diff --git a/404.html b/404.html index 73acf19..f296790 100644 --- a/404.html +++ b/404.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/CONDUCT.html b/CONDUCT.html index ea5f7c6..39edbb3 100644 --- a/CONDUCT.html +++ b/CONDUCT.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/LICENSE-text.html b/LICENSE-text.html index a17e43d..66316b9 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/articles/competingRisk.html b/articles/competingRisk.html index 6b11c5a..a5a2e56 100644 --- a/articles/competingRisk.html +++ b/articles/competingRisk.html @@ -31,7 +31,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -100,7 +100,7 @@

Competing risk analysis

Maxime Turgeon

-

2021-02-07

+

2021-02-08

Source: vignettes/competingRisk.Rmd @@ -458,7 +458,7 @@

## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] casebase_0.9.1 +## [1] casebase_0.9.1.9999 ## ## loaded via a namespace (and not attached): ## [1] highr_0.8 compiler_4.0.2 pillar_1.4.7 tools_4.0.2 diff --git a/articles/customizingpopTime.html b/articles/customizingpopTime.html index 9bb2dc3..bed3466 100644 --- a/articles/customizingpopTime.html +++ b/articles/customizingpopTime.html @@ -31,7 +31,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -100,7 +100,7 @@

Customizing Population Time Plots

Sahir R. Bhatnagar

-

2021-02-07

+

2021-02-08

Source: vignettes/customizingpopTime.Rmd @@ -450,8 +450,8 @@

## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] colorspace_2.0-0 data.table_1.13.6 ggplot2_3.3.3 casebase_0.9.1 -## [5] survival_3.1-12 +## [1] colorspace_2.0-0 data.table_1.13.6 ggplot2_3.3.3 +## [4] casebase_0.9.1.9999 survival_3.1-12 ## ## loaded via a namespace (and not attached): ## [1] highr_0.8 pillar_1.4.7 compiler_4.0.2 tools_4.0.2 diff --git a/articles/customizingpopTime_files/figure-html/unnamed-chunk-12-1.png b/articles/customizingpopTime_files/figure-html/unnamed-chunk-12-1.png index ccccbd4..0d55f4b 100644 Binary files a/articles/customizingpopTime_files/figure-html/unnamed-chunk-12-1.png and b/articles/customizingpopTime_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/articles/customizingpopTime_files/figure-html/unnamed-chunk-15-1.png b/articles/customizingpopTime_files/figure-html/unnamed-chunk-15-1.png index 8b3c1d5..4167aeb 100644 Binary files a/articles/customizingpopTime_files/figure-html/unnamed-chunk-15-1.png and b/articles/customizingpopTime_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/customizingpopTime_files/figure-html/unnamed-chunk-16-1.png b/articles/customizingpopTime_files/figure-html/unnamed-chunk-16-1.png index ef45a4d..23a4eed 100644 Binary files a/articles/customizingpopTime_files/figure-html/unnamed-chunk-16-1.png and b/articles/customizingpopTime_files/figure-html/unnamed-chunk-16-1.png differ diff --git a/articles/customizingpopTime_files/figure-html/unnamed-chunk-17-1.png b/articles/customizingpopTime_files/figure-html/unnamed-chunk-17-1.png index fba9706..16d965b 100644 Binary files a/articles/customizingpopTime_files/figure-html/unnamed-chunk-17-1.png and b/articles/customizingpopTime_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/articles/index.html b/articles/index.html index 89c05b6..967de9f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/articles/plotabsRisk.html b/articles/plotabsRisk.html index 6c3e3bc..131d432 100644 --- a/articles/plotabsRisk.html +++ b/articles/plotabsRisk.html @@ -31,7 +31,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -100,7 +100,7 @@

Plot Cumulative Incidence and Survival Curves

Sahir Rai Bhatnagar

-

2021-02-07

+

2021-02-08

Source: vignettes/plotabsRisk.Rmd diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-2-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-2-1.png index 63d6ace..2bb69de 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-2-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-3-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-3-1.png index 1cee220..78ba6b9 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-3-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-4-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-4-1.png index c9de050..f7216ad 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-4-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-5-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-5-1.png index 0a7bcdd..351109b 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-5-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-6-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-6-1.png index f9f938b..b029e12 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-6-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-7-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-7-1.png index e0d342b..ac6aa03 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-7-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/plotabsRisk_files/figure-html/unnamed-chunk-8-1.png b/articles/plotabsRisk_files/figure-html/unnamed-chunk-8-1.png index 98d84e2..0f8d9ac 100644 Binary files a/articles/plotabsRisk_files/figure-html/unnamed-chunk-8-1.png and b/articles/plotabsRisk_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/plotsmoothHazard.html b/articles/plotsmoothHazard.html index 25b6a49..5d7cb09 100644 --- a/articles/plotsmoothHazard.html +++ b/articles/plotsmoothHazard.html @@ -31,7 +31,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -100,7 +100,7 @@

