rm(list=ls())
# Load libraries ---------------------------
library(foreign)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
# Set wd for generated output ---------------------------
setwd("/Volumes/caas/CMHIV/WISE/AK-R-output")
# Load data ---------------------------
load(file="table1.RData")
options(na.action='na.pass')
# Obtain outcomes with correct 0-1 coding ---------------------------
# see https://stackoverflow.com/questions/38678378/factor-levels-default-to-1-and-2-in-r-dummy-variable
## smoking plans
vuln_dt$scrn7r_b
## [1] plans to not smoke plans to not smoke plans to not smoke
## [4] plans to smoke plans to smoke plans to not smoke
## [7] plans to smoke plans to smoke plans to not smoke
## [10] plans to not smoke plans to smoke plans to not smoke
## [13] plans to not smoke plans to smoke plans to smoke
## [16] plans to smoke plans to not smoke plans to not smoke
## [19] plans to not smoke plans to not smoke plans to not smoke
## [22] plans to smoke plans to not smoke plans to smoke
## [25] plans to not smoke plans to not smoke plans to not smoke
## [28] plans to not smoke plans to not smoke plans to not smoke
## [31] plans to not smoke plans to smoke plans to not smoke
## [34] plans to not smoke plans to not smoke plans to not smoke
## [37] plans to not smoke plans to not smoke plans to not smoke
## [40] plans to smoke plans to not smoke plans to not smoke
## [43] plans to smoke plans to smoke plans to not smoke
## [46] plans to not smoke plans to not smoke plans to not smoke
## [49] plans to smoke plans to not smoke plans to smoke
## [52] plans to smoke plans to not smoke plans to not smoke
## [55] plans to smoke plans to smoke plans to not smoke
## [58] plans to smoke plans to not smoke plans to smoke
## [61] plans to not smoke plans to not smoke plans to smoke
## [64] plans to not smoke plans to not smoke plans to not smoke
## [67] plans to smoke plans to smoke plans to smoke
## [70] plans to not smoke plans to not smoke plans to smoke
## [73] plans to not smoke plans to not smoke plans to smoke
## [76] plans to smoke plans to not smoke plans to smoke
## [79] plans to not smoke plans to not smoke plans to smoke
## [82] plans to not smoke plans to not smoke plans to smoke
## [85] plans to smoke plans to smoke plans to not smoke
## [88] plans to not smoke plans to smoke plans to not smoke
## [91] plans to smoke plans to smoke plans to not smoke
## [94] plans to smoke plans to not smoke plans to smoke
## [97] plans to smoke plans to not smoke plans to smoke
## [100] plans to smoke plans to not smoke plans to smoke
## [103] plans to not smoke plans to not smoke plans to smoke
## [106] plans to smoke plans to not smoke plans to not smoke
## [109] plans to not smoke plans to not smoke plans to not smoke
## [112] plans to smoke plans to not smoke plans to smoke
## [115] plans to not smoke plans to not smoke plans to not smoke
## [118] plans to smoke plans to smoke plans to smoke
## [121] plans to smoke plans to smoke plans to not smoke
## [124] plans to not smoke plans to smoke plans to smoke
## [127] plans to not smoke plans to smoke plans to not smoke
## [130] plans to smoke plans to smoke plans to smoke
## [133] plans to not smoke plans to not smoke plans to not smoke
## [136] plans to not smoke plans to not smoke plans to smoke
## [139] plans to not smoke plans to smoke plans to not smoke
## [142] plans to smoke plans to smoke plans to not smoke
## [145] plans to smoke plans to not smoke plans to smoke
## [148] plans to not smoke plans to smoke plans to not smoke
## [151] plans to not smoke plans to smoke plans to not smoke
## [154] plans to smoke plans to not smoke plans to not smoke
## [157] plans to smoke plans to not smoke plans to smoke
## [160] plans to not smoke plans to not smoke plans to smoke
## [163] plans to smoke plans to smoke plans to smoke
## [166] plans to smoke plans to smoke plans to smoke
## [169] plans to smoke plans to smoke plans to smoke
## [172] plans to not smoke plans to not smoke plans to not smoke
## [175] plans to not smoke plans to not smoke plans to smoke
## [178] plans to not smoke plans to not smoke plans to smoke
## [181] plans to smoke plans to smoke plans to smoke
## [184] <NA> plans to smoke plans to not smoke
## [187] plans to smoke plans to smoke plans to smoke
## [190] plans to smoke plans to not smoke plans to smoke
## [193] plans to smoke plans to smoke plans to not smoke
## [196] plans to smoke plans to smoke plans to not smoke
## [199] plans to smoke plans to smoke plans to smoke
## [202] plans to smoke plans to smoke plans to smoke
## [205] plans to smoke plans to not smoke plans to smoke
## [208] plans to smoke plans to smoke plans to smoke
## [211] plans to not smoke plans to not smoke plans to smoke
## [214] plans to not smoke plans to smoke plans to smoke
## [217] plans to smoke plans to smoke plans to smoke
## [220] plans to not smoke plans to not smoke plans to smoke
## [223] plans to not smoke plans to smoke plans to not smoke
## [226] plans to not smoke plans to smoke plans to smoke
## [229] plans to smoke plans to smoke plans to smoke
## [232] plans to smoke plans to not smoke plans to not smoke
## [235] plans to smoke plans to smoke plans to not smoke
## [238] plans to not smoke plans to smoke plans to smoke
## [241] plans to not smoke plans to not smoke plans to not smoke
## [244] plans to smoke plans to smoke plans to smoke
## [247] plans to smoke
## Levels: plans to smoke plans to not smoke
levels(vuln_dt$scrn7r_b)
## [1] "plans to smoke" "plans to not smoke"
str(vuln_dt$scrn7r_b)
