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R/OpenStatsReportRR.R
In OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
Defines functions
OpenStatsReportRR
OpenStatsReportRR <- function(object) {
if (!is.null(object$messages)) {
return(NULL)
}
#####################################################################
Labels <- OpenStatsListLevels(object = object)
Fmodel <- object$extra$Cleanedformula
frm <- formula(Fmodel)
depVariable <- all_vars0(frm)[1]
refVariable <- all_vars0(frm)[2]
# equation = NULL
formula <- printformula(frm)
framework <- paste0(
"Reference Range Plus Test framework; quantile = ",
object$input$prop,
" (Tails probability = ",
1 - MakeRRQuantileFromTheValue(object$input$prop, messages = FALSE),
")"
)
# fittingMethod = NULL
#####################################################################
Vsplit <- object$output$SplitModels
low <- pastedot("Low", depVariable, refVariable)
high <- pastedot("High", depVariable, refVariable)
VsplitLow <- Vsplit[[low]]
VsplitHig <- Vsplit[[high]]
#### Sex
VsplitLowFemale <- Vsplit[[pastedot(low, "Female")]]
VsplitHigFemale <- Vsplit[[pastedot(high, "Female")]]
VsplitLowMale <- Vsplit[[pastedot(low, "Male")]]
VsplitHigMale <- Vsplit[[pastedot(high, "Male")]]
### Lifestage
VsplitLowEarly <- Vsplit[[pastedot(low, "Early")]]
VsplitHigEarly <- Vsplit[[pastedot(high, "Early")]]
VsplitLowLate <- Vsplit[[pastedot(low, "Late")]]
VsplitHigLate <- Vsplit[[pastedot(high, "Late")]]
### LifeStage x Sex
# Female
VsplitLowEarlyFemale <- Vsplit[[pastedot(low, "Female", "Early")]]
VsplitHigEarlyFemale <- Vsplit[[pastedot(high, "Female", "Early")]]
VsplitLowLateFemale <- Vsplit[[pastedot(low, "Female", "Late")]]
VsplitHigLateFemale <- Vsplit[[pastedot(high, "Female", "Late")]]
# Male
VsplitLowEarlyMale <- Vsplit[[pastedot(low, "Male", "Early")]]
VsplitHigEarlyMale <- Vsplit[[pastedot(high, "Male", "Early")]]
VsplitLowLateMale <- Vsplit[[pastedot(low, "Male", "Late")]]
VsplitHigLateMale <- Vsplit[[pastedot(high, "Male", "Late")]]
###
GenotypeDiscLabel <- "Data is discritised by `Genotype` levels"
SexDiscLabel <- "Data is first split by `Sex` levels then discritised by `Genotype` levels"
LifeStageDiscLabel <- "Data is first split by `LifeStage` levels then discritised by `Genotype` levels"
LifeStageSexDiscLabel <- "Data is first split by `LifeStage-Sex` levels then discritised by `Genotype` levels"
#####################################################################
x <- object$input$data
columnOfInterest <- x[, c(depVariable)]
#####################################################################
variability <- list(
"Value" = length(unique(columnOfInterest)) / max(length(columnOfInterest), 1),
"Type" = "Total unique response divided by total number of response"
)
#####################################################################
extractFisherSubTableResults1 <- function(x, what = "p.value") {
r <- extractFisherSubTableResults(x = x, what = what)
if (length(r) == 1) {
r <- r[[1]]
}
return(r)
}
lapply1 <- function(X, FUN, ...) {
r <- lapply0(X = X, FUN = FUN, ...)
