Remove broken URLs

Author: mikolajsp

R/metrics.R

@@ -12,7 +12,7 @@ utils::globalVariables(c("PredictionSurv"))
 #' @return a function that can be used to calculate metrics (with parameters `y_true`, `risk`, `surv`, and `times`)
 #'
 #' @section References:
-#' - \[1\] Graf, Erika, et al. ["Assessment and comparison of prognostic classification schemes for survival data."](https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0258%2819990915/30%2918%3A17/18%3C2529%3A%3AAID-SIM274%3E3.0.CO%3B2-5) Statistics in Medicine 18.17‐18 (1999): 2529-2545.
+#' - \[1\] Graf, Erika, et al. "Assessment and comparison of prognostic classification schemes for survival data." Statistics in Medicine 18.17‐18 (1999): 2529-2545.
 #'
 #' @export
 loss_integrate <- function(loss_function, ..., normalization = NULL, max_quantile = 1) {
@@ -57,7 +57,7 @@ loss_integrate <- function(loss_function, ..., normalization = NULL, max_quantil
 #' @return numeric from 0 to 1, higher values indicate better performance
 #'
 #' @section References:
-#' - \[1\] Harrell, F.E., Jr., et al. ["Regression modelling strategies for improved prognostic prediction."](https://onlinelibrary.wiley.com/doi/10.1002/sim.4780030207) Statistics in Medicine 3.2 (1984): 143-152.
+#' - \[1\] Harrell, F.E., Jr., et al. "Regression modelling strategies for improved prognostic prediction." Statistics in Medicine 3.2 (1984): 143-152.
 #'
 #' @rdname c_index
 #' @seealso [loss_one_minus_c_index()]
@@ -109,7 +109,7 @@ attr(c_index, "loss_type") <- "risk-based"
 #' @return numeric from 0 to 1, lower values indicate better performance
 #'
 #' @section References:
-#' - \[1\] Harrell, F.E., Jr., et al. ["Regression modelling strategies for improved prognostic prediction."](https://onlinelibrary.wiley.com/doi/10.1002/sim.4780030207) Statistics in Medicine 3.2 (1984): 143-152.
+#' - \[1\] Harrell, F.E., Jr., et al. "Regression modelling strategies for improved prognostic prediction." Statistics in Medicine 3.2 (1984): 143-152.
 #'
 #' @rdname loss_one_minus_c_index
 #' @seealso [c_index()]
@@ -152,8 +152,8 @@ attr(loss_one_minus_c_index, "loss_type") <- "risk-based"
 #' @return numeric from 0 to 1, lower scores are better (Brier score of 0.25 represents a model which returns always returns 0.5 as the predicted survival function)
 #'
 #' @section References:
-#' - \[1\] Brier, Glenn W. ["Verification of forecasts expressed in terms of probability."](https://journals.ametsoc.org/view/journals/mwre/78/1/1520-0493_1950_078_0001_vofeit_2_0_co_2.xml) Monthly Weather Review 78.1 (1950): 1-3.
-#' - \[2\] Graf, Erika, et al. ["Assessment and comparison of prognostic classification schemes for survival data."](https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19990915/30)18:17/18%3C2529::AID-SIM274%3E3.0.CO;2-5) Statistics in Medicine 18.17‐18 (1999): 2529-2545.
+#' - \[1\] Brier, Glenn W. "Verification of forecasts expressed in terms of probability." Monthly Weather Review 78.1 (1950): 1-3.
+#' - \[2\] Graf, Erika, et al. "Assessment and comparison of prognostic classification schemes for survival data." Statistics in Medicine 18.17‐18 (1999): 2529-2545.
 #'
 #' @rdname brier_score
 #' @seealso [cd_auc()]
@@ -217,8 +217,8 @@ attr(loss_brier_score, "loss_type") <- "time-dependent"
 #' Calculate Cumulative/Dynamic AUC
 #'
 #' This function calculates the Cumulative/Dynamic AUC metric for a survival model. It is done using the
-#' estimator proposed proposed by Uno et al. \[[1](https://www.jstor.org/stable/27639883)\],
-#' and Hung and Chang \[[2](https://www.jstor.org/stable/41000414)\].
+#' estimator proposed proposed by Uno et al. \[1\],
+#' and Hung and Chang \[2\].
 #'
 #' C/D AUC is an extension of the AUC metric known from classification models.
 #' Its values represent the model's performance at specific time points.
@@ -232,8 +232,8 @@ attr(loss_brier_score, "loss_type") <- "time-dependent"
 #' @return a numeric vector of length equal to the length of the times vector, each value (from the range from 0 to 1) represents the AUC metric at a specific time point, with higher values indicating better performance.
 #'
 #' @section References:
-#' - \[1\] Uno, Hajime, et al. ["Evaluating prediction rules for t-year survivors with censored regression models."](https://www.jstor.org/stable/27639883) Journal of the American Statistical Association 102.478 (2007): 527-537.
-#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. ["Optimal composite markers for time dependent receiver operating characteristic curves with censored survival data."](https://www.jstor.org/stable/41000414) Scandinavian Journal of Statistics 37.4 (2010): 664-679.
+#' - \[1\] Uno, Hajime, et al. "Evaluating prediction rules for t-year survivors with censored regression models." Journal of the American Statistical Association 102.478 (2007): 527-537.