Plot Hazards and Hazard Ratios

Sahir Rai Bhatnagar

-

2021-02-07

+

2021-02-08

Source: vignettes/plotsmoothHazard.Rmd @@ -150,23 +150,23 @@

#> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.1801 -0.1601 -0.1476 -0.1245 3.8257 +#> -0.1816 -0.1593 -0.1481 -0.1242 3.8526 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -64.7753 14.0107 -4.623 3.78e-06 *** -#> ns(log(time), df = 3)1 38.0764 9.1596 4.157 3.22e-05 *** -#> ns(log(time), df = 3)2 110.1617 27.3181 4.033 5.52e-05 *** -#> ns(log(time), df = 3)3 22.8441 5.5983 4.081 4.49e-05 *** -#> hormon -0.3829 0.1256 -3.048 0.0023 ** +#> (Intercept) -96.2161 21.2673 -4.524 6.06e-06 *** +#> ns(log(time), df = 3)1 59.2477 14.0381 4.220 2.44e-05 *** +#> ns(log(time), df = 3)2 170.4264 41.2648 4.130 3.63e-05 *** +#> ns(log(time), df = 3)3 35.6660 8.5413 4.176 2.97e-05 *** +#> hormon -0.3678 0.1255 -2.931 0.00338 ** #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3354.9 on 30198 degrees of freedom -#> Residual deviance: 3276.1 on 30194 degrees of freedom -#> AIC: 3286.1 +#> Residual deviance: 3274.6 on 30194 degrees of freedom +#> AIC: 3284.6 #> #> Number of Fisher Scoring iterations: 10
@@ -211,12 +211,12 @@ 

 head(plot_results$fit)
 #>           time hormon offset cens    visregFit    visregLwr    visregUpr
-#> 1   0.05326367      0      0    0 7.386267e-29 7.242465e-39 7.532924e-19
-#> 2  26.63920357      0      0    0 3.792034e-07 2.556597e-08 5.624478e-06
-#> 3  53.22514348      0      0    0 8.442803e-06 1.892414e-06 3.766665e-05
-#> 4  79.81108338      0      0    0 3.633305e-05 1.404300e-05 9.400344e-05
-#> 5 106.39702329      0      0    0 8.629346e-05 4.537116e-05 1.641254e-04
-#> 6 132.98296319      0      0    0 1.524907e-04 9.679866e-05 2.402246e-04
+#> 1 7.216138e-03 0 0 0 1.636425e-42 1.051015e-57 2.547904e-27 +#> 2 2.655812e+01 0 0 0 2.593749e-07 1.603962e-08 4.194323e-06 +#> 3 5.310902e+01 0 0 0 7.091968e-06 1.528734e-06 3.290044e-05 +#> 4 7.965993e+01 0 0 0 3.314281e-05 1.253892e-05 8.760290e-05 +#> 5 1.062108e+02 0 0 0 8.221740e-05 4.269836e-05 1.583129e-04 +#> 6 1.327617e+02 0 0 0 1.490949e-04 9.398736e-05 2.365137e-04

