diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..d392f0e --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +*.jar diff --git a/PeerReviewGPS-v07.nlogo b/PeerReviewGPS-v07.nlogo new file mode 100644 index 0000000..813155f --- /dev/null +++ b/PeerReviewGPS-v07.nlogo @@ -0,0 +1,2192 @@ +; NOTES: +; Instalation notes: +; pr-utils is a custom extension that must be present in the Netlogo extensions folder in a directory of the same name. +; A folder called "results" has to be present in the same location of the main netlogo file. This directory is used to store detailed results of each simulation. +; Every simulation execution rewrites the content of the "results" folder + +; The code blocks marked as ------ PR ------ are exectued only in the Peer review simulation +; The code blocks marked as ------ REP ----- are executed only in the Reputation simulation +; The code blocks marked as ------ PR-REP -- are executed in both simulations, Peer review and Reputation + + +; primary entities +breed [scientists scientist] +scientists-own[role quality productivity tmp-prod initial-reputation reputation id age] +breed [papers paper] +papers-own [quality published? inherited-reputation reputation age curr-pr-reads curr-rep-reads tot-pr-reads tot-rep-reads mistaken?] +breed [journals journal] +journals-own [editor quality-average quality] + +; support-connection entities +directed-link-breed [read-prs read-pr] +directed-link-breed [read-reps read-rep] +read-reps-own [score] +breed [drafts draft] +drafts-own [quality] +breed [obsoletes obsolete] +obsoletes-own [quality published? inherited-reputation reputation age curr-pr-reads curr-rep-reads tot-pr-reads tot-rep-reads] +undirected-link-breed [paper-to-authors paper-to-author] +undirected-link-breed [reviewers reviewer] +directed-link-breed [they-appear-in appears-in] + +; NOTE: pr-utils is a custom extension that must be present in the Netlogo extensions folder in a directory of the same name. +extensions [pr-utils rnd stats csv] + +globals [ + types + version + topics + itm-paper + itm-scientist + papers-plot-following + journals-list + checking-zipf + checking-exp + scientists-correlation + papers-correlation +] + + +;-----------SETUP--------------------------------------------------------------------------------------------- + + +to setup + ; Initializes the simulation + + clear-all + reset-ticks + set version "07" + set itm-paper 10 + set itm-scientist 5 + ifelse random-seed? [ + random-seed random 1000000 + let zero pr-utils:zipfGenInit random 1000000 initial-Zipf-exponent] + [ + random-seed 1432 + let uno pr-utils:zipfGenInit 1432 initial-Zipf-exponent + ] + if behaviorspace-experiment-name = "" [plot-zipf-and-exp-just-because] + + create-scientists initial-scientists [setup-scientist set shape "circle"] + if simulationType = "PR" or simulationType = "both" [ + setup-journals + ] + set papers-plot-following no-turtles +end + +to plot-zipf-and-exp-just-because + let how-many 500 + let current-type excellence-criterion + set excellence-criterion "exponentialrandom" + set checking-exp n-values how-many [log generate-quality 10] + set excellence-criterion "zipf" + set checking-zipf n-values how-many [log generate-quality 10] + set excellence-criterion current-type + + set-current-plot "comparing generate-qualities" + set-plot-x-range 0 max sentence checking-zipf checking-exp + set-current-plot-pen"zipf" histogram checking-zipf + set-current-plot-pen "exp" histogram checking-exp +end + +to setup-scientist + ; Initialize a scientist + + set role "author" + set productivity random-exponential production-mean + set quality generate-quality + set initial-reputation generate-quality + set reputation initial-reputation + set age 1 + if count journals > 0 [create-reviewer-with one-of journals] +end + + +;----- PR ------------------- + +to setup-journals + ; Creates the journals where the scientists can publish their papers + + create-journals n-of-journals [ + set shape "triangle" + set editor one-of scientists + ask n-of (2 * num-reviewers) scientists [create-reviewer-with myself] + ] + set journals-list sort journals + let random-sample sort n-values (n-of-journals * 20) [generate-quality] + adapt-journal-quality random-sample +end + +to adapt-journal-quality [sorted_pqualities] + ; Stablishes the journal qualities + ; The space of existing journal qualities is divided in n bins with the same number of papers inside (approximatively) + + let index 0; + foreach journals-list [ + ask ? [set quality item floor ((index + 1 / 2) * (length sorted_pqualities / n-of-journals) ) sorted_pqualities] + set index index + 1 + ] +end + +;----- REP ------------------ + +to-report weight-inherited-vs-eval [inherit itm-limit evals] + ; Calculates the reputation of a paper based on the evaluations it has received and the reputation coming from its authors + + let num-eval length evals + let eval-weight -1 ; weights evaluations vs. inherited + ifelse num-eval = 0 [ + report inherit ; if there are no evaluations of that paper we use inherited-reputation only + ] + [ + if-else num-eval < itm-limit [ ; if there are less than 'itm-paper' evaluations of that paper we use inherited-reputation and the evaluations + set eval-weight sin((pi * num-eval) / (2 * itm-limit)) + ] + [ ; if there are more than 'itm-paper' evaluations we use only the info from the evaluations + set eval-weight 1 + ] + let evalCalc mean evals; (sum evals) / (length evals) + report (inherit * (1 - eval-weight) + evalCalc * eval-weight) + ] +end + +to-report evaluations + let scores [score] of my-in-read-reps + report ifelse-value (length scores > 0) [reduce sentence [score] of my-in-read-reps][[]] +end + +to-report evaluators + report in-read-rep-neighbors +end + + +;----- PR-REP ----------------- +to go + ; Simulation step + + generate-papers ; papers are generated as drafts. + + if (ticks mod 5 = 0 ) [save-distributions] + + if (ticks = 0 ) [set papers-plot-following (turtle-set one-of drafts) ; + set-current-plot "papers read per turn - red PR blue REP" + create-temporary-plot-pen word [who] of one-of papers-plot-following "pr" set-plot-pen-color red + create-temporary-plot-pen word [who] of one-of papers-plot-following "rep" set-plot-pen-color blue + ] + if (ticks = 20) [ + let new-followed one-of papers with [ age = 1] ; max-one-of papers with [ age <= 2] [quality] + set papers-plot-following turtle-set new-followed + set-current-plot "papers read per turn - red PR blue REP" + create-temporary-plot-pen word [who] of new-followed "pr" set-plot-pen-color red + create-temporary-plot-pen word [who] of new-followed "rep" set-plot-pen-color blue + ] + ask papers [set curr-pr-reads 0 set curr-rep-reads 0] + + if simulationType = "PR" or simulationType = "both" [ + review-drafts ; transforms drafts into papers or into unpublished things. Drafts are empty at this point, all of them changed into papers. + ask scientists [read-and-think-pr] ; Papers are read but not evaluated. + adapt-journal-quality sort [quality] of papers + ] + + if simulationType = "REP" or simulationType = "both" + [ ; this is the REP branch of the if + + ; calculate the inherited-reputation, reputation and visibility of all papers + if any? drafts [ask drafts [set breed papers set published? false set age 0 set mistaken? false]] ; rep only branch, everything published. In the "both" branch will not fire. + ask papers [ + + ; inherited-reputation + set inherited-reputation mean [reputation] of paper-to-author-neighbors + + ; reputation + set reputation weight-inherited-vs-eval inherited-reputation itm-paper evaluations + ;set reputation ifelse-value (empty? evaluations) [inherited-reputation][mean evaluations] + ] + ; Papers are evaluated. + ask scientists [read-and-think-rep] + + ; calculate the reputation of the authors + ask scientists [ + set reputation weight-inherited-vs-eval initial-reputation itm-scientist ([reputation] of paper-to-author-neighbors with [breed = papers ]) + ] + ] + + ; new scientists + ask scientists [set age age + 1] + ask n-of (scientists-leaving) scientists [set productivity 0] ; not age related because people just change field. + create-scientists new-scientists-per-turn [setup-scientist set shape "circle"] + + ; increase the age of the paper, update paper accumulators + ask papers [set age age + 1 set tot-rep-reads tot-rep-reads + curr-rep-reads + set tot-pr-reads tot-pr-reads + curr-pr-reads] + + ask papers with [age > obsolescence-threshold] [set breed obsoletes] + + calculateCorrelationsScientists + calculateCorrelationsPapers + + + if behaviorspace-experiment-name = "" [do-plots] + tick + print word "Tick n. " ticks +end + +;-----PR------------------- + +to-report reading-weight-pr ;self=paper + report ([quality] of one-of out-appears-in-neighbors) * ifelse-value (age-weight?) [age-weight age][1] ; it's the journal quality - only one appears-in +end + +;-----REP------------------- + +to-report reading-weight-rep ;self=paper + let r reputation * ifelse-value (age-weight?) [age-weight age][1] + report ifelse-value (r > 0) [r][0] +end + +;------PR-REP---------------- + +to-report age-weight [the-age] ; this is justfied by the fact that after three years novelty wears off. + ifelse (the-age <= 2) [report item (the-age) [0.25 0.6 1]] [ ; first three years of paper life, 0 1 and 2 + report ( 1 / exp ((the-age - 2) / 5) )] ; after five years it gets 50% +end + +;-----REP------------------- + +to read-and-think-rep ;self=scientist + let not-yet-read no-turtles + ifelse (read-cap?) [ + let already-read out-read-rep-neighbors + set not-yet-read papers with [not member? self already-read] + ] + [ + set not-yet-read papers + ] + let num-to-read min list (productivity * productivity-to-reads-multiplier) count not-yet-read + let to-read rnd:weighted-n-of num-to-read not-yet-read [ reading-weight-rep ] + ask to-read [ + let paper-evaluation evaluate-paper-forREP myself self; myself = the_evaluator, self = the_paper + if not in-read-rep-neighbor? myself [create-read-rep-from myself [set score []]] + ask in-read-rep-from myself [set score fput paper-evaluation score ] + set curr-rep-reads curr-rep-reads + 1 + ] +end + +;-----PR------------------- + +to read-and-think-pr ;self=scientist + let not-yet-read no-turtles + ifelse (read-cap?) [ + let already-read out-read-pr-neighbors + set not-yet-read papers with [published? and not member? self already-read] + ] + [ + set not-yet-read papers with [published?] + ] + let num-to-read min list (productivity * productivity-to-reads-multiplier) count not-yet-read + let to-read rnd:weighted-n-of num-to-read not-yet-read [ reading-weight-pr ] + ask to-read [ + if not in-read-pr-neighbor? myself [create-read-pr-from myself] + set curr-pr-reads curr-pr-reads + 1 + ] +end + +;-----REP------------------- + + to-report evaluate-paper-forREP [evaluator a-paper] + report ([quality] of a-paper + (ifelse-value(random-float 1.0 > 0.5) [-1][1] * generate-quality * generate-quality / quality)) + end + +;-----PR-------------------- + +to-report evaluate-paper-forPR [a-paper journal-quality] ; context: the scientist who evaluate. + report ifelse-value ([quality] of a-paper > (journal-quality + (ifelse-value(random-float 1 > 0.5) [-1][1] * generate-quality * generate-quality / quality) )) ["yes"]["no"] +end + + + +;-----PR-------------------- + +to review-drafts + ; Simulates the review of a paper and decides about publication or rejection + + ask drafts [ + if-else strategic-submission? [ ;one of the authors chooses the journal. Which one? He chooses a journal that is the nearest to his quality. You can assume it was a resubmission if you go for a journal of lower quality. + let the-journal [ + choose-journal + ] of one-of paper-to-author-neighbors + ask the-journal [review myself] + ][ + ask one-of journals [review myself] + ] + ] +end + +to-report choose-journal + ; An author chooses a journal near his or her quality + + let theJ min-one-of journals [abs (quality + ifelse-value(random-float 1 > 0.5)[-1][1] * generate-quality - [quality] of myself)] +report theJ +end + + +to review [a-paper] ; self=journal + let revs n-of num-reviewers reviewer-neighbors ; people could end out evaluating their own paper, but as they would not do it differently, it'ìs not a big issue. + let evals [evaluate-paper-forPR a-paper [quality] of myself ] of revs + if-else length filter [? = "yes"] evals > length filter [? = "no"] evals [ + ask a-paper [set breed papers create-appears-in-to myself + set age 0 + set published? true + set mistaken? ifelse-value (quality < [quality] of myself) [true][false] + ] ; published, yay + ] + [ + ask a-paper [set breed papers set age 0 set published? false set mistaken? false + set mistaken? ifelse-value (quality >= [quality] of myself) [true][false] + ] ; rejected, groan. + ] +end + +;-----PR-REP---------------- + +to generate-papers + ; Generates the (draft) papers according to the total production of the active scientists. + ; Each paper is assigned a set of co-authors and then assigned an initial quality. Here we + ; also generate the exceptionally good papers that appear in the system from time to time. + + let production-total floor sum [productivity] of scientists + ; First we create all the drafts with random quality + create-drafts floor production-total / average-authors-per-paper [ + set quality generate-quality ; The quality of the paper starts indipendently of the quality of the authors (heck the authors aren't even yet assigned) + ] + if (artificial-big-paper? and (ticks mod time-artificial-big-paper) = 0) and ticks > 0 [ + ask one-of drafts [set quality 10 * max [quality] of papers + print (word "Exceptional paper n. " who " with quality: " quality) + ] + ] + if-else keep-co-workers [create-co-authors-on-network] [create-co-authors-randomly] + ; At this point the paper has the authors assigned. + ; Next, average the quality between paper and authors. + ask drafts [ + let num-of-authors count paper-to-author-neighbors ;with [quality != -1] + set quality (quality + sum [quality] of paper-to-author-neighbors) / (num-of-authors + 1) ; In this averaging the paper - which is, the idea - counts exactly as the quality of one author. + ; Then authors change. They can learn something, but they can't forget something. So: + ask paper-to-author-neighbors [ if quality < ([quality] of myself) [set quality (1 - rate-of-adaptation) * quality + rate-of-adaptation * [quality] of myself] ] + ] +end + + +to create-co-authors-randomly + ; Assigns co-authors to a paper. The co-authors are assigned randomly. A scientist can + ; be the co-author of a paper only if he/she still has production capacity. + + ask scientists [ set tmp-prod productivity ] + let drafts-list [ self ] of drafts with [ not any? paper-to-author-neighbors ] + let candidates-list reduce sentence [ n-values tmp-prod [ self ] ] of scientists + let n min (list (length drafts-list) (length candidates-list)) + set drafts-list sublist drafts-list 0 n + (foreach (n-of n candidates-list) (drafts-list) [ + ask ?1 [ + create-paper-to-author-with ?2 + decrease-tmp-prod + ] + ]) + foreach drafts-list [ + let the-draft ? + repeat (floor random-exponential average-authors-per-paper - 1) [ + let candidates scientists with [ tmp-prod > 0 ] + if any? candidates [ + ask rnd:weighted-one-of candidates [ tmp-prod ] [ + create-paper-to-author-with the-draft + decrease-tmp-prod + ] + ] + ] + ] + ask drafts with [ not any? paper-to-author-neighbors ] [ die ] +end + + +to decrease-tmp-prod + set tmp-prod max list 0 (tmp-prod - 1) + if (tmp-prod < 0) [print "ERROR"] +end + + +to create-co-authors-on-network + ; Assings co-authors to a paper. The co-authors are taken from the network of + ; previous co-authors of the progressively assigned authors (with the first + ; one assigned randomly) + + ask scientists [ set tmp-prod productivity ] + let drafts-list [ self ] of drafts with [ not any? paper-to-author-neighbors ] + + let make-me-integer min [tmp-prod] of scientists + let candidates-list reduce sentence [ n-values round (tmp-prod / make-me-integer) [ self ] ] of scientists + + let n min (list (length drafts-list) (length candidates-list)) + set drafts-list sublist drafts-list 0 n + (foreach (n-of n candidates-list) (drafts-list) [ + ask ?1 [ + create-paper-to-author-with ?2 + decrease-tmp-prod + ] + ]) + foreach drafts-list [ + let the-draft ? + repeat (floor random-exponential average-authors-per-paper - 1) [ + let current-authors [ paper-to-author-neighbors ] of the-draft + let candidates (turtle-set [ coauthors ] of current-authors) with [ + tmp-prod > 0 and not member? self current-authors + ] + if not any? candidates [ + set candidates scientists with [ tmp-prod > 0 ] + ] + if any? candidates [ + ask rnd:weighted-one-of candidates [ tmp-prod ] [ + create-paper-to-author-with the-draft + decrease-tmp-prod + ] + ] + ] + ] + ask drafts with [ not any? paper-to-author-neighbors ] [ die ] +end + + +to-report coauthors + report [ paper-to-author-neighbors ] of paper-to-author-neighbors +end + + +to-report generate-quality + ; Quality generator. Generates qualities using either exponential random or a + ; zipf distribution (as selected by the user in the user interface) + + ifelse (excellence-criterion = "exponentialrandom")[ + report random-exponential r-exp-mean + 1 + ] + [ + ifelse (excellence-criterion = "zipf") [ + let theZ pr-utils:zipfGen + report ifelse-value sawoff-zipf? [min (list 100 theZ)][theZ] + ] + [ ; must be initialized (in the setup) + report "uh, not implemented" + ] + ] +end + +;------------PLOTTING------------------------ + + +to do-plots + +set-current-plot "papers read per turn - red PR blue REP" + +ask papers-plot-following with [breed = papers][ + set-current-plot-pen word who "pr" plotxy ticks curr-pr-reads + set-current-plot-pen word who "rep" plotxy ticks curr-rep-reads +] +let to-replace papers-plot-following with [breed = obsoletes] +if any? to-replace [ + ask to-replace [ + ask max-one-of papers with [age <= 2] [quality] [ + set papers-plot-following (turtle-set self papers-plot-following) + create-temporary-plot-pen word who "pr" set-plot-pen-color red + create-temporary-plot-pen word who "rep" set-plot-pen-color blue + ] + ] + set papers-plot-following papers-plot-following with [breed != obsoletes] +] + +set-current-plot "readings by paper quality (blue: rep, red:PR)" +clear-plot + +if simulationType = "REP" [ set-plot-pen-color blue ask papers [plotxy quality count evaluators] ] +if simulationType = "PR" [set-plot-pen-color red ask papers with [published?] [ plotxy quality count in-read-pr-neighbors] ] +if simulationType = "both" [ + +set-plot-pen-color red ask papers with [published?] [ plotxy quality count in-read-pr-neighbors] +set-plot-pen-color blue ask papers [plotxy quality count evaluators]] + +set-current-plot "mistakes" +plot count papers with [mistaken? and age = 1] + +set-current-plot "published, mistakes" +set-current-plot-pen "mistakes" +plot count papers with [mistaken?] +set-current-plot-pen "published" +plot count papers with [published?] + +set-current-plot "readings by paper quality (blue: rep, red:PR)" +clear-plot +if simulationType = "REP" [ set-plot-pen-color blue ask papers [plotxy quality count evaluators] ] +if simulationType = "PR" [set-plot-pen-color red ask papers with [published?] [ plotxy quality count in-read-pr-neighbors] ] +if simulationType = "both" [ + set-plot-pen-color red ask papers with [published?] [ plotxy quality count in-read-pr-neighbors] + set-plot-pen-color blue ask papers [plotxy quality count evaluators]] + +set-current-plot "Obsoletes" +clear-plot +if simulationType = "REP" [ set-plot-pen-color blue ask obsoletes [plotxy quality count evaluators] ] +if simulationType = "PR" [set-plot-pen-color red ask obsoletes with [published?] [ plotxy quality count in-read-pr-neighbors] ] +if simulationType = "both" [ + set-plot-pen-color red ask obsoletes with [published?] [ plotxy quality count in-read-pr-neighbors] + set-plot-pen-color blue ask obsoletes [plotxy quality count evaluators]] + +set-current-plot "readings by author quality" +clear-plot +if simulationType = "REP" [set-plot-pen-color blue ask scientists [plotxy quality sum [count evaluators] of paper-to-author-neighbors with [breed = papers] ] ] +if simulationType = "PR" [set-plot-pen-color red ask scientists [plotxy quality sum [count in-read-pr-neighbors] of paper-to-author-neighbors with [breed = papers] ] ] +if simulationType = "both" [ + set-plot-pen-color blue ask scientists [plotxy quality sum [count evaluators] of paper-to-author-neighbors with [breed = papers] ] + set-plot-pen-color red ask scientists [plotxy quality sum [count in-read-pr-neighbors] of paper-to-author-neighbors with [breed = papers] ] + ] + +set-current-plot "quality distribution authors" +set-plot-x-range 0 max [quality] of scientists + 1 +histogram [quality] of scientists + +set-current-plot "reputation" +set-plot-x-range 0 max [reputation] of papers + 1 +histogram [reputation] of papers + +set-current-plot "quality of papers" +set-plot-x-range 0 max [quality] of papers + 1 + histogram [quality] of papers + +set-current-plot "quality of published papers" +set-plot-x-range 0 max [quality] of papers + 1 + histogram [quality] of papers with [published?] + + +set-current-plot "quality of papers (log)" +set-plot-x-range 0 max [log quality 10] of papers + 1 + histogram [log quality 10] of papers + +set-current-plot "quality-by-productivity" +ask scientists [plotxy productivity quality] + +set-current-plot "authors-per-paper" +set-plot-x-range 0 max [count paper-to-author-neighbors] of papers + 1 +histogram [count paper-to-author-neighbors] of papers + +set-current-plot "quality of journals" +set-plot-x-range 0 max [quality] of journals + 1 +let quality-j-list [] +ask papers [ + let j-quality [quality] of out-appears-in-neighbors + if length j-quality > 0 [ + set quality-j-list fput