fix: CRAN issues, remove tmle based methods, update citation info

Author: Robin Enrico Denz

DESCRIPTION

@@ -1,22 +1,22 @@
 Package: adjustedCurves
 Title: Confounder-Adjusted Survival Curves and Cumulative Incidence
     Functions
-Version: 0.9.1
+Version: 0.10.0
 Authors@R: 
     person("Robin", "Denz", , "robin.denz@rub.de", role = c("aut", "cre"))
 Maintainer: Robin Denz <robin.denz@rub.de>
 Description: Estimate and plot confounder-adjusted survival curves using
     either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values',
     various forms of 'Inverse Probability of Treatment Weighting', two
-    forms of 'Augmented Inverse Probability of Treatment Weighting',
-    'Empirical Likelihood Estimation' and 'Targeted Maximum Likelihood
-    Estimation'. Also includes a significance test for the difference
+    forms of 'Augmented Inverse Probability of Treatment Weighting' and
+    'Empirical Likelihood Estimation'.
+	Also includes a significance test for the difference
     between two adjusted survival curves and the calculation of adjusted
     restricted mean survival times.  Additionally enables the user to
     estimate and plot cause-specific confounder-adjusted cumulative
     incidence functions in the competing risks setting using the same
     methods (with some exceptions).
-	For details, see Denz et. al (2022) <arXiv:2203.10002v1>.
+	For details, see Denz et. al (2023) <doi:10.1002/sim.9681>.
 License: GPL (>= 3)
 URL: https://github.com/RobinDenz1/adjustedCurves,
     https://robindenz1.github.io/adjustedCurves/
@@ -31,8 +31,6 @@ Imports:
 Suggests: 
     MASS,
     Matching (>= 4.9),
-    R6,
-    SuperLearner (>= 2.0.0),
     WeightIt (>= 0.11.0),
     cmprsk (>= 2.2),
     eventglm (>= 1.1.1),
@@ -47,7 +45,6 @@ Suggests:
     riskRegression (>= 2020.12.08),
     rmarkdown,
     survival (>= 3.0.0),
-    survtmle (>= 1.1),
     testthat (>= 3.0.0),
     tidyr,
 	ggpp (>= 0.4.3),
@@ -59,4 +56,4 @@ Config/testthat/edition: 3
 Contact: <robin.denz@rub.de>
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

NAMESPACE

@@ -31,7 +31,6 @@ export(cif_direct_pseudo)
 export(cif_iptw)
 export(cif_iptw_pseudo)
 export(cif_matching)
-export(cif_tmle)
 export(plot_curve_diff)
 export(plot_rmst_curve)
 export(plot_rmtl_curve)
@@ -47,11 +46,9 @@ export(surv_iptw_km)
 export(surv_iptw_pseudo)
 export(surv_km)
 export(surv_matching)
-export(surv_ostmle)
 export(surv_strat_amato)
 export(surv_strat_cupples)
 export(surv_strat_nieto)
-export(surv_tmle)
 importFrom(doRNG,"%dorng%")
 importFrom(dplyr,"%>%")
 importFrom(foreach,"%dopar%")

NEWS.md

@@ -8,3 +8,9 @@
 * Updated code and tests to run with updated versions of the mice and ggplot2 packages
 * Updated documentation of package man page to include features not supported at the moment
 
+# adjustedCurves 0.10.0
+
+* Removed support for tmle, ostmle methods
+* Changed citation information because manuscript was published
+* Changed `print` method to be equal to `summary` method
+* Fixed issues with unit-tests that require packages under "Suggests" only

R/adjustedcif.r

@@ -404,12 +404,6 @@ adjustedcif_boot <- function(data, variable, ev_time, event, cause, method,
 
 }
 
-## S3 print method for adjustedcif objects
-#' @export
-print.adjustedcif <- function(x, ...) {
-  print(x$adjcif, ...)
-}
-
 ## S3 summary method for adjustedcif objects
 #' @export
 summary.adjustedcif <- function(object, ...) {
@@ -429,8 +423,6 @@ summary.adjustedcif <- function(object, ...) {
   } else if (object$method=="aiptw_pseudo") {
     method_name <- paste0("Augmented Inverse Probability of Treatment",
                           " Weighting: Pseudo-Values")
-  } else if (object$method=="tmle") {
-    method_name <- "Targeted Maximum Likelihood Estimation"
   } else if (object$method=="aalen_johansen") {
     method_name <- "Aalen-Johansen Estimator"
   }
@@ -473,6 +465,12 @@ summary.adjustedcif <- function(object, ...) {
   }
 }
 
+## S3 print method for adjustedcif objects
+#' @export
+print.adjustedcif <- function(x, ...) {
+  summary(x, ...)
+}
+
 ## S3 print method for adjustedcif.method objects
 #' @export
 print.adjustedcif.method <- function(x, ...) {

R/adjustedsurv.r

@@ -424,12 +424,6 @@ adjustedsurv_boot <- function(data, variable, ev_time, event, method,
   return(adjsurv_boot)
 }
 