if (length(r) == 1) {
r <- r[[1]]
}
return(r)
}
#####################################################################
DSsize <- SummaryStats(
x = x,
formula = object$input$formula,
# label = 'Summary statistics',
lower = TRUE,
drop = TRUE,
sep = "_"
)
MultiBatch <- ifelse(multiBatch(x),
"Dataset contains multiple batches",
"Dataset contains single batch"
)
addInfo <- list(
Data = list(
"Data signature" = dataSignature(
formula = frm,
data = x
),
"Variability" = variability,
"Summary statistics" = DSsize
),
Analysis = list(
"Model setting" = extractFERRTerms(object),
"Implementation specification" = RRextraDetailsExtractor(object),
"Is model optimised" = NULL,
"Multibatch in analysis" = MultiBatch,
"Gender included in analysis" = GenderIncludedInAnalysis(x),
"Further models" = if (!is.null(Vsplit)) {
setNames(lapply0(Vsplit, function(v) {
lapply1(
v,
FUN = function(v2) {
list(
Result = extractFisherSubTableResults1(
x = v2$result,
what = c("p.value", "effect")
),
RRextra = v2$RRextra
)
}
)
}), nm = names(Vsplit))
} else {
NULL
},
"Effect sizes" = "Look at the individual models",
"Other residual normality tests" = NULL
)
)
#####################################################################
percentageChanges <- NULL
#####################################################################
OpenStatsReportRR0 <- list(
"Applied method" = framework,
"Dependent variable" = depVariable,
"Batch included" = NULL,
"Batch p-value" = NULL,
"Residual variances homogeneity" = NULL,
"Residual variances homogeneity p-value" = NULL,
#####################################################################
"Genotype contribution" = list(
"Overall" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result),
extractFisherSubTableResults1(VsplitHig$Genotype$result),
"Details" = GenotypeDiscLabel
),
"Sex FvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex MvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result),
"Details" = SexDiscLabel
),
"Sexual dimorphism detected" = list(
"Criteria" = TRUE,
"Note" = "Sex specific results for Low/High tables are always reported."
)
),
"Genotype estimate" = lowHighList(
lapply1(VsplitLow$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHig$Genotype$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"Genotype standard error" = NULL,
"Genotype p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result),
extractFisherSubTableResults1(VsplitHig$Genotype$result),
"Details" = GenotypeDiscLabel
),
"Genotype percentage change" = percentageChanges,
"Genotype effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHig$Genotype$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"Sex estimate" = lowHighList(
lapply1(VsplitLow$Sex$result, CatEstimateAndCI),
lapply1(VsplitHig$Sex$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"Sex standard error" = NULL,
"Sex p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Sex$result),
extractFisherSubTableResults1(VsplitHig$Sex$result),
"Details" = GenotypeDiscLabel
),
"Sex effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Sex$result, "effect"),
extractFisherSubTableResults1(VsplitHig$Sex$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"LifeStage estimate" = lowHighList(
lapply1(VsplitLow$LifeStage$result, CatEstimateAndCI),
lapply1(VsplitHig$LifeStage$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"LifeStage standard error" = NULL,
"LifeStage p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$LifeStage$result),
extractFisherSubTableResults1(VsplitHig$LifeStage$result),
"Details" = GenotypeDiscLabel
),
"LifeStage effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$LifeStage$result, "effect"),
extractFisherSubTableResults1(VsplitHig$LifeStage$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"Weight estimate" = NULL,
"Weight standard error" = NULL,
"Weight p-value" = NULL,
"Weight effect size" = NULL,
#####################################################################
"Gp1 genotype" = Labels$Genotype$Control,
"Gp1 Residuals normality test" = NULL,
"Gp2 genotype" = Labels$Genotype$Mutant,
"Gp2 Residuals normality test" = NULL,
#####################################################################
"Blups test" = NULL,
"Rotated residuals normality test" = NULL,
#####################################################################
"Intercept estimate" = NULL,
"Intercept standard error" = NULL,
"Intercept p-value" = NULL,
#####################################################################
"Interactions included" = list(
"Genotype Sex" = NULL,
"Genotype LifeStage" = NULL,
"Sex LifeStage" = NULL,
"Genotype Sex LifeStage" = NULL
),
#####################################################################
################ interaction
"Interactions p-value" = list(
"Genotype Sex" = NULL,
"Genotype LifeStage" = NULL,
"Sex LifeStage" = NULL,
"Genotype Sex LifeStage" = NULL
),
#####################################################################
################ Sex interactions
"Sex FvKO estimate" = lowHighList(
lapply1(VsplitLowFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigFemale$Genotype$result, CatEstimateAndCI),
"Details" = SexDiscLabel
),
"Sex FvKO standard error" = NULL,
"Sex FvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex FvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result, "effect"),
"Details" = SexDiscLabel
),
#####################################################################
"Sex MvKO estimate" = lowHighList(
lapply1(VsplitLowMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigMale$Genotype$result, CatEstimateAndCI),
"Details" = SexDiscLabel
),
"Sex MvKO standard error" = NULL,
"Sex MvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex MvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result, "effect"),
"Details" = SexDiscLabel
),
#####################################################################
################ LifeStage interaction
"LifeStage EvKO estimate" = lowHighList(
lapply1(VsplitLowEarly$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarly$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageDiscLabel
),
"LifeStage EvKO standard error" = NULL,
"LifeStage EvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarly$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarly$Genotype$result),
"Details" = LifeStageDiscLabel
),
"LifeStage EvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarly$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarly$Genotype$result, "effect"),
"Details" = LifeStageDiscLabel
),
#####################################################################
"LifeStage LvKO estimate" = lowHighList(
lapply1(VsplitLowLate$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLate$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageDiscLabel
),
"LifeStage LvKO standard error" = NULL,
"LifeStage LvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLate$Genotype$result),
extractFisherSubTableResults1(VsplitHigLate$Genotype$result),
"Details" = LifeStageDiscLabel
),
"LifeStage LvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLate$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLate$Genotype$result, "effect"),
