From af99149558e7e447d5caebf0f0d4e0a9fbe48737 Mon Sep 17 00:00:00 2001 From: Paul Schmidt Date: Fri, 29 Sep 2023 15:43:50 +0200 Subject: [PATCH] better get_anova(), added add_group_column() --- DESCRIPTION | 4 +- NAMESPACE | 4 +- R/add_group_column.R | 31 +++++ R/describe.R | 4 +- R/get_anova.R | 139 ++++++++++++++------ R/get_varcomp.R | 4 +- R/project_setup.R | 13 +- _pkgdown.yml | 1 + docs/404.html | 2 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/BioMathR-package.html | 2 +- docs/reference/add_group_column.html | 115 ++++++++++++++++ docs/reference/add_sheet.html | 2 +- docs/reference/cond_format.html | 2 +- docs/reference/create_wb.html | 2 +- docs/reference/desc_tabs.html | 2 +- docs/reference/describe.html | 4 +- docs/reference/desplot_across.html | 2 +- docs/reference/docx_tab.html | 8 +- docs/reference/emmeans_BM.html | 2 +- docs/reference/format_p.html | 2 +- docs/reference/get_anova.html | 66 +++++++--- docs/reference/get_d3_colourScale.html | 2 +- docs/reference/get_residual_plots.html | 2 +- docs/reference/get_unique_references.html | 2 +- docs/reference/get_varcomp.html | 8 +- docs/reference/gg_export.html | 2 +- docs/reference/grapes-not_in-grapes.html | 2 +- docs/reference/index.html | 8 +- docs/reference/palette_getset-1.png | Bin 21236 -> 21201 bytes docs/reference/palette_getset.html | 2 +- docs/reference/partial_block_pour_docx.html | 2 +- docs/reference/project_setup.html | 2 +- docs/reference/round_smart.html | 2 +- docs/reference/save_wb.html | 2 +- docs/reference/smart_fit.html | 2 +- docs/reference/str_unGer.html | 2 +- docs/reference/str_wrap_br.html | 8 +- docs/reference/theme_BioMath.html | 2 +- docs/reference/theme_UBA.html | 2 +- docs/reference/tidy_reg.html | 2 +- docs/reference/write_ascii.html | 2 +- docs/sitemap.xml | 3 + man/add_group_column.Rd | 28 ++++ man/get_anova.Rd | 75 ++++++++--- man/get_varcomp.Rd | 6 +- man/str_wrap_br.Rd | 4 +- tests/testthat/test-get_anova.R | 50 +++++++ 50 files changed, 508 insertions(+), 135 deletions(-) create mode 100644 R/add_group_column.R create mode 100644 docs/reference/add_group_column.html create mode 100644 man/add_group_column.Rd create mode 100644 tests/testthat/test-get_anova.R diff --git a/DESCRIPTION b/DESCRIPTION index d7f6639..dcd2005 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: BioMathR Title: Utility functions used at BioMath -Version: 0.6.0 +Version: 0.7.0 Authors@R: c( person("Paul", "Schmidt", email = "paul.schmidt@biomath.de", role = c("aut", "cre")), person("BioMath", role = "fnd") @@ -46,6 +46,7 @@ Suggests: lme4, lmerTest, MetBrewer, + nlme, openair, pdftools, performance, @@ -59,3 +60,4 @@ Config/testthat/edition: 3 Encoding: UTF-8 LazyData: true RoxygenNote: 7.2.3 +Roxygen: list(markdown = TRUE) diff --git a/NAMESPACE b/NAMESPACE index 241e277..b65875c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,13 +1,11 @@ # Generated by roxygen2: do not edit by hand -S3method(get_anova,glmmTMB) -S3method(get_anova,lm) -S3method(get_anova,lmerMod) S3method(get_varcomp,glmmTMB) S3method(get_varcomp,merMod) S3method(tidy_reg,lm) S3method(tidy_reg,openair) export("%not_in%") +export(add_group_column) export(add_sheet) export(cond_format) export(create_wb) diff --git a/R/add_group_column.R b/R/add_group_column.R new file mode 100644 index 0000000..71f8bf3 --- /dev/null +++ b/R/add_group_column.R @@ -0,0 +1,31 @@ +#' Add Group Column +#' +#' This function adds a new column to a data frame with a specified name. The new column indicates groups based on the grouping variables provided. When no grouping variable is provided, a default value is assigned to the new column. +#' +#' @param data A data frame. +#' @param name The