From 0dfb5a4612c0f6021883931f36155c03225ecf2b Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:48:58 -0400
Subject: [PATCH 1/7] needs improvement

---
 NAMESPACE                  |  2 +-
 R/provoc_methods.R         | 19 +++++++++++++++++--
 man/autoplot.provoc.Rd     |  2 +-
 man/predict.provoc.Rd      |  2 ++
 man/variants_similarity.Rd |  2 +-
 5 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index a69c754..6164f57 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(autoplot,provoc)
 S3method(plot,provoc)
 S3method(predict,provoc)
 S3method(print,provoc)
 S3method(summary,provoc)
 export(add_coverage)
 export(astronomize)
+export(autoplot.provoc)
 export(coverage_at_aa)
 export(filter_varmat)
 export(fuse)
diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index bfddfc5..4e175c3 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -17,20 +17,35 @@
 #' @examples
 #' predicted_results <- predict(provoc_obj)
 predict.provoc <- function(provoc_obj,
+    b1, b2,
     newdata = NULL, type = NULL,
     dispersion = NULL, terms = NULL) {
 
+    # TEMP example usage
+    # library(provoc)
+    # data("Baaijens")
+    # Baaijens$mutation <- parse_mutations(Baaijens$label)
+    # res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+    # print(get_convergence(res))
+    # predicted_values <- predict.provoc(res)
+
     if (!"provoc" %in% class(provoc_obj)) {
         stop("Object must be of class 'provoc'")
     }
 
+    b1_index <- match("b1", colnames(provoc_obj$variant))
+    b2_index <- match("b2", colnames(provoc_obj$variant))
+
     proportions <- as.numeric(provoc_obj$rho)
-    variant_matrix <- get_varmat(provoc_obj)
+    variant_matrix <- attr(provoc_obj, "variant_matrix")
+    #variant_matrix <- get_varmat(provoc_obj)
+
     if (any(!rownames(variant_matrix) %in% provoc_obj$variant)) {
         stop("Variant matrix does not match variants in results")
     }
 
-    results <- proportions %*% variant_matrix[provoc_obj$variant, ]
+    results <- proportions[b1_index] %*% variant_matrix[b2_index, ]
+    #results <- proportions %*% variant_matrix[provoc_obj$variant, ]
 
     return(results)
 }
diff --git a/man/autoplot.provoc.Rd b/man/autoplot.provoc.Rd
index 6293010..40ac897 100644
--- a/man/autoplot.provoc.Rd
+++ b/man/autoplot.provoc.Rd
@@ -4,7 +4,7 @@
 \alias{autoplot.provoc}
 \title{Plot a provoc object using ggplot2}
 \usage{
-\method{autoplot}{provoc}(provoc_obj, date_col = NULL)
+autoplot.provoc(provoc_obj, date_col = NULL)
 }
 \arguments{
 \item{provoc_obj}{The result of provoc(), or an object coerced via as.provoc().}
diff --git a/man/predict.provoc.Rd b/man/predict.provoc.Rd
index b502d47..29bad91 100644
--- a/man/predict.provoc.Rd
+++ b/man/predict.provoc.Rd
@@ -6,6 +6,8 @@
 \usage{
 \method{predict}{provoc}(
   provoc_obj,
+  b1,
+  b2,
   newdata = NULL,
   type = NULL,
   dispersion = NULL,
diff --git a/man/variants_similarity.Rd b/man/variants_similarity.Rd
index 937247f..b9fdeea 100644
--- a/man/variants_similarity.Rd
+++ b/man/variants_similarity.Rd
@@ -9,7 +9,7 @@ variants_similarity(data, is_varmat)
 \arguments{
 \item{data}{A dataframe either before or after it has been fused with varmat}
 
-\item{is_varmat}{TRUE if data is a varaint matrix, FALSE if data is a fused dataframe}
+\item{is_varmat}{TRUE if data is a variant matrix, FALSE if data is a fused dataframe}
 }
 \value{
 none

From 0f11dfe1164e41c8cade88d0bda8252022afe7a5 Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:51:21 -0400
Subject: [PATCH 2/7] complete temp example usage

