female male help("predict") yhat age

Transcription

1 female male 1.0 help("predict") 0.5 yhat age

2 female male help("predict") 0.5 yhat age

3 2 Wald Statistics Response: y Factor Chi Square d.f. P treat (Factor+Higher Order Factors) All Interactions age (Factor+Higher Order Factors) <.0001 All Interactions Nonlinear (Factor+Higher Order Factors) treat * age (Factor+Higher Order Factors) Nonlinear Nonlinear Interaction : f(a,b) vs. AB TOTAL NONLINEAR TOTAL NONLINEAR + INTERACTION TOTAL <.0001 help("anova.rms") 1 log odds Age

4 help("anova.rms") age treat treat * age χ 2 df

5 0: Wald Statistics Response: y Factor Chi Square d.f. P treat (Factor+Higher Order Factors) <.0001 All Interactions <.0001 age (Factor+Higher Order Factors) <.0001 All Interactions <.0001 Nonlinear (Factor+Higher Order Factors) <.0001 bp <.0001 Nonlinear treat * age (Factor+Higher Order Factors) <.0001 Nonlinear <.0001 Nonlinear Interaction : f(a,b) vs. AB <.0001 TOTAL NONLINEAR <.0001 TOTAL NONLINEAR + INTERACTION <.0001 TOTAL <.0001 help("anova.rms") Index

6 help("anova.rms") treat bp age treat * age χ 2 df

7 TOTAL a b help("anova.rms") x1 * x2 x2 x partial R 2

8 b x1 * x2 TOTAL help("anova.rms") a x1 x2 b a partial R 2

9 TOTAL help("anova.rms") x1 * x2 a b x2 x partial R 2

10 Ranks and 0.95 Confidence Limits for χ 2 d.f. x2 help("anova.rms") predictor sex x Rank

11 help("bj") b a age log(t)

12 Survival Probability help("bj")

13 Survival Probability help("bj") cut2(age, g = 2)=[69. cut2(age, g = 2)=[41.1,69.9)

14 help("bootcov") Histogram of beta beta Frequency

15 help("bootcov") Normal Q Q Plot Theoretical Quantiles Sample Quantiles

16 help("bootcov") age log odds

17 Normal Q Q Plot Theoretical Quantiles Normal Q Q Plot Theoretical Quantiles Normal Q Q Plot Intercept Coefficient of sex=male help("bootcov") Theoretical Quantiles Coefficient of age Normal Q Q Plot Theoretical Quantiles Normal Q Q Plot Theoretical Quantiles Normal Q Q Plot Theoretical Quantiles Coefficient of age^ Coefficient of sex=male * age Coefficient of sex=male * age^

18 Histogram of y Histogram of y Histogram of y Density Density Density help("bootcov") Intercept Fraction of effects>0 = 0 Coefficient of sex=male Fraction of effects>0 = 0.9 Coefficient of age Fraction of effects>0 = 1 Histogram of y Histogram of y Histogram of y Density Density Density Coefficient of age^2 Fraction of effects>0 = Coefficient of sex=male * age Fraction of effects>0 = Coefficient of sex=male * age^2 Fraction of effects>0 = 0.78

19 help("bootcov") age log odds

20 help("bootcov") b c a b c d x a d y

21 help("bootcov") Age F:M Log Odds Ratio

22 female male help("bplot") Total Cholesterol, mg dl Age Adjusted to: blood.pressure=119.3

23 help("bplot") Age female Adjusted to: blood.pressure= Age male Total Cholesterol, mg dl log odds log odds Total Cholesterol, mg dl

24 help("bplot") Age female Adjusted to: blood.pressure= Age male 2 Total Cholesterol, mg dl log odds log odds Total Cholesterol, mg dl

25 help("bplot") female male Age Adjusted to: blood.pressure=119.3 Total Cholesterol, mg dl

26 help("bplot") age cholesterol

27 help("bplot") Total Cholesterol, mg dl Age Adjusted to: blood.pressure=119.3 sex=female

28 help("bplot") Total Cholesterol, mg dl Age Adjusted to: blood.pressure=119.3 sex=female

29 Fraction Surviving 2 Day help("calibrate") Black: observed Gray: ideal Blue : optimism corrected Predicted 2 Day Survival B=20 based on observed predicted Mean error = Quantile=0.039

30 Actual Probability Apparent Bias corrected Ideal help("calibrate") B= 40 repetitions, boot Predicted Pr{y>=2} Mean absolute error=0.023 n=200