## Factor w/ 2 levels "plans to smoke",..: 2 2 2 1 1 2 1 1 2 2 ...
storage.mode(vuln_dt$scrn7r_b)
## [1] "integer"
as.integer(vuln_dt$scrn7r_b)
## [1] 2 2 2 1 1 2 1 1 2 2 1 2 2 1 1 1 2 2 2 2 2 1 2 1 2
## [26] 2 2 2 2 2 2 1 2 2 2 2 2 2 2 1 2 2 1 1 2 2 2 2 1 2
## [51] 1 1 2 2 1 1 2 1 2 1 2 2 1 2 2 2 1 1 1 2 2 1 2 2 1
## [76] 1 2 1 2 2 1 2 2 1 1 1 2 2 1 2 1 1 2 1 2 1 1 2 1 1
## [101] 2 1 2 2 1 1 2 2 2 2 2 1 2 1 2 2 2 1 1 1 1 1 2 2 1
## [126] 1 2 1 2 1 1 1 2 2 2 2 2 1 2 1 2 1 1 2 1 2 1 2 1 2
## [151] 2 1 2 1 2 2 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 2 2 2 2
## [176] 2 1 2 2 1 1 1 1 NA 1 2 1 1 1 1 2 1 1 1 2 1 1 2 1 1
## [201] 1 1 1 1 1 2 1 1 1 1 2 2 1 2 1 1 1 1 1 2 2 1 2 1 2
## [226] 2 1 1 1 1 1 1 2 2 1 1 2 2 1 1 2 2 2 1 1 1 1
scrn7r_b.out <- as.numeric(model.matrix(~vuln_dt$scrn7r_b)[,2]) #key step
length(scrn7r_b.out)
## [1] 247
length(vuln_dt$scrn7r_b)
## [1] 247
xtabs(~factor(vuln_dt$scrn7r_b) + factor(scrn7r_b.out))
## factor(scrn7r_b.out)
## factor(vuln_dt$scrn7r_b) 0 1
## plans to smoke 126 0
## plans to not smoke 0 120
## quit status
vuln_dt$Final_QuitStatus
## [1] Smoking Quit at 3 weeks Smoking Smoking
## [5] Smoking Smoking Smoking Smoking
## [9] Smoking Smoking Smoking Smoking
## [13] Smoking Quit at 3 weeks Smoking Smoking
## [17] Smoking Smoking Quit at 3 weeks Smoking
## [21] Smoking Smoking Smoking Smoking
## [25] Smoking Smoking Smoking Smoking
## [29] Smoking Smoking Smoking Smoking
## [33] Smoking Quit at 3 weeks Quit at 3 weeks Quit at 3 weeks
## [37] Smoking Smoking Smoking Smoking
## [41] Smoking Smoking Smoking Smoking
## [45] Smoking Quit at 3 weeks Smoking Smoking
## [49] Smoking Smoking Smoking Smoking
## [53] Quit at 3 weeks Quit at 3 weeks Smoking Smoking
## [57] Smoking Smoking Smoking Quit at 3 weeks
## [61] Smoking Smoking Smoking Quit at 3 weeks
## [65] Quit at 3 weeks Smoking Smoking Smoking
## [69] Smoking Smoking Smoking Smoking
## [73] Smoking Smoking Smoking Smoking
## [77] Smoking Smoking Smoking Smoking
## [81] Smoking Smoking Quit at 3 weeks Smoking
## [85] Smoking Quit at 3 weeks Smoking Smoking
## [89] Quit at 3 weeks Smoking Smoking Smoking
## [93] Smoking Smoking Smoking Smoking
## [97] Smoking Smoking Smoking Smoking
## [101] Quit at 3 weeks Smoking Smoking Quit at 3 weeks
## [105] Quit at 3 weeks Smoking Smoking Smoking
## [109] Smoking Smoking Smoking Smoking
## [113] Smoking Smoking Smoking Smoking
## [117] Smoking Smoking Smoking Smoking
## [121] Smoking Smoking Smoking Smoking
## [125] Smoking Smoking Quit at 3 weeks Smoking
## [129] Smoking Smoking Smoking Smoking
## [133] Quit at 3 weeks Smoking Quit at 3 weeks Quit at 3 weeks
## [137] Smoking Smoking Quit at 3 weeks Smoking
## [141] Quit at 3 weeks Smoking Quit at 3 weeks Smoking
## [145] Smoking Smoking Smoking Smoking
## [149] Smoking Smoking Smoking Smoking
## [153] Quit at 3 weeks Smoking Smoking Smoking
## [157] Smoking Smoking Smoking Smoking
## [161] Smoking Smoking Smoking Quit at 3 weeks
## [165] Smoking Quit at 3 weeks Smoking Smoking
## [169] Smoking Smoking Smoking Smoking
## [173] Quit at 3 weeks Smoking Smoking Smoking
## [177] Smoking Smoking Smoking Smoking
## [181] Smoking Smoking Quit at 3 weeks Smoking
## [185] Smoking Quit at 3 weeks Smoking Smoking
## [189] Smoking Smoking Smoking Quit at 3 weeks
## [193] Smoking Smoking Smoking Smoking
## [197] Smoking Smoking Quit at 3 weeks Smoking
## [201] Smoking Smoking Quit at 3 weeks Smoking
## [205] Smoking Smoking Smoking Smoking
## [209] Smoking Smoking Smoking Smoking
## [213] Smoking Smoking Smoking Smoking
## [217] Smoking Smoking Smoking Smoking
## [221] Smoking Smoking Smoking Smoking
## [225] Smoking Smoking Quit at 3 weeks Quit at 3 weeks
## [229] Smoking Smoking Smoking Smoking
## [233] Quit at 3 weeks Quit at 3 weeks Quit at 3 weeks Smoking
## [237] Smoking Smoking Smoking Smoking
## [241] Smoking Quit at 3 weeks Smoking Smoking
## [245] Smoking Smoking Smoking
## Levels: Smoking Quit at 3 weeks
vuln_dt$Final_QuitStatus
## [1] Smoking Quit at 3 weeks Smoking Smoking
## [5] Smoking Smoking Smoking Smoking
## [9] Smoking Smoking Smoking Smoking
## [13] Smoking Quit at 3 weeks Smoking Smoking
## [17] Smoking Smoking Quit at 3 weeks Smoking
## [21] Smoking Smoking Smoking Smoking
## [25] Smoking Smoking Smoking Smoking
## [29] Smoking Smoking Smoking Smoking
## [33] Smoking Quit at 3 weeks Quit at 3 weeks Quit at 3 weeks
## [37] Smoking Smoking Smoking Smoking
## [41] Smoking Smoking Smoking Smoking
## [45] Smoking Quit at 3 weeks Smoking Smoking
## [49] Smoking Smoking Smoking Smoking
## [53] Quit at 3 weeks Quit at 3 weeks Smoking Smoking
## [57] Smoking Smoking Smoking Quit at 3 weeks
## [61] Smoking Smoking Smoking Quit at 3 weeks
## [65] Quit at 3 weeks Smoking Smoking Smoking
## [69] Smoking Smoking Smoking Smoking
## [73] Smoking Smoking Smoking Smoking
## [77] Smoking Smoking Smoking Smoking
## [81] Smoking Smoking Quit at 3 weeks Smoking
## [85] Smoking Quit at 3 weeks Smoking Smoking
## [89] Quit at 3 weeks Smoking Smoking Smoking
## [93] Smoking Smoking Smoking Smoking
## [97] Smoking Smoking Smoking Smoking
## [101] Quit at 3 weeks Smoking Smoking Quit at 3 weeks
## [105] Quit at 3 weeks Smoking Smoking Smoking
## [109] Smoking Smoking Smoking Smoking
## [113] Smoking Smoking Smoking Smoking
## [117] Smoking Smoking Smoking Smoking
## [121] Smoking Smoking Smoking Smoking
## [125] Smoking Smoking Quit at 3 weeks Smoking
## [129] Smoking Smoking Smoking Smoking
## [133] Quit at 3 weeks Smoking Quit at 3 weeks Quit at 3 weeks
## [137] Smoking Smoking Quit at 3 weeks Smoking
## [141] Quit at 3 weeks Smoking Quit at 3 weeks Smoking
## [145] Smoking Smoking Smoking Smoking
## [149] Smoking Smoking Smoking Smoking
## [153] Quit at 3 weeks Smoking Smoking Smoking
## [157] Smoking Smoking Smoking Smoking
## [161] Smoking Smoking Smoking Quit at 3 weeks
## [165] Smoking Quit at 3 weeks Smoking Smoking
## [169] Smoking Smoking Smoking Smoking
## [173] Quit at 3 weeks Smoking Smoking Smoking
## [177] Smoking Smoking Smoking Smoking
## [181] Smoking Smoking Quit at 3 weeks Smoking
## [185] Smoking Quit at 3 weeks Smoking Smoking
## [189] Smoking Smoking Smoking Quit at 3 weeks
## [193] Smoking Smoking Smoking Smoking
## [197] Smoking Smoking Quit at 3 weeks Smoking
## [201] Smoking Smoking Quit at 3 weeks Smoking
## [205] Smoking Smoking Smoking Smoking
## [209] Smoking Smoking Smoking Smoking
## [213] Smoking Smoking Smoking Smoking
## [217] Smoking Smoking Smoking Smoking
## [221] Smoking Smoking Smoking Smoking
## [225] Smoking Smoking Quit at 3 weeks Quit at 3 weeks
## [229] Smoking Smoking Smoking Smoking
## [233] Quit at 3 weeks Quit at 3 weeks Quit at 3 weeks Smoking
## [237] Smoking Smoking Smoking Smoking
## [241] Smoking Quit at 3 weeks Smoking Smoking
## [245] Smoking Smoking Smoking
## Levels: Smoking Quit at 3 weeks
levels(vuln_dt$Final_QuitStatus)