name of the new column to be added. +#' @param group_by A vector of strings specifying the column names used for grouping. Default is NULL. +#' +#' @return A data frame with the new column added. +#' @examples +#' \dontrun{ +#' data <- data.frame(x = c(1,2,3,1,2,3), y = c("a","b","c","a","b","c")) +#' data %>% add_group_column(name = "group_id", group_by = c("x", "y")) +#' } +#' +#' @export +#' +add_group_column <- function(data, name, group_by = NULL) { + if (is.null(group_by)) { + data[[name]] <- as.factor("-") + return(data) + } else { + data <- data %>% + group_by(across(all_of(group_by))) %>% + mutate(temp____col = paste0(name, str_pad(cur_group_id(), width = 2, pad = "0")) %>% as.factor()) %>% + ungroup() + + names(data)[which(names(data) == "temp____col")] <- name + return(data) + } +} diff --git a/R/describe.R b/R/describe.R index 08b15cc..3cf33ab 100644 --- a/R/describe.R +++ b/R/describe.R @@ -79,14 +79,14 @@ describe <- if (is.numeric(digits)) { out <- out %>% mutate(across( - cols_to_round, + all_of(cols_to_round), ~ round(., digits = digits) )) } if (digits == "round_smart") { out <- out %>% mutate(across( - cols_to_round, + all_of(cols_to_round), ~ BioMathR::round_smart(., ...) )) } diff --git a/R/get_anova.R b/R/get_anova.R index dbb6d60..f4dbea7 100644 --- a/R/get_anova.R +++ b/R/get_anova.R @@ -2,69 +2,126 @@ #' #' @description This function obtains the ANOVA table for a model. #' -#' @param model a fitted model object. Supported classes: \code{"lm"}, \code{"lmerMod"} & \code{"glmmTMB"}. +#' @param model a fitted model object. Supported classes: \code{"lm"}, \code{"lmerModLmerTest"}, \code{"glmmTMB"}, \code{"gls"}, \code{"lme"}. #' @param type Type of ANOVA test: \code{"I"}, \code{"II"} or \code{"III"} (default). #' @param ... additional arguments to be passed to the specific anova function. +#' @param info Logical, if \code{TRUE}, information about the type of ANOVA and +#' test statistic used is printed to the console. Default is \code{FALSE}. #' -#' @details The function utilizes \code{car::Anova()} for all supported model classes. For models of class 'lm' and 'lmerMod', the F-test is employed. In contrast, for models of the 'glmmTMB' class, the Chi-Square test is used since the F-test is \href{https://github.com/glmmTMB/glmmTMB/blob/bd1932addbfb4edf2ce933675f5a8bf72abc0e7c/glmmTMB/R/Anova.R#L73C8-L73C8}{currently unavailable}. It's worth noting that only the 'lmerMod' models support (and default to) the Kenward-Roger method as a degrees of freedom method. +#' @details The function utilizes \code{car::Anova()} for all supported model +#' classes and defaults to type III of sum of squares. For models of class +#' 'lm' and 'lmerModLmerTest', the F-test is employed. In contrast, for models of the +#' 'glmmTMB', 'gls', and 'lme' class, the Chi-Square test is used since the +#' F-test is +#' \href{https://github.com/glmmTMB/glmmTMB/blob/bd1932addbfb4edf2ce933675f5a8bf72abc0e7c/glmmTMB/R/Anova.R#L73C8-L73C8}{currently +#' unavailable}. It's worth noting that only the 'lmerModLmerTest' models support (and +#' default to) the Kenward-Roger method as a degrees of freedom method. +#' +#' \itemize{ +#' \item{\code{lm} (Package: stats):} {Types I/II/III; F-Test; Standard df.} +#' \item{\code{lmer/lmerTest} (Packages: lme4/lmerTest):} {Types I/II/III; F-Test; Kenward-Roger (KR) df.} +#' \item{\code{lme} (Package: nlme):} {Types I/II/III; Chi-Square Test (Chisq*); Standard df.} +#' \item{\code{gls} (Package: nlme):} {Types I/II/III; Chi-Square Test (Chisq*); Standard df.} +#' \item{\code{glmmTMB} (Package: glmmTMB):} {Types I/II/III; Chi-Square Test; Standard df.