31 help("contrast") drug placebo age y

32 help("contrast") placebo drug age y

33 help("contrast") female age male Drug Placebo

34 help("contrast") age Drug Placebo

35 help("cph") Female Male Age log Relative Hazard

36 help("cph") Male Female Adjusted to: age=48.8 Years Survival Probability

37 help("cph") time fitted(z)

38 help("cph") Time Beta(t) for age

39 help("cph") Time Beta(t) for age

40 help("cph") Time Beta(t) for age

41 help("cph") Time Beta(t) for sex=male

42 12 help("cph") Age Adjusted to:sex=male

43 From cph Female Male 2.5 help("cph") se age

44 From coxph Female Male 1.0 help("cph") 0.8 se age

45 help("cph") Days Survival Prob

46 help("groupkm") age n=1000 d=139, avg. 100 patients per group Kaplan Meier 5 Year Survival

47 help("hazard.ratio.plot") t Event:e Log Hazard Ratio

48 1 help("lrm") log odds 0 male 1 female Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

49 1.0 help("lrm") 0.5 log odds Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

50 Penalty Penalty Dxy R help("lrm") Penalty Intercept Penalty Penalty Penalty Slope Emax D Penalty Penalty Penalty U Q B

51 Points age help("nomogram") cholesterol 220 (sex=female) cholesterol (sex=male) blood.pressure 170 Total Points Linear Predictor Risk of Death

52 Points age help("nomogram") cholesterol 220 (sex=female) cholesterol (sex=male) blood.pressure 170 Total Points Linear Predictor

53 Points cholesterol (age=20) help("nomogram") cholesterol 220 (age=40) cholesterol (age=60) sex female male Total Points Linear Predictor

54 Points age (sex=female) help("nomogram") age (sex=male) Total Points Linear Predictor Median Survival Time

55 Points age (sex=female) help("nomogram") age (sex=male) Total Points Linear Predictor Month Survival Probability month Survival Probability

56 Points Age in Years help("nomogram") cholesterol (sex=female) cholesterol (sex=male) Total Points Linear Predictor Prob Y>= Prob Y>= Prob Y=

57 help("pentrace") Penalty Effective d.f

58 help("pentrace") Penalty Solid: AIC_c Dotted: AIC Dashed: BIC Information Criterion

59 help("pentrace") Solid: AIC_c Penalty Information Criterion

60 cholesterol sex 1 0 help("plot.predict") 1 log odds age female blood.pressure male

61 cholesterol sex 1 0 help("plot.predict") 1 log odds age female blood.pressure male

62 log odds help("plot.predict") age cholesterol

63 help("plot.predict") log odds male female Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

64 1 help("plot.predict") log odds Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

65 0.8 help("plot.predict") 0.7 P^ Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

66 0.8 help("plot.predict") Age Adjusted to:blood.pressure=119.3 cholesterol=200.5

67 cholesterol:215 blood.pressure:120 cholesterol:215 blood.pressure:140 cholesterol:215 blood.pressure:160 help("plot.predict") cholesterol:200 blood.pressure:120 cholesterol:200 blood.pressure:140 cholesterol:200 blood.pressure:160 log odds cholesterol:180 blood.pressure:120 cholesterol:180 blood.pressure:140 cholesterol:180 blood.pressure: Age

68 blood.pressure:160 cholesterol:180 blood.pressure:160 cholesterol:200 blood.pressure:160 cholesterol:215 help("plot.predict") blood.pressure:140 cholesterol:180 blood.pressure:140 cholesterol:200 blood.pressure:140 cholesterol:215 log odds blood.pressure:120 cholesterol:180 blood.pressure:120 cholesterol:200 blood.pressure:120 cholesterol: Age

69 round(age, 1) cholesterol:180 round(age, 1) cholesterol:180 round(age, 1) cholesterol:200 round(age, 1) cholesterol:200 round(age, 1) cholesterol:215 round(age, 1) cholesterol:215 help("plot.predict") round(age, 1) cholesterol:180 round(age, 1) cholesterol:200 round(age, 1) cholesterol:215 log odds round(age, 1) cholesterol:180 round(age, 1) cholesterol:200 round(age, 1) cholesterol: round(age, 1) cholesterol:180 round(age, 1) cholesterol:200 round(age, 1) cholesterol: Systolic Blood Pressure, mmhg

70 male emale cholesterol:215 blood.pressure:120 male emale cholesterol:215 blood.pressure:140 male emale cholesterol:215 blood.pressure:160 help("plot.predict") cholesterol:200 blood.pressure:120 cholesterol:200 blood.pressure:140 cholesterol:200 blood.pressure:160 1 log odds male emale male emale male emale 0 1 cholesterol:180 blood.pressure:120 cholesterol:180 blood.pressure:140 cholesterol:180 blood.pressure: male emale male emale male emale Age

