Merge pull request #70 from nt-williams/devel

Devel

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-07-10.
-Once it is accepted, delete this file and tag the release (commit 0a05bebcfe).
+This package was submitted to CRAN on 2020-07-13.
+Once it is accepted, delete this file and tag the release (commit c397f48bbf).

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: lmtp
 Title: Non-Parametric Causal Effects of Feasible Interventions Based on Modified Treatment Policies
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: 
     c(person(given = "Nicholas",
              family = "Williams",
@@ -10,7 +10,7 @@ Authors@R:
       person(given = "Iván", 
              family = "Díaz", 
              email = "[email protected]",
-             role = c("aut"),
+             role = c("aut", "cph"),
              comment = c(ORCID = "0000-0001-9056-2047")))
 Description: Non-parametric estimators for casual effects based on longitudinal modified treatment 
   policies as described in Diaz, Williams, and Hoffman (<arXiv:2006.01366>), traditional point treatment, 

R/shift.R

@@ -34,7 +34,7 @@ shift_trt <- function(data, trt, .f) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' data("iptwExWide", package = "twang")
 #' a <- paste0("tx", 1:3)
 #' baseline <- c("gender", "age")
@@ -59,7 +59,7 @@ static_binary_on <- function(data, trt) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' data("iptwExWide", package = "twang")
 #' a <- paste0("tx", 1:3)
 #' baseline <- c("gender", "age")

R/theta.R

@@ -25,7 +25,9 @@ theta_sub <- function(eta) {
               low = NA_real_,
               high = NA_real_,
               shift = eta$shift,
-              outcome_reg = rescale_y_continuous(eta$m, eta$bounds),
+              outcome_reg = switch(eta$outcome_type,
+                                   continuous = rescale_y_continuous(eta$m, eta$bounds),
+                                   binomial = eta$m),
               weights_m = eta$weights_m,
               outcome_type = eta$outcome_type)
 
@@ -92,7 +94,9 @@ theta_dr <- function(eta) {
               high = ci_high,
               eif = inflnce,
               shift = eta$shift,
-              outcome_reg = rescale_y_continuous(eta$m$shifted, eta$bounds),
+              outcome_reg = switch(eta$outcome_type,
+                                   continuous = rescale_y_continuous(eta$m$shifted, eta$bounds),
+                                   binomial = eta$m$shifted),
               density_ratios = eta$r,
               weights_m = eta$weights_m,
               weights_r = eta$weights_r,

R/tidy.R

@@ -10,12 +10,12 @@ generics::tidy
 #' @param ... Unused, included for generic consistency only.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' a <- c("A1", "A2")
 #' nodes <- list(c("L1"), c("L2"))
 #' cens <- c("C1", "C2")
 #' y <- "Y"
-#' fit <- lmtp_tmle(sim_cens, a, y, nodes, cens = cens, shift = NULL, folds = 2)
+#' fit <- lmtp_tmle(sim_cens, a, y, time_vary = nodes, cens = cens, shift = NULL, folds = 2)
 #' tidy(fit)
 #' }
 #'

README.Rmd

@@ -130,7 +130,7 @@ Please cite the following when using `lmtp` in publications. Citation should inc
     title = {lmtp: {Non}-parametric {Causal} {Effects} of {Feasible} {Interventions} {Based} on {Modified} {Treatment} {Policies}},
     author = {Nicholas T Williams and Iván Díaz},
     year = {2020},
-    note = {R package version 0.0.4},
+    note = {R package version 0.0.5},
     doi = {10.5281/zenodo.3874931}, 
     url = {https://github.com/nt-williams/lmtp}
 }

README.md

@@ -157,7 +157,7 @@ statistical methodology.
         title = {lmtp: {Non}-parametric {Causal} {Effects} of {Feasible} {Interventions} {Based} on {Modified} {Treatment} {Policies}},
         author = {Nicholas T Williams and Iván Díaz},
         year = {2020},
-        note = {R package version 0.0.4},
+        note = {R package version 0.0.5},
         doi = {10.5281/zenodo.3874931}, 
         url = {https://github.com/nt-williams/lmtp}
     }

cran-comments.md

@@ -16,6 +16,11 @@
 
 ## Additional comments
 
+### Submission 4
+
+Ivan Diaz has been identified as a copyright holder in DESCRIPTION
+All instances of `\dontrun{}` have been removed
+
 ### Submission 3
 
 Only undirected quotation marks are now used in DESCRIPTION