## [1] "Smoking" "Quit at 3 weeks"
str(vuln_dt$Final_QuitStatus)
## Factor w/ 2 levels "Smoking","Quit at 3 weeks": 1 2 1 1 1 1 1 1 1 1 ...
storage.mode(vuln_dt$Final_QuitStatus)
## [1] "integer"
as.integer(vuln_dt$Final_QuitStatus)
## [1] 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1
## [38] 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1
## [75] 1 1 1 1 1 1 1 1 2 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 2 1 1 1 1 1 1
## [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 2 2 1 1 2 1 2 1 2 1 1 1 1 1
## [149] 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1
## [186] 2 1 1 1 1 1 2 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
## [223] 1 1 1 1 2 2 1 1 1 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 1
Final_QuitStatus.out <- as.numeric(model.matrix(~vuln_dt$Final_QuitStatus)[,2]) #key step
length(Final_QuitStatus.out)
## [1] 247
length(vuln_dt$Final_QuitStatus)
## [1] 247
xtabs(~factor(vuln_dt$Final_QuitStatus) + factor(Final_QuitStatus.out))
## factor(Final_QuitStatus.out)
## factor(vuln_dt$Final_QuitStatus) 0 1
## Smoking 207 0
## Quit at 3 weeks 0 40
# Control Variable: TRT_Group ---------------------------
vuln_dt$trt_grp
## [1] Intervention Intervention Control Intervention Control
## [6] Intervention Intervention Control Control Control
## [11] Control Intervention Intervention Intervention Control
## [16] Control Control Control Control Control
## [21] Intervention Intervention Intervention Intervention Intervention
## [26] Control Intervention Control Intervention Control
## [31] Intervention Intervention Intervention Intervention Control
## [36] Control Control Control Control Intervention
## [41] Intervention Intervention Control Control Control
## [46] Intervention Control Control Intervention Intervention
## [51] Intervention Control Intervention Intervention Intervention
## [56] Control Control Intervention Intervention Intervention
## [61] Control Control Control Intervention Intervention
## [66] Control Control Intervention Control Control
## [71] Intervention Intervention Intervention Control Intervention
## [76] Intervention Control Control Control Intervention
## [81] Control Control Intervention Intervention Control
## [86] Intervention Intervention Intervention Intervention Control
## [91] Control Control Control Control Intervention
## [96] Intervention Intervention Intervention Intervention Control
## [101] Control Control Intervention Intervention Intervention
## [106] Intervention Control Control Intervention Intervention
## [111] Control Control Intervention Intervention Intervention
## [116] Control Control Control Control Control
## [121] Intervention Intervention Control Control Control
## [126] Intervention Intervention Control Control Control
## [131] Intervention Intervention Intervention Control Intervention
## [136] Intervention Control Intervention Control Control
## [141] Intervention Control Intervention Intervention Control
## [146] Control Control Control Intervention Intervention
## [151] Control Control Control Control Intervention
## [156] Control Intervention Control Intervention Control
## [161] Intervention Control Intervention Intervention Intervention
## [166] Control Control Intervention Intervention Intervention
## [171] Intervention Control Intervention Control Intervention
## [176] Control Intervention Control Control Control
## [181] Control Intervention Intervention Control Control
## [186] Control Intervention Control Control Intervention
## [191] Control Intervention Intervention Control Intervention
## [196] Control Control Intervention Intervention Control
## [201] Intervention Intervention Control Intervention Control
## [206] Control Control Intervention Control Intervention
## [211] Intervention Intervention Control Control Intervention
## [216] Control Control Intervention Control Control
## [221] Intervention Intervention Intervention Control Control
## [226] Control Intervention Intervention Control Control
## [231] Intervention Intervention Intervention Intervention Intervention
## [236] Control Control Control Intervention Control
## [241] Intervention Intervention Control Control Control
## [246] Intervention Control
## Levels: Control Intervention
# Adjustment variables ---------------------------
drugp1 <- na_if(vuln_dt$drugp1, "Not Applicable")
levels(drugp1)
## [1] "No" "Yes" "Don't Know" "Refuse to Answer"
## [5] "Not Applicable"
# Logistic Regressions (Smoking plans) ---------------------------
outcomes <- cbind(scrn7r_b.out, Final_QuitStatus.out)
## Future Vulnerability
FPV.logreg.scrn7rb <-
glm(scrn7r_b.out ~ FPV +
vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2,
family="binomial",
na.action = 'na.omit'
)
FPV.logreg.finalquit <-
glm(Final_QuitStatus.out ~ FPV + vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2+
scrn7r_b.out,
family="binomial",
na.action = 'na.omit'
)
summary(FPV.logreg.scrn7rb)
##
## Call:
## glm(formula = scrn7r_b.out ~ FPV + vuln_dt$trt_grp + drugp1 +
## vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2, family = "binomial",
## na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.7336 -1.0083 -0.0002 1.0586 1.8590
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 15.62091 3956.18058 0.004 0.9968