71 help("plot.predict") Age Adjusted to:blood.pressure=119.3 sex=female cholesterol=200.5 Age=x:Age=30 Odds Ratio

72 cholesterol male help("plot.predict") 1 female 2 log odds age blood.pressure male male 1 2 female female

73 cholesterol female cholesterol male help("plot.predict") blood.pressure female blood.pressure male 2 log odds age female age male

74 help("plot.predict") Age Median Survival Time

75 help("plot.predict") x1 Adjusted to:x2=0.494 Predicted Mean on y scale

76 help("plot.predict") male female a b anxiety gender

77 help("plot.predict") b a female male gender anxiety

78 help("plot.predict") female male a b m anxiety

79 help("plot.predict") female male a b female male gender anxiety

80 C C C n=400 y age help("plot.xmean.ordinaly") C C C n=400 y blood.pressure C C C n=400 y C C C n=400 y region=north region=west

81 help("predict.lrm") x1 Adjusted to:x2=0.446 Predicted Mean

82 b age female c a b c a age male help("predictrms") 4 linear.predictors 6 age female b ac a c age male b age female age male b ac a b c cholesterol

83 help("predictrms") bp^0.5 logit

84 help("predictrms") bp^1.5 logit

85 help("predictrms") sqrt(bp 60) logit

86 blood.pressure cholesterol blood.pressure cholesterol blood.pressure cholesterol help("predictrms") 4 blood.pressure cholesterol blood.pressure cholesterol blood.pressure cholesterol 4 2 pred blood.pressure cholesterol blood.pressure cholesterol blood.pressure cholesterol age

87 cholesterol help("predictrms") pred cholesterol cholesterol age

88 help("predictrms") pred age

89 cholesterol help("predictrms") 0 2 linear.predictors cholesterol 4 cholesterol age

90 Sex: female Age b:a Odds Ratio help("predictrms") Sex: male Age b:a Odds Ratio Sex: female Age Sex: male Age c:a Odds Ratio c:a Odds Ratio Sex: female Age Sex: male Age c:b Odds Ratio c:b Odds Ratio

91 help("psm") Male Female age log(t)

92 help("psm") Adjusted to: sex=female Days Survival Probability

93 help("psm") Xβ^ S(6, Xβ^)

94 help("psm") times S(times, 0)

95 help("psm") times lam(times, 0)

96 help("psm") lp Median Survival Time

97 help("psm") Time S(t)

98 Survival Probability help("psm")

99 Survival Probability cut2(age, g = 2)=[15.3,49.8) cut2(age, g = 2)=[49.8,81.8] help("psm")

100 help("psm") x=[15.3,49.8) x=[49.8,81.8] Residual Survival Probability

101 Residual help("residuals.cph") Smoothed Martingale Residuals Residual Residual

102 I(r[, i]) Transformed I(r[, i]) help("residuals.cph") tt Transformed tt I(r[, i]) tt Transformed I(r[, i]) Transformed tt I(r[, i]) tt Transformed I(r[, i]) Transformed tt

103 Time Beta(t) for age help("residuals.cph") Time Beta(t) for sex=male Time Beta(t) for blood.pressure

104 x1 r[, i] help("residuals.lrm") x2 r[, i]

105 x1 Partial Residual help("residuals.lrm") x2 Partial Residual

106 x1 Partial Residual help("residuals.lrm") x2 Partial Residual

107 1 2 y y age help("residuals.lrm") 1 2 y blood.pressure y>=1 y>= age y>=2 y>= blood.pressure Partial Residual Partial Residual

108 help("residuals.lrm") f1 f age f1 f blood.pressure Partial Residual Partial Residual 5 3 1

109 True Proportional Odds Ordinal Model Score Residuals y Score Residual for x True Proportional Odds Binary Score Residuals y x help("residuals.lrm") True Proportional Odds Partial Residuals y>=5 y>=4 y>=2 y>=1 y>= x Partial Residual Non Proportional Odds Slopes= y Score Residual for x Non Proportional Odds Slopes= y Non Proportional Odds Slopes= y>=1 y>=5 y>=3 y>=4 y>= x x Partial Residual

110 help("robcov") age log odds

111 help("sensuc") Prevalence of U: 0.5 Odds Ratio for X:U Odds Ratio for Y:U

112 blood.pressure : Odds Ratio help("summary.rms") age 70:50 cholesterol : sex male:female Adjusted to:sex=female age=60 cholesterol=200.48

