Update vignettes + NEWS w.r.t. new interface change in as_ped. Fixes …

…#88

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pammtools
 Title: Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis
-Version: 0.1.14
-Date: 2019-09-05
+Version: 0.1.15
+Date: 2019-11-02
 Authors@R: c(
     person("Andreas", "Bender", , "[email protected]", role = c("aut", "cre"), comment=c(ORCID = "0000-0001-5628-8611")),
     person("Fabian", "Scheipl", , "[email protected]", role = c("aut")))

NEWS.md

@@ -1,3 +1,6 @@
+# pammtools 0.1.15
+* Interface for specification of data transformation in `as_ped` changed. The vertical bar `|` is no longer necessary to indicate concurrent or cumulative effects
+
 # pammtools 0.1.14
 
 * Support for new interface to tidyr

vignettes/cumulative-effects.Rmd

@@ -262,7 +262,7 @@ and need to be considered at the beginning of the analysis as this information
 goes into the code for the data transformation:
 
 ```{r, message = FALSE}
-ped <- as_ped(list(event_df, tdc_df), Surv(time, outcome)~ . |
+ped <- as_ped(list(event_df, tdc_df), Surv(time, outcome)~ . +
     cumulative(latency(day), SOFA, tz_var = "day",
       ll_fun = function(t, tz) t >= tz &  t <= tz + 5),
     cut = 0:49, # administrative censoring at t = 49

vignettes/data-transformation.Rmd

@@ -75,7 +75,7 @@ Using the `pammtools` package this is easily achieved with the `as_ped` function
 as follows:
 
 ```{r}
-ped <- as_ped(Surv(time, status)~., data = veteran, id = "id")
+ped <- as_ped(Surv(time, status) ~ ., data = veteran, id = "id")
 ped %>% filter(id %in% c(42, 85, 112)) %>% select(-diagtime, -prior)
 ```
 
@@ -114,7 +114,7 @@ $\kappa_0 = 0, \kappa_1 = 50, \kappa_2 = 200, \kappa_3 = 400$,
 resulting in $J = 3$ intervals:
 
 ```{r}
-ped2 <- as_ped(Surv(time, status)~., data = veteran, cut = c(0, 50, 200, 400),
+ped2 <- as_ped(Surv(time, status) ~ ., data = veteran, cut = c(0, 50, 200, 400),
   id = "id")
 ped2 %>% filter(id %in% c(42, 85, 112)) %>% select(-diagtime, -prior)
 ```
@@ -162,7 +162,7 @@ updated.
 ```{r}
 ped_pbc <- as_ped(
   data    = list(pbc, pbcseq),
-  formula = Surv(time, status) ~ . | concurrent(bili, protime, tz_var = "day"),
+  formula = Surv(time, status) ~ . + concurrent(bili, protime, tz_var = "day"),
   id      = "id")
 ```
 
@@ -172,7 +172,7 @@ lags. This will increase the data set, as an (additional) split point will be ge
 
 ```{r, eval = FALSE}
 pbc_ped <- as_ped(data = list(pbc, pbcseq),
-  formula = Surv(time, status) ~ . | concurrent(bili, tz_var = "day") +
+  formula = Surv(time, status) ~ . + concurrent(bili, tz_var = "day") +
     concurrent(protime, tz_var = "day", lag = 10),
     id = "id")
 ```
@@ -292,7 +292,7 @@ however, you can override the suffix by specifying the
 ```{r}
 ped <- as_ped(
   data    = list(patient, daily),
-  formula = Surv(survhosp, PatientDied) ~ . |
+  formula = Surv(survhosp, PatientDied) ~ . +
     cumulative(latency(Study_Day), caloriesPercentage, tz_var = "Study_Day"),
   cut     = 0:30,
   id = "CombinedID")
@@ -316,7 +316,7 @@ $t-t_z$ occurs in both partial effects, we only need to specify one `cumulative`
 ```{r}
 ped <- as_ped(
   data = list(patient, daily),
-  formula = Surv(survhosp, PatientDied) ~ . |
+  formula = Surv(survhosp, PatientDied) ~ . +
     cumulative(survhosp, latency(Study_Day), caloriesPercentage, proteinGproKG,
       tz_var = "Study_Day"),
   cut = 0:30,
@@ -355,7 +355,7 @@ specifications as illustrated below:
 ```{r}
 ped_sim <- as_ped(
   data = simdf_elra,
-  formula = Surv(time, status) ~ . |
+  formula = Surv(time, status) ~ . +
     cumulative(time, latency(tz1), z.tz1, tz_var = "tz1") +
     cumulative(latency(tz2), z.tz2, tz_var = "tz2"),
   cut = 0:10,

vignettes/smj-tutorial.Rmd

@@ -17,6 +17,6 @@ In: Statistical Modelling 18.3-4 (Jun. 2018), pp. 299-321. ISSN: 1471-082X. DOI:
 
 <br>&nbsp;
 
-<embed src="pamtutorial.pdf" width="100%" height="600" type="application/pdf">
+<embed src="https://adibender.netlify.com/files/pamtutorial.pdf" width="100%" height="600" type="application/pdf">
 
 <!-- \includepdf[pages=-]{pamtutorial.pdf} -->

vignettes/tdcovar.Rmd

@@ -234,7 +234,7 @@ pbc <- pbc %>% filter(id <= 312) %>%
   mutate(status = 1L * (status == 2))
 pbc_ped <- as_ped(
   data = list(pbc, pbcseq),
-  formula = Surv(time, status) ~ . | concurrent(bili, protime, tz_var = "day"),
+  formula = Surv(time, status) ~ . + concurrent(bili, protime, tz_var = "day"),
   id = "id")
 ```