## FPV 0.10165 0.03983 2.552 0.0107 *
## vuln_dt$trt_grpIntervention -0.10410 0.30054 -0.346 0.7291
## drugp1Yes 0.46075 0.30924 1.490 0.1362
## vuln_dt$smhis1_6mMore than 6 months 0.78532 0.30935 2.539 0.0111 *
## vuln_dt$hispanic -0.72153 0.40745 -1.771 0.0766 .
## vuln_dt$ftnd25 0.07651 4845.25570 0.000 1.0000
## vuln_dt$ftnd26 0.11549 5594.88402 0.000 1.0000
## vuln_dt$ftnd27 -1.02647 5594.88399 0.000 0.9999
## vuln_dt$ftnd29 -35.85612 5594.88400 -0.006 0.9949
## vuln_dt$ftnd210 -17.75064 3956.18051 -0.004 0.9964
## vuln_dt$ftnd211 -1.02647 5594.88399 0.000 0.9999
## vuln_dt$ftnd212 0.15581 5594.88399 0.000 1.0000
## vuln_dt$ftnd213 -17.01402 3956.18075 -0.004 0.9966
## vuln_dt$ftnd215 -17.74642 3956.18052 -0.004 0.9964
## vuln_dt$ftnd218 -34.95051 4184.67742 -0.008 0.9933
## vuln_dt$ftnd220 -17.96155 3956.18050 -0.005 0.9964
## vuln_dt$ftnd221 0.11549 5594.88402 0.000 1.0000
## vuln_dt$ftnd222 -16.81283 3956.18069 -0.004 0.9966
## vuln_dt$ftnd225 -18.08144 3956.18055 -0.005 0.9964
## vuln_dt$ftnd228 -0.92482 5594.88399 0.000 0.9999
## vuln_dt$ftnd230 -17.36596 3956.18052 -0.004 0.9965
## vuln_dt$ftnd233 -35.01664 5594.88402 -0.006 0.9950
## vuln_dt$ftnd235 -17.87687 3956.18063 -0.005 0.9964
## vuln_dt$ftnd238 -34.98878 5594.88402 -0.006 0.9950
## vuln_dt$ftnd240 -17.51812 3956.18052 -0.004 0.9965
## vuln_dt$ftnd245 -34.54468 4841.67990 -0.007 0.9943
## vuln_dt$ftnd260 0.04674 4258.96462 0.000 1.0000
## vuln_dt$ftnd290 -0.34526 5594.88401 0.000 1.0000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 322.66 on 232 degrees of freedom
## Residual deviance: 261.40 on 204 degrees of freedom
## (14 observations deleted due to missingness)
## AIC: 319.4
##
## Number of Fisher Scoring iterations: 16
summary(FPV.logreg.finalquit)
##
## Call:
## glm(formula = Final_QuitStatus.out ~ FPV + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2 +
## scrn7r_b.out, family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.86779 -0.56513 -0.31000 -0.00013 2.94720
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 13.06749 6522.63889 0.002 0.99840
## FPV -0.01628 0.05233 -0.311 0.75571
## vuln_dt$trt_grpIntervention 1.59468 0.48706 3.274 0.00106 **
## drugp1Yes 0.54351 0.47034 1.156 0.24786
## vuln_dt$smhis1_6mMore than 6 months 1.41618 0.50170 2.823 0.00476 **
## vuln_dt$hispanic 1.13885 0.55667 2.046 0.04077 *
## vuln_dt$ftnd25 -34.56024 7987.22375 -0.004 0.99655
## vuln_dt$ftnd26 -32.39008 9224.40412 -0.004 0.99720
## vuln_dt$ftnd27 1.18770 9224.40408 0.000 0.99990
## vuln_dt$ftnd29 -33.36532 9224.40412 -0.004 0.99711
## vuln_dt$ftnd210 -17.59088 6522.63877 -0.003 0.99785
## vuln_dt$ftnd211 1.18770 9224.40408 0.000 0.99990
## vuln_dt$ftnd212 0.59235 9224.40408 0.000 0.99995
## vuln_dt$ftnd213 -33.63442 7941.80779 -0.004 0.99662
## vuln_dt$ftnd215 -17.52327 6522.63878 -0.003 0.99786
## vuln_dt$ftnd218 -16.13871 6522.63885 -0.002 0.99803
## vuln_dt$ftnd220 -17.25088 6522.63876 -0.003 0.99789
## vuln_dt$ftnd221 -32.39008 9224.40412 -0.004 0.99720
## vuln_dt$ftnd222 -17.27267 6522.63889 -0.003 0.99789
## vuln_dt$ftnd225 -34.67321 6745.87661 -0.005 0.99590
## vuln_dt$ftnd228 -35.96072 9224.40408 -0.004 0.99689
## vuln_dt$ftnd230 -18.10693 6522.63880 -0.003 0.99779
## vuln_dt$ftnd233 -31.34051 9224.40415 -0.003 0.99729
## vuln_dt$ftnd235 -16.06195 6522.63887 -0.002 0.99804
## vuln_dt$ftnd238 -32.88693 9224.40414 -0.004 0.99716
## vuln_dt$ftnd240 -17.76466 6522.63878 -0.003 0.99783
## vuln_dt$ftnd245 -33.15972 7760.43911 -0.004 0.99659
## vuln_dt$ftnd260 -35.24758 6981.12038 -0.005 0.99597
## vuln_dt$ftnd290 -32.93359 9224.40411 -0.004 0.99715
## scrn7r_b.out 1.04957 0.48004 2.186 0.02879 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 207.26 on 232 degrees of freedom
## Residual deviance: 144.19 on 203 degrees of freedom
## (14 observations deleted due to missingness)
## AIC: 204.19
##
## Number of Fisher Scoring iterations: 17
## Future Precaution
FUTPREC.logreg.scrn7rb <-
glm(scrn7r_b.out ~ FUTPREC +
vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2,
family="binomial",
na.action = 'na.omit'
)
FUTPREC.logreg.finalquit <-
glm(Final_QuitStatus.out ~ FUTPREC + vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2+
scrn7r_b.out,
family="binomial",
na.action = 'na.omit'
)
summary(FUTPREC.logreg.scrn7rb)
##
## Call:
## glm(formula = scrn7r_b.out ~ FUTPREC + vuln_dt$trt_grp + drugp1 +
## vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2, family = "binomial",
## na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.62143 -0.99281 -0.00022 1.07350 2.06745
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 15.9950 3956.1805 0.004 0.9968