113 help("survfit.formula") Maintained Nonmaintained

114 help("survfit.formula") Years Survival

115 Competing Risk: death KM:prog Competing Risk: progression help("survfit.formula") Years post diagnosis of MGUS

116 help("survplot") Years Survival Probability

117 help("survplot") Years Survival Probability

118 Survival Probability male female female male help("survplot") Adjusted to: age=48.8 Years

119 help("survplot") female male Adjusted to: age=48.8 log Survival Time in Years log( log Survival Probability)

120 help("survplot") male female Years Survival Probability

121 help("survplot") female male Adjusted to: age=48.8 Years Survival Probability

122 help("survplot") f m m female f male Adjusted to: age=48.8 Years Survival Probability

123 help("survplot") Years Survival Probability

124 help("survplot") Years Survival Probability

125 help("survplot") sex=male sex=female Years Survival Probability

126 help("survplot") sex=female Inverse Normal Transform sex=male Years

127 help("survplot") sex=female Logit S(t) sex=male Years

128 help("survplot") sex=female sex=male Years Difference in Survival Probability

129 Actual Probability Dxy C (ROC) R2 D U Q Brier Intercept Slope Emax S:z S:p Ideal Logistic calibration Nonparametric Grouped observations help("val.prob") Predicted Probability

130 Actual Probability Group [0.0131,0.526) [0.5260,0.993] Overall n [0.0131,0.526) Overall Pavg Obs ChiSq ChiSq [0.5260,0.993] Eavg Eavg/P Med OR C B B ChiSq help("val.prob") Predicted Probability

131 Actual Probability Group [0.0131,0.526) [0.5260,0.993] Overall n [0.0131,0.526) Overall Pavg Obs ChiSq ChiSq [0.5260,0.993] Eavg Eavg/P Med OR C B B ChiSq help("val.prob") Predicted Probability

132 Actual Probability Group [0.0131,0.526) [0.5260,0.993] Overall n [0.0131,0.526) Overall Pavg Obs ChiSq ChiSq [0.5260,0.993] Eavg Eavg/P Med OR C B B ChiSq help("val.prob") Predicted Probability

133 help("val.surv") Predicted Probability of Surviving 1 Year n=1000 d=187, avg. 100 patients per group Actual Probability of Surviving 1 Year

134 help("val.surv") Predicted Pr[T <= observed T] Fraction <= x

135 help("val.surv") Male Overall Female Predicted Pr[T <= observed T] Fraction <= x

136 help("val.surv") Male Overall Female Predicted Pr[T <= observed T] Fraction <= x

137 help("val.surv") Linear Predictor F(T X,T<=C).5F(C X)

138 help("val.surv") [45.4,55.0) [55.0,88.9] [16.3,45.4) Linear Predictor F(T X,T<=C).5F(C X)

139 mean age [15.1,43.6) [43.6,50.3) [50.3,56.7) [56.7,89.4] help("zzzrmsoverview") N help("zzzrmsoverview") sex female male sys.bp [102,115) [115,120) [120,125) [125,141] Overall N=500 dz.bp

140 Lowess smoothed Estimates with True Regression Functions dz True male male True female female help("zzzrmsoverview") age

141 Spline Fits with True Regression Functions 2 True male male help("zzzrmsoverview") 1 log odds 0 1 True female 2 female age

142 Calibration of Unpenalized Model Actual Probability Apparent Bias corrected Ideal help("zzzrmsoverview") B= 25 repetitions, boot Predicted Pr{dz=1} Mean absolute error=0.017 n=500

143 Penalized Spline Fits with True Regression Functions 2 1 male help("zzzrmsoverview") log odds female age

144 help("zzzrmsoverview") Odds Ratio age 56.6:43.6 sex female:male Adjusted to:age=50.3 sex=male

145 help("zzzrmsoverview") Odds Ratio age 56.6:43.6 sex female:male Adjusted to:age=50.3 sex=male

146 Calibration of Penalized Model Actual Probability Apparent Bias corrected Ideal help("zzzrmsoverview") B= 40 repetitions, boot Predicted Pr{dz=1} Mean absolute error=0.017 n=500

147 Points age (sex=female) age (sex=male) help("zzzrmsoverview") sys.bp Total Points Linear Predictor Prob(dz)

148 help("zzzrmsoverview") age treat num.diseases cholesterol treat * cholesterol χ 2 df

149 cholesterol 217:184 age 57.1:43.1 treat b:a Odds Ratio help("zzzrmsoverview") treat c:a num.diseases 0:2 num.diseases 1:2 num.diseases 3:2 num.diseases 4:2 Adjusted to:treat=a cholesterol=200

