Some small changes in functions

mwheymans · May 31, 2023 · c76437a · c76437a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,37 +3,35 @@ Type: Package
 Depends:
   R (>= 4.0.0),
 Imports:
-    ggplot2 (>= 3.3.6),
-    norm (>= 1.0-10.0),
-    survival (>= 3.4-0),
-    mitools (>= 2.4),
-    pROC (>= 1.18.0),
-    rms (>= 6.3-0),
-    ResourceSelection (>= 0.3-5),
-    magrittr (>= 2.0.3),
-    rsample (>= 1.1.0),
-    mice (>= 3.14.0),
-    mitml (>= 0.4-3),
-    cvAUC (>= 1.1.4),
-    dplyr (>= 1.0.10), 
-    purrr (>= 0.3.5),
-    tidyr (>= 1.2.1),
-    tibble (>= 3.1.8),
-    stringr (>= 1.4.1),
-    lme4 (>= 1.1-30),
-    car(>= 3.1-1)
+    ggplot2,
+    norm,
+    survival,
+    mitools,
+    pROC,
+    rms,
+    magrittr,
+    rsample,
+    mice,
+    mitml,
+    cvAUC,
+    dplyr, 
+    purrr,
+    tidyr,
+    tibble,
+    stringr,
+    lme4,
+    car
 Suggests: 
     foreign (>= 0.8-80),
     knitr,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     bookdown,
     readr,
     gtools,
-    covr,
-    ucminf
+    covr
 Title: Prediction Model Pooling, Selection and Performance Evaluation Across Multiply Imputed Datasets
-Version: 1.1.0
+Version: 1.3.0
 Authors@R: c(
   person("Martijn", "Heymans", email = "mw.heymans@amsterdamumc.nl", role=c("cre", "aut"),
   comment = c(ORCID = "0000-0002-3889-0921")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,49 +1,52 @@
 
-export(psfmi_lr)
-export(psfmi_lm)
-export(psfmi_coxr)
-export(psfmi_lr_bw)
-export(psfmi_lr_fw)
-export(psfmi_lm_bw)
-export(psfmi_lm_fw)
-export(psfmi_coxr_bw)
-export(psfmi_coxr_fw)
-export(psfmi_validate)
-export(mivalext_lr)
-export(nri_cox)
-export(nri_est)
-export(psfmi_mm)
-export(psfmi_mm_multiparm)
-export(psfmi_stab)
-export(pool_performance)
-export(pool_intadj)
-export(pool_RR)
-export(boot_MI)
 export(MI_boot)
-export(cv_MI)
-export(cv_MI_RR)
 export(MI_cv_naive)
-export(scaled_brier)
-export(rsq_nagel)
-export(rsq_surv)
-export(pool_auc)
-export(miceImp)
+export(RR_diff_prop)
+export(boot_MI)
+export(bw_single)
 export(clean_P)
-export(pool_compare_models)
-export(pool_reclassification)
+export(coxph_bw)
+export(coxph_fw)
+export(cv_MI)
+export(cv_MI_RR)
+export(glm_bw)
+export(glm_fw)
 export(hoslem_test)
 export(km_estimates)
 export(km_fit)
+export(mean_auc_log)
+export(miceImp)
+export(mivalext_lr)
+export(nri_cox)
+export(nri_est)
 export(pool_D2)
 export(pool_D4)
-export(glm_bw)
-export(glm_fw)
-export(coxph_bw)
-export(coxph_fw)
-export(bw_single)
+export(pool_RR)
+export(pool_auc)
+export(pool_compare_models)
+export(pool_intadj)
+export(pool_performance)
+export(pool_performance_internal)
+export(pool_reclassification)
+export(psfmi_coxr)
+export(psfmi_coxr_bw)
+export(psfmi_coxr_fw)
+export(psfmi_lm)
+export(psfmi_lm_bw)
+export(psfmi_lm_fw)
+export(psfmi_lr)
+export(psfmi_lr_bw)
+export(psfmi_lr_fw)
+export(psfmi_mm)
+export(psfmi_mm_multiparm)
 export(psfmi_perform)
-export(stab_single)
+export(psfmi_stab)
+export(psfmi_validate)
 export(risk_coxph)
+export(rsq_nagel)
+export(rsq_surv)
+export(scaled_brier)
+export(stab_single)
 
