
to transform the weight variable of bubble plots. The acceptable arguments and
their meanings are: {p_end}
{marker edawgts}{col 20}{hline 80}
{col 20}{hi:Argument} {col 35}{hi: Transformation}
{col 20}{hline 80}
{col 20}0{col 35}{it:Raw Data (not transformed)}
{col 20}1{col 35}{it:Natural Logarithm of the Variable}
{col 20}2{col 35}{it:Square Root of the Variable}
{col 20}3{col 35}{it:Exponential Function of the Variable}
{col 20}4{col 35}{it:Inverse of the Logit Function of the Variable}
{col 20}5{col 35}{it:Complementary Log Log of the Variable}
{col 20}6{col 35}{it:Digamma Function of the Variable}
{col 20}7{col 35}{it:Inverse of the Complementary Log Log of the Variable}
{col 20}8{col 35}{it:Natural Logarithm of the Gamma Function of the Variable}
{col 20}9{col 35}{it:Base 10 Logarithm of the Variable}
{col 20}10{col 35}{it:Log of the Odds-Ratio of the Variable}
{col 20}11{col 35}{it:2nd Derivative of the Log of the Gamma Function of the Variable}
{col 20}{hline 80}{break}
{p 14 14 14}The transformations are applied to copies of the original data at
runtime and the copies are removed after the graph is created. Changing the
weighting of the variable will affect the scaling of the "bubbles" or points in
the weighted scatterplot. These variables are used as arguments to the {help weight}
parameter of the scatterplot commands (specifically entered as {hi:aweight}s).{p_end}
{marker edatex}{dlgtab 8 8:LaTeX Options}{p_end}{break}
{p 20 20 20}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 14 14 14}{cmdab:comp:ile} is an option used to write a batch (if called from
a machine running Windoze) or bash (for any *nix-based system) script to compile
the LaTeX source code document and subsequently to execute the script. If called
from a *nix-based platform, the {help shell:shellout} will fail if the user does
not have sudo permissions w/o password entry. {subscript:{it:This is required to modify the file permissions and make it executable for all users with a call to ! sudo chmod a+x scriptname.sh.}} {p_end}
{p 14 14 14}{cmdab:pdfl:atex} is an option used to specify the location of the
pdflatex binary. If pdflatex is already on your operating system's path, you
should not need to specify this option (the script will just call pdflatex on
any *nix-based system or pdflatex.exe on Windoze).{p_end}
{marker edarefs}{p 2 2 2}{title:{hi:References}}{p_end}{break}
{p 4 4 4}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 4 4 8}Tukey, J. W. (1977). {it:Exploratory Data Analysis}. {p_end}
{marker edaex}{p 2 2 2}{title:{hi:Examples}}{p_end}{break}
{p 4 4 4}{help eda##edasyntax:Syntax} {space 15} {help eda##edadesc:Description} {space 15} {help eda##edaex:Examples} {p_end}{break}
{p 4 4 8}All of these examples will assume the same starting point: {stata sysuse auto.dta, clear}
since the data set is smaller/easier to manage. You should also install {search brewscheme} and
create an example palette called {hi: edatest} that will be used in the following
examples. My version of this file was created using: {p_end}
{p 8 8 8}brewscheme, scheme(edatest) const(orange) cone(blue) consat(20) scatst(set1) scatc(8) piest(pastel2) piec(6) barst(pastel1) barc(7) linest(accent) linec(7) areast(set2) areac(5) boxst(pastel2) boxc(6) somest(paired) somec(12) {p_end}
{p 4 4 8}The most minimal example is:{p_end}
{p 8 8 8}{stata sysuse auto.dta, clear}{p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp}{p_end}
{p 4 4 8}To apply the styling from the scheme created above to the graphs, simply
pass the name of the scheme to the scheme parameter: {p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest)}{p_end}
{p 4 4 8}To add reference lines for Tukey's five number summary to histograms:{p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest) fivenum}{p_end}
{p 4 4 8}To suppress the creation of a heatmap of the correlations: {p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest) noheat}{p_end}
{p 4 4 8}To use log transformed variable values for weights in the bubble plots: {p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest) weight(1)}{p_end}
{p 4 4 8}To get percentages printed in the bargraphs and pie charts: {p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest) perc}{p_end}
{p 4 4 8}To suppress the creation of bar graphs and pie charts: {p_end}
{p 8 8 8}{stata eda, r(`"`c(pwd)'/edaexamples"') o("minexample") comp scheme(edatest) nobargr nopiec}{p_end}
{marker edaack}{p 2 2 2}{title:{hi:Acknowledgements}}{p_end}
{p 4 4 8}This program makes use of several user written commands including: {p_end}
{marker edadeps}{col 10}{hline 80}
{col 10}{hi:Program} {col 35}{hi: Authors}
{col 10}{hline 80}
{col 10}{search brewscheme:brewscheme}{col 35}{it:Billy Buchanan}
{col 10}{search tuples:tuples}{col 35}{it:Joseph N. Luchman & Nick J. Cox}
{col 10}{search spineplot:spineplot}{col 35}{it:Nick J. Cox}
{col 10}{search estout:estout}{col 35}{it:Ben Jann}
{col 10}{hline 80}
{marker contact}{p 2 2 2}{title:{hi:Author}}{p_end}
{p 4 4 4}Billy Buchanan {p_end}
{p 4 4 4}Data Scientist{p_end}
{p 4 4 4}{browse "http://mpls.k12.mn.us":Minneapolis Public Schools}{p_end}