---
 R/provoc_methods.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index 4e175c3..cbdd59b 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -22,12 +22,23 @@ predict.provoc <- function(provoc_obj,
     dispersion = NULL, terms = NULL) {
 
     # TEMP example usage
+    # -------
     # library(provoc)
     # data("Baaijens")
+    
     # Baaijens$mutation <- parse_mutations(Baaijens$label)
+    
     # res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+    
     # print(get_convergence(res))
+    
+    # b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
+    # b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
+    
     # predicted_values <- predict.provoc(res)
+    # print(predicted_values)
+    # -------
+    # END OF TEMP
 
     if (!"provoc" %in% class(provoc_obj)) {
         stop("Object must be of class 'provoc'")

From 13d532a24bd702fe11cbe489e0a6ed731dc34363 Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:55:57 -0400
Subject: [PATCH 3/7] still shows NAs

---
 R/provoc_methods.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index cbdd59b..973b5a6 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -35,7 +35,7 @@ predict.provoc <- function(provoc_obj,
     # b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
     # b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
     
-    # predicted_values <- predict.provoc(res)
+    # predicted_values <- predict.provoc(res, b1, b2)
     # print(predicted_values)
     # -------
     # END OF TEMP
@@ -44,8 +44,11 @@ predict.provoc <- function(provoc_obj,
         stop("Object must be of class 'provoc'")
     }
 
-    b1_index <- match("b1", colnames(provoc_obj$variant))
-    b2_index <- match("b2", colnames(provoc_obj$variant))
+    # b1_index <- match("b1", colnames(provoc_obj$variant))
+    # b2_index <- match("b2", colnames(provoc_obj$variant))
+
+    b1_index <- match(b1, provoc_obj$group)
+    b2_index <- match(b2, provoc_obj$group)
 
     proportions <- as.numeric(provoc_obj$rho)
     variant_matrix <- attr(provoc_obj, "variant_matrix")

From 002d45131342abee36490122e946d64295beb609 Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:48:58 -0400
Subject: [PATCH 4/7] needs improvement

---
 NAMESPACE                  |  2 +-
 R/provoc_methods.R         | 19 +++++++++++++++++--
 man/autoplot.provoc.Rd     |  2 +-
 man/predict.provoc.Rd      |  2 ++
 man/variants_similarity.Rd |  2 +-
 5 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e4b4354..c15fdea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(autoplot,provoc)
 S3method(plot,provoc)
 S3method(predict,provoc)
 S3method(print,provoc)
 S3method(summary,provoc)
 export(add_coverage)
 export(astronomize)
+export(autoplot.provoc)
 export(coverage_at_aa)
 export(filter_varmat)
 export(fuse)
diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index bfddfc5..4e175c3 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -17,20 +17,35 @@
 #' @examples
 #' predicted_results <- predict(provoc_obj)
 predict.provoc <- function(provoc_obj,
+    b1, b2,
     newdata = NULL, type = NULL,
     dispersion = NULL, terms = NULL) {
 
+    # TEMP example usage
+    # library(provoc)
+    # data("Baaijens")
+    # Baaijens$mutation <- parse_mutations(Baaijens$label)
+    # res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+    # print(get_convergence(res))
+    # predicted_values <- predict.provoc(res)
+
     if (!"provoc" %in% class(provoc_obj)) {
         stop("Object must be of class 'provoc'")
     }
 
+    b1_index <- match("b1", colnames(provoc_obj$variant))
+    b2_index <- match("b2", colnames(provoc_obj$variant))
+
     proportions <- as.numeric(provoc_obj$rho)
-    variant_matrix <- get_varmat(provoc_obj)
+    variant_matrix <- attr(provoc_obj, "variant_matrix")
+    #variant_matrix <- get_varmat(provoc_obj)
+
     if (any(!rownames(variant_matrix) %in% provoc_obj$variant)) {
         stop("Variant matrix does not match variants in results")
     }
 