item 0 j-quality quality-j-list + ] +] +histogram quality-j-list + +end + + +;------------REPORTING------------------------ + + + +to-report filename + let expname ifelse-value (behaviorspace-experiment-name = "") [""][(word behaviorspace-experiment-name "-" behaviorspace-run-number "-")] + report (word "./results/" expname version "-" simulationType "-" excellence-criterion "." "-z" initial-Zipf-exponent "-e" r-exp-mean + ".ns." initial-scientists "+" new-scientists-per-turn "-" scientists-leaving + "-aw." age-weight? "-kc." keep-co-workers "-nr." num-reviewers "-pm." production-mean ) +end + +to happy-ending + let the-name filename + export-world (word the-name "-world.csv") +end + +to save-distributions + save-authors + save-papers + save-journals +end + +to save-papers + let the-breed papers + let variables ["behaviorspace-run-number" "ticks" "who" "count evaluators" "reputation" "quality" "age"] + let names ["runnumber" "ticks" "ID" "reads" "reputation" "quality" "age"] + save-stuff-2 the-breed variables names + end + +to save-journals + let the-breed journals + let variables ["behaviorspace-run-number" "ticks" "who" "count in-appears-in-neighbors" "quality" ] + let names ["runnumber" "ticks" "ID" "reads" "quality" ] + save-stuff-2 the-breed variables names +end + +to save-authors + let the-breed scientists + let variables ["behaviorspace-run-number" "ticks" "who" "sum [count evaluators] of paper-to-author-neighbors with [breed = papers]" "count paper-to-author-neighbors" "reputation" "quality" "productivity" "age"] + let names ["runnumber" "ticks" "ID" "reads" "papers" "reputation" "quality" "productivity" "age"] + save-stuff-2 the-breed variables names +end + +to save-stuff-2 [the-breed variables names] + let the-filename (word filename "." the-breed ".csv") + let values [ map runresult variables ] of the-breed + file-open the-filename + ;print values + if not file-exists? the-filename [ + csv:to-file the-filename fput names values + ] + file-print csv:to-string values +file-close +end + +to-report export-network-string + let the-net "" + ask papers [ + ask paper-to-author-neighbors [ + ask [paper-to-author-neighbors] of myself [ + set the-net (word the-net [who + 1] of myself " " (who + 1) "\\n" ) + ] + ] + ] + report the-net +end + +to-report export-network-list + let the-net [] + ask papers [ + ask paper-to-author-neighbors [ + ask [paper-to-author-neighbors] of myself [;myself being, I hope, the paper + set the-net fput (list ( [who + 1] of myself) (who + 1) ) the-net + ] + ] + ] + report the-net +end + + +to-report export-network-type + let the-net "" + ask papers [ + ask paper-to-author-neighbors [ + ask [paper-to-author-neighbors] of myself [;myself being the paper + type [who + 1] of myself ; now myself is the author under consideration + type " " + type who + 1 ; the co-author + print "" + ] + ] + ] +end + +to-report correlationMatrix [which i j] + ifelse (ticks = 0) + [report 0] + [report item i item j ifelse-value (which = "papers") [papers-correlation ] [ scientists-correlation]] +end + +to-report correlationScientistQualityRep + report correlationMatrix "scientist" 0 1 +end + +to-report correlationScientistQualityReadPR + report correlationMatrix "scientist" 0 2 +end + +to-report correlationScientistReputationReadREP + report correlationMatrix "scientist" 1 3 + end + +to calculateCorrelationsScientists ; side effect, matrix ready + let tbl stats:newtable + ask Scientists [stats:add tbl (list quality reputation + sum [count evaluators] of paper-to-author-neighbors with [breed = papers] + sum [count in-read-pr-neighbors] of paper-to-author-neighbors with [breed = papers] )] + set scientists-correlation stats:correlation tbl +end + +to-report correlationPapersQualityRep + report correlationMatrix "paper" 0 1 +end + +to-report correlationPapersQualityReadPR + report correlationMatrix "paper" 0 2 +end + +to-report correlationPapersReputationReadREP + report correlationMatrix "paper" 1 3 +end + +to calculateCorrelationsPapers ; side effect, matrix ready + let tbl stats:newtable + if count papers > 2 [ + ask papers [stats:add tbl (list quality reputation + count my-in-read-prs + count my-in-read-reps)] + set papers-correlation stats:correlation tbl + ] +end +@#$#@#$#@ +GRAPHICS-WINDOW +204 +10 +449 +229 +-1 +-1 +7.833333333333333 +1 +10 +1 +1 +1 +0 +1 +1 +1 +0 +23 +0 +23 +1 +1 +1 +ticks +30.0 + +BUTTON +35 +125 +157 +158 +NIL +setup +NIL +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +BUTTON +35 +165 +157 +198 +go +go\n +T +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +PLOT +1175 +10 +1375 +160 +authors-per-paper +NIL +NIL +0.0 +30.0 +0.0 +40.0 +true +true +"" "" +PENS +"authors" 1.0 1 -16777216 true "" "" + +BUTTON +35 +205 +160 +238 +go-once +go +NIL +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +CHOOSER +410 +55 +595 +100 +excellence-criterion +excellence-criterion +"exponentialrandom" "zipf" +1 + +PLOT +255 +370 +455 +520 +quality-by-productivity +NIL +NIL +0.0 +10.0 +0.0 +150.0 +true +false +"" "" +PENS +"qbp" 1.0 2 -16777216 true "" "" + +PLOT +675 +630 +1170 +780 +quality of papers +NIL +NIL +0.0 +300.0 +0.0 +10.0 +true +false +"" "" +PENS +"pen-0" 1.0 1 -16777216 true "" "" + +PLOT +460 +370 +660 +520 +quality distribution authors +NIL +NIL +0.0 +110.