DataONE:Notebook/Data Citation and Sharing Policy/2010/07/27
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Cleaner Analysis
> 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 1 236 71 > Afil = ifelse(Affiliation.Code > 0, 1, 0) > table(Afil) Afil 0 1 148 158 > table(PubCode) PubCode other elsevier springer wiley 149 52 58 48 > PubCode = relevel(PubCode, ref="other") > 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 -1.0326 -0.5140 -0.3973 -0.3177 2.5392 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.8726 0.7481 -3.840 0.000123 *** log(ImFa) 0.2252 0.2738 0.822 0.410910 Afil 0.4374 0.4100 1.067 0.285966 PubCodeelsevier 1.4796 0.4888 3.027 0.002472 ** PubCodespringer -0.3144 0.6995 -0.450 0.653050 PubCodewiley 0.9403 0.5256 1.789 0.073634 . is.Eco -0.2317 0.5807 -0.399 0.689973 is.EnvSci 0.2959 0.6399 0.462 0.643746 is.EvoBio -0.1708 0.7475 -0.228 0.819299 --- 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: 205.36 on 291 degrees of freedom (7 observations deleted due to missingness) AIC: 223.36 Number of Fisher Scoring iterations: 5 > confint(mylogit) Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) -4.3924248 -1.4488793 log(ImFa) -0.3014913 0.7736730 Afil -0.3572635 1.2583180 PubCodeelsevier 0.5290583 2.4588049 PubCodespringer -1.8708292 0.9588558 PubCodewiley -0.1174621 1.9669483 is.Eco -1.4100069 0.8765251 is.EnvSci -0.9617093 1.5543530 is.EvoBio -1.7375732 1.2369173 > exp(mylogit$coefficients) (Intercept) log(ImFa) Afil PubCodeelsevier PubCodespringer PubCodewiley is.Eco is.EnvSci 0.05654958 1.25255157 1.54872058 4.39102729 0.73020193 2.56077481 0.79322294 1.34440052 is.EvoBio 0.84301868 > exp(confint(mylogit)) Waiting for profiling to be done... 2.5 % 97.5 % (Intercept) 0.01237070 0.2348333 log(ImFa) 0.73971425 2.1677138 Afil 0.69958816 3.5194967 PubCodeelsevier 1.69733323 11.6908318 PubCodespringer 0.15399592 2.6087098 PubCodewiley 0.88917420 7.1488273 is.Eco 0.24414160 2.4025365 is.EnvSci 0.38223896 4.7320241 is.EvoBio 0.17594686 3.4449772
<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 |