OpenSciencePandemic/PMC_data_parsing.m at master · lonnibesancon/OpenSciencePandemic · GitHub

Name: OpenSciencePandemic/PMC_data_parsing.m at master · lonnibesancon/OpenSciencePandemic · GitHub
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%%Runs on Matlab R2018b
%%Author: Maxime Deforet CC-BY-SA 2020

%%Identify blocks in raw data

str = fileread( '/Users/maxdeforet 1/Downloads/pmc_result.txt');
str=splitlines(str);
blocks_pmc = find(contains( str, 'PMC - PMC' ));
blocks_received = find(contains( str, '[received]' ));
blocks_accepted = find(contains( str, '[accepted]' ));
blocks_doi = find(contains( str, '[doi]' ));
blocks_articletype = find(contains( str, 'PT - ' ));

T = table('Size',[numel(blocks_pmc),6],'VariableTypes',{'string','string','string','datetime','datetime','double'},'VariableNames',{'PMCID','DOI','ArticleType','Received','Accepted','ReviewTime'});
%%
for i=1:numel(blocks_pmc)-1
% progress bar:
if mod(i,100)==0
i
end
 counter=0;

% PMC:
 pmc=str{blocks_pmc(i)};
 Tpmc=pmc(7:end);

% DOI:
 ff = find(blocks_doi<blocks_pmc(i+1) & blocks_pmc(i)<blocks_doi);
if ~isempty(ff)
 doi = str{blocks_doi(ff)};
 Tdoi = doi(7:end-6);
else
 Tdoi='';
end

% Article Type:
 ff = find(blocks_articletype<blocks_pmc(i+1) & blocks_pmc(i)<blocks_articletype);
if ~isempty(ff)
 arttype = str{blocks_articletype(ff(1))};
 arttype = arttype(7:end);
if length(ff)==2
 arttype2 = str{blocks_articletype(ff(2))};
 arttype = [arttype,' / ',arttype2(7:end)];
end
 Tarttype =arttype;
else
 Tarttype='';
end

% Received:
 ff = find(blocks_received<blocks_pmc(i+1) & blocks_pmc(i)<blocks_received);
if ~isempty(ff)
 rec = str{blocks_received(ff)};
if rec(18)=='['
 Trec = datetime(rec(7:16),'InputFormat','yyyy/MM/dd');
 counter=counter+1;
else
 Trec=NaT;
end

else
 Trec=NaT;
end

% Accepted:
 ff = find(blocks_accepted<blocks_pmc(i+1) & blocks_pmc(i)<blocks_accepted);
if ~isempty(ff)
 acc = str{blocks_accepted(ff)};
if acc(18)=='['
 Tacc = datetime(acc(7:16),'InputFormat','yyyy/MM/dd');
 counter=counter+1;
else
 Tacc=NaT;
end
else
 Tacc=NaT;
end

% Review time
ifcounter==2
 Tday=days(Tacc-Trec);
else
 Tday=NaN;
end
 T(i,:)={Tpmc,Tdoi,Tarttype,Trec,Tacc,Tday};
end


%%Only zero day
T0=T;
T0(isnan(T.ReviewTime) |T.ReviewTime>0 |T.ReviewTime<0 |T.Accepted==NaT,:)=[];
writetable(T0,'ReviewTime_0day.csv')

%%Only one day
T1=T;
T1(isnan(T.ReviewTime) |T.ReviewTime>1 |T.ReviewTime<1 |T.Accepted==NaT,:)=[];
writetable(T1,'ReviewTime_1day.csv')