DataONE:Notebook/Data Citation and Sharing Policy/2010/07/27
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Cleaner Analysis
<pre?> filename = "/Users/nicholasweber/Desktop/New Folder for Stats/JournalData1.csv" > mydata = read.csv(filename) > ImFa = Impact.Factor > ImFa[ImFa==0] = NA > hist(ImFa) > summary(ImFa) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.064 1.000 1.578 2.132 2.762 16.690 6.000 > SomeOA = ifelse(Subscription.Model == "Sub", 0, 1) > table(SomeOA) SomeOA 0 1 223 84 > Afil = ifelse(Affiliation.Code > 0, 1, 0)] # Society Affiliation Error: unexpected ']' in "Afil = ifelse(Affiliation.Code > 0, 1, 0)]" > table(Afil) Afil 0 1 148 158 > table(PubCode) PubCode elsevier other springer taylor wiley 52 125 58 24 48 > relevel(PubCode, ref="other") [1] other other other other other other other other other other other other other other [15] other other other other other other other other other other other other other other [29] other other other other other other other other other other other other other elsevier [43] elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier [57] elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier [71] elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier [85] elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier elsevier other other other other other [99] other other other other other other other other other other other other other other [113] other other other other other other other other other other other other other other [127] other other other other other other other other other other other other other other [141] other other other other other other other other other other other other other other [155] other other other other other other other other other other other other springer springer [169] springer springer springer springer springer springer springer springer springer springer springer springer springer springer [183] springer springer springer springer springer springer springer springer springer springer springer springer springer springer [197] springer springer springer springer springer springer springer springer springer springer springer springer springer springer [211] springer springer springer springer springer springer springer springer springer springer springer springer springer springer [225] taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor [239] taylor taylor taylor taylor taylor taylor taylor taylor taylor taylor other other other other [253] other other other other other other other wiley wiley wiley wiley wiley wiley wiley [267] wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley [281] wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley [295] wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley wiley Levels: other elsevier springer taylor wiley > is.EnvSci = rep(0, length(ISI.Category)) > is.EnvSci[grep("*Environmental Sciences*", ISI.Category)] = 1 > table(is.EnvSci) is.EnvSci 0 1 143 164 > is.Eco = rep(0, length(ISI.Category)) > is.Eco[grep("*Ecology*", ISI.Category)] = 1 > table(is.Eco) is.Eco 0 1 181 126 > is.EvoBio = rep(0, length(ISI.Category)) > is.EvoBio[grep("*Evolutionary Biology*", ISI.Category)] =1 > table(is.EvoBio) is.EvoBio 0 1 267 40 > > > > mylogit = glm(requests~log(ImFa)+ Afil+ PubCode+ is.Eco+ is.EnvSci+ is.EvoBio, family=binomial(link="logit"), na.action=na.omit) ## log creates even distribution for IF > summary(mylogit) Call: glm(formula = requests ~ log(ImFa) + Afil + PubCode + is.Eco + is.EnvSci + is.EvoBio, family = binomial(link = "logit"), na.action = na.omit) Deviance Residuals: Min 1Q Median 3Q Max -1.5923 -0.5175 -0.3049 -0.1650 2.9789 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.47821 0.94286 -4.750 2.04e-06 *** log(ImFa) 1.03947 0.28999 3.584 0.000338 *** Afil 1.06656 0.46263 2.305 0.021142 * PubCodeother 1.51846 0.68919 2.203 0.027577 * PubCodespringer -0.63246 1.19125 -0.531 0.595471 PubCodetaylor -0.07985 1.20958 -0.066 0.947364 PubCodewiley 1.11416 0.75835 1.469 0.141783 is.Eco -0.33277 0.57250 -0.581 0.561067 is.EnvSci 0.46830 0.64702 0.724 0.469200 is.EvoBio 0.75310 0.67683 1.113 0.265841 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 