 importFrom(stats, glm)
 importFrom(stats, coef)
@@ -81,7 +84,6 @@ importFrom(stats, AIC)
 importFrom(stats, stepfun)
 importFrom(pROC, roc)
 importFrom(pROC, var)
-importFrom(ResourceSelection, hoslem.test)
 importFrom(ggplot2, theme_set)
 importFrom(ggplot2, theme_bw)
 importFrom(ggplot2, element_blank)
@@ -138,4 +140,3 @@ importFrom(cvAUC, cvAUC)
 importFrom(cvAUC, ci.cvAUC)
 importFrom(car, Anova)
 importFrom(stats, approx)
-importFrom(stats, stepfun)
diff --git a/R/pool_D4.R b/R/pool_D4.R
@@ -49,7 +49,7 @@ pool_D4 <- function(data,
 {
   m <- nimp
   data <-
-    filter(data, data[impvar] <= nimp)
+    subset(data, data[impvar] <= nimp)
 
   if(model_type=="binomial") family="binomial"
   if(model_type=="linear") family="gaussian"

diff --git a/R/psfmi_lm_bw.R b/R/psfmi_lm_bw.R
@@ -112,7 +112,7 @@ psfmi_lm_bw <- function(data, nimp, impvar, Outcome, P, p.crit, method, keep.P)
         }
         if(method=="D4"){
           data <-
-            filter(data, data[impvar] <= nimp)
+            subset(data, data[impvar] <= nimp)
           imp_list <-
             data %>% group_split(data[, impvar], .keep = FALSE) %>%
             mitools::imputationList(imp_list)

diff --git a/R/psfmi_lm_fw.R b/R/psfmi_lm_fw.R
@@ -124,7 +124,7 @@ psfmi_lm_fw <- function(data, nimp, impvar, Outcome, P, p.crit, method, keep.P)
         }
         if(method=="D4"){
           data <-
-            filter(data, data[impvar] <= nimp)
+            subset(data, data[impvar] <= nimp)
           imp_list <-
             data %>% group_split(data[, impvar], .keep = FALSE) %>%
             mitools::imputationList(imp_list)

diff --git a/R/psfmi_lr_bw.R b/R/psfmi_lr_bw.R
@@ -123,7 +123,7 @@ psfmi_lr_bw <- function(data, nimp, impvar, Outcome, P, p.crit, method, keep.P)
         }
         if(method=="D4"){
           data <-
-            filter(data, data[impvar] <= nimp)
+            subset(data, data[impvar] <= nimp)
           imp_list <-
             data %>% group_split(data[, impvar], .keep = FALSE) %>%
             mitools::imputationList(imp_list)
@@ -162,7 +162,7 @@ psfmi_lr_bw <- function(data, nimp, impvar, Outcome, P, p.crit, method, keep.P)
         }
         if(method=="D3"){
           data <-
-            filter(data, data[impvar] <= nimp)
+            subset(data, data[impvar] <= nimp)
           imp_list <-
             data %>% group_split(data[, impvar], .keep = FALSE) %>%
             mitools::imputationList(imp_list)

diff --git a/R/psfmi_lr_fw.R b/R/psfmi_lr_fw.R
@@ -129,7 +129,7 @@ psfmi_lr_fw <- function(data, nimp, impvar, Outcome, P, p.crit, method, keep.P)
         }
         if(method=="D4"){
           data <-
-            filter(data, data[impvar] <= nimp)
+            subset(data, data[impvar] <= nimp)
           imp_list <-
             data %>% group_split(data[, impvar], .keep = FALSE) %>%
             mitools::imputationList(imp_list)

diff --git a/tests/testthat/testthat.R b/tests/testthat/testthat.R
@@ -1,6 +1,12 @@
-context("testthat.R")
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
 
 library(testthat)
 library(psfmi)
 
-
+test_check("psfmi")