} +#' } +#' +#' * You can obtain the F-Test only for type I/II via \code{stats::anova()} +#' +#' The \code{type} argument specifies the type of sum of squares to be used in the analysis: +#' \itemize{ +#' \item{Type I (Sequential) sum of squares:}{ +#' The order in which factors are entered into the model does matter. Each factor is adjusted for the factors listed before it. +#' } +#' \item{Type II (Marginal) sum of squares:}{ +#' The order in which factors are entered into the model does not matter. Each factor is adjusted for all of the other factors in the model. +#' } +#' \item{Type III sum of squares:}{ +#' The order in which factors are entered into the model does not matter, similar to Type II. However, each factor is adjusted for all +#' of the other factors as well as for itself, which allows for the testing of each factor in the presence of interactions. +#' } +#' } +#' +#' Kenward-Roger Degrees of Freedom: The Kenward-Roger (KR) method is +#' a sophisticated approach to approximating the degrees of freedom in mixed +#' models, particularly in the presence of small sample sizes or unbalanced +#' data. It is not applicable to non-mixed models. Unlike the classical +#' degrees of freedom methods which may overestimate the significance of +#' effects, the KR approximation tends to provide a more conservative and +#' accurate estimation. This method adjusts the degrees of freedom to account +#' for the complexity of the mixed model structure, thereby enhancing the +#' robustness of the resulting inference. The Kenward-Roger method is +#' especially beneficial when working with complex models that include +#' multiple random effects and/or nested structures, as it helps to mitigate +#' the risk of Type I errors, offering a more reliable foundation for +#' hypothesis testing. Importantly, employing the KR method is never +#' disadvantageous when compared to using the default method; it provides a +#' more accurate reflection of the model's complexity and the data structure, +#' thus leading to more reliable statistical inferences. #' #' @seealso #' [car::Anova()], #' [lmerTest::lmer()], -#' [glmmTMB::glmmTMB()] +#' [glmmTMB::glmmTMB()], +#' [nlme::gls()], +#' [nlme::lme()] #' #' @export -get_anova <- function(model, type, ...) { - assertthat::assert_that(inherits(model, c("lm", "lmerMod", "glmmTMB")), +get_anova <- function(model, type = "III", ..., info = FALSE) { + assertthat::assert_that(inherits(model, c("lm", "lmerMod", "lmerModLmerTest", "glmmTMB", "gls", "lme")), msg = "This is not a supported model class.") - if (!requireNamespace("car", quietly = TRUE)) { - stop("Package 'car' must be installed.") - } + model_class <- class(model)[1] # Extract the primary class name of the model - UseMethod("get_anova") -} - - -#' @export -#' @rdname get_anova -get_anova.lm <- function(model, - type = c("I", "II", "III")[3], - ...) { + if (model_class == "lmerMod" && !requireNamespace("lmerTest", quietly = TRUE)) { + stop("Please fit your model via lmerTest::lmer() instead of lme4::lmer().") + } - anova_table <- car::Anova(model, type, ...) - return(anova_table) -} + test_statistic <- switch( + model_class, + lm = "F", + lmerModLmerTest = "F", + glmmTMB = "Chisq", + gls = "Chisq", + lme = "Chisq", + stop("Unsupported model class") + ) + ddf <- if (model_class == "lmerModLmerTest") "Kenward-Roger" else NULL -#' @export -#' @rdname get_anova -get_anova.lmerMod <- function(model, - type = c("I", "II", "III")[3], - ...) { + necessary_package <- switch( + model_class, + lm = "stats", + lmerModLmerTest = c("lmerTest", "lme4"), + glmmTMB = "glmmTMB", + gls = "nlme", + lme = "nlme", + NULL + ) - if (!requireNamespace("lme4", quietly = TRUE)) { - stop("When model object is 'lmerMod', package 