diff --git a/DESCRIPTION b/DESCRIPTION index 14535b9a0..a7a21eae1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: parsnip Title: A Common API to Modeling and Analysis Functions -Version: 0.1.7.9006 +Version: 0.2.0 Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", role = c("aut", "cre")), person("Davis", "Vaughan", , "davis@rstudio.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index cc536061f..62edb2bcd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# parsnip (development version) +# parsnip 0.2.0 ## Model Specification Changes diff --git a/man/details_C5_rules_C5.0.Rd b/man/details_C5_rules_C5.0.Rd index f9039d589..1c333e18c 100644 --- a/man/details_C5_rules_C5.0.Rd +++ b/man/details_C5_rules_C5.0.Rd @@ -61,7 +61,7 @@ are not required for this model. \item Quinlan R (1992). “Learning with Continuous Classes.” Proceedings of the 5th Australian Joint Conference On Artificial Intelligence, pp. 343-348. -\item Quinlan R (1993).“Combining Instance-Based and Model-Based +\item Quinlan R (1993).”Combining Instance-Based and Model-Based Learning.” Proceedings of the Tenth International Conference on Machine Learning, pp. 236-243. \item Kuhn M and Johnson K (2013). \emph{Applied Predictive Modeling}. diff --git a/man/details_boost_tree_mboost.Rd b/man/details_boost_tree_mboost.Rd index df9dfa215..a26b5ed01 100644 --- a/man/details_boost_tree_mboost.Rd +++ b/man/details_boost_tree_mboost.Rd @@ -43,7 +43,7 @@ boost_tree() \%>\% ## family = mboost::CoxPH()) } -\code{\link[=blackboost_train]{blackboost_train()}} is a wrapper around +\code{censored::blackboost_train()} is a wrapper around \code{\link[mboost:blackboost]{mboost::blackboost()}} (and other functions) that makes it easier to run this model. } diff --git a/man/details_cubist_rules_Cubist.Rd b/man/details_cubist_rules_Cubist.Rd index beeef85da..29e8f9665 100644 --- a/man/details_cubist_rules_Cubist.Rd +++ b/man/details_cubist_rules_Cubist.Rd @@ -60,7 +60,7 @@ are not required for this model. \item Quinlan R (1992). “Learning with Continuous Classes.” Proceedings of the 5th Australian Joint Conference On Artificial Intelligence, pp. 343-348. -\item Quinlan R (1993).“Combining Instance-Based and Model-Based +\item Quinlan R (1993).”Combining Instance-Based and Model-Based Learning.” Proceedings of the Tenth International Conference on Machine Learning, pp. 236-243. \item Kuhn M and Johnson K (2013). \emph{Applied Predictive Modeling}. diff --git a/man/details_decision_tree_party.Rd b/man/details_decision_tree_party.Rd index 8d38f802a..be7a55bf2 100644 --- a/man/details_decision_tree_party.Rd +++ b/man/details_decision_tree_party.Rd @@ -49,9 +49,9 @@ decision_tree(tree_depth = integer(1), min_n = integer(1)) \%>\% ## data)) } -\code{\link[=cond_inference_surv_ctree]{cond_inference_surv_ctree()}} is a -wrapper around \code{\link[party:ctree]{party::ctree()}} (and other functions) -that makes it easier to run this model. +\code{censored::cond_inference_surv_ctree()} is a wrapper around +\code{\link[party:ctree]{party::ctree()}} (and other functions) that makes it +easier to run this model. } \subsection{Preprocessing requirements}{ diff --git a/man/details_discrim_linear_sda.Rd b/man/details_discrim_linear_sda.Rd index 49d56fe77..52857aa48 100644 --- a/man/details_discrim_linear_sda.Rd +++ b/man/details_discrim_linear_sda.Rd @@ -65,7 +65,7 @@ before fitting the model. \item Ahdesmaki, A., and K. Strimmer. 