-    results <- proportions %*% variant_matrix[provoc_obj$variant, ]
+    results <- proportions[b1_index] %*% variant_matrix[b2_index, ]
+    #results <- proportions %*% variant_matrix[provoc_obj$variant, ]
 
     return(results)
 }
diff --git a/man/autoplot.provoc.Rd b/man/autoplot.provoc.Rd
index 6293010..40ac897 100644
--- a/man/autoplot.provoc.Rd
+++ b/man/autoplot.provoc.Rd
@@ -4,7 +4,7 @@
 \alias{autoplot.provoc}
 \title{Plot a provoc object using ggplot2}
 \usage{
-\method{autoplot}{provoc}(provoc_obj, date_col = NULL)
+autoplot.provoc(provoc_obj, date_col = NULL)
 }
 \arguments{
 \item{provoc_obj}{The result of provoc(), or an object coerced via as.provoc().}
diff --git a/man/predict.provoc.Rd b/man/predict.provoc.Rd
index b502d47..29bad91 100644
--- a/man/predict.provoc.Rd
+++ b/man/predict.provoc.Rd
@@ -6,6 +6,8 @@
 \usage{
 \method{predict}{provoc}(
   provoc_obj,
+  b1,
+  b2,
   newdata = NULL,
   type = NULL,
   dispersion = NULL,
diff --git a/man/variants_similarity.Rd b/man/variants_similarity.Rd
index 937247f..b9fdeea 100644
--- a/man/variants_similarity.Rd
+++ b/man/variants_similarity.Rd
@@ -9,7 +9,7 @@ variants_similarity(data, is_varmat)
 \arguments{
 \item{data}{A dataframe either before or after it has been fused with varmat}
 
-\item{is_varmat}{TRUE if data is a varaint matrix, FALSE if data is a fused dataframe}
+\item{is_varmat}{TRUE if data is a variant matrix, FALSE if data is a fused dataframe}
 }
 \value{
 none

From 846d035d553a1b284c021b64088485bcc9e9c933 Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:51:21 -0400
Subject: [PATCH 5/7] complete temp example usage

---
 R/provoc_methods.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index 4e175c3..cbdd59b 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -22,12 +22,23 @@ predict.provoc <- function(provoc_obj,
     dispersion = NULL, terms = NULL) {
 
     # TEMP example usage
+    # -------
     # library(provoc)
     # data("Baaijens")
+    
     # Baaijens$mutation <- parse_mutations(Baaijens$label)
+    
     # res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+    
     # print(get_convergence(res))
+    
+    # b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
+    # b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
+    
     # predicted_values <- predict.provoc(res)
+    # print(predicted_values)
+    # -------
+    # END OF TEMP
 
     if (!"provoc" %in% class(provoc_obj)) {
         stop("Object must be of class 'provoc'")

From 81afd2dd9db6f4a5ce321cd5536097e241cd70a4 Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Sun, 24 Mar 2024 04:55:57 -0400
Subject: [PATCH 6/7] still shows NAs

---
 R/provoc_methods.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index cbdd59b..973b5a6 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -35,7 +35,7 @@ predict.provoc <- function(provoc_obj,
     # b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
     # b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
     
-    # predicted_values <- predict.provoc(res)
+    # predicted_values <- predict.provoc(res, b1, b2)
     # print(predicted_values)
     # -------
     # END OF TEMP
@@ -44,8 +44,11 @@ predict.provoc <- function(provoc_obj,
         stop("Object must be of class 'provoc'")
     }
 
-    b1_index <- match("b1", colnames(provoc_obj$variant))
-    b2_index <- match("b2", colnames(provoc_obj$variant))
+    # b1_index <- match("b1", colnames(provoc_obj$variant))
+    # b2_index <- match("b2", colnames(provoc_obj$variant))
+
+    b1_index <- match(b1, provoc_obj$group)
+    b2_index <- match(b2, provoc_obj$group)
 
     proportions <- as.numeric(provoc_obj$rho)
     variant_matrix <- attr(provoc_obj, "variant_matrix")

From d16132fe6ef65f1bf50f81edbefc70e8d12f299f Mon Sep 17 00:00:00 2001
From: Daner Yasin <77366878+danerkestey@users.noreply.github.com>
Date: Tue, 26 Mar 2024 03:13:05 -0400
Subject: [PATCH 7/7] Rebase and clean up