## FUTPREC 0.4325 0.1788 2.419 0.0156 *
## vuln_dt$trt_grpIntervention -0.2460 0.2974 -0.827 0.4081
## drugp1Yes 0.3951 0.3046 1.297 0.1945
## vuln_dt$smhis1_6mMore than 6 months 0.6318 0.3063 2.063 0.0391 *
## vuln_dt$hispanic -0.6515 0.4093 -1.592 0.1115
## vuln_dt$ftnd25 -0.7127 4798.7096 0.000 0.9999
## vuln_dt$ftnd26 -0.1590 5594.8840 0.000 1.0000
## vuln_dt$ftnd27 -0.9399 5594.8839 0.000 0.9999
## vuln_dt$ftnd29 -35.8855 5594.8839 -0.006 0.9949
## vuln_dt$ftnd210 -18.0692 3956.1804 -0.005 0.9964
## vuln_dt$ftnd211 -0.9399 5594.8839 0.000 0.9999
## vuln_dt$ftnd212 0.1068 5594.8839 0.000 1.0000
## vuln_dt$ftnd213 -17.6901 3956.1807 -0.004 0.9964
## vuln_dt$ftnd215 -18.2201 3956.1804 -0.005 0.9963
## vuln_dt$ftnd218 -35.1026 4184.9605 -0.008 0.9933
## vuln_dt$ftnd220 -18.1778 3956.1804 -0.005 0.9963
## vuln_dt$ftnd221 0.9944 5594.8840 0.000 0.9999
## vuln_dt$ftnd222 -17.2474 3956.1806 -0.004 0.9965
## vuln_dt$ftnd225 -18.0720 3956.1805 -0.005 0.9964
## vuln_dt$ftnd228 -0.5074 5594.8839 0.000 0.9999
## vuln_dt$ftnd230 -17.5039 3956.1805 -0.004 0.9965
## vuln_dt$ftnd233 -35.0028 5594.8840 -0.006 0.9950
## vuln_dt$ftnd235 -17.8890 3956.1805 -0.005 0.9964
## vuln_dt$ftnd238 -35.9229 5594.8840 -0.006 0.9949
## vuln_dt$ftnd240 -17.6356 3956.1805 -0.004 0.9964
## vuln_dt$ftnd245 -35.2811 4845.1933 -0.007 0.9942
## vuln_dt$ftnd260 0.1066 4247.8417 0.000 1.0000
## vuln_dt$ftnd290 -0.5541 5594.8840 0.000 0.9999
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 326.74 on 235 degrees of freedom
## Residual deviance: 266.38 on 207 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 324.38
##
## Number of Fisher Scoring iterations: 16
summary(FUTPREC.logreg.finalquit)
##
## Call:
## glm(formula = Final_QuitStatus.out ~ FUTPREC + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2 +
## scrn7r_b.out, family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.88804 -0.55374 -0.29858 -0.00014 3.07147
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 13.2157 6522.6388 0.002 0.998383
## FUTPREC -0.2149 0.2718 -0.791 0.429208
## vuln_dt$trt_grpIntervention 1.6754 0.4985 3.361 0.000776 ***
## drugp1Yes 0.6006 0.4689 1.281 0.200265
## vuln_dt$smhis1_6mMore than 6 months 1.5415 0.5143 2.997 0.002726 **
## vuln_dt$hispanic 1.1721 0.5590 2.097 0.036032 *
## vuln_dt$ftnd25 -34.2098 7987.5317 -0.004 0.996583
## vuln_dt$ftnd26 -31.9994 9224.4041 -0.003 0.997232
## vuln_dt$ftnd27 1.3153 9224.4040 0.000 0.999886
## vuln_dt$ftnd29 -33.2792 9224.4041 -0.004 0.997121
## vuln_dt$ftnd210 -17.3774 6522.6387 -0.003 0.997874
## vuln_dt$ftnd211 1.3153 9224.4040 0.000 0.999886
## vuln_dt$ftnd212 0.7439 9224.4040 0.000 0.999936
## vuln_dt$ftnd213 -33.1558 7945.7884 -0.004 0.996671
## vuln_dt$ftnd215 -17.3456 6522.6387 -0.003 0.997878
## vuln_dt$ftnd218 -15.9758 6522.6388 -0.002 0.998046
## vuln_dt$ftnd220 -17.0641 6522.6387 -0.003 0.997913
## vuln_dt$ftnd221 -32.5724 9224.4041 -0.004 0.997183
## vuln_dt$ftnd222 -17.0174 6522.6388 -0.003 0.997918
## vuln_dt$ftnd225 -34.6249 6739.7002 -0.005 0.995901
## vuln_dt$ftnd228 -36.0317 9224.4040 -0.004 0.996883
## vuln_dt$ftnd230 -17.8601 6522.6387 -0.003 0.997815
## vuln_dt$ftnd233 -31.0655 9224.4041 -0.003 0.997313
## vuln_dt$ftnd235 -16.0341 6522.6388 -0.002 0.998039
## vuln_dt$ftnd238 -32.4637 9224.4041 -0.004 0.997192
## vuln_dt$ftnd240 -17.5809 6522.6387 -0.003 0.997849
## vuln_dt$ftnd245 -32.8030 7739.1968 -0.004 0.996618
## vuln_dt$ftnd260 -35.1284 6982.9978 -0.005 0.995986
## vuln_dt$ftnd290 -32.6000 9224.4041 -0.004 0.997180
## scrn7r_b.out 1.0771 0.4797 2.245 0.024741 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 208.32 on 235 degrees of freedom
## Residual deviance: 144.37 on 206 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 204.37
##
## Number of Fisher Scoring iterations: 17
## Relative Pessimism
RELPESS.logreg.scrn7rb <-
glm(scrn7r_b.out ~ RELPESS +
vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2,
family="binomial",
na.action = 'na.omit'
)
RELPESS.logreg.finalquit <-
glm(Final_QuitStatus.out ~ RELPESS + vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2+
scrn7r_b.out,
family="binomial",
na.action = 'na.omit'
)
summary(RELPESS.logreg.scrn7rb)
##
## Call:
## glm(formula = scrn7r_b.out ~ RELPESS + vuln_dt$trt_grp + drugp1 +
## vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2, family = "binomial",
## na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.4963 -1.0576 -0.0002 1.0964 1.8345
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 16.76192 3956.18046 0.004 0.9966