@@ -265,26 +265,26 @@

#> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.1802 -0.1605 -0.1462 -0.1255 3.7653 +#> -0.1818 -0.1601 -0.1457 -0.1261 3.7916 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -57.097 14.642 -3.899 9.64e-05 *** -#> hormon -28.348 33.679 -0.842 0.399960 -#> ns(log(time), df = 3)1 33.176 9.596 3.457 0.000546 *** -#> ns(log(time), df = 3)2 95.332 28.626 3.330 0.000868 *** -#> ns(log(time), df = 3)3 19.372 5.768 3.358 0.000784 *** -#> hormon:ns(log(time), df = 3)1 18.538 22.260 0.833 0.404954 -#> hormon:ns(log(time), df = 3)2 54.350 65.478 0.830 0.406512 -#> hormon:ns(log(time), df = 3)3 11.333 13.344 0.849 0.395724 +#> (Intercept) -85.321 22.783 -3.745 0.000180 *** +#> hormon -39.539 51.713 -0.765 0.444516 +#> ns(log(time), df = 3)1 52.188 15.055 3.466 0.000527 *** +#> ns(log(time), df = 3)2 149.400 44.293 3.373 0.000744 *** +#> ns(log(time), df = 3)3 30.928 9.078 3.407 0.000657 *** +#> hormon:ns(log(time), df = 3)1 26.200 34.384 0.762 0.446068 +#> hormon:ns(log(time), df = 3)2 75.570 100.097 0.755 0.450267 +#> hormon:ns(log(time), df = 3)3 16.081 20.713 0.776 0.437525 #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3354.9 on 30198 degrees of freedom -#> Residual deviance: 3274.0 on 30191 degrees of freedom -#> AIC: 3290 +#> Residual deviance: 3271.9 on 30191 degrees of freedom +#> AIC: 3287.9 #> #> Number of Fisher Scoring iterations: 11

Now we can easily plot the hazard function over time for each hormon group:

@@ -319,26 +319,26 @@

#> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.1863 -0.1619 -0.1420 -0.1360 4.0239 +#> -0.1879 -0.1621 -0.1426 -0.1355 4.0680 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -85.6883 24.2364 -3.536 0.000407 *** -#> estrec -0.8276 0.4397 -1.882 0.059815 . -#> ns(log(time), df = 3)1 51.7118 16.0424 3.223 0.001267 ** -#> ns(log(time), df = 3)2 151.2305 47.0434 3.215 0.001306 ** -#> ns(log(time), df = 3)3 30.3825 9.6759 3.140 0.001689 ** -#> estrec:ns(log(time), df = 3)1 0.5662 0.2964 1.910 0.056107 . -#> estrec:ns(log(time), df = 3)2 1.5671 0.8425 1.860 0.062866 . -#> estrec:ns(log(time), df = 3)3 0.3488 0.1805 1.933 0.053231 . +#> (Intercept) -62.7884 16.8829 -3.719 0.00020 *** +#> estrec -0.6145 0.3129 -1.964 0.04953 * +#> ns(log(time), df = 3)1 36.1663 11.0712 3.267 0.00109 ** +#> ns(log(time), df = 3)2 107.3742 32.9163 3.262 0.00111 ** +#> ns(log(time), df = 3)3 21.1891 6.7225 3.152 0.00162 ** +#> estrec:ns(log(time), df = 3)1 0.4205 0.2102 2.001 0.04538 * +#> estrec:ns(log(time), df = 3)2 1.1623 0.6003 1.936 0.05286 . +#> estrec:ns(log(time), df = 3)3 0.2596 0.1285 2.021 0.04329 * #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3354.9 on 30198 degrees of freedom -#> Residual deviance: 3264.2 on 30191 degrees of freedom -#> AIC: 3280.2 +#> Residual deviance: 3259.0 on 30191 degrees of freedom +#> AIC: 3275 #> #> Number of Fisher Scoring iterations: 13

There are now many ways to plot the time-varying effect of estrogen receptor on the hazard function. The default is to plot the 10th, 50th and 90th quantiles of the by variable:

@@ -429,34 +429,34 @@

#> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.6743 -0.1621 -0.1339 -0.0963 4.0591 +#> -0.6718 -0.1616 -0.1345 -0.0956 4.0786 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -5.650e+01 1.528e+01 -3.698 0.000218 *** -#> estrec -4.112e-01 2.564e-01 -1.604 0.108725 -#> ns(log(time), df = 3)1 3.218e+01 9.983e+00 3.223 0.001268 ** -#> ns(log(time), df = 3)2 9.490e+01 2.983e+01 3.181 0.001469 ** -#> ns(log(time), df = 3)3 1.932e+01 6.080e+00 3.177 0.001486 ** -#> horThyes -3.537e-01 1.298e-01 -2.726 0.006416 ** -#> age -1.048e-02 9.296e-03 -1.127 0.259712 -#> menostatPost 2.640e-01 1.848e-01 1.429 0.153020 -#> tsize 7.158e-03 3.989e-03 1.795 0.072723 . -#> tgrade.L 5.344e-01 1.912e-01 2.795 0.005185 ** -#> tgrade.Q -2.152e-01 1.226e-01 -1.756 0.079143 . -#> pnodes 5.266e-02 7.928e-03 6.642 3.09e-11 *** -#> progrec -2.252e-03 5.802e-04 -3.882 0.000104 *** -#> estrec:ns(log(time), df = 3)1 2.828e-01 1.717e-01 1.647 0.099502 . -#> estrec:ns(log(time), df = 3)2 7.784e-01 4.926e-01 1.580 0.114080 -#> estrec:ns(log(time), df = 3)3 1.749e-01 1.051e-01 1.663 0.096248 . +#> (Intercept) -6.747e+01 1.841e+01 -3.665 0.000247 *** +#> estrec -5.177e-01 3.279e-01 -1.579 0.114405 +#> ns(log(time), df = 3)1 3.944e+01 1.206e+01 3.270 0.001074 ** +#> ns(log(time), df = 3)2 1.159e+02 3.584e+01 3.233 0.001225 ** +#> ns(log(time), df = 3)3 2.383e+01 7.369e+00 3.234 0.001222 ** +#> horThyes -3.352e-01 1.297e-01 -2.585 0.009734 ** +#> age -9.951e-03 9.220e-03 -1.079 0.280478 +#> menostatPost 3.056e-01 1.833e-01 1.667 0.095557 . +#> tsize 7.209e-03 3.953e-03 1.823 0.068238 . +#> tgrade.L 5.434e-01 1.907e-01 2.849 0.004387 ** +#> tgrade.Q -1.996e-01 1.227e-01 -1.627 0.103813 +#> pnodes 5.240e-02 7.984e-03 6.564 5.25e-11 *** +#> progrec -2.140e-03 5.717e-04 -3.743 0.000182 *** +#> estrec:ns(log(time), df = 3)1 3.555e-01 2.198e-01 1.617 0.105835 +#> estrec:ns(log(time), df = 3)2 9.786e-01 6.289e-01 1.556 0.119699 +#> estrec:ns(log(time), df = 3)3 2.214e-01 1.353e-01 1.636 0.101753 #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3354.9 on 30198 degrees of freedom -#> Residual deviance: 3164.0 on 30183 degrees of freedom -#> AIC: 3196 +#> Residual deviance: 3164.1 on 30183 degrees of freedom +#> AIC: 3196.1 #> #> Number of Fisher Scoring iterations: 13

In the following plot, we show the time-varying effect of estrec while controlling for all other variables. By default, the other terms in the model are set to their median if the term is numeric or the most common category if the term is a factor. The values of the other variables are shown in the output:

@@ -468,14 +468,14 @@

breaks = 2, ylab = "Hazard")) #> Conditions used in construction of plot -#> estrec: 8 / 175 +#> estrec: 8 / 173 #> horTh: no #> age: 53 #> menostat: Post #> tsize: 25 #> tgrade: II #> pnodes: 3 -#> progrec: 51 +#> progrec: 48 #> offset: 0

You can of course set the values of the other covariates as before, i.e. by specifying the cond argument as a named list to the hazard.params argument:

@@ -488,14 +488,14 @@

breaks = 2, ylab = "Hazard")) #> Conditions used in construction of plot -#> estrec: 8 / 175 +#> estrec: 8 / 173 #> horTh: no #> age: 49 #> menostat: Post #> tsize: 25 #> tgrade: III #> pnodes: 3 -#> progrec: 51 +#> progrec: 48 #> offset: 0

@@ -541,22 +541,22 @@

#> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.1679 -0.1490 -0.1453 -0.1316 3.1816 +#> -0.1686 -0.1495 -0.1461 -0.1308 3.1884 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -6.09132 0.17549 -34.710 <2e-16 *** -#> treatmentestPro 0.60864 0.22408 2.716 0.0066 ** -#> time 0.11562 0.04773 2.422 0.0154 * -#> treatmentestPro:time -0.13528 0.06331 -2.137 0.0326 * +#> (Intercept) -6.11336 0.17532 -34.870 < 2e-16 *** +#> treatmentestPro 0.63431 0.22485 2.821 0.00479 ** +#> time 0.12002 0.04767 2.518 0.01182 * +#> treatmentestPro:time -0.13776 0.06367 -2.164 0.03048 * #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3635.4 on 32723 degrees of freedom -#> Residual deviance: 3626.1 on 32720 degrees of freedom -#> AIC: 3634.1 +#> Residual deviance: 3625.1 on 32720 degrees of freedom +#> AIC: 3633.1 #> #> Number of Fisher Scoring iterations: 7

To plot the hazard ratio, we must specify the newdata argument with a covariate pattern for the reference group. In this example, we treat the placebo as the reference group. Because we have fit an interaction with time, we also provide a sequence of times at which we would like to calculate the hazard ratio.