"Details" = LifeStageDiscLabel
),
#####################################################################
################ Sex LifeStage Genotype interactions
#####################################################################
# 1.
"LifeStageSexGenotype FvEvKO estimate" = lowHighList(
lapply1(VsplitLowEarlyFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarlyFemale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvEvKO standard error" = NULL,
"LifeStageSexGenotype FvEvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarlyFemale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvEvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarlyFemale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
# 2.
"LifeStageSexGenotype MvEvKO estimate" = lowHighList(
lapply1(VsplitLowEarlyMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarlyMale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvEvKO standard error" = NULL,
"LifeStageSexGenotype MvEvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarlyMale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvEvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarlyMale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
# 3.
"LifeStageSexGenotype FvLvKO estimate" = lowHighList(
lapply1(VsplitLowLateFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLateFemale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvLvKO standard error" = NULL,
"LifeStageSexGenotype FvLvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigLateFemale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvLvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLateFemale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO estimate" = lowHighList(
lapply1(VsplitLowLateMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLateMale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO standard error" = NULL,
"LifeStageSexGenotype MvLvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigLateMale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLateMale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
################
"Classification tag" = NULL,
"Transformation" = NULL,
"Additional information" = addInfo
)
return(OpenStatsReportRR0)
}
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Defines functions OpenStatsReportRR
OpenStatsReportRR <- function(object) {
if (!is.null(object$messages)) {
return(NULL)
}
#####################################################################
Labels <- OpenStatsListLevels(object = object)
Fmodel <- object$extra$Cleanedformula
frm <- formula(Fmodel)
depVariable <- all_vars0(frm)[1]
refVariable <- all_vars0(frm)[2]
# equation = NULL
formula <- printformula(frm)
framework <- paste0(
"Reference Range Plus Test framework; quantile = ",
object$input$prop,
" (Tails probability = ",
1 - MakeRRQuantileFromTheValue(object$input$prop, messages = FALSE),
")"
)
# fittingMethod = NULL
#####################################################################
Vsplit <- object$output$SplitModels
low <- pastedot("Low", depVariable, refVariable)
high <- pastedot("High", depVariable, refVariable)
VsplitLow <- Vsplit[[low]]
VsplitHig <- Vsplit[[high]]
#### Sex
VsplitLowFemale <- Vsplit[[pastedot(low, "Female")]]
VsplitHigFemale <- Vsplit[[pastedot(high, "Female")]]
VsplitLowMale <- Vsplit[[pastedot(low, "Male")]]
VsplitHigMale <- Vsplit[[pastedot(high, "Male")]]
### Lifestage
VsplitLowEarly <- Vsplit[[pastedot(low, "Early")]]
VsplitHigEarly <- Vsplit[[pastedot(high, "Early")]]
VsplitLowLate <- Vsplit[[pastedot(low, "Late")]]
VsplitHigLate <- Vsplit[[pastedot(high, "Late")]]
### LifeStage x Sex
# Female
VsplitLowEarlyFemale <- Vsplit[[pastedot(low, "Female", "Early")]]
VsplitHigEarlyFemale <- Vsplit[[pastedot(high, "Female", "Early")]]
VsplitLowLateFemale <- Vsplit[[pastedot(low, "Female", "Late")]]
VsplitHigLateFemale <- Vsplit[[pastedot(high, "Female", "Late")]]
# Male
VsplitLowEarlyMale <- Vsplit[[pastedot(low, "Male", "Early")]]
VsplitHigEarlyMale <- Vsplit[[pastedot(high, "Male", "Early")]]
VsplitLowLateMale <- Vsplit[[pastedot(low, "Male", "Late")]]
VsplitHigLateMale <- Vsplit[[pastedot(high, "Male", "Late")]]
###
GenotypeDiscLabel <- "Data is discritised by `Genotype` levels"
SexDiscLabel <- "Data is first split by `Sex` levels then discritised by `Genotype` levels"
LifeStageDiscLabel <- "Data is first split by `LifeStage` levels then discritised by `Genotype` levels"
LifeStageSexDiscLabel <- "Data is first split by `LifeStage-Sex` levels then discritised by `Genotype` levels"
#####################################################################
x <- object$input$data
columnOfInterest <- x[, c(depVariable)]
#####################################################################
variability <- list(
"Value" = length(unique(columnOfInterest)) / max(length(columnOfInterest), 1),
"Type" = "Total unique response divided by total number of response"
)
#####################################################################
extractFisherSubTableResults1 <- function(x, what = "p.value") {
r <- extractFisherSubTableResults(x = x, what = what)
if (length(r) == 1) {
r <- r[[1]]
}
return(r)
}
lapply1 <- function(X, FUN, ...) {
r <- lapply0(X = X, FUN = FUN, ...)