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 1 -16777216 true "" "" + +SLIDER +410 +180 +595 +213 +average-authors-per-paper +average-authors-per-paper +0.01 +10 +2.275 +0.01 +1 +NIL +HORIZONTAL + +SWITCH +410 +145 +595 +178 +keep-co-workers +keep-co-workers +0 +1 +-1000 + +SLIDER +410 +285 +594 +318 +initial-Zipf-exponent +initial-Zipf-exponent +1.1 +10 +1.88 +0.1 +1 +NIL +HORIZONTAL + +PLOT +1175 +320 +1489 +470 +quality of papers (log) +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 1 -16777216 true "" "" + +SLIDER +410 +215 +595 +248 +num-reviewers +num-reviewers +1 +10 +3 +1 +1 +NIL +HORIZONTAL + +CHOOSER +35 +10 +173 +55 +simulationType +simulationType +"PR" "REP" "both" +2 + +MONITOR +35 +65 +94 +110 +NIL +version +17 +1 +11 + +MONITOR +35 +255 +200 +300 +quality mean (pub) +mean [quality] of papers with [published?] +1 +1 +11 + +MONITOR +35 +305 +200 +350 +unpublished quality +mean [quality] of papers with [not published?] +1 +1 +11 + +SLIDER +410 +10 +595 +43 +new-scientists-per-turn +new-scientists-per-turn +0 +100 +0 +1 +1 +NIL +HORIZONTAL + +PLOT +680 +165 +1169 +315 +readings by paper quality (blue: rep, red:PR) +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 2 -16777216 true "" "" + +PLOT +675 +320 +1170 +470 +readings by author quality +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 2 -16777216 true "" "" + +SLIDER +410 +320 +595 +353 +production-mean +production-mean +0 +20 +0.07 +0.001 +1 +NIL +HORIZONTAL + +SLIDER +410 +250 +595 +283 +r-exp-mean +r-exp-mean +0 +200 +11.1 +1 +1 +NIL +HORIZONTAL + +SLIDER +410 +110 +595 +143 +initial-scientists +initial-scientists +0 +4000 +848 +100 +1 +NIL +HORIZONTAL + +MONITOR +35 +355 +200 +400 +quality mass rep +sum [quality * count evaluators] of papers + sum [quality * count evaluators] of obsoletes +0 +1 +11 + +MONITOR +35 +405 +200 +450 +quality mass pr +sum [quality * count my-in-read-prs] of papers + sum [quality * count my-in-read-prs] of obsoletes +0 +1 +11 + +PLOT +1175 +165 +1375 +315 +reputation +NIL +NIL +0.0 +20.0 +0.0 +0.0 +true +false +"" "" +PENS +"pen-0" 1.0 1 -7500403 true "" "" + +SLIDER +605 +45 +750 +78 +n-of-journals +n-of-journals +1 +100 +36 +5 +1 +NIL +HORIZONTAL + +PLOT +970 +10 +1170 +160 +Obsoletes +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 2 -16777216 true "" "" + +MONITOR +35 +455 +200 +500 +rep sq q +sum [quality ^ 2 * count evaluators] of papers + sum [quality ^ 2 * count evaluators] of obsoletes +0 +1 +11 + +MONITOR +35 +505 +200 +550 +pr sq q +sum [quality ^ 2 * count my-in-read-prs] of papers + sum [quality ^ 2 * count my-in-read-prs] of obsoletes +0 +1 +11 + +PLOT +765 +10 +965 +160 +mistakes +NIL +NIL +0.0 +10.0 +0.0 +1.0 +true +false +"" "" +PENS +"default" 1.0 0 -16777216 true "" "" + +PLOT +675 +475 +1169 +625 +published, mistakes +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +true +"" "" +PENS +"mistakes" 1.0 2 -16777216 true "" "" +"published" 1.0 0 -13840069 true "" "" + +PLOT +255 +680 +660 +830 +papers read per turn - red PR blue REP +NIL +NIL +0.0 +50.0 +0.0 +6.0 +true +false +"" "" +PENS +"pen-0" 1.0 2 -7500403 true "" "" + +SWITCH +35 +660 +170 +693 +age-weight? +age-weight? +0 +1 +-1000 + +SWITCH +36 +624 +169 +657 +sawoff-zipf? +sawoff-zipf? +1 +1 +-1000 + +SWITCH +605 +80 +750 +113 +read-cap? +read-cap? +1 +1 +-1000 + +SWITCH +35 +695 +200 +728 +strategic-submission? +strategic-submission? +0 +1 +-1000 + +PLOT +1175 +475 +1485 +625 +quality of journals +NIL +NIL +0.0 +2.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 1 -16777216 true "" "" + +MONITOR +255 +245 +380 +290 +Papers +count papers +17 +1 +11 + +MONITOR +255 +295 +380 +340 +Published papers +count papers with [published?] +17 +1 +11 + +PLOT +675 +785 +1172 +935 +quality of published papers +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +false +"" "" +PENS +"default" 1.0 1 -16777216 true "" "" + +PLOT +255 +525 +660 +675 +comparing generate-qualities +NIL +NIL +0.0 +10.0 +0.0 +10.0 +true +true +"" "" +PENS +"zipf" 1.0 0 -16777216 true "" "" +"exp" 1.0 0 -5298144 true "" "" + +SLIDER +35 +820 +225 +853 +productivity-to-reads-multiplier +productivity-to-reads-multiplier +1 +10 +5 +1 +1 +NIL +HORIZONTAL + +SLIDER +605 +10 +750 +43 +scientists-leaving +scientists-leaving +0 +50 +0 +1 +1 +NIL +HORIZONTAL + +MONITOR +35 +555 +200 +600 +number of scientsts +count scientists +0 +1 +11 + +SLIDER +35 +740 +207 +773 +rate-of-adaptation +rate-of-adaptation +0 +1 +0.1 +0.1 +1 +NIL +HORIZONTAL + +SWITCH +35 +910 +189 +943 +random-seed? +random-seed? +0 +1 +-1000 + +SWITCH +255 +860 +436 +893 +artificial-big-paper? +artificial-big-paper? +1 +1 +-1000 + +SLIDER +255 +895 +460 +928 +time-artificial-big-paper +time-artificial-big-paper +1 +100 +30 +1 +1 +NIL +HORIZONTAL + +SLIDER +35 +860 +225 +893 +obsolescence-threshold +obsolescence-threshold +5 +100 +100 +1 +1 +NIL +HORIZONTAL + +@#$#@#$#@ +## WHAT IS IT? + +This is a model of paper publication and consumption that allows to study the effect of two different evaluation mechanisms, peer review and reputation, on the quality of the manuscripts accessed by a scientific community. + +## HOW IT WORKS + +In order to compare the two filters - reputation and peer review - the model includes a common paper production mechanism and then runs two distinct sub-models for accessing papers: one driven by reputation and the other by peer review. + +The simulation cycle of the model begins with paper production, generating the papers for the current time step and adding them to the papers pool. Afterwards, it applies either a simulated peer review process or a simulated reputation mechanism, both driving parallel reading processes. In the