'lme4' must be installed.") + if (!is.null(necessary_package)) { + for (pkg in necessary_package) { + assertthat::assert_that(requireNamespace(pkg, quietly = TRUE), + msg = sprintf("When model object is '%s', package '%s' must be installed.", model_class, pkg)) + } } - if (!requireNamespace("lmerTest", quietly = TRUE)) { - stop("When model object is 'lmerMod', package 'lmerTest' must be installed.") - } + anova_table <- car::Anova(model, type = type, test.statistic = test_statistic, ddf = ddf, ...) - anova_table <- car::Anova(model, type = type, test.statistic = "F", ...) - return(anova_table) -} + # Get an info summary above the table + anova_summary <- sprintf( + "The ANOVA performed is of Type %s, utilizing a %s test statistic.", + type, + test_statistic + ) -#' @export -#' @rdname get_anova -get_anova.glmmTMB <- function(model, - type = c("I", "II", "III")[3], - ...) { + if (!is.null(ddf)) { + anova_summary <- paste(anova_summary, sprintf("Degrees of freedom were adjusted using the %s method.", ddf)) + } - if (!requireNamespace("glmmTMB", quietly = TRUE)) { - stop("When model object is 'glmmTMB', package 'glmmTMB' must be installed.") + # Output the summary only if info = TRUE + if (info) { + cat(paste0(anova_summary, "\n")) } - anova_table <- car::Anova(model, type = type, test.statistic = "Chisq", ...) return(anova_table) } diff --git a/R/get_varcomp.R b/R/get_varcomp.R index c6d81f2..6006e9d 100644 --- a/R/get_varcomp.R +++ b/R/get_varcomp.R @@ -12,7 +12,7 @@ #' @seealso #' [lme4::VarCorr()], #' [glmmTMB::VarCorr()], -#' [mixedup::extract_vc()] +#' [mixedup::extract_vc()](https://github.com/m-clark/mixedup) #' #' @export get_varcomp <- function(model, @@ -73,7 +73,7 @@ get_varcomp.merMod <- function(model, get_varcomp.glmmTMB <- function(model, digits = 3) { - if (!requireNamespace("glmmTMB", quietly = TRUE)) { + if (!suppressWarnings(requireNamespace("glmmTMB", quietly = TRUE))) { stop("When model object is 'glmmTMB', package 'glmmTMB' must be installed.") } diff --git a/R/project_setup.R b/R/project_setup.R index 7d81b03..8851ec0 100644 --- a/R/project_setup.R +++ b/R/project_setup.R @@ -40,9 +40,9 @@ project_setup <- function() { # Create setup file setup_file <- file.path(root_dir, "code", "00 setup.R") setup_content <- 'library(BioMathR) # remotes::install_github("SchmidtPaul/BioMathR") -library(conflicted) # install.packages("conflicted") -library(here) # install.packages("here") -library(tidyverse) # install.packages("tidyverse") +library(conflicted) +library(here) +library(tidyverse) # conflicts conflicts_prefer(dplyr::filter, .quiet = TRUE) @@ -57,6 +57,11 @@ here_out <- function(...) {here("10 RCode", "out", ...)} BMcols <- BioMathR::palette_getset("BioMath")' writeLines(setup_content, setup_file) + # Create import file + import_file <- file.path(root_dir, "code", "01 import.R") + import_content <- 'source(here::here("10 RCode", "code", "00 setup.R"), encoding = "UTF-8")' + writeLines(import_content, import_file) + # send message - message("Directories and 00 setup.R created successfully!") + message("Directories, '00 setup.R' and '01 import.R' created successfully!") } diff --git a/_pkgdown.yml b/_pkgdown.yml index deabaab..070b8a6 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -74,6 +74,7 @@ reference: - title: utility contents: + - add_group_column - project_setup - round_smart - write_ascii diff --git a/docs/404.html b/docs/404.html index 9251628..7dcdb88 100644 --- a/docs/404.html +++ b/docs/404.html @@ -40,7 +40,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/authors.html b/docs/authors.html index 0e9f17b..1967e54 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -70,13 +70,13 @@