---
 NAMESPACE                   |  3 ++-
 R/provoc_methods.R          | 42 ++++++++++++-------------------------
 man/autoplot.provoc.Rd      |  2 +-
 man/find_mutation_column.Rd | 21 +++++++++++++++++++
 man/parse_ivar.Rd           | 14 +++++++++++++
 man/parse_one_ivar.Rd       | 16 ++++++++++++++
 man/predict.provoc.Rd       | 13 +++++++++++-
 man/provoc.Rd               |  2 +-
 8 files changed, 80 insertions(+), 33 deletions(-)
 create mode 100644 man/find_mutation_column.Rd
 create mode 100644 man/parse_ivar.Rd
 create mode 100644 man/parse_one_ivar.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c15fdea..e56cca0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(autoplot,provoc)
 S3method(plot,provoc)
 S3method(predict,provoc)
 S3method(print,provoc)
 S3method(summary,provoc)
 export(add_coverage)
 export(astronomize)
-export(autoplot.provoc)
 export(coverage_at_aa)
 export(filter_varmat)
 export(fuse)
@@ -15,6 +15,7 @@ export(get_convergence)
 export(get_lineage_info)
 export(get_mutation_defs)
 export(get_res)
+export(parse_ivar)
 export(parse_mutations)
 export(pos_from_aa)
 export(provoc)
diff --git a/R/provoc_methods.R b/R/provoc_methods.R
index 973b5a6..a74da86 100644
--- a/R/provoc_methods.R
+++ b/R/provoc_methods.R
@@ -1,4 +1,3 @@
-
 #' Predict using Proportions of Variants of Concern
 #'
 #' Takes a named list with an estimate of the proportions and the
@@ -6,6 +5,8 @@
 #' predict outcomes, and returns results in the same order as the original data.
 #'
 #' @param provoc_obj Named list with `proportions` and `variant_matrix`.
+#' @param b1 Name of the first sra sample group.
+#' @param b2 Name of the second sra sample group.
 #' @param newdata Not yet implemented.
 #' @param type Not yet implemented.
 #' @param se.fit Not yet implemented.
@@ -13,53 +14,36 @@
 #' @param terms Not yet implemented.
 #' @param na.action Not yet implemented.
 #' @return Predicted values in the same order as the input data.
-#' @export
 #' @examples
-#' predicted_results <- predict(provoc_obj)
-predict.provoc <- function(provoc_obj,
+#' library(provoc)
+#' data("Baaijens")
+#' Baaijens$mutation <- parse_mutations(Baaijens$label)
+#' res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+#' b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
+#' b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
+#' predicted_values <- predict.provoc(res, b1, b2)
+#' print(predicted_values)
+#' @export
+predict.provoc <- function(
+    provoc_obj,
     b1, b2,
     newdata = NULL, type = NULL,
     dispersion = NULL, terms = NULL) {
-
-    # TEMP example usage
-    # -------
-    # library(provoc)
-    # data("Baaijens")
-    
-    # Baaijens$mutation <- parse_mutations(Baaijens$label)
-    
-    # res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
-    
-    # print(get_convergence(res))
-    
-    # b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
-    # b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
-    
-    # predicted_values <- predict.provoc(res, b1, b2)
-    # print(predicted_values)
-    # -------
-    # END OF TEMP
-
     if (!"provoc" %in% class(provoc_obj)) {
         stop("Object must be of class 'provoc'")
     }
 
-    # b1_index <- match("b1", colnames(provoc_obj$variant))
-    # b2_index <- match("b2", colnames(provoc_obj$variant))
-
     b1_index <- match(b1, provoc_obj$group)
     b2_index <- match(b2, provoc_obj$group)
 
     proportions <- as.numeric(provoc_obj$rho)
     variant_matrix <- attr(provoc_obj, "variant_matrix")
-    #variant_matrix <- get_varmat(provoc_obj)
 
     if (any(!rownames(variant_matrix) %in% provoc_obj$variant)) {
         stop("Variant matrix does not match variants in results")
     }
 
     results <- proportions[b1_index] %*% variant_matrix[b2_index, ]
-    #results <- proportions %*% variant_matrix[provoc_obj$variant, ]
 