former case, scientists read papers as prioritized by journal's quality whereas, in the latter case, they read papers as prioritized by their reputation. + +The two sub-models share the same ground truth for what regards paper and scientist quality. This guarantees a clean comparison, made with exactly the same papers in the system, at the cost of ignoring the feedback from reading towards paper production. + +## INSTALLATION NOTES (IMPORTANT!) + +* **pr-utils** is a custom extension that must be present in the Netlogo extensions folder in a directory of the same name. +* A folder called **results** has to be present in the same location of the main netlogo file. This directory is used to store detailed results of each simulation. + +## HOW TO USE IT + +SETUP button — sets up the model by creating the agents. + +GO button — runs the model + +GO-ONCE - runs one step of the simulation + +## THINGS TO TRY + +In order to reproduce the results presented in the paper you will find defined the different set of experiments in the BehaviorSpace. Detailed results are stored in the folder "results" that previously must be created in the directory where the application is installed (see installation notes) + +## HOW TO CITE + +## CREDITS AND REFERENCES + +Copyright 2015 Mario Paolucci & Jordi Sabater-Mir & Francisco Grimaldo under the GPL licence. Developed at LABSS (http://labss.istc.cnr.it/), ETSE-UV, IIIA-CSIC. +@#$#@#$#@ +default +true +0 +Polygon -7500403 true true 150 5 40 250 150 205 260 250 + +airplane +true +0 +Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15 + +arrow +true +0 +Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150 + +box +false +0 +Polygon -7500403 true true 150 285 285 225 285 75 150 135 +Polygon -7500403 true true 150 135 15 75 150 15 285 75 +Polygon -7500403 true true 15 75 15 225 150 285 150 135 +Line -16777216 false 150 285 150 135 +Line -16777216 false 150 135 15 75 +Line -16777216 false 150 135 285 75 + +bug +true +0 +Circle -7500403 true true 96 182 108 +Circle -7500403 true true 110 127 80 +Circle -7500403 true true 110 75 80 +Line -7500403 true 150 100 80 30 +Line -7500403 true 150 100 220 30 + +butterfly +true +0 +Polygon -7500403 true true 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true true 65 21 108 +Circle -7500403 true true 116 41 127 +Circle -7500403 true true 45 90 120 +Circle -7500403 true true 104 74 152 + +triangle +false +0 +Polygon -7500403 true true 150 30 15 255 285 255 + +triangle 2 +false +0 +Polygon -7500403 true true 150 30 15 255 285 255 +Polygon -16777216 true false 151 99 225 223 75 224 + +truck +false +0 +Rectangle -7500403 true true 4 45 195 187 +Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194 +Rectangle -1 true false 195 60 195 105 +Polygon -16777216 true false 238 112 252 141 219 141 218 112 +Circle -16777216 true false 234 174 42 +Rectangle -7500403 true true 181 185 214 194 +Circle -16777216 true false 144 174 42 +Circle -16777216 true false 24 174 42 +Circle -7500403 false true 24 174 42 +Circle -7500403 false true 144 174 42 +Circle -7500403 false true 234 174 42 + +turtle +true +0 +Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 +Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 +Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 +Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 +Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 +Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99 + +wheel +false +0 +Circle -7500403 true true 3 3 294 +Circle -16777216 true false 30 30 240 +Line -7500403 true 150 285 150 15 +Line -7500403 true 15 150 285 150 +Circle -7500403 true true 120 120 60 +Line -7500403 true 216 40 79 269 +Line -7500403 true 40 84 269 221 +Line -7500403 true 40 216 269 79 +Line -7500403 true 84 40 221 269 + +x +false +0 +Polygon -7500403 true true 270 75 225 30 30 225 75 270 +Polygon -7500403 true true 30 75 75 30 270 225 225 270 + +@#$#@#$#@ +NetLogo 5.3.1 +@#$#@#$#@ +@#$#@#$#@ +@#$#@#$#@ + + + setup + go + + sum [quality * count my-in-read-prs] of papers + sum [quality * count my-in-read-prs] of obsoletes + sum [quality * count my-in-read-reps] of papers + sum [quality * count my-in-read-reps] of obsoletes + sum [quality ^ 2 * count my-in-read-prs] of papers + sum [quality ^ 2 * count my-in-read-prs] of obsoletes + sum [quality ^ 2 * count my-in-read-reps] of papers + sum [quality ^ 2 * count my-in-read-reps] of obsoletes + count papers + count papers with [mistaken?] + count papers with [published?] + count papers with [not any? my-in-read-prs] + count papers with [not any? my-in-read-reps] + count papers with [published? and not any? my-in-read-prs] + correlationScientistQualityRep + correlationScientistQualityReadPR + correlationScientistReputationReadREP + correlationPapersQualityRep + correlationPapersReputationReadREP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + setup + go + + sum [quality * count my-in-read-prs] of papers + sum [quality * count my-in-read-prs] of obsoletes + sum [quality * count my-in-read-reps] of papers + sum [quality * count my-in-read-reps] of obsoletes + sum [quality ^ 2 * count my-in-read-prs] of papers + sum [quality ^ 2 * count my-in-read-prs] of obsoletes + sum [quality ^ 2 * count my-in-read-reps] of papers + sum [quality ^ 2 * count my-in-read-reps] of obsoletes + count papers + count papers with [mistaken?] + count papers with [published?] + count papers with [not any? my-in-read-prs] + count papers with [not any? my-in-read-reps] + count