-## S3 print method for adjustedsurv objects
-#' @export
-print.adjustedsurv <- function(x, ...) {
-  print(x$adjsurv, ...)
-}
-
 ## S3 summary method for adjustedsurv objects
 #' @export
 summary.adjustedsurv <- function(object, ...) {
@@ -453,10 +447,6 @@ summary.adjustedsurv <- function(object, ...) {
   } else if (object$method=="aiptw_pseudo") {
     method_name <- paste0("Augmented Inverse Probability of Treatment",
                           " Weighting: Pseudo-Values")
-  } else if (object$method=="tmle") {
-    method_name <- "Targeted Maximum Likelihood Estimation"
-  } else if (object$method=="ostmle") {
-    method_name <- "One-Step Targeted Maximum Likelihood Estimation"
   } else if (object$method=="km") {
     method_name <- "Kaplan-Meier Estimator"
   } else if (object$method=="strat_cupples") {
@@ -504,6 +494,12 @@ summary.adjustedsurv <- function(object, ...) {
   }
 }
 
+## S3 print method for adjustedsurv objects
+#' @export
+print.adjustedsurv <- function(x, ...) {
+  summary(x, ...)
+}
+
 ## S3 print method for adjustedsurv.method objects
 #' @export
 print.adjustedsurv.method <- function(x, ...) {

R/helper_functions.r

@@ -280,12 +280,6 @@ remove_unnecessary_covars <- function(data, method, variable, ev_time,
   } else if (method=="aiptw_pseudo") {
     needed_covars <- c(needed_covars, args$outcome_vars, args$censoring_vars,
                        treatment_vars)
-  } else if (method=="tmle" | method=="ostmle") {
-    if (!is.null(args$adjust_vars)) {
-      needed_covars <- c(needed_covars, args$adjust_vars)
-    } else {
-      needed_covars <- colnames(data)
-    }
   } else if (method=="strat_cupples" | method=="strat_amato" |
              method=="strat_nieto") {
     needed_covars <- c(needed_covars, args$adjust_vars)
@@ -347,17 +341,6 @@ load_needed_packages <- function(method, kind, treatment_model,
       requireNamespace("MASS")
     }
 
-    # survtmle, SuperLearner
-    if (method=="tmle") {
-      requireNamespace("survtmle")
-      requireNamespace("SuperLearner")
-    }
-
-    # SuperLearner
-    if (method=="ostmle") {
-      requireNamespace("SuperLearner")
-    }
-
   } else {
 
     # cmprsk
@@ -391,12 +374,6 @@ load_needed_packages <- function(method, kind, treatment_model,
     if (method=="direct_pseudo" | method=="aiptw_pseudo") {
       requireNamespace("geepack")
     }
-
-    # survtmle, SuperLearner
-    if (method=="tmle") {
-      requireNamespace("survtmle")
-      requireNamespace("SuperLearner")
-    }
   }
 }
 

R/input_checks.r

@@ -66,7 +66,7 @@ check_inputs_adjustedsurv <- function(data, variable, ev_time, event, method,
   # method
   } else if (!method %in% c("km", "iptw_km", "iptw_cox", "iptw_pseudo",
                             "direct", "direct_pseudo", "aiptw_pseudo",
-                            "aiptw", "tmle", "ostmle", "matching",
+                            "aiptw", "matching",
                             "emp_lik", "strat_cupples", "strat_amato",
                             "strat_nieto")) {
     stop("Method '", method, "' is undefined. See documentation for ",
@@ -114,8 +114,7 @@ check_inputs_adjustedsurv <- function(data, variable, ev_time, event, method,
     levs_len <- length(unique(data[, variable]))
     if (levs_len < 2) {
       stop("There have to be at least two groups in 'variable'.")
-    } else if (levs_len > 2 & method %in% c("matching", "emp_lik", "tmle",
-                                            "ostmle", "aiptw")) {
+    } else if (levs_len > 2 & method %in% c("matching", "emp_lik", "aiptw")) {
       stop("Categorical treatments are currently not supported for ",
            "method='", method, "'.")
     }
@@ -248,13 +247,6 @@ check_inputs_adjustedsurv <- function(data, variable, ev_time, event, method,
       }
     }
 
-  ## TMLE / OSTMLE
-  } else if (method=="tmle" | method=="ostmle") {
-    # times
-    if (!is.null(times) && (!all(times==floor(times)))) {
-      stop("Only integer time is allowed when using method='tmle' or",
-           " method='ostmle'.")
-    }
   ## Empirical Likelihood
   } else if (method=="emp_lik") {
     # need treatment_vars
@@ -677,7 +669,7 @@ check_inputs_adjustedcif <- function(data, variable, ev_time, event, method,
          "character strings, specifying variables in 'data'.")
   } else if (!method %in% c("aalen_johansen", "iptw", "iptw_pseudo", "direct",
                             "direct_pseudo", "aiptw_pseudo",
-                            "aiptw", "tmle", "matching")) {
+                            "aiptw", "matching")) {
     stop("Method '", method, "' is undefined. See documentation for ",
          "details on available methods.")
   # conf_int
@@ -750,7 +742,7 @@ check_inputs_adjustedcif <- function(data, variable, ev_time, event, method,
     levs_len <- length(unique(data[, variable]))
     if (levs_len < 2) {
       stop("There have to be at least two groups in 'variable'.")
-    } else if (levs_len > 2 & method %in% c("matching", "tmle", "aiptw")) {
+    } else if (levs_len > 2 & method %in% c("matching", "aiptw")) {
       stop("Categorical treatments are currently not supported for ",
            "method='", method, "'.")
     }
@@ -861,11 +853,6 @@ check_inputs_adjustedcif <- function(data, variable, ev_time, event, method,
       }
     }
 
-  ## TMLE
-  } else if (method=="tmle") {
-    if (!is.null(times) && (!all(times==floor(times)))) {
-      stop("Only integer time is allowed when using method='tmle'.")
-    }
   ## Matching
   } else if (method=="matching") {
     # treatment_model