224.11 on 299 degrees of freedom Residual deviance: 179.30 on 290 degrees of freedom (7 observations deleted due to missingness) AIC: 199.30 Number of Fisher Scoring iterations: 6 > confint(mylogit) Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) -6.4891243 -2.7483337 log(ImFa) 0.4997142 1.6439447 Afil 0.1927414 2.0210161 PubCodeother 0.2835126 3.0654572 PubCodespringer -3.6782146 1.5068642 PubCodetaylor -3.1462362 2.0985217 PubCodewiley -0.3023809 2.7566380 is.Eco -1.4871180 0.7674237 is.EnvSci -0.7926678 1.7566885 is.EvoBio -0.5935155 2.0812672 > exp(mylogit$coefficients) (Intercept) log(ImFa) Afil PubCodeother PubCodespringer PubCodetaylor PubCodewiley is.Eco 0.01135371 2.82772192 2.90537996 4.56517827 0.53128225 0.92325210 3.04699545 0.71693464 is.EnvSci is.EvoBio 1.59727355 2.12357998 > exp(confint(mylogit)) Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) 0.001519879 0.06403447 log(ImFa) 1.648250089 5.17554541 Afil 1.212569143 7.54598828 PubCodeother 1.327785624 21.44426327 PubCodespringer 0.025268047 4.51255803 PubCodetaylor 0.043013719 8.15410670 PubCodewiley 0.739056529 15.74681379 is.Eco 0.226023115 2.15420925 is.EnvSci 0.452635621 5.79322142 is.EvoBio 0.552381958 8.01461828
<html><script src="http://gist.github.com/491173.js?file=JournalAnalysis_MultReg"></script> </html>
Estimate Std. Error z value Pr(>|z|) (Intercept) -4.55278 1.23451 -3.688 0.000226 *** log(ImFa) 1.04003 0.29007 3.585 0.000337 *** Afil 1.06761 0.46302 2.306 0.021125 * OthPub 1.60747 1.09173 1.472 0.140913
Estimate Std. Error z value Pr(>|z|) (Intercept) -4.55278 1.23451 -3.688 0.000226 *** log(ImFa) 1.04003 0.29007 3.585 0.000337 *** Afil 1.06761 0.46302 2.306 0.021125 * OthPub 1.60747 1.09173 1.472 0.140913
(Intercept) log(ImFa) S Afil OthPub 0.01053787 2.82930675 2.90840677 4.99014645
2.5 % 97.5 % log(ImFa) 1.6484164883 5.1777868 Afil 1.2128683481 7.5593332 OthPub 0.8527096723 95.7104652
> filename = "/Users/nicholasweber/Desktop/JournalData1.csv" > mydata = read.csv(filename) > ImFa = Impact.Factor > ImFa[ImFa==0] = NA > hist(ImFa) > summary(ImFa) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.064 1.000 1.578 2.132 2.762 16.690 6.000 > SomeOA = ifelse(Subscription.Model == "Sub", 0, 1) > table(SomeOA) SomeOA 0 1 223 84 > Afil = ifelse(Affiliation.Code > 0, 1, 0)] # Society Affiliation Error: unexpected ']' in "Afil = ifelse(Affiliation.Code > 0, 1, 0)]" > table(Afil) Afil 0 1 148 158 > is.EnvSci = rep(0, length(ISI.Category)) > is.EnvSci[grep("*Environmental Sciences*", ISI.Category)] = 1 > table(is.EnvSci) is.EnvSci 0 1 143 164 > is.Eco = rep(0, length(ISI.Category)) > is.Eco[grep("*Ecology*", ISI.Category)] = 1 > table(is.Eco) is.Eco 0 1 181 126 > is.EvoBio = rep(0, length(ISI.Category)) > is.EvoBio[grep("*Evolutionary Biology*", ISI.Category)] =1 > table(is.EvoBio) is.EvoBio 0 1 267 40 > > Springer = rep(0, length(PubCode)) > Springer [grep("*springer*", PubCode)] =1 > table(Springer) Springer 0 1 249 58 > Elsevier = rep(0, length(PubCode)) > Elsevier [grep("*elsevier*", PubCode)] =1 > table(Elsevier)Wiley Error: unexpected symbol in "table(Elsevier)Wiley" > Wiley = rep(0, length(PubCode)) > Wiley [grep("*wiley*", PubCode)] =1 > table(Wiley) Wiley 0 1 259 48 > OthPub = rep(0, length(PubCode)) > OthPub [grep("*other*", PubCode)] =1 > table(OthPub) #Includes all other publishers from dataset OthPub 0 1 182 125 > > mylogit = glm(requests~log(ImFa) + SomeOA+ Afil+ Elsevier+ Springer+ Wiley+ OthPub+ is.Eco+ is.EnvSci + is.EvoBio, family=binomial(link="logit"), na.action=na.omit) ## log creates even distribution for IF > summary(mylogit) Call: glm(formula = requests ~ log(ImFa) + SomeOA + Afil + Elsevier + Springer + Wiley + OthPub + is.Eco + is.EnvSci + is.EvoBio, family = binomial(link = "logit"), na.action = na.omit) Deviance Residuals: Min 1Q Median 3Q Max -1.5987 -0.5199 -0.3057 -0.1653 2.9759 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.55278 1.23451 -3.688 0.000226 *** log(ImFa) 1.04003 0.29007 3.585 0.000337 *** SomeOA -0.02429 0.43966 -0.055 0.955949 Afil 1.06761 0.46302 2.306 0.021125 * Elsevier 0.07862 1.20986 0.065 0.948188 Springer -0.54932 1.45679 -0.377 0.706117 Wiley 1.19822 1.14467 1.047 0.295199 OthPub 1.60747 1.09173 1.472 0.140913 is.Eco -0.33555 0.57484 -0.584 0.559403 is.EnvSci 0.46216 0.65644 0.704 0.481416 is.EvoBio 0.75327 0.67710 1.112 0.265925 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 224.11 on 299 degrees of freedom Residual deviance: 179.30 on 289 degrees of freedom (7 observations deleted due to missingness) AIC: 201.3 Number of Fisher Scoring iterations: 6 > confint(mylogit) Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) -7.6716071 -2.4547973 log(ImFa) 0.4998151 1.6443777 SomeOA -0.9051808 0.8301939 Afil 0.1929881 2.0227830 Elsevier -2.1005325 3.1452976 Springer -3.8359538 2.7374242 Wiley -0.7306740 4.2048215 OthPub -0.1593362 4.5613276 is.Eco -1.4946319 0.7684235 is.EnvSci -0.8165620 1.7687779 is.EvoBio -0.5939997 2.0820360 > exp(mylogit$coefficients) (Intercept) log(ImFa) SomeOA Afil Elsevier Springer Wiley OthPub is.Eco is.EnvSci is.EvoBio 0.01053787 2.82930675 0.97600675 2.90840677 1.08179389 0.57734165 3.31422494 4.99014645 0.71494624 1.58749158 2.12394266 > exp(confint(mylogit)) # conf int for exp Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) 0.0004658685 0.0858806 log(ImFa) 1.6484164883 5.1777868 SomeOA 0.4044687314 2.2937636 Afil 1.2128683481 7.5593332 Elsevier 0.1223912330 23.2265858 Springer 0.0215807450 15.4471456 Wiley 0.4815843005 67.0086336 OthPub 0.8527096723 95.7104652 is.Eco 0.2243311619 2.1563641 is.EnvSci 0.4419484746 5.8636828 is.EvoBio 0.5521145557 8.0207830
<html><script src="http://gist.github.com/491173.js"> </script></html>
Coefficients: Estimate Std. Error z value Pr(>|z|) log(ImFa) 1.04003 0.29007 3.585 0.000337 *** Afil 1.06761 0.46302 2.306 0.021125 * PubCodeother 1.52884 0.71422 2.141 0.032309 *
2.5 % 97.5 % log(ImFa) 0.4998151 1.6443777 Afil 0.1929881 2.0227830 PubCodeother 0.2325047 3.1117025
log(ImFa) Afil PubCodeother 2.82930675 2.90840677 4.61284400
2.5 % 97.5 % log(ImFa) 1.648416488 5.1777868 Afil 1.212868348 7.5593332 PubCodeother 1.261756334 22.4592496
> summary(mylogit) Call: glm(formula = requests ~ log(ImFa) + SomeOA + Afil + PubCode + is.Eco + is.EnvSci + is.EvoBio, family = binomial(link = "logit"), na.action = na.omit) Deviance Residuals: Min 1Q Median 3Q Max -1.5987 -0.5199 -0.3057 -0.1653 2.9759 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.47416 0.94554 -4.732 2.22e-06 *** log(ImFa) 1.04003 0.29007 3.585 0.000337 *** SomeOA -0.02429 0.43966 -0.055 0.955949 Afil 1.06761 0.46302 2.306 0.021125 * PubCodeother 1.52884 0.71422 2.141 0.032309 * PubCodespringer -0.62794 1.19405 -0.526 0.598963 PubCodetaylor -0.07862 1.20986 -0.065 0.948188 PubCodewiley 1.11960 0.76456 1.464 0.143093 is.Eco -0.33555 0.57484 -0.584 0.559403 is.EnvSci 0.46216 0.65644 0.704 0.481416 is.EvoBio 0.75327 0.67710 1.112 0.265925 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 224.11 on 299 degrees of freedom Residual deviance: 179.30 on 289 degrees of freedom (7 observations deleted due to missingness) AIC: 201.3 Number of Fisher Scoring iterations: 6 > confint(mylogit) Waiting for profiling to be done... 2.5 % 97.5 % <b>(Intercept) -6.4901304 -2.7394727</b> log(ImFa) 0.4998151 1.6443777 SomeOA -0.9051808 0.8301939 Afil 0.1929881 2.0227830 PubCodeother 0.2325047 3.1117025 PubCodespringer -3.6768695 1.5175314 PubCodetaylor -3.1452976 2.1005325 PubCodewiley -0.3119753 2.7709763 is.Eco -1.4946319 0.7684235 is.EnvSci -0.8165620 1.7687779 is.EvoBio -0.5939997 2.0820360 > exp(mylogit$coefficients) (Intercept) log(ImFa) SomeOA Afil PubCodeother PubCodespringer PubCodetaylor PubCodewiley 0.01139980 2.82930675 0.97600675 2.90840677 4.61284400 0.53368914 0.92439051 3.06363807 is.Eco is.EnvSci is.EvoBio 0.71494624 1.58749158 2.12394266 > exp(confint(mylogit)) # conf int for exp Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) 0.001518351 0.0646044 log(ImFa) 1.648416488 5.1777868 SomeOA 0.404468731 2.2937636 Afil 1.212868348 7.5593332 PubCodeother 1.261756334 22.4592496 PubCodespringer 0.025302058 4.5609519 PubCodetaylor 0.043054111 8.1705199 PubCodewiley 0.731999586 15.9742218 is.Eco 0.224331162 2.1563641 is.EnvSci 0.441948475 5.8636828 is.EvoBio 0.552114556 8.0207830 |