150 num.diseases treat 1 0 help("zzzrmsoverview") 1 log odds age a b c cholesterol

151 2 a b c help("zzzrmsoverview") 1 log odds Age Adjusted to:cholesterol=200.5 num.diseases=2

152 help("zzzrmsoverview") Total Cholesterol, mg dl Age Adjusted to: treat=a num.diseases=2

153 help("zzzrmsoverview") Prob Adjusted to:treat=a cholesterol=200.5 age=49.56 Number of Comorbid Diseases

154 help("zzzrmsoverview") ag^0.5 logit

155 help("zzzrmsoverview") ag^1.5 logit

156 Points cholesterol (treat=a) cholesterol (treat=b) cholesterol (treat=c) help("zzzrmsoverview") Age Number of Comorbid 1 3 Diseases Total Points Linear Predictor Prob[Y=1]

157 weight cholesterol weight cholesterol weight cholesterol help("zzzrmsoverview") weight cholesterol weight cholesterol weight cholesterol 4 pred 2 0 weight cholesterol weight cholesterol weight cholesterol age

158 cholesterol help("zzzrmsoverview") pred cholesterol cholesterol age

159 help("zzzrmsoverview") pred age

160 cholesterol: help("zzzrmsoverview") log odds cholesterol:170 cholesterol: Age Adjusted to:num.diseases=2 sex=male

161 weight:250 cholesterol:170 weight:250 cholesterol:200 weight:250 cholesterol:230 help("zzzrmsoverview") weight:200 cholesterol:170 weight:200 cholesterol:200 weight:200 cholesterol:230 4 log odds weight:150 cholesterol:170 weight:150 cholesterol:200 weight:150 cholesterol: Age Adjusted to:num.diseases=2 sex=male

162 help("zzzrmsoverview") Age log[ log S(3)]

163 help("zzzrmsoverview") Female Age Male log[ log S(3)]

164 help("zzzrmsoverview") Female agen Male yhat

165 Survival Probability Male Female Female Male help("zzzrmsoverview") Adjusted to: age=48.99 Years

166 Fraction Surviving 1 Years help("zzzrmsoverview") Black: observed Gray: ideal Blue : optimism corrected Predicted 1 Year Survival B=10 based on observed predicted Mean error = Quantile=0.019

167 help("zzzrmsoverview") Time Beta(t) for age

168 help("zzzrmsoverview") Time Beta(t) for age

169 help("zzzrmsoverview") Time Beta(t) for age

170 help("zzzrmsoverview") Female Male Age log[ log S(3)]

171 help("zzzrmsoverview") Female Male Age log[ log S(3)]

172 help("zzzrmsoverview") Male Female Age 3 Year Survival Probability

173 Points Age Total Points help("zzzrmsoverview") Linear Predictor S(3 Male) S(3 Female) Median (Male) 12 Median (Female)

174 help("zzzrmsoverview") x1 x2 x χ 2 df

175 help("zzzrmsoverview") x1 15.2:5.75 Odds Ratio 1.0e e x2 7.25:2.75 x3 1:0 x3 2:0

176 log odds help("zzzrmsoverview") x x x

177 Points x help("zzzrmsoverview") x x Total Points Linear Predictor

178 Apparent Bias corrected Ideal help("zzzrmsoverview") B= 10 repetitions, boot Predicted Pr{y=1} Mean absolute error=0.103 n=20

179 help("zzzrmsoverview") x1 x2 x χ 2 df

180 help("zzzrmsoverview") x1 15.2:5.75 exp(y) x2 7.25:2.75 x3 1:0 x3 2:0

181 y help("zzzrmsoverview") x x x

182 Points x help("zzzrmsoverview") x x Total Points Linear Predictor

183 Apparent Bias corrected Ideal help("zzzrmsoverview") B= 10 repetitions, boot Predicted y Mean absolute error=0.056 n=20

184 help("zzzrmsoverview") x3=0 x3=1 x3= Days

185 help("zzzrmsoverview") x1 Adjusted to:x2=5 x3=0 5 Day Survival Probability

186 help("zzzrmsoverview") n=20 d=20 p=5, 10 subjects per group Gray: ideal Predicted 5 Day Survival X resampling optimism added, B=10 Based on observed predicted

187 help("zzzrmsoverview") Residual

188 help("zzzrmsoverview") x1 Adjusted to:x2=5 x3=0 5 Day Survival Probability

189 help("zzzrmsoverview") Adjusted to: x2=5 x3=0 Days