if (length(r) == 1) {
r <- r[[1]]
}
return(r)
}
#####################################################################
DSsize <- SummaryStats(
x = x,
formula = object$input$formula,
# label = 'Summary statistics',
lower = TRUE,
drop = TRUE,
sep = "_"
)
MultiBatch <- ifelse(multiBatch(x),
"Dataset contains multiple batches",
"Dataset contains single batch"
)
addInfo <- list(
Data = list(
"Data signature" = dataSignature(
formula = frm,
data = x
),
"Variability" = variability,
"Summary statistics" = DSsize
),
Analysis = list(
"Model setting" = extractFERRTerms(object),
"Implementation specification" = RRextraDetailsExtractor(object),
"Is model optimised" = NULL,
"Multibatch in analysis" = MultiBatch,
"Gender included in analysis" = GenderIncludedInAnalysis(x),
"Further models" = if (!is.null(Vsplit)) {
setNames(lapply0(Vsplit, function(v) {
lapply1(
v,
FUN = function(v2) {
list(
Result = extractFisherSubTableResults1(
x = v2$result,
what = c("p.value", "effect")
),
RRextra = v2$RRextra
)
}
)
}), nm = names(Vsplit))
} else {
NULL
},
"Effect sizes" = "Look at the individual models",
"Other residual normality tests" = NULL
)
)
#####################################################################
percentageChanges <- NULL
#####################################################################
OpenStatsReportRR0 <- list(
"Applied method" = framework,
"Dependent variable" = depVariable,
"Batch included" = NULL,
"Batch p-value" = NULL,
"Residual variances homogeneity" = NULL,
"Residual variances homogeneity p-value" = NULL,
#####################################################################
"Genotype contribution" = list(
"Overall" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result),
extractFisherSubTableResults1(VsplitHig$Genotype$result),
"Details" = GenotypeDiscLabel
),
"Sex FvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex MvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result),
"Details" = SexDiscLabel
),
"Sexual dimorphism detected" = list(
"Criteria" = TRUE,
"Note" = "Sex specific results for Low/High tables are always reported."
)
),
"Genotype estimate" = lowHighList(
lapply1(VsplitLow$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHig$Genotype$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"Genotype standard error" = NULL,
"Genotype p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result),
extractFisherSubTableResults1(VsplitHig$Genotype$result),
"Details" = GenotypeDiscLabel
),
"Genotype percentage change" = percentageChanges,
"Genotype effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHig$Genotype$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"Sex estimate" = lowHighList(
lapply1(VsplitLow$Sex$result, CatEstimateAndCI),
lapply1(VsplitHig$Sex$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"Sex standard error" = NULL,
"Sex p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Sex$result),
extractFisherSubTableResults1(VsplitHig$Sex$result),
"Details" = GenotypeDiscLabel
),
"Sex effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$Sex$result, "effect"),
extractFisherSubTableResults1(VsplitHig$Sex$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"LifeStage estimate" = lowHighList(
lapply1(VsplitLow$LifeStage$result, CatEstimateAndCI),
lapply1(VsplitHig$LifeStage$result, CatEstimateAndCI),
"Details" = GenotypeDiscLabel
),
"LifeStage standard error" = NULL,
"LifeStage p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLow$LifeStage$result),
extractFisherSubTableResults1(VsplitHig$LifeStage$result),
"Details" = GenotypeDiscLabel
),
"LifeStage effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLow$LifeStage$result, "effect"),
extractFisherSubTableResults1(VsplitHig$LifeStage$result, "effect"),
"Details" = GenotypeDiscLabel
),
#####################################################################
"Weight estimate" = NULL,
"Weight standard error" = NULL,
"Weight p-value" = NULL,
"Weight effect size" = NULL,
#####################################################################
"Gp1 genotype" = Labels$Genotype$Control,
"Gp1 Residuals normality test" = NULL,
"Gp2 genotype" = Labels$Genotype$Mutant,
"Gp2 Residuals normality test" = NULL,
#####################################################################
"Blups test" = NULL,
"Rotated residuals normality test" = NULL,
#####################################################################
"Intercept estimate" = NULL,
"Intercept standard error" = NULL,
"Intercept p-value" = NULL,
#####################################################################
"Interactions included" = list(
"Genotype Sex" = NULL,
"Genotype LifeStage" = NULL,
"Sex LifeStage" = NULL,
"Genotype Sex LifeStage" = NULL
),
#####################################################################
################ interaction
"Interactions p-value" = list(
"Genotype Sex" = NULL,
"Genotype LifeStage" = NULL,
"Sex LifeStage" = NULL,
"Genotype Sex LifeStage" = NULL
),
#####################################################################
################ Sex interactions
