refactor main runner function's name

qmarcou · Jun 1, 2024 · 12591c0 · 12591c0
1 parent 6ba79a6
commit 12591c0
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Showing 7 changed files with 14 additions and 14 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,13 +5,13 @@ S3method(print,TPreg)
 S3method(summary,TPreg)
 export(.filter_times)
 export(compute_survprob_pch)
+export(fit_netTPreg)
 export(generate_exponential_time_to_event)
 export(generate_poisson_time_to_event)
 export(generate_uncensored_ind_exp_idm_data)
 export(iddata)
 export(invalid_argument)
 export(multi_assert)
-export(renewnetTPreg)
 importFrom(data.table,":=")
 importFrom(data.table,.BY)
 importFrom(data.table,.EACHI)

diff --git a/R/renewnetTPreg.R → R/fit_netTPreg.R b/R/renewnetTPreg.R → R/fit_netTPreg.R
@@ -215,7 +215,7 @@ mod.glm.fit.callingwrapper <-
 #' doi:10.1177/09622802211003608
 #' @examples
 #' # ADD_EXAMPLES_HERE
-renewnetTPreg <- function(s = 0,
+fit_netTPreg <- function(s = 0,
                           t = NULL,
                           trans,
                           formula,

diff --git a/README.Rmd b/README.Rmd
@@ -98,7 +98,7 @@ Now let's carry the of net survival estimation:
 # Estimation can be sped up and carried in parrallel using futures:
 future::plan("multisession") # will work on any OS
 # future::plan("multicore") # more efficient but only works on UNIX systems
-net_estimate <- renewnetTPreg(
+net_estimate <- fit_netTPreg(
   formula = ~1, # intercept only model, similar to Pohar-Perme estimation
   data = crude_synth_idm_data,
   # Use a standard ratetable

diff --git a/README.md b/README.md
@@ -101,7 +101,7 @@ Now let’s carry the of net survival estimation:
 # Estimation can be sped up and carried in parrallel using futures:
 future::plan("multisession") # will work on any OS
 # future::plan("multicore") # more efficient but only works on UNIX systems
-net_estimate <- renewnetTPreg(
+net_estimate <- fit_netTPreg(
   formula = ~1, # intercept only model, similar to Pohar-Perme estimation
   data = crude_synth_idm_data,
   # Use a standard ratetable

diff --git a/tests/testthat/test-netidmtpreg_fit.R b/tests/testthat/test-netidmtpreg_fit.R
@@ -60,7 +60,7 @@ testthat::test_that("IDM crude survival model estimates", {
   estimates <- list()
   for (transition in c("11", "12", "22", "13", "23")) {
     estimates[transition] <-
-      renewnetTPreg(~1, synth_idm_data,
+      fit_netTPreg(~1, synth_idm_data,
         ratetable = NULL,
         rmap = NULL,
         time_dep_popvars = NULL,
@@ -154,7 +154,7 @@ testthat::test_that("IDM Net survival model fitting runs inside futures", {
   for (session_type in c("sequential", "multisession")){
     future::plan(session_type)
     for (transition in c("all", "11", "12", "22", "13", "23")) {
-      renewnetTPreg(
+      fit_netTPreg(
         formula = ~1,
         synth_idm_data,
         # Use a standard ratetable
@@ -201,7 +201,7 @@ testthat::test_that("IDM Net survival fitting arguments handling", {
 
   # vector-like t with adjusted_t gives is estimated at expected times
   t <- c(1.3, 1.4, 1.5)
-  estim <- renewnetTPreg(
+  estim <- fit_netTPreg(
     s = .5,
     t = t,
     trans = "11",
@@ -213,7 +213,7 @@ testthat::test_that("IDM Net survival fitting arguments handling", {
   )
   testthat::expect_equal(object = estim$co$time, expected = t)
   testthat::expect_error( # large t in unadjusted vector of times
-    estim <- renewnetTPreg(
+    estim <- fit_netTPreg(
       s = .5,
       t = c(t, 1e5),
       trans = "11",
@@ -275,7 +275,7 @@ population mortality are equal",
     )
 
     for (transition in c("11", "12", "22", "13", "23")) {
-      net_truth <- renewnetTPreg(
+      net_truth <- fit_netTPreg(
         formula = ~1,
         synth_idm_data,
         # Use a standard ratetable
@@ -294,7 +294,7 @@ population mortality are equal",
         R = 1 # Number of bootstraps
       )
 
-      net_estimated <- renewnetTPreg(
+      net_estimated <- fit_netTPreg(
         formula = ~1,
         crude_synth_idm_data,
         # Use a standard ratetable

diff --git a/tests/testthat/test-plot.TPreg.R b/tests/testthat/test-plot.TPreg.R
@@ -21,7 +21,7 @@ test_that("Plotting TPreg objects does not throw any error", {
   # for (transition in c("11", "all")) {
   for (transition in c("11")) {
     estimate <-
-      renewnetTPreg(~1, synth_idm_data,
+      fit_netTPreg(~1, synth_idm_data,
         ratetable = NULL,
         rmap = NULL,
         time_dep_popvars = NULL,
@@ -38,7 +38,7 @@ test_that("Plotting TPreg objects does not throw any error", {
 
     # Check with more than just an intercept
     estimate <-
-      renewnetTPreg(~sex, synth_idm_data,
+      fit_netTPreg(~sex, synth_idm_data,
         ratetable = NULL,
         rmap = NULL,
         time_dep_popvars = NULL,

diff --git a/tests/testthat/test-print.TPreg.R b/tests/testthat/test-print.TPreg.R
@@ -20,7 +20,7 @@ test_that("Printing TPreg objects does not throw any error", {
     )
   for (transition in c("11", "all")) {
     estimate <-
-      renewnetTPreg(~1, synth_idm_data,
+      fit_netTPreg(~1, synth_idm_data,
         ratetable = NULL,
         rmap = NULL,
         time_dep_popvars = NULL,
@@ -37,7 +37,7 @@ test_that("Printing TPreg objects does not throw any error", {
 
     # Check with more than just an intercept
     estimate <-
-      renewnetTPreg(~sex, synth_idm_data,
+      fit_netTPreg(~sex, synth_idm_data,
         ratetable = NULL,
         rmap = NULL,
         time_dep_popvars = NULL,