## RELPESS 0.11468 0.13522 0.848 0.3964
## vuln_dt$trt_grpIntervention -0.15180 0.29090 -0.522 0.6018
## drugp1Yes 0.45397 0.30062 1.510 0.1310
## vuln_dt$smhis1_6mMore than 6 months 0.73962 0.30344 2.437 0.0148 *
## vuln_dt$hispanic -0.61990 0.40044 -1.548 0.1216
## vuln_dt$ftnd25 -0.23969 4737.36977 0.000 1.0000
## vuln_dt$ftnd26 0.46012 5594.88395 0.000 0.9999
## vuln_dt$ftnd27 -0.35232 5594.88393 0.000 0.9999
## vuln_dt$ftnd29 -35.94207 5594.88393 -0.006 0.9949
## vuln_dt$ftnd210 -17.70991 3956.18041 -0.004 0.9964
## vuln_dt$ftnd211 -0.58168 5594.88392 0.000 0.9999
## vuln_dt$ftnd212 0.72155 5594.88393 0.000 0.9999
## vuln_dt$ftnd213 -16.94708 3956.18065 -0.004 0.9966
## vuln_dt$ftnd215 -17.84834 3956.18042 -0.005 0.9964
## vuln_dt$ftnd218 -35.04495 4198.15927 -0.008 0.9933
## vuln_dt$ftnd220 -17.84006 3956.18040 -0.005 0.9964
## vuln_dt$ftnd221 0.68947 5594.88396 0.000 0.9999
## vuln_dt$ftnd222 -16.79194 3956.18059 -0.004 0.9966
## vuln_dt$ftnd225 -17.85450 3956.18045 -0.005 0.9964
## vuln_dt$ftnd228 -0.73458 5594.88393 0.000 0.9999
## vuln_dt$ftnd230 -17.20060 3956.18043 -0.004 0.9965
## vuln_dt$ftnd233 -34.82492 5594.88395 -0.006 0.9950
## vuln_dt$ftnd235 -17.70929 3956.18052 -0.004 0.9964
## vuln_dt$ftnd238 -35.25874 5594.88395 -0.006 0.9950
## vuln_dt$ftnd240 -17.38535 3956.18042 -0.004 0.9965
## vuln_dt$ftnd245 -34.77264 4843.47720 -0.007 0.9943
## vuln_dt$ftnd260 0.23683 4261.44082 0.000 1.0000
## vuln_dt$ftnd290 -0.07031 5594.88394 0.000 1.0000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 326.74 on 235 degrees of freedom
## Residual deviance: 271.87 on 207 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 329.87
##
## Number of Fisher Scoring iterations: 16
summary(RELPESS.logreg.finalquit)
##
## Call:
## glm(formula = Final_QuitStatus.out ~ RELPESS + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2 +
## scrn7r_b.out, family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.79075 -0.53462 -0.28540 -0.00015 2.97047
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 13.40035 6522.63887 0.002 0.99836
## RELPESS -0.20900 0.20268 -1.031 0.30245
## vuln_dt$trt_grpIntervention 1.58670 0.48662 3.261 0.00111 **
## drugp1Yes 0.55458 0.46570 1.191 0.23372
## vuln_dt$smhis1_6mMore than 6 months 1.45174 0.50422 2.879 0.00399 **
## vuln_dt$hispanic 1.22363 0.56286 2.174 0.02971 *
## vuln_dt$ftnd25 -34.46943 7923.60425 -0.004 0.99653
## vuln_dt$ftnd26 -32.38516 9224.40412 -0.004 0.99720
## vuln_dt$ftnd27 0.73596 9224.40408 0.000 0.99994
## vuln_dt$ftnd29 -33.20640 9224.40412 -0.004 0.99713
## vuln_dt$ftnd210 -17.68392 6522.63877 -0.003 0.99784
## vuln_dt$ftnd211 1.15396 9224.40408 0.000 0.99990
## vuln_dt$ftnd212 0.06691 9224.40408 0.000 0.99999
## vuln_dt$ftnd213 -33.67382 7921.85910 -0.004 0.99661
## vuln_dt$ftnd215 -17.63255 6522.63878 -0.003 0.99784
## vuln_dt$ftnd218 -15.98204 6522.63885 -0.002 0.99804
## vuln_dt$ftnd220 -17.24266 6522.63876 -0.003 0.99789
## vuln_dt$ftnd221 -32.80316 9224.40413 -0.004 0.99716
## vuln_dt$ftnd222 -17.24334 6522.63890 -0.003 0.99789
## vuln_dt$ftnd225 -34.72789 6742.82788 -0.005 0.99589
## vuln_dt$ftnd228 -35.69951 9224.40408 -0.004 0.99691
## vuln_dt$ftnd230 -17.98121 6522.63880 -0.003 0.99780
## vuln_dt$ftnd233 -31.06075 9224.40415 -0.003 0.99731
## vuln_dt$ftnd235 -16.21125 6522.63887 -0.002 0.99802
## vuln_dt$ftnd238 -33.06982 9224.40414 -0.004 0.99714
## vuln_dt$ftnd240 -17.78915 6522.63878 -0.003 0.99782
## vuln_dt$ftnd245 -33.07418 7761.21400 -0.004 0.99660
## vuln_dt$ftnd260 -35.26936 6988.72710 -0.005 0.99597
## vuln_dt$ftnd290 -32.80041 9224.40411 -0.004 0.99716
## scrn7r_b.out 1.04574 0.47637 2.195 0.02815 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 208.32 on 235 degrees of freedom
## Residual deviance: 143.90 on 206 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 203.9
##
## Number of Fisher Scoring iterations: 17
## Current Vulnerability
ropbais5.logreg.scrn7rb <-
glm(scrn7r_b.out ~ ropbais5 +
vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2,
family="binomial",
na.action = 'na.omit'
)
ropbais5.logreg.finalquit <-
glm(Final_QuitStatus.out ~ ropbais5 + vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2+
scrn7r_b.out,
family="binomial",
na.action = 'na.omit'
)
summary(ropbais5.logreg.scrn7rb)
##
## Call:
## glm(formula = scrn7r_b.out ~ ropbais5 + vuln_dt$trt_grp + drugp1 +
## vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2, family = "binomial",
## na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.67318 -0.98262 -0.00018 0.99929 2.05350
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 15.93033 3956.18050 0.004 0.996787