@@ -633,7 +633,20 @@ 

 head(result)
-#> NULL
+#> treatment time log_hazard_ratio standarderror hazard_ratio lowerbound +#> 1% estPro 0.9166667 -0.50803484 0.1768734 0.6016768 0.4254107 +#> 2% estPro 1.7500000 -0.39323869 0.1402646 0.6748676 0.5126549 +#> 3% estPro 2.5000000 -0.28992214 0.1184836 0.7483218 0.5932462 +#> 4% estPro 3.1666667 -0.19808522 0.1133880 0.8202999 0.6568355 +#> 5% estPro 3.4166667 -0.16364637 0.1155103 0.8490422 0.6770282 +#> 6% estPro 3.9166667 -0.09476868 0.1258340 0.9095833 0.7107754 +#> upperbound +#> 1% 0.8509777 +#> 2% 0.8884072 +#> 3% 0.9439345 +#> 4% 1.0244452 +#> 5% 1.0647603 +#> 6% 1.1639989
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@@ -100,7 +100,7 @@

Population Time Plots

Sahir R. Bhatnagar

-

2021-02-07

+

2021-02-08

Source: vignettes/popTime.Rmd @@ -588,7 +588,8 @@

## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] data.table_1.13.6 ggplot2_3.3.3 casebase_0.9.1 survival_3.1-12 +## [1] data.table_1.13.6 ggplot2_3.3.3 casebase_0.9.1.9999 +## [4] survival_3.1-12 ## ## loaded via a namespace (and not attached): ## [1] highr_0.8 pillar_1.4.7 compiler_4.0.2 tools_4.0.2 diff --git a/articles/popTime_files/figure-html/unnamed-chunk-10-1.png b/articles/popTime_files/figure-html/unnamed-chunk-10-1.png index 9e5d7a2..3fccce9 100644 Binary files a/articles/popTime_files/figure-html/unnamed-chunk-10-1.png and b/articles/popTime_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/articles/popTime_files/figure-html/unnamed-chunk-15-1.png b/articles/popTime_files/figure-html/unnamed-chunk-15-1.png index 6d8492b..84e1684 100644 Binary files a/articles/popTime_files/figure-html/unnamed-chunk-15-1.png and b/articles/popTime_files/figure-html/unnamed-chunk-15-1.png differ diff --git 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a/articles/smoothHazard.html b/articles/smoothHazard.html index b39b3cc..51198e9 100644 --- a/articles/smoothHazard.html +++ b/articles/smoothHazard.html @@ -31,7 +31,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -100,7 +100,7 @@

Introduction to casebase sampling

Maxime Turgeon

-

2021-02-07

+

2021-02-08

Source: vignettes/smoothHazard.Rmd @@ -739,7 +739,8 @@

## [8] base ## ## other attached packages: -## [1] visreg_2.7.0 eha_2.8.5 survival_3.1-12 casebase_0.9.1 +## [1] visreg_2.7.0 eha_2.8.5 survival_3.1-12 +## [4] casebase_0.9.1.9999 ## ## loaded via a namespace (and not attached): ## [1] highr_0.8 pillar_1.4.7 compiler_4.0.2 tools_4.0.2 diff --git a/authors.html b/authors.html index 6bfb0e3..c9e7d49 100644 --- a/authors.html +++ b/authors.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/index.html b/index.html index f2d8663..8c997fc 100644 --- a/index.html +++ b/index.html @@ -39,7 +39,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/news/index.html b/news/index.html index 6f5ebdf..a6df3de 100644 --- a/news/index.html +++ b/news/index.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -141,6 +141,14 @@