+#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. "Optimal composite markers for time dependent receiver operating characteristic curves with censored survival data." Scandinavian Journal of Statistics 37.4 (2010): 664-679.
 #'
 #' @rdname cd_auc
 #' @seealso [loss_one_minus_cd_auc()] [integrated_cd_auc()] [brier_score()]
@@ -297,8 +297,8 @@ attr(cd_auc, "loss_type") <- "time-dependent"
 #' @return a numeric vector of length equal to the length of the times vector, each value (from the range from 0 to 1) represents 1 - AUC metric at a specific time point, with lower values indicating better performance.
 #'
 #' #' @section References:
-#' - \[1\] Uno, Hajime, et al. ["Evaluating prediction rules for t-year survivors with censored regression models."](https://www.jstor.org/stable/27639883) Journal of the American Statistical Association 102.478 (2007): 527-537.
-#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. ["Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data."](https://www.jstor.org/stable/41000414) Scandinavian Journal of Statistics 37.4 (2010): 664-679.
+#' - \[1\] Uno, Hajime, et al. "Evaluating prediction rules for t-year survivors with censored regression models." Journal of the American Statistical Association 102.478 (2007): 527-537.
+#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. "Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data." Scandinavian Journal of Statistics 37.4 (2010): 664-679.
 #'
 #' @rdname loss_one_minus_cd_auc
 #' @seealso [cd_auc()]
@@ -337,8 +337,8 @@ attr(loss_one_minus_cd_auc, "loss_type") <- "time-dependent"
 #' @return numeric from 0 to 1, higher values indicate better performance
 #'
 #' #' @section References:
-#' - \[1\] Uno, Hajime, et al. ["Evaluating prediction rules for t-year survivors with censored regression models."](https://www.jstor.org/stable/27639883) Journal of the American Statistical Association 102.478 (2007): 527-537.
-#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. ["Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data."](https://www.jstor.org/stable/41000414) Scandinavian Journal of Statistics 37.4 (2010): 664-679.
+#' - \[1\] Uno, Hajime, et al. "Evaluating prediction rules for t-year survivors with censored regression models." Journal of the American Statistical Association 102.478 (2007): 527-537.
+#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. "Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data." Scandinavian Journal of Statistics 37.4 (2010): 664-679.
 #'
 #' @rdname integrated_cd_auc
 #' @seealso [cd_auc()] [loss_one_minus_cd_auc()]
@@ -373,8 +373,8 @@ attr(integrated_cd_auc, "loss_type") <- "integrated"
 #' @return numeric from 0 to 1, lower values indicate better performance
 #'
 #' #' @section References:
-#' - \[1\] Uno, Hajime, et al. ["Evaluating prediction rules for t-year survivors with censored regression models."](https://www.jstor.org/stable/27639883) Journal of the American Statistical Association 102.478 (2007): 527-537.
-#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. ["Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data."](https://www.jstor.org/stable/41000414) Scandinavian Journal of Statistics 37.4 (2010): 664-679.
+#' - \[1\] Uno, Hajime, et al. "Evaluating prediction rules for t-year survivors with censored regression models." Journal of the American Statistical Association 102.478 (2007): 527-537.
+#' - \[2\] Hung, Hung, and Chin‐Tsang Chiang. "Optimal composite markers for time‐dependent receiver operating characteristic curves with censored survival data." Scandinavian Journal of Statistics 37.4 (2010): 664-679.
 #'
 #' @rdname loss_one_minus_integrated_cd_auc
 #' @seealso [integrated_cd_auc()] [cd_auc()] [loss_one_minus_cd_auc()]
@@ -417,8 +417,8 @@ attr(loss_one_minus_integrated_cd_auc, "loss_type") <- "integrated"
 #' @return numeric from 0 to 1, lower values indicate better performance
 #'
 #' @section References:
-#' - \[1\] Brier, Glenn W. ["Verification of forecasts expressed in terms of probability."](https://journals.ametsoc.org/view/journals/mwre/78/1/1520-0493_1950_078_0001_vofeit_2_0_co_2.xml) Monthly Weather Review 78.1 (1950): 1-3.
-#' - \[2\] Graf, Erika, et al. ["Assessment and comparison of prognostic classification schemes for survival data."](https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19990915/30)18:17/18%3C2529::AID-SIM274%3E3.0.CO;2-5) Statistics in Medicine 18.17‐18 (1999): 2529-2545.
+#' - \[1\] Brier, Glenn W. "Verification of forecasts expressed in terms of probability." Monthly Weather Review 78.1 (1950): 1-3.
+#' - \[2\] Graf, Erika, et al. "Assessment and comparison of prognostic classification schemes for survival data." Statistics in Medicine 18.17‐18 (1999): 2529-2545.
 #'
 #' @rdname integrated_brier_score
 #' @seealso [brier_score()] [integrated_cd_auc()] [loss_one_minus_integrated_cd_auc()]