     return(results)
 }
diff --git a/man/autoplot.provoc.Rd b/man/autoplot.provoc.Rd
index 40ac897..6293010 100644
--- a/man/autoplot.provoc.Rd
+++ b/man/autoplot.provoc.Rd
@@ -4,7 +4,7 @@
 \alias{autoplot.provoc}
 \title{Plot a provoc object using ggplot2}
 \usage{
-autoplot.provoc(provoc_obj, date_col = NULL)
+\method{autoplot}{provoc}(provoc_obj, date_col = NULL)
 }
 \arguments{
 \item{provoc_obj}{The result of provoc(), or an object coerced via as.provoc().}
diff --git a/man/find_mutation_column.Rd b/man/find_mutation_column.Rd
new file mode 100644
index 0000000..2a3e090
--- /dev/null
+++ b/man/find_mutation_column.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/provoc.R
+\name{find_mutation_column}
+\alias{find_mutation_column}
+\title{Finds the right mutation column in mutation_defs.}
+\usage{
+find_mutation_column(data, mutation_defs)
+}
+\arguments{
+\item{data}{Data frame containing count, coverage, and lineage columns}
+
+\item{mutation_defs}{Optional mutation definitions}
+}
+\value{
+A list of length 2 containing the possibly transposed mutation_defs and
+the right mutation column.
+}
+\description{
+Checks the columns of mutation_defs and if not found in columns will check the rows
+and transpose mutation_defs.
+}
diff --git a/man/parse_ivar.Rd b/man/parse_ivar.Rd
new file mode 100644
index 0000000..cabb349
--- /dev/null
+++ b/man/parse_ivar.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parse_mutations.R
+\name{parse_ivar}
+\alias{parse_ivar}
+\title{Parse Mutations from the ivar pipeline}
+\usage{
+parse_ivar(ivar_output)
+}
+\arguments{
+\item{ivar_output}{A data frame imported from the ivar output. Must have columns POS and ALT}
+}
+\description{
+Parse Mutations from the ivar pipeline
+}
diff --git a/man/parse_one_ivar.Rd b/man/parse_one_ivar.Rd
new file mode 100644
index 0000000..4313460
--- /dev/null
+++ b/man/parse_one_ivar.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parse_mutations.R
+\name{parse_one_ivar}
+\alias{parse_one_ivar}
+\title{Parse mutations from ivar pipeline}
+\usage{
+parse_one_ivar(pos, alt)
+}
+\arguments{
+\item{pos}{The position on the genome}
+
+\item{alt}{The alternate genotype}
+}
+\description{
+Parse mutations from ivar pipeline
+}
diff --git a/man/predict.provoc.Rd b/man/predict.provoc.Rd
index 29bad91..dcf752d 100644
--- a/man/predict.provoc.Rd
+++ b/man/predict.provoc.Rd
@@ -17,6 +17,10 @@
 \arguments{
 \item{provoc_obj}{Named list with \code{proportions} and \code{variant_matrix}.}
 
+\item{b1}{Name of the first sra sample group.}
+
+\item{b2}{Name of the second sra sample group.}
+
 \item{newdata}{Not yet implemented.}
 
 \item{type}{Not yet implemented.}
@@ -38,5 +42,12 @@ associated variant matrix, performs matrix multiplication to
 predict outcomes, and returns results in the same order as the original data.
 }
 \examples{
-predicted_results <- predict(provoc_obj)
+library(provoc)
+data("Baaijens")
+Baaijens$mutation <- parse_mutations(Baaijens$label)
+res <- provoc(formula = cbind(count, coverage) ~ B.1.1.7 + B.1.617.2, data = Baaijens)
+b1 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[1], ]
+b2 <- Baaijens[Baaijens$sra == unique(Baaijens$sra)[2], ]
+predicted_values <- predict.provoc(res, b1, b2)
+print(predicted_values)
 }
diff --git a/man/provoc.Rd b/man/provoc.Rd
index d540fe6..595dd16 100644
--- a/man/provoc.Rd
+++ b/man/provoc.Rd
@@ -10,7 +10,7 @@ provoc(
   mutation_defs = NULL,
   by = NULL,
   update_interval = 20,
-  verbose = TRUE,
+  verbose = FALSE,
   annihilate = FALSE
 )
 }