Changelog

Source: NEWS.md +
+

+casebase 0.9.1.9999 Unreleased +

+ +

casebase 0.9.1 2021-02-07 diff --git a/pkgdown.yml b/pkgdown.yml index f2150d0..a1da0c3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -8,7 +8,7 @@ articles: plotsmoothHazard: plotsmoothHazard.html popTime: popTime.html smoothHazard: smoothHazard.html -last_built: 2021-02-07T17:44Z +last_built: 2021-02-08T17:41Z urls: reference: http://sahirbhatnagar.com/casebase/reference article: http://sahirbhatnagar.com/casebase/articles diff --git a/reference/CompRisk-class.html b/reference/CompRisk-class.html index 12d9d40..c43dee3 100644 --- a/reference/CompRisk-class.html +++ b/reference/CompRisk-class.html @@ -72,7 +72,7 @@ casebase - 0.9.1 + 0.9.1.9999

diff --git a/reference/ERSPC.html b/reference/ERSPC.html index 595c0c2..733953c 100644 --- a/reference/ERSPC.html +++ b/reference/ERSPC.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/absoluteRisk.html b/reference/absoluteRisk.html index cfbe4ec..5afd8ad 100644 --- a/reference/absoluteRisk.html +++ b/reference/absoluteRisk.html @@ -77,7 +77,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/bmtcrr.html b/reference/bmtcrr.html index 4cbd85d..35068a0 100644 --- a/reference/bmtcrr.html +++ b/reference/bmtcrr.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/brcancer.html b/reference/brcancer.html index a8fa3c8..eb48e50 100644 --- a/reference/brcancer.html +++ b/reference/brcancer.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/checkArgsEventIndicator.html b/reference/checkArgsEventIndicator.html index 3bacefa..87e8654 100644 --- a/reference/checkArgsEventIndicator.html +++ b/reference/checkArgsEventIndicator.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/eprchd.html b/reference/eprchd.html index 7549830..1641c01 100644 --- a/reference/eprchd.html +++ b/reference/eprchd.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/fitSmoothHazard.html b/reference/fitSmoothHazard.html index 26bc0e9..bd628f4 100644 --- a/reference/fitSmoothHazard.html +++ b/reference/fitSmoothHazard.html @@ -75,7 +75,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/hazardPlot.html b/reference/hazardPlot.html index 270f1fe..dcc6daa 100644 --- a/reference/hazardPlot.html +++ b/reference/hazardPlot.html @@ -77,7 +77,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/index.html b/reference/index.html index 72092d8..fad9317 100644 --- a/reference/index.html +++ b/reference/index.html @@ -71,7 +71,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/plot.singleEventCB.html b/reference/plot.singleEventCB.html index 23a6297..5abb821 100644 --- a/reference/plot.singleEventCB.html +++ b/reference/plot.singleEventCB.html @@ -75,7 +75,7 @@ casebase - 0.9.1 + 0.9.1.9999 @@ -379,7 +379,20 @@

Examp # see data used to create plot head(result) } -
#> NULL
+
#> treat eventtime log_hazard_ratio standarderror hazard_ratio lowerbound +#> 5% treatment 0.3488444 0.5617254 0.7422200 1.753696 0.4094260 +#> 6% treatment 0.3902785 0.6649501 0.7012281 1.944394 0.4919237 +#> 7% treatment 0.4148271 0.7239973 0.6788513 2.062662 0.5452413 +#> 8% treatment 0.4512202 0.8086798 0.6482910 2.244942 0.6300556 +#> 9% treatment 0.4636149 0.8367497 0.6385929 2.308850 0.6604266 +#> 10% treatment 0.4862850 0.8870854 0.6217826 2.428043 0.7177844 +#> upperbound +#> 5% 7.511610 +#> 6% 7.685473 +#> 7% 7.803102 +#> 8% 7.998922 +#> 9% 8.071737 +#> 10% 8.213317
diff --git a/reference/sampleCaseBase.html b/reference/sampleCaseBase.html index 903f992..8b2c5e5 100644 --- a/reference/sampleCaseBase.html +++ b/reference/sampleCaseBase.html @@ -74,7 +74,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/simdat.html b/reference/simdat.html index 1bd50cb..e6052d7 100644 --- a/reference/simdat.html +++ b/reference/simdat.html @@ -73,7 +73,7 @@ casebase - 0.9.1 + 0.9.1.9999 diff --git a/reference/support.html b/reference/support.html index dcdafa2..5efb6a4 100644 --- a/reference/support.html +++ b/reference/support.html @@ -77,7 +77,7 @@ casebase - 0.9.1 + 0.9.1.9999