sam::Journal

Journal Class. More...

#include <Journal.h>

Public Functions

	Name
	Journal() =default
	~Journal() =default
	Journal(json & journal_config) Constructs a Journal from a JSON object.
bool	review(std::vector< Submission > & s) Review the Submission.
void	accept(const std::vector< Submission > & s) Accepts the Submission.
void	reject(const std::vector< Submission > & s) Rejects the Submission.
bool	isStillAccepting() const Indicates whether the Journal is still accepting outcomes or not.
size_t	nStudies() const Returns the number of studies.
size_t	nSubmissions() const Returns the number of publications.
size_t	nRejected() const Returns the number of rejected publications.
void	saveMetaAnalysis() Saves MetaAnalysis Results.
void	saveSummaries() Saves Overall Summaries.
void	storeMetaAnalysisResult(const MetaAnalysisOutcome & res) Stores the MetaAnalysisOutcome.
void	savePublicationsPerSimSummaries() Saves the Per Simulation summary of Publications.
void	clear() Clear the Journal.
void	reset() Completely resets the Journal.
void	prepareForMetaAnalysis() Prepares the Journal for running meta-analysis.
void	runMetaAnalysis() Runs the meta-analysis methods.
void	updateMetaStatsRunners() Updates the overall stats runners.
std::vector< std::string >	Columns() Returns Journal's CSV header.

Public Attributes

	Name
std::vector< Submission >	publications_list List of all accepted submissions, i.e., outcomes.
std::vector< Submission >	rejection_list Rejected Submissions.
arma::Row< float >	yi
arma::Row< float >	vi The variance of the accepted submissions.
arma::Row< float >	wi The weight of the accepted submissions, computed as 1./vi;.
std::unique_ptr< ReviewStrategy >	review_strategy Journal's Selection Model/Strategy.

Detailed Description

class sam::Journal;

Journal Class.

The Journal class mimics the behavior of a Journal. It deals with new publications as they are being submitted for review. It is equipped with a review strategy which is used to make a decision over the destiny of the newly submitted manuscript, ie., being accepted or rejected.

Additionally, it handles the meta-analysis calculation and reporting of those at the end of the simulation.

Public Functions Documentation

function Journal

Journal() =default

function ~Journal

~Journal() =default

function Journal

explicit Journal(
    json & journal_config
)

Constructs a Journal from a JSON object.

Parameters:

• journal_config The journal configuration

This makes sure that everything in the Journal are set up correctly:

• Instantiates the Review Strategy
• Prepares the output files, and their column names
• Prepares the stat runners based on users preference

Removing the higher level information because I don't want them to be written to the config file again.

function review

bool review(
    std::vector< Submission > & s
)

Review the Submission.

Parameters:

• subs A list of submissions

Return: Returns true if the submission is accepted, otherwise it returns false.

Sends the submission to the review strategy, and based on its verdict it either accept() or reject() the submission.

function accept

void accept(
    const std::vector< Submission > & s
)

Accepts the Submission.

Parameters:

• subs A list of submissions

Adds the accepted submission to the list of publications, and updates some of the necessary internals of the Journal to be able to keep track of the number of publications, studies, etc.

function reject

void reject(
    const std::vector< Submission > & s
)

Rejects the Submission.

Parameters:

• subs A list of submissions

Adds the rejected submissions to the list of rejected submissions, and keeps the internal of the Journal up-to-date.

function isStillAccepting

inline bool isStillAccepting() const

Indicates whether the Journal is still accepting outcomes or not.

function nStudies

inline size_t nStudies() const

Returns the number of studies.

function nSubmissions

inline size_t nSubmissions() const

Returns the number of publications.

function nRejected

inline size_t nRejected() const

Returns the number of rejected publications.

function saveMetaAnalysis

void saveMetaAnalysis()

Saves MetaAnalysis Results.

Saves the meta analytics results.

function saveSummaries

void saveSummaries()

Saves Overall Summaries.

Saves the publications and meta stats runners.

function storeMetaAnalysisResult

void storeMetaAnalysisResult(
    const MetaAnalysisOutcome & res
)

Stores the MetaAnalysisOutcome.

Adds the given meta analysis outcome to the list of collected meta-analysis.

function savePublicationsPerSimSummaries

void savePublicationsPerSimSummaries()

Saves the Per Simulation summary of Publications.

Saving the runner statistics of each batch of publications in Journal.

Resetting the runner statistics

function clear

void clear()

Clear the Journal.

Clears the history of publications, rejections, and runner statistics...

function reset

void reset()

Completely resets the Journal.

In addition to clearing the Journal, it resets some of the overall stats runners that are not usually being cleared by clear()

function prepareForMetaAnalysis

void prepareForMetaAnalysis()

Prepares the Journal for running meta-analysis.

This prepares the Journal for running meta-analysis. I mainly designed this to introduce some caching that I don't have to compute everything every time. So, with this, Journal prepares the vi, yi, and wi once and pass them to the meta analysis methods.

function runMetaAnalysis

void runMetaAnalysis()

Runs the meta-analysis methods.

Loops through the meta-analysis methods and run them, and update their stats runners

function updateMetaStatsRunners

void updateMetaStatsRunners()

Updates the overall stats runners.

Updates the overall meta stats runners.

function Columns

static std::vector< std::string > Columns()

Returns Journal's CSV header.

Public Attributes Documentation

variable publications_list

std::vector< Submission > publications_list;

List of all accepted submissions, i.e., outcomes.

variable rejection_list

std::vector< Submission > rejection_list;

Rejected Submissions.

variable yi

arma::Row< float > yi;

Caching variables The effect sizes of the accepted submissions.

variable vi

arma::Row< float > vi;

The variance of the accepted submissions.

variable wi

arma::Row< float > wi;

The weight of the accepted submissions, computed as 1./vi;.

variable review_strategy

std::unique_ptr< ReviewStrategy > review_strategy;

Journal's Selection Model/Strategy.

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Updated on 29 June 2021 at 16:13:46 CEST

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Last update: 2021-09-18