## ropbais51 1.06379 0.31536 3.373 0.000743 ***
## ropbais5Don't Know -17.08468 3956.18036 -0.004 0.996554
## vuln_dt$trt_grpIntervention -0.06408 0.30135 -0.213 0.831608
## drugp1Yes 0.53413 0.31311 1.706 0.088028 .
## vuln_dt$smhis1_6mMore than 6 months 0.75828 0.31168 2.433 0.014980 *
## vuln_dt$hispanic -0.65639 0.41569 -1.579 0.114330
## vuln_dt$ftnd25 -0.27516 4807.21115 0.000 0.999954
## vuln_dt$ftnd26 0.57195 5594.88398 0.000 0.999918
## vuln_dt$ftnd27 -0.65639 5594.88396 0.000 0.999906
## vuln_dt$ftnd29 -34.78881 5594.88397 -0.006 0.995039
## vuln_dt$ftnd210 -17.18885 3956.18046 -0.004 0.996533
## vuln_dt$ftnd211 -0.65639 5594.88396 0.000 0.999906
## vuln_dt$ftnd212 1.59792 5594.88396 0.000 0.999772
## vuln_dt$ftnd213 -16.36906 3956.18072 -0.004 0.996699
## vuln_dt$ftnd215 -17.17000 3956.18047 -0.004 0.996537
## vuln_dt$ftnd218 -34.59309 4170.37354 -0.008 0.993382
## vuln_dt$ftnd220 -17.39441 3956.18046 -0.004 0.996492
## vuln_dt$ftnd221 0.57195 5594.88398 0.000 0.999918
## vuln_dt$ftnd222 -16.32785 3956.18064 -0.004 0.996707
## vuln_dt$ftnd225 -17.64028 3956.18051 -0.004 0.996442
## vuln_dt$ftnd228 -0.65639 5594.88396 0.000 0.999906
## vuln_dt$ftnd230 -16.47622 3956.18048 -0.004 0.996677
## vuln_dt$ftnd233 -34.56019 5594.88398 -0.006 0.995071
## vuln_dt$ftnd235 -17.22744 3956.18059 -0.004 0.996526
## vuln_dt$ftnd238 -34.25468 5594.88399 -0.006 0.995115
## vuln_dt$ftnd240 -16.75025 3956.18048 -0.004 0.996622
## vuln_dt$ftnd245 -34.15343 4777.66914 -0.007 0.994296
## vuln_dt$ftnd260 0.69903 4242.60040 0.000 0.999869
## vuln_dt$ftnd290 0.03782 5594.88397 0.000 0.999995
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 326.74 on 235 degrees of freedom
## Residual deviance: 259.19 on 206 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 319.19
##
## Number of Fisher Scoring iterations: 16
summary(ropbais5.logreg.finalquit)
##
## Call:
## glm(formula = Final_QuitStatus.out ~ ropbais5 + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2 +
## scrn7r_b.out, family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.91272 -0.52983 -0.30110 -0.00013 2.93121
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 13.0947 6522.6388 0.002 0.99840
## ropbais51 -0.3580 0.4481 -0.799 0.42432
## ropbais5Don't Know -15.4257 6522.6387 -0.002 0.99811
## vuln_dt$trt_grpIntervention 1.5705 0.4865 3.228 0.00125 **
## drugp1Yes 0.5058 0.4664 1.084 0.27821
## vuln_dt$smhis1_6mMore than 6 months 1.4870 0.5029 2.957 0.00311 **
## vuln_dt$hispanic 1.1660 0.5618 2.076 0.03794 *
## vuln_dt$ftnd25 -34.4379 7988.1176 -0.004 0.99656
## vuln_dt$ftnd26 -32.4029 9224.4041 -0.004 0.99720
## vuln_dt$ftnd27 1.1660 9224.4040 0.000 0.99990
## vuln_dt$ftnd29 -33.6535 9224.4041 -0.004 0.99709
## vuln_dt$ftnd210 -17.7728 6522.6387 -0.003 0.99783
## vuln_dt$ftnd211 1.1660 9224.4040 0.000 0.99990
## vuln_dt$ftnd212 0.1477 9224.4040 0.000 0.99999
## vuln_dt$ftnd213 -33.7149 7956.3971 -0.004 0.99662
## vuln_dt$ftnd215 -17.7221 6522.6387 -0.003 0.99783
## vuln_dt$ftnd218 -16.1808 6522.6388 -0.002 0.99802
## vuln_dt$ftnd220 -17.3770 6522.6387 -0.003 0.99787
## vuln_dt$ftnd221 -32.4029 9224.4041 -0.004 0.99720
## vuln_dt$ftnd222 -17.4164 6522.6388 -0.003 0.99787
## vuln_dt$ftnd225 -34.7192 6747.4620 -0.005 0.99589
## vuln_dt$ftnd228 -35.9661 9224.4040 -0.004 0.99689
## vuln_dt$ftnd230 -18.2821 6522.6387 -0.003 0.99776
## vuln_dt$ftnd233 -31.3028 9224.4041 -0.003 0.99729
## vuln_dt$ftnd235 -16.1697 6522.6388 -0.002 0.99802
## vuln_dt$ftnd238 -33.1477 9224.4041 -0.004 0.99713
## vuln_dt$ftnd240 -17.9590 6522.6387 -0.003 0.99780
## vuln_dt$ftnd245 -33.2029 7794.2402 -0.004 0.99660
## vuln_dt$ftnd260 -35.3656 6985.7003 -0.005 0.99596
## vuln_dt$ftnd290 -32.9086 9224.4041 -0.004 0.99715
## scrn7r_b.out 1.1001 0.4871 2.258 0.02393 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 208.32 on 235 degrees of freedom
## Residual deviance: 144.28 on 205 degrees of freedom
## (11 observations deleted due to missingness)
## AIC: 206.28
##
## Number of Fisher Scoring iterations: 17
## Future Pessimism
OPBIAS4R_2way.logreg.scrn7rb <-
glm(scrn7r_b.out ~ OPBIAS4R_2way +
vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2,
family="binomial",
na.action = 'na.omit'
)
OPBIAS4R_2way.logreg.finalquit <-
glm(Final_QuitStatus.out ~ OPBIAS4R_2way + vuln_dt$trt_grp+
drugp1+
vuln_dt$smhis1_6m+
vuln_dt$hispanic+
vuln_dt$ftnd2+
scrn7r_b.out,
family="binomial",
