From d47baa546e49ead3f3e463a98f9bb15690bd6b09 Mon Sep 17 00:00:00 2001
From: Philipp Baumann <philipp.baumann@usys.ethz.ch>
Date: Tue, 16 Jan 2018 20:44:31 +0100
Subject: [PATCH] Update manuals because of new `resampling_seed` argument of
 `fit_pls` and `fit_rf`

---
 man/fit_pls.Rd | 15 +++++++++++----
 man/fit_rf.Rd  |  9 +++++++--
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/man/fit_pls.Rd b/man/fit_pls.Rd
index 0008a7f..43222c1 100644
--- a/man/fit_pls.Rd
+++ b/man/fit_pls.Rd
@@ -9,15 +9,17 @@ fit_pls(spec_chem, response, variable = NULL, center = TRUE, scale = TRUE,
   evaluation_method = "test_set", validation = TRUE,
   split_method = "ken_stone", ratio_val = 1/3, ken_sto_pc = 2, pc,
   invert = TRUE, tuning_method = "resampling",
-  resampling_method = "kfold_cv", cv = NULL, pls_ncomp_max = 20,
-  ncomp_fixed = 5, print = TRUE, env = parent.frame())
+  resampling_method = "kfold_cv", cv = NULL, resampling_seed = 123,
+  pls_ncomp_max = 20, ncomp_fixed = 5, print = TRUE,
+  env = parent.frame())
 
 pls_ken_stone(spec_chem, response, variable = NULL, center = TRUE,
   scale = TRUE, evaluation_method = "test_set", validation = TRUE,
   split_method = "ken_stone", ratio_val = 1/3, ken_sto_pc = 2, pc,
   invert = TRUE, tuning_method = "resampling",
-  resampling_method = "kfold_cv", cv = NULL, pls_ncomp_max = 20,
-  ncomp_fixed = 5, print = TRUE, env = parent.frame())
+  resampling_method = "kfold_cv", cv = NULL, resampling_seed = 123,
+  pls_ncomp_max = 20, ncomp_fixed = 5, print = TRUE,
+  env = parent.frame())
 }
 \arguments{
 \item{spec_chem}{Tibble that contains spectra, metadata and chemical
@@ -88,6 +90,11 @@ a fixed number of components.}
 
 \item{cv}{Depreciated. Use \code{resampling_method} instead.}
 
+\item{resampling_seed}{Random seed (integer) that will be used for generating
+resampling indices, which will be supplied to \code{caret::trainControl}.
+This makes sure that modeling results are constant when re-fitting.
+Default is \code{resampling_seed = 123}.}
+
 \item{pls_ncomp_max}{Maximum number of PLS components that are evaluated
 by caret::train. Caret will aggregate a performance profile using resampling
 for an integer sequence from 1 to \code{pls_ncomp_max}}
diff --git a/man/fit_rf.Rd b/man/fit_rf.Rd
index 65c88a3..64fd902 100644
--- a/man/fit_rf.Rd
+++ b/man/fit_rf.Rd
@@ -7,8 +7,8 @@
 fit_rf(spec_chem, response, variable = NULL, evaluation_method = "test_set",
   validation = NULL, split_method = "ken_stone", ratio_val,
   ken_sto_pc = 2, pc = NULL, invert = TRUE,
-  tuning_method = "resampling", cv = NULL, ntree_max = 500,
-  print = TRUE, env = parent.frame())
+  tuning_method = "resampling", resampling_seed = 123, cv = NULL,
+  ntree_max = 500, print = TRUE, env = parent.frame())
 }
 \arguments{
 \item{spec_chem}{Tibble that contains spectra, metadata and chemical
@@ -62,6 +62,11 @@ parameter number of PLS components. In this case, the value
 supplied by \code{ncomp_fixed}` is used to set model complexity at
 a fixed number of components.}
 
+\item{resampling_seed}{Random seed (integer) that will be used for generating
+resampling indices, which will be supplied to \code{caret::trainControl}.
+This makes sure that modeling results are constant when re-fitting.
+Default is \code{resampling_seed = 123}.}
+
 \item{cv}{Depreciated. Use \code{resampling_method} instead.}
 
 \item{ntree_max}{Maximum random forest trees