From a4bd1d3746c7f03229a5e6a5940cd9645f9f9270 Mon Sep 17 00:00:00 2001
From: Matthew Stephens <stephens999@gmail.com>
Date: Sun, 28 Jul 2019 15:42:56 -0500
Subject: [PATCH] fix some documentation issues

---
 R/susie.R                 | 19 ++++++++++++-------
 man/susie.Rd              | 18 +++++++++++-------
 man/update_each_effect.Rd |  4 ++--
 3 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/R/susie.R b/R/susie.R
index a182ae0d..ebdce23f 100644
--- a/R/susie.R
+++ b/R/susie.R
@@ -26,11 +26,11 @@
 #'    either a scalar, or a vector of length \code{L}. The prior variance
 #'   of each non-zero element of b is set to
 #'   \code{var(Y)*scaled_prior_variance}. If
-#'   \code{estimate_prior_variance = TRUE}, this input provides the
+#'   \code{estimate_prior_variance = TRUE}, this input simply provides
 #'   initial estimates of the prior variances.
 #'
 #' @param residual_variance The variance of the residual. If
-#'   \code{estimate_residual_variance = TRUE}, this value provides the
+#'   \code{estimate_residual_variance = TRUE}, this value simply provides the
 #'   initial estimate of the residual variance. By default, it is set to
 #'   \code{var(Y)}.
 #'
@@ -56,13 +56,18 @@
 #'   FALSE} is generally not recommended.
 #'
 #' @param estimate_residual_variance If
-#'   \code{estimate_residual_variance = TRUE}, the variance of the
-#'   residual is estimated separately for each of the \code{L}
-#'   components, and \code{scaled_prior_variance} is used as an initial
-#'   estimate of the variances.
+#'   \code{estimate_residual_variance = TRUE}, the residual variance
+#'   is estimated (using \code{residual_variance} as an initial  value).
+#'   If \code{estimate_residual_variance = FALSE}
+#'   then the residual variance is fixed to the value supplied by \code{residual_variance}.
 #'
 #' @param estimate_prior_variance If \code{estimate_prior_variance =
-#'   TRUE}, the prior variance is estimated father than fixed.
+#'   TRUE}, the prior variance is estimated (a separate parameter for each of the \code{L}
+#'   effects). If provided, \code{scaled_prior_variance} is then used as an initial
+#'   point for the optimization. If \code{estimate_prior_variance = FALSE}
+#'   then the prior variance (for each of the \code{L} effects) is determined by the value
+#'   supplied to \code{scaled_prior_variance}.
+#
 #'
 #' @param estimate_prior_method The method used for estimating prior
 #'   variance.
diff --git a/man/susie.Rd b/man/susie.Rd
index 6d7bf048..9aaf0e4d 100644
--- a/man/susie.Rd
+++ b/man/susie.Rd
@@ -26,11 +26,11 @@ covariate (p), \code{L} is set to p.}
  either a scalar, or a vector of length \code{L}. The prior variance
 of each non-zero element of b is set to
 \code{var(Y)*scaled_prior_variance}. If
-\code{estimate_prior_variance = TRUE}, this input provides the
+\code{estimate_prior_variance = TRUE}, this input simply provides
 initial estimates of the prior variances.}
 
 \item{residual_variance}{The variance of the residual. If
-\code{estimate_residual_variance = TRUE}, this value provides the
+\code{estimate_residual_variance = TRUE}, this value simply provides the
 initial estimate of the residual variance. By default, it is set to
 \code{var(Y)}.}
 
@@ -56,13 +56,17 @@ fitted; otherwise, it is set to zero. Setting \code{intercept =
 FALSE} is generally not recommended.}
 
 \item{estimate_residual_variance}{If
-\code{estimate_residual_variance = TRUE}, the variance of the
-residual is estimated separately for each of the \code{L}
-components, and \code{scaled_prior_variance} is used as an initial
-estimate of the variances.}
+\code{estimate_residual_variance = TRUE}, the residual variance
+is estimated (using \code{residual_variance} as an initial  value).
+If \code{estimate_residual_variance = FALSE}
+then the residual variance is fixed to the value supplied by \code{residual_variance}.}
 
 \item{estimate_prior_variance}{If \code{estimate_prior_variance =
-TRUE}, the prior variance is estimated father than fixed.}
+TRUE}, the prior variance is estimated (a separate parameter for each of the \code{L}
+effects). If provided, \code{scaled_prior_variance} is then used as an initial
+point for the optimization. If \code{estimate_prior_variance = FALSE}
+then the prior variance (for each of the \code{L} effects) is determined by the value
+supplied to \code{scaled_prior_variance}.}
 
 \item{estimate_prior_method}{The method used for estimating prior
 variance.}
diff --git a/man/update_each_effect.Rd b/man/update_each_effect.Rd
index bd229af8..2db58f4b 100644
--- a/man/update_each_effect.Rd
+++ b/man/update_each_effect.Rd
@@ -8,9 +8,9 @@ update_each_effect(X, Y, s, estimate_prior_variance = FALSE,
   estimate_prior_method = "optim")
 }
 \arguments{
-\item{X}{an n by p matrix of covariantes}
+\item{X}{an n by p matrix of regressor variables}
 
-\item{Y}{an n vector of data}
+\item{Y}{an n vector of response variable}
 
 \item{s}{a SuSiE fit}