"Sex FvKO estimate" = lowHighList(
lapply1(VsplitLowFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigFemale$Genotype$result, CatEstimateAndCI),
"Details" = SexDiscLabel
),
"Sex FvKO standard error" = NULL,
"Sex FvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex FvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigFemale$Genotype$result, "effect"),
"Details" = SexDiscLabel
),
#####################################################################
"Sex MvKO estimate" = lowHighList(
lapply1(VsplitLowMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigMale$Genotype$result, CatEstimateAndCI),
"Details" = SexDiscLabel
),
"Sex MvKO standard error" = NULL,
"Sex MvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result),
"Details" = SexDiscLabel
),
"Sex MvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigMale$Genotype$result, "effect"),
"Details" = SexDiscLabel
),
#####################################################################
################ LifeStage interaction
"LifeStage EvKO estimate" = lowHighList(
lapply1(VsplitLowEarly$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarly$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageDiscLabel
),
"LifeStage EvKO standard error" = NULL,
"LifeStage EvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarly$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarly$Genotype$result),
"Details" = LifeStageDiscLabel
),
"LifeStage EvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarly$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarly$Genotype$result, "effect"),
"Details" = LifeStageDiscLabel
),
#####################################################################
"LifeStage LvKO estimate" = lowHighList(
lapply1(VsplitLowLate$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLate$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageDiscLabel
),
"LifeStage LvKO standard error" = NULL,
"LifeStage LvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLate$Genotype$result),
extractFisherSubTableResults1(VsplitHigLate$Genotype$result),
"Details" = LifeStageDiscLabel
),
"LifeStage LvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLate$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLate$Genotype$result, "effect"),
"Details" = LifeStageDiscLabel
),
#####################################################################
################ Sex LifeStage Genotype interactions
#####################################################################
# 1.
"LifeStageSexGenotype FvEvKO estimate" = lowHighList(
lapply1(VsplitLowEarlyFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarlyFemale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvEvKO standard error" = NULL,
"LifeStageSexGenotype FvEvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarlyFemale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvEvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarlyFemale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
# 2.
"LifeStageSexGenotype MvEvKO estimate" = lowHighList(
lapply1(VsplitLowEarlyMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigEarlyMale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvEvKO standard error" = NULL,
"LifeStageSexGenotype MvEvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigEarlyMale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvEvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowEarlyMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigEarlyMale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
# 3.
"LifeStageSexGenotype FvLvKO estimate" = lowHighList(
lapply1(VsplitLowLateFemale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLateFemale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvLvKO standard error" = NULL,
"LifeStageSexGenotype FvLvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateFemale$Genotype$result),
extractFisherSubTableResults1(VsplitHigLateFemale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype FvLvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateFemale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLateFemale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO estimate" = lowHighList(
lapply1(VsplitLowLateMale$Genotype$result, CatEstimateAndCI),
lapply1(VsplitHigLateMale$Genotype$result, CatEstimateAndCI),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO standard error" = NULL,
"LifeStageSexGenotype MvLvKO p-value" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateMale$Genotype$result),
extractFisherSubTableResults1(VsplitHigLateMale$Genotype$result),
"Details" = LifeStageSexDiscLabel
),
"LifeStageSexGenotype MvLvKO effect size" = lowHighList(
extractFisherSubTableResults1(VsplitLowLateMale$Genotype$result, "effect"),
extractFisherSubTableResults1(VsplitHigLateMale$Genotype$result, "effect"),
"Details" = LifeStageSexDiscLabel
),
################
"Classification tag" = NULL,
"Transformation" = NULL,
"Additional information" = addInfo
)
return(OpenStatsReportRR0)
}
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