papers with [published? and not any? my-in-read-prs] + correlationScientistQualityRep + correlationScientistQualityReadPR + correlationScientistReputationReadREP + correlationPapersQualityRep + correlationPapersReputationReadREP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + setup + go + + sum [quality * count my-in-read-prs] of papers + sum [quality * count my-in-read-prs] of obsoletes + sum [quality * count my-in-read-reps] of papers + sum [quality * count my-in-read-reps] of obsoletes + sum [quality ^ 2 * count my-in-read-prs] of papers + sum [quality ^ 2 * count my-in-read-prs] of obsoletes + sum [quality ^ 2 * count my-in-read-reps] of papers + sum [quality ^ 2 * count my-in-read-reps] of obsoletes + count papers + count papers with [mistaken?] + count papers with [published?] + count papers with [not any? my-in-read-prs] + count papers with [not any? my-in-read-reps] + count papers with [published? and not any? my-in-read-prs] + correlationScientistQualityRep + correlationScientistQualityReadPR + correlationScientistReputationReadREP + correlationPapersQualityRep + correlationPapersReputationReadREP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + setup + go + + sum [quality * count my-in-read-prs] of papers + sum [quality * count my-in-read-prs] of obsoletes + sum [quality * count my-in-read-reps] of papers + sum [quality * count my-in-read-reps] of obsoletes + sum [quality ^ 2 * count my-in-read-prs] of papers + sum [quality ^ 2 * count my-in-read-prs] of obsoletes + sum [quality ^ 2 * count my-in-read-reps] of papers + sum [quality ^ 2 * count my-in-read-reps] of obsoletes + count papers + count papers with [mistaken?] + count papers with [published?] + count papers with [not any? my-in-read-prs] + count papers with [not any? my-in-read-reps] + count papers with [published? and not any? my-in-read-prs] + correlationScientistQualityRep + correlationScientistQualityReadPR + correlationScientistReputationReadREP + correlationPapersQualityRep + correlationPapersReputationReadREP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@#$#@#$#@ +@#$#@#$#@ +default +0.0 +-0.2 0 0.0 1.0 +0.0 1 1.0 0.0 +0.2 0 0.0 1.0 +link direction +true +0 +Line -7500403 true 150 150 90 180 +Line -7500403 true 150 150 210 180 + +@#$#@#$#@ +1 +@#$#@#$#@ diff --git a/README.md b/README.md new file mode 100644 index 0000000..50a7a22 --- /dev/null +++ b/README.md @@ -0,0 +1,40 @@ +# What is it? + +This is a model of paper publication and consumption that allows to study the effect of two different evaluation mechanisms, peer review and reputation, on the quality of the manuscripts accessed by a scientific community. + +# How it works + +In order to compare the two filters - reputation and peer review - the model includes a common paper production mechanism and then runs two distinct sub-models for accessing papers: one driven by reputation and the other by peer review. + +The simulation cycle of the model begins with paper production, generating the papers for the current time step and adding them to the papers pool. Afterwards, it applies either a simulated peer review process or a simulated reputation mechanism, both driving parallel reading processes. In the former case, scientists read papers as prioritized by journal’s quality whereas, in the latter case, they read papers as prioritized by their reputation. + +The two sub-models share the same ground truth for what regards paper and scientist quality. This guarantees a clean comparison, made with exactly the same papers in the system, at the cost of ignoring the feedback from reading towards paper production. + +# Installation notes (important!) + +* This model needs NetLogo 5.3.1. +* The model makes use of four different NetLogo extensions: + * `pr-utils` is a custom extension developped specifically for this model. + * [`stats`](https://github.com/cstaelin/Stats-Extension) provides NetLogo with a tables for holding data gathered during runs, a number of statistical procedures to use on those data, and access to a number of useful distributions. + * [`csv`](https://github.com/NetLogo/CSV-Extension) facilitates the reading and writing of CSV files. + * [`rnd`](https://github.com/NetLogo/Rnd-Extension) provides primitive for weighted random selection. + + These extensions must be present, either under NetLogo's `extensions/` folder, or under the folder from which you run the model. (Note that `rnd` and `csv` are bundled with NetLogo version 6.0 and later but were not in NetLogo 5.3.1, thus the need to provide them here.) + +* A folder called `results/` has to be present in the same location of the main NetLogo file. This directory is used to store detailed results of each simulation. + +# How to use it + +SETUP button — sets up the model by creating the agents. + +GO button — runs the model + +GO-ONCE - runs one step of the simulation + +# Things to try + +In order to reproduce the results presented in the paper you will find defined the different set of experiments in the BehaviorSpace. Detailed results are stored in the folder `results/` that previously must be created in the directory where the application is installed (see installation notes). + +# Credits and references + +Copyright 2015 Mario Paolucci, Jordi Sabater-Mir & Francisco Grimaldo under the GPL licence. Developed at LABSS (http://labss.istc.cnr.it/), ETSE-UV, IIIA-CSIC. diff --git a/results/.gitignore b/results/.gitignore new file mode 100644 index 0000000..e69de29