2010. Feature selection in omics prediction problems using cat scores and false non-discovery rate control. Ann. Appl. Stat. 4: 503-519. -\href{http://arxiv.org/abs/0903.2003}{Preprint}. +\href{https://arxiv.org/abs/0903.2003}{Preprint}. } } } diff --git a/man/details_rand_forest_party.Rd b/man/details_rand_forest_party.Rd index 6951629bf..489351502 100644 --- a/man/details_rand_forest_party.Rd +++ b/man/details_rand_forest_party.Rd @@ -37,9 +37,9 @@ rand_forest() \%>\% ## data = missing_arg()) } -\code{\link[=cond_inference_surv_cforest]{cond_inference_surv_cforest()}} is a -wrapper around \code{\link[party:cforest]{party::cforest()}} (and other -functions) that makes it easier to run this model. +\code{censored::cond_inference_surv_cforest()} is a wrapper around +\code{\link[party:cforest]{party::cforest()}} (and other functions) that makes +it easier to run this model. } \subsection{Preprocessing requirements}{ diff --git a/man/details_surv_reg_flexsurv.Rd b/man/details_surv_reg_flexsurv.Rd index e39e6d032..b654470e3 100644 --- a/man/details_surv_reg_flexsurv.Rd +++ b/man/details_surv_reg_flexsurv.Rd @@ -40,9 +40,9 @@ model specification typically involved the use of \code{\link[survival:Surv]{survival::Surv()}}. For this engine, stratification cannot be specified via -\code{\link[=strata]{strata()}}, please see the documentation of the -\code{\link[flexsurv:flexsurv-package]{flexsurv::flexsurv-package}} -package for alternative specifications. +\code{\link[=strata]{strata()}}, please see +\code{\link[flexsurv:flexsurvreg]{flexsurv::flexsurvreg()}} for alternative +specifications. } \subsection{References}{ diff --git a/man/details_survival_reg_flexsurv.Rd b/man/details_survival_reg_flexsurv.Rd index 084ff7ecf..d50009458 100644 --- a/man/details_survival_reg_flexsurv.Rd +++ b/man/details_survival_reg_flexsurv.Rd @@ -44,8 +44,9 @@ model specification typically involved the use of \code{\link[survival:Surv]{survival::Surv()}}. For this engine, stratification cannot be specified via -\code{\link[=strata]{strata()}}; please see the documentation of the -\link{flexsurv} package for alternative specifications. +\code{\link[=strata]{strata()}}, please see +\code{\link[flexsurv:flexsurvreg]{flexsurv::flexsurvreg()}} for alternative +specifications. } \subsection{References}{ diff --git a/man/rmd/boost_tree_mboost.Rmd b/man/rmd/boost_tree_mboost.Rmd index 0d2ddabfd..d9c1b8d41 100644 --- a/man/rmd/boost_tree_mboost.Rmd +++ b/man/rmd/boost_tree_mboost.Rmd @@ -38,7 +38,7 @@ boost_tree() %>% translate() ``` -[blackboost_train()] is a wrapper around [mboost::blackboost()] (and other functions) that makes it easier to run this model. +`censored::blackboost_train()` is a wrapper around [mboost::blackboost()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/boost_tree_mboost.md b/man/rmd/boost_tree_mboost.md index 6bacca070..387fd3496 100644 --- a/man/rmd/boost_tree_mboost.md +++ b/man/rmd/boost_tree_mboost.md @@ -45,7 +45,7 @@ boost_tree() %>% ## family = mboost::CoxPH()) ``` -[blackboost_train()] is a wrapper around [mboost::blackboost()] (and other functions) that makes it easier to run this model. +`censored::blackboost_train()` is a wrapper around [mboost::blackboost()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/decision_tree_party.Rmd b/man/rmd/decision_tree_party.Rmd index 06fa585fe..fbcd98694 100644 --- a/man/rmd/decision_tree_party.Rmd +++ b/man/rmd/decision_tree_party.Rmd @@ -42,7 +42,7 @@ decision_tree(tree_depth = integer(1), min_n = integer(1)) %>% translate() ``` -[cond_inference_surv_ctree()] is a wrapper around [party::ctree()] (and other functions) that makes it easier to run this model. +`censored::cond_inference_surv_ctree()` is a wrapper around [party::ctree()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/decision_tree_party.md b/man/rmd/decision_tree_party.md index acb160d67..38274833b 100644 --- a/man/rmd/decision_tree_party.md +++ b/man/rmd/decision_tree_party.md @@ -48,7 +48,7 @@ decision_tree(tree_depth = integer(1), min_n = integer(1)) %>% ## data)) ``` -[cond_inference_surv_ctree()] is a wrapper around [party::ctree()] (and other functions) that makes it easier to run this model. +`censored::cond_inference_surv_ctree()` is a wrapper around [party::ctree()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/discrim_linear_sda.md b/man/rmd/discrim_linear_sda.md index b94cb28c9..9c283f3e2 100644 --- a/man/rmd/discrim_linear_sda.md +++ b/man/rmd/discrim_linear_sda.md @@ -51,4 +51,4 @@ Variance calculations are used in these computations so _zero-variance_ predicto ## References - - Ahdesmaki, A., and K. Strimmer. 