fixed partial matching for call to print.data.table, and others

Author: joshhwuu

R/data_extension.R

@@ -51,7 +51,7 @@ data_extension <- function(data,
       N <- N + nrow(switch_data)
       for (p in unique(switch_data[["trial_period"]])) {
         file_p <- file.path(data_dir, paste0("trial_", p, ".csv"))
-        fwrite(switch_data[trial_period == p, ], file_p, append = TRUE)
+        fwrite(switch_data[trial_period == p, ], file = file_p, append = TRUE)
       }
     }
     files <- file.path(data_dir, paste0("trial_", first_period:last_period, ".csv"))
@@ -188,9 +188,9 @@ expand <- function(sw_data,
     switch_data[(switch_new == 0 & time_of_event == period_new & outcome_new == 1), case := 1]
   }
 
-  setnames(switch_data, c("case"), c("outcome"))
-  setnames(switch_data, c("init"), c("assigned_treatment"))
-  setnames(switch_data, c("treatment_new"), c("treatment"))
+  setnames(switch_data, old = c("case"), new = c("outcome"))
+  setnames(switch_data, old = c("init"), new = c("assigned_treatment"))
+  setnames(switch_data, old = c("treatment_new"), new = c("treatment"))
   switch_data <- switch_data[expand == 1]
   switch_data <- switch_data[, keeplist, with = FALSE]
 

R/generics.R

@@ -47,7 +47,7 @@ summary.TE_data_prep_sep <- function(object, ...) {
 
   n_files <- length(object$data)
   cat("Expanded data saved in ", n_files, " csv file", if (n_files > 1) "s" else "", ":\n", sep = "")
-  print(data.table(data = object$data), topn = 3, n = 5, col.names = "none", ...)
+  print(data.table(data = object$data), topn = 3, nrows = 5, col.names = "none", ...)
   cat("\n\n")
   NextMethod()
 }

R/predict.R

@@ -112,7 +112,7 @@ predict.TE_msm <- function(object,
           c("followup_time", col_names, "2.5%", "97.5%")
         )
       } else {
-        setNames(data.frame(predict_times, pred_matrix[, 1]), c("followup_time", col_names))
+        setNames(data.frame(predict_times, pred_matrix[, 1]), nm = c("followup_time", col_names))
       }
     }
   )

R/sampling.R

@@ -103,7 +103,7 @@ sample_from_period <- function(period_data,
                                subset_expr,
                                sort = FALSE) {
   if (use_subset) period_data <- subset(period_data, eval(subset_expr))
-  if (isTRUE(sort)) setorderv(period_data, c("followup_time", "id"))
+  if (isTRUE(sort)) setorderv(period_data, cols = c("followup_time", "id"))
   followup_split <- split(period_data, by = "followup_time")
 
   all_samples <- lapply(p_control, function(p) {