remove p1807 example data by replacing with simulated data.

fgcz · May 22, 2024 · eb7369d · eb7369d
1 parent 93c5831
commit eb7369d
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Showing 23 changed files with 12 additions and 141 deletions.
diff --git a/R/A_dataset_docu.R b/R/A_dataset_docu.R
@@ -59,9 +59,6 @@ NULL
 #' @name PACKAGE_DATA
 NULL
 
-# data_basicModel_p1807 <- prolfqua::basicModel_p1807
-# usethis::use_data(data_basicModel_p1807, compress = TRUE, overwrite = TRUE)
-# file.remove("data/basicModel_p1807.rda")
 
 #' SAINT express output
 #'
@@ -77,14 +74,7 @@ NULL
 
 
 
-#' Model for debugging
-#' @family data
-#' @keywords internal
-#' @docType data
-#' @format a linear model
-"data_basicModel_p1807"
 
-# #@usage data_basicModel_p1807 <- prolfqua_data("data_basicModel_p1807")
 
 # data_benchmarkExample <- prolfqua::benchmarkDataExample
 # usethis::use_data(data_benchmarkExample, compress = TRUE, overwrite = TRUE)
@@ -167,13 +157,6 @@ NULL
 
 
 
-
-#' example data for check
-#' @family data
-#' @docType data
-#' @keywords internal
-'data_interactionModel_p1807'
-
 # #@usage data_interactionModel_p1807 <- prolfqua_data("data_interactionModel_p1807")
 
 

diff --git a/R/tidyMS_R6_Modelling.R b/R/tidyMS_R6_Modelling.R
@@ -359,7 +359,6 @@ model_analyse <- function(pepIntensity,
 #' @family modelling
 #' @keywords internal
 #' @examples
-#' # m <- prolfqua_data('data_interactionModel_p1807')
 #' m <- sim_make_model_lmer()
 #' plot_lmer_peptide_predictions(m, intensity = "abundance")
 #' m <- sim_make_model_lmer("interaction")
@@ -823,25 +822,21 @@ my_contrast_V2 <- function(m, linfct,confint = 0.95){
 #' @keywords internal
 #' @examples
 #'
-#' mb <- prolfqua_data('data_basicModel_p1807')
+#' mb <- sim_make_model_lmer("interaction")
 #' summary(mb)
 #'
 #' linfct <- linfct_from_model(mb)
 #' names(linfct)
 #' my_contest(mb, linfct$linfct_factors)
 #' my_contest(mb, linfct$linfct_interactions)
-#'
-#' # my_glht(mb, linfct$linfct_factors)
-#' # my_glht(mb, linfct$linfct_interactions)
+#' if(require(multcomp)){
+#' my_glht(mb, linfct$linfct_factors)
+#' my_glht(mb, linfct$linfct_interactions)
+#' }
+#' length(mb@beta)
 #' lmerTest::contest(mb, c( 0 ,1 , 0 , 0),joint = FALSE)
 #' summary(mb)
 #'
-#'
-#' #library(pbkrtest)
-#' #(fm1 <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy))
-#' #class(fm1)
-#' #pbkrtest::get_ddf_Lb.lmerMod(fm1)
-#'
 my_contest <- function(model, linfct, ddf = c("Satterthwaite", "Kenward-Roger")){
   ddf <- match.arg(ddf)
   if (length(lme4::fixef(model)) != ncol(linfct) ) {

diff --git a/data/data_basicModel_p1807.rda b/data/data_basicModel_p1807.rda
diff --git a/data/data_interactionModel_p1807.rda b/data/data_interactionModel_p1807.rda
diff --git a/man/PACKAGE_DATA.Rd b/man/PACKAGE_DATA.Rd
diff --git a/man/data_IonstarProtein_subsetNorm.Rd b/man/data_IonstarProtein_subsetNorm.Rd
diff --git a/man/data_SAINTe_output.Rd b/man/data_SAINTe_output.Rd
diff --git a/man/data_basicModel_p1807.Rd b/man/data_basicModel_p1807.Rd
diff --git a/man/data_benchmarkExample.Rd b/man/data_benchmarkExample.Rd
diff --git a/man/data_checksummarizationrobust87.Rd b/man/data_checksummarizationrobust87.Rd
diff --git a/man/data_checksummarizerobust.Rd b/man/data_checksummarizerobust.Rd
diff --git a/man/data_checksummarizerobust69.Rd b/man/data_checksummarizerobust69.Rd
diff --git a/man/data_correlatedPeptideList.Rd b/man/data_correlatedPeptideList.Rd
diff --git a/man/data_interactionModel_p1807.Rd b/man/data_interactionModel_p1807.Rd
diff --git a/man/data_ionstar.Rd b/man/data_ionstar.Rd
diff --git a/man/data_multigroupFC.Rd b/man/data_multigroupFC.Rd
diff --git a/man/data_skylinePRMSample_A.Rd b/man/data_skylinePRMSample_A.Rd
diff --git a/man/data_skylineSRM_HL_A.Rd b/man/data_skylineSRM_HL_A.Rd
diff --git a/man/data_spectronautDIA250_A.Rd b/man/data_spectronautDIA250_A.Rd
diff --git a/man/data_test_confusion_matrix_scores.Rd b/man/data_test_confusion_matrix_scores.Rd
diff --git a/man/my_contest.Rd b/man/my_contest.Rd
diff --git a/man/plot_lmer_peptide_predictions.Rd b/man/plot_lmer_peptide_predictions.Rd
diff --git a/man/prolfqua_data.Rd b/man/prolfqua_data.Rd