2010. Feature selection in omics prediction problems using cat scores and false non-discovery rate control. Ann. Appl. Stat. 4: 503-519. [Preprint](http://arxiv.org/abs/0903.2003). + - Ahdesmaki, A., and K. Strimmer. 2010. Feature selection in omics prediction problems using cat scores and false non-discovery rate control. Ann. Appl. Stat. 4: 503-519. [Preprint](https://arxiv.org/abs/0903.2003). diff --git a/man/rmd/rand_forest_party.Rmd b/man/rmd/rand_forest_party.Rmd index 68e0fddd4..5462aaa96 100644 --- a/man/rmd/rand_forest_party.Rmd +++ b/man/rmd/rand_forest_party.Rmd @@ -36,7 +36,7 @@ rand_forest() %>% translate() ``` -[cond_inference_surv_cforest()] is a wrapper around [party::cforest()] (and other functions) that makes it easier to run this model. +`censored::cond_inference_surv_cforest()` is a wrapper around [party::cforest()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/rand_forest_party.md b/man/rmd/rand_forest_party.md index 227641b17..719d12f26 100644 --- a/man/rmd/rand_forest_party.md +++ b/man/rmd/rand_forest_party.md @@ -39,7 +39,7 @@ rand_forest() %>% ## data = missing_arg()) ``` -[cond_inference_surv_cforest()] is a wrapper around [party::cforest()] (and other functions) that makes it easier to run this model. +`censored::cond_inference_surv_cforest()` is a wrapper around [party::cforest()] (and other functions) that makes it easier to run this model. ## Preprocessing requirements diff --git a/man/rmd/surv_reg_flexsurv.Rmd b/man/rmd/surv_reg_flexsurv.Rmd index 0fd521f4a..278d26493 100644 --- a/man/rmd/surv_reg_flexsurv.Rmd +++ b/man/rmd/surv_reg_flexsurv.Rmd @@ -37,7 +37,7 @@ surv_reg(dist = character(1)) %>% The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. -For this engine, stratification cannot be specified via [`strata()`], please see the documentation of the [`flexsurv::flexsurv-package`] package for alternative specifications. +For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvreg()] for alternative specifications. ## References diff --git a/man/rmd/surv_reg_flexsurv.md b/man/rmd/surv_reg_flexsurv.md index e98a23aa6..a0d27f61e 100644 --- a/man/rmd/surv_reg_flexsurv.md +++ b/man/rmd/surv_reg_flexsurv.md @@ -39,7 +39,7 @@ surv_reg(dist = character(1)) %>% The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. -For this engine, stratification cannot be specified via [`strata()`], please see the documentation of the [`flexsurv::flexsurv-package`] package for alternative specifications. +For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvreg()] for alternative specifications. ## References diff --git a/man/rmd/survival_reg_flexsurv.Rmd b/man/rmd/survival_reg_flexsurv.Rmd index 3e244ae26..9a0c2b31b 100644 --- a/man/rmd/survival_reg_flexsurv.Rmd +++ b/man/rmd/survival_reg_flexsurv.Rmd @@ -40,7 +40,7 @@ survival_reg(dist = character(1)) %>% The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. -For this engine, stratification cannot be specified via [strata()]; please see the documentation of the [flexsurv] package for alternative specifications. +For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvreg()] for alternative specifications. ## References diff --git a/man/rmd/survival_reg_flexsurv.md b/man/rmd/survival_reg_flexsurv.md index 51bf3f9b9..b2e900126 100644 --- a/man/rmd/survival_reg_flexsurv.md +++ b/man/rmd/survival_reg_flexsurv.md @@ -42,7 +42,7 @@ survival_reg(dist = character(1)) %>% The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. -For this engine, stratification cannot be specified via [strata()]; please see the documentation of the [flexsurv] package for alternative specifications. +For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvreg()] for alternative specifications. ## References