R/model_performance.R

@@ -9,17 +9,17 @@
 #' @param times a numeric vector of times. If `type == "metrics"` then the survival function is evaluated at these times, if `type == "roc"` then the ROC curves are calculated at these times.
 #'
 #' @return An object of class `"model_performance_survival"`. It's a list of metric values calculated for the model. It contains:
-#' - Harrell's concordance index \[[1](https://onlinelibrary.wiley.com/doi/abs/10.1002/sim.4780030207)\]
-#' - Brier score \[[2](https://journals.ametsoc.org/view/journals/mwre/78/1/1520-0493_1950_078_0001_vofeit_2_0_co_2.xml), [3](https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0258%2819990915/30%2918%3A17/18%3C2529%3A%3AAID-SIM274%3E3.0.CO%3B2-5)\]
-#' - C/D AUC using the estimator proposed by Uno et. al \[[4](https://www.jstor.org/stable/27639883#metadata_info_tab_contents)\]
+#' - Harrell's concordance index \[1\]
+#' - Brier score \[2, 3\]
+#' - C/D AUC using the estimator proposed by Uno et. al \[4\]
 #' - integral of the Brier score
 #' - integral of the C/D AUC
 #'
 #' @section References:
-#' - \[1\] Harrell, F.E., Jr., et al. ["Regression modelling strategies for improved prognostic prediction."](https://onlinelibrary.wiley.com/doi/abs/10.1002/sim.4780030207) Statistics in Medicine 3.2 (1984): 143-152.
-#' - \[2\] Brier, Glenn W. ["Verification of forecasts expressed in terms of probability."](https://journals.ametsoc.org/view/journals/mwre/78/1/1520-0493_1950_078_0001_vofeit_2_0_co_2.xml) Monthly Weather Review 78.1 (1950): 1-3.
-#' - \[3\] Graf, Erika, et al. ["Assessment and comparison of prognostic classification schemes for survival data."](https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0258%2819990915/30%2918%3A17/18%3C2529%3A%3AAID-SIM274%3E3.0.CO%3B2-5) Statistics in Medicine 18.17‐18 (1999): 2529-2545.
-#' - \[4\] Uno, Hajime, et al. ["Evaluating prediction rules for t-year survivors with censored regression models."](https://www.jstor.org/stable/27639883#metadata_info_tab_contents) Journal of the American Statistical Association 102.478 (2007): 527-537.
+#' - \[1\] Harrell, F.E., Jr., et al. "Regression modelling strategies for improved prognostic prediction." Statistics in Medicine 3.2 (1984): 143-152.
+#' - \[2\] Brier, Glenn W. "Verification of forecasts expressed in terms of probability." Monthly Weather Review 78.1 (1950): 1-3.
+#' - \[3\] Graf, Erika, et al. "Assessment and comparison of prognostic classification schemes for survival data." Statistics in Medicine 18.17‐18 (1999): 2529-2545.
+#' - \[4\] Uno, Hajime, et al. "Evaluating prediction rules for t-year survivors with censored regression models." Journal of the American Statistical Association 102.478 (2007): 527-537.
 #'
 #' @examples
 #' \donttest{