na.action = 'na.omit'
)
summary(OPBIAS4R_2way.logreg.scrn7rb)
##
## Call:
## glm(formula = scrn7r_b.out ~ OPBIAS4R_2way + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2,
## family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.59109 -1.02683 -0.00021 1.08572 1.80243
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 17.0774 3956.1803 0.004 0.99656
## OPBIAS4R_2way1 0.2831 0.3184 0.889 0.37396
## vuln_dt$trt_grpIntervention -0.1810 0.2953 -0.613 0.53997
## drugp1Yes 0.4650 0.3049 1.525 0.12724
## vuln_dt$smhis1_6mMore than 6 months 0.7886 0.3061 2.576 0.00999 **
## vuln_dt$hispanic -0.5839 0.4083 -1.430 0.15264
## vuln_dt$ftnd25 -0.3549 4754.7441 0.000 0.99994
## vuln_dt$ftnd26 0.4887 5594.8839 0.000 0.99993
## vuln_dt$ftnd27 -0.5839 5594.8838 0.000 0.99992
## vuln_dt$ftnd29 -35.8971 5594.8838 -0.006 0.99488
## vuln_dt$ftnd210 -18.0005 3956.1803 -0.005 0.99637
## vuln_dt$ftnd211 -0.5839 5594.8838 0.000 0.99992
## vuln_dt$ftnd212 0.4650 5594.8838 0.000 0.99993
## vuln_dt$ftnd213 -16.9274 3956.1805 -0.004 0.99659
## vuln_dt$ftnd215 -17.8794 3956.1803 -0.005 0.99639
## vuln_dt$ftnd218 -35.1042 4195.8621 -0.008 0.99332
## vuln_dt$ftnd220 -17.9305 3956.1803 -0.005 0.99638
## vuln_dt$ftnd221 0.4887 5594.8839 0.000 0.99993
## vuln_dt$ftnd222 -16.9147 3956.1805 -0.004 0.99659
## vuln_dt$ftnd225 -17.9793 3956.1803 -0.005 0.99637
## vuln_dt$ftnd228 -0.8670 5594.8838 0.000 0.99988
## vuln_dt$ftnd230 -17.2898 3956.1803 -0.004 0.99651
## vuln_dt$ftnd233 -34.6435 5594.8839 -0.006 0.99506
## vuln_dt$ftnd235 -17.7782 3956.1804 -0.004 0.99641
## vuln_dt$ftnd238 -35.4321 5594.8839 -0.006 0.99495
## vuln_dt$ftnd240 -17.5382 3956.1803 -0.004 0.99646
## vuln_dt$ftnd245 -34.8997 4831.5410 -0.007 0.99424
## vuln_dt$ftnd260 0.1616 4260.2653 0.000 0.99997
## vuln_dt$ftnd290 0.0237 5594.8838 0.000 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 321.00 on 231 degrees of freedom
## Residual deviance: 264.71 on 203 degrees of freedom
## (15 observations deleted due to missingness)
## AIC: 322.71
##
## Number of Fisher Scoring iterations: 16
summary(OPBIAS4R_2way.logreg.finalquit)
##
## Call:
## glm(formula = Final_QuitStatus.out ~ OPBIAS4R_2way + vuln_dt$trt_grp +
## drugp1 + vuln_dt$smhis1_6m + vuln_dt$hispanic + vuln_dt$ftnd2 +
## scrn7r_b.out, family = "binomial", na.action = "na.omit")
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.90923 -0.51967 -0.30496 -0.00014 2.98321
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 12.3929 6522.6387 0.002 0.998484
## OPBIAS4R_2way1 -0.8019 0.5104 -1.571 0.116143
## vuln_dt$trt_grpIntervention 1.7523 0.5073 3.454 0.000552 ***
## drugp1Yes 0.4872 0.4660 1.045 0.295827
## vuln_dt$smhis1_6mMore than 6 months 1.4349 0.5141 2.791 0.005252 **
## vuln_dt$hispanic 1.3897 0.5883 2.362 0.018167 *
## vuln_dt$ftnd25 -33.8542 7932.7916 -0.004 0.996595
## vuln_dt$ftnd26 -32.0679 9224.4040 -0.003 0.997226
## vuln_dt$ftnd27 1.3897 9224.4040 0.000 0.999880
## vuln_dt$ftnd29 -32.8811 9224.4040 -0.004 0.997156
## vuln_dt$ftnd210 -17.1902 6522.6386 -0.003 0.997897
## vuln_dt$ftnd211 1.3897 9224.4040 0.000 0.999880
## vuln_dt$ftnd212 0.4872 9224.4040 0.000 0.999958
## vuln_dt$ftnd213 -33.4582 7924.4311 -0.004 0.996631
## vuln_dt$ftnd215 -17.0321 6522.6386 -0.003 0.997917
## vuln_dt$ftnd218 -15.4217 6522.6387 -0.002 0.998114
## vuln_dt$ftnd220 -16.8310 6522.6386 -0.003 0.997941
## vuln_dt$ftnd221 -32.0679 9224.4040 -0.003 0.997226
## vuln_dt$ftnd222 -16.3816 6522.6387 -0.003 0.997996
## vuln_dt$ftnd225 -34.2734 6731.4338 -0.005 0.995938
## vuln_dt$ftnd228 -34.9405 9224.4040 -0.004 0.996978
## vuln_dt$ftnd230 -17.4816 6522.6386 -0.003 0.997862
## vuln_dt$ftnd233 -30.9590 9224.4040 -0.003 0.997322
## vuln_dt$ftnd235 -15.8108 6522.6387 -0.002 0.998066
## vuln_dt$ftnd238 -32.3939 9224.4040 -0.004 0.997198
## vuln_dt$ftnd240 -17.1661 6522.6386 -0.003 0.997900
## vuln_dt$ftnd245 -32.2839 7825.7776 -0.004 0.996708
## vuln_dt$ftnd260 -35.1661 6953.8682 -0.005 0.995965
## vuln_dt$ftnd290 -32.5551 9224.4040 -0.004 0.997184
## scrn7r_b.out 1.1089 0.4943 2.243 0.024866 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 203.61 on 231 degrees of freedom
## Residual deviance: 138.54 on 202 degrees of freedom
## (15 observations deleted due to missingness)
## AIC: 198.54
##
## Number of Fisher Scoring iterations: 17
# Save object ---------------------------
save.image(file="table2-adjusted.RData")