From 1fc552e9a3fef768679ca38f88aa4b08fe24291e Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Tue, 14 May 2024 14:11:35 +0200
Subject: [PATCH] fix error in examples

---
 R/tidyMS_R6_Modelling.R  |  2 +-
 R/tidyMS_missigness_V2.R | 14 +++++++-------
 man/MissingHelpers.Rd    | 10 +++++-----
 man/build_models.Rd      |  2 +-
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/tidyMS_R6_Modelling.R b/R/tidyMS_R6_Modelling.R
index 446ef680..e1260b7a 100644
--- a/R/tidyMS_R6_Modelling.R
+++ b/R/tidyMS_R6_Modelling.R
@@ -3,7 +3,7 @@
 #' @export
 #' @keywords internal
 #' @examples
-#' mod <- build_models(model = " ~ Treatment * Background", weight_missing = 1)
+#' mod <- build_models(model = "interaction", weight_missing = 1)
 #' stopifnot(dim(mod$modelDF) == c(10,9))
 #'
 build_models <- function(model = c("factors", "interaction"), Nprot = 10, with_missing = TRUE, weight_missing = 1) {
diff --git a/R/tidyMS_missigness_V2.R b/R/tidyMS_missigness_V2.R
index 4cdb36f5..df22d03b 100644
--- a/R/tidyMS_missigness_V2.R
+++ b/R/tidyMS_missigness_V2.R
@@ -7,11 +7,11 @@
 #' Contrasts <- c("group.b-a" = "group_A - group_B", "group.a-ctrl" = "group_A - group_Ctrl")
 #' dd <- prolfqua::sim_lfq_data_protein_config(Nprot = 100,weight_missing = 2)
 #' mh <- prolfqua::MissingHelpers$new(dd$data, dd$config, prob = 0.8,weighted = TRUE)
-#' mh$get_stats()
-#' mh$get_LOD()
-#' mh$impute_weighted_lod()
-#' mh$impute_lod()
-#' mh$get_poolvar()
+#' xx <- mh$get_stats()
+#' xx <- mh$get_LOD()
+#' xx <- mh$impute_weighted_lod()
+#' xx <- mh$impute_lod()
+#' xx <- mh$get_poolvar()
 #' bb <- mh$get_contrast_estimates(Contrasts)
 #' mh$get_contrasts(Contrasts)
 #'
@@ -112,8 +112,8 @@ MissingHelpers <- R6::R6Class(
       meandf$sd <-  ifelse(meandf$sd > 0, meandf$sd, minsd)
       meandf$sdT <-  ifelse(meandf$sdT > 0, meandf$sdT, minsd)
 
-      pooled <- pooled |> mutate(sd = ifelse(is.na(sd) ,meandf$sd, sd))
-      pooled <- pooled |> mutate(sdT = ifelse(is.na(sdT) , meandf$sdT, sdT ))
+      pooled <- pooled |> mutate(sd = ifelse(is.na(sd) | sd == 0 ,meandf$sd, sd))
+      pooled <- pooled |> mutate(sdT = ifelse(is.na(sdT) | sdT == 0, meandf$sdT, sdT ))
       pooled <- pooled |> mutate(df = ifelse(df == 0, 1, df))
       return(pooled)
     },
diff --git a/man/MissingHelpers.Rd b/man/MissingHelpers.Rd
index 253751b3..56414e08 100644
--- a/man/MissingHelpers.Rd
+++ b/man/MissingHelpers.Rd
@@ -15,11 +15,11 @@ weight lod by nr of NA's $(LOD * nrNas + meanAbundance *nrObs)/(nrMeasured)$
 Contrasts <- c("group.b-a" = "group_A - group_B", "group.a-ctrl" = "group_A - group_Ctrl")
 dd <- prolfqua::sim_lfq_data_protein_config(Nprot = 100,weight_missing = 2)
 mh <- prolfqua::MissingHelpers$new(dd$data, dd$config, prob = 0.8,weighted = TRUE)
-mh$get_stats()
-mh$get_LOD()
-mh$impute_weighted_lod()
-mh$impute_lod()
-mh$get_poolvar()
+xx <- mh$get_stats()
+xx <- mh$get_LOD()
+xx <- mh$impute_weighted_lod()
+xx <- mh$impute_lod()
+xx <- mh$get_poolvar()
 bb <- mh$get_contrast_estimates(Contrasts)
 mh$get_contrasts(Contrasts)
 
diff --git a/man/build_models.Rd b/man/build_models.Rd
index 5a061112..b04de988 100644
--- a/man/build_models.Rd
+++ b/man/build_models.Rd
@@ -15,7 +15,7 @@ build_models(
 build dataframe with models for testing
 }
 \examples{
-mod <- build_models(model = " ~ Treatment * Background", weight_missing = 1)
+mod <- build_models(model = "interaction", weight_missing = 1)
 stopifnot(dim(mod$modelDF) == c(10,9))
 
 }