Citation

Schmidt P (2023). BioMathR: Utility functions used at BioMath. -R package version 0.6.0. +R package version 0.7.0. 

@Manual{,
   title = {BioMathR: Utility functions used at BioMath},
   author = {Paul Schmidt},
   year = {2023},
-  note = {R package version 0.6.0},
+  note = {R package version 0.7.0},
 }
diff --git a/docs/index.html b/docs/index.html index 9b7b1a2..05899a9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,7 +41,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 2aba46d..ccb49b7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-09-15T10:25Z +last_built: 2023-09-29T13:40Z urls: reference: schmidtpaul.github.io/BioMathR/reference article: schmidtpaul.github.io/BioMathR/articles diff --git a/docs/reference/BioMathR-package.html b/docs/reference/BioMathR-package.html index a2c87c5..5e7be02 100644 --- a/docs/reference/BioMathR-package.html +++ b/docs/reference/BioMathR-package.html @@ -18,7 +18,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/add_group_column.html b/docs/reference/add_group_column.html new file mode 100644 index 0000000..4798aa4 --- /dev/null +++ b/docs/reference/add_group_column.html @@ -0,0 +1,115 @@ + +Add Group Column — add_group_column • BioMathR + + +
+
+ + + +
+
+
+

Add Group Column

+ + +
+ +
+

This function adds a new column to a data frame with a specified name. The new column indicates groups based on the grouping variables provided. When no grouping variable is provided, a default value is assigned to the new column.

+
+ +
+ 
add_group_column(data, name, group_by = NULL)
+
+ +
+

Arguments

+
data
+

A data frame.

+ + +
name
+

The name of the new column to be added.

+ + +
group_by
+

A vector of strings specifying the column names used for grouping. Default is NULL.

+ +
+
+

Value

+ + +

A data frame with the new column added.

+
+ +
+

Examples

+ 
if (FALSE) {
+data <- data.frame(x = c(1,2,3,1,2,3), y = c("a","b","c","a","b","c"))
+data %>% add_group_column(name = "group_id", group_by = c("x", "y"))
+}
+
+
+
+
+ +
+ + +
+ + + + + + + + diff --git a/docs/reference/add_sheet.html b/docs/reference/add_sheet.html index c9d0039..3b45b33 100644 --- a/docs/reference/add_sheet.html +++ b/docs/reference/add_sheet.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/cond_format.html b/docs/reference/cond_format.html index 53ae213..cbb2a27 100644 --- a/docs/reference/cond_format.html +++ b/docs/reference/cond_format.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/create_wb.html b/docs/reference/create_wb.html index 6b9bea7..0962135 100644 --- a/docs/reference/create_wb.html +++ b/docs/reference/create_wb.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/desc_tabs.html b/docs/reference/desc_tabs.html index 9adc286..3f317f3 100644 --- a/docs/reference/desc_tabs.html +++ b/docs/reference/desc_tabs.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/describe.html b/docs/reference/describe.html index 523cc8a..51d4691 100644 --- a/docs/reference/describe.html +++ b/docs/reference/describe.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -127,7 +127,7 @@

Examples

group_by(group, group2) %>% describe(c("weight", "weight2", "weight3"), lang = "ger") %>% docx_tab() -

Variable

group

group2

N

Fehl

MW

StdAbw

IQA

Min

Median

Max

weight

ctrl

A

4

0

4.9

0.6

0.80

4.2

4.90

5.60

weight

ctrl

B

6

0

5.1

0.6

0.60

4.5

5.20

6.10

weight

trt1

A

4

0

4.7

1.0

1.03

3.8

4.50

6.03

weight

trt1

B

6

0

4.6

0.8

0.50

3.6

4.60

5.87

weight

trt2

A

4

0

5.4

0.6

0.50

4.9

5.20

6.30

weight

trt2

B

6

0

5.6

0.3

0.30

5.3

5.52

6.10

weight2

ctrl

A

4

0

9.8

1.2

1.50

8.3

9.80

11.20

weight2

ctrl

B

6

0

10.3

1.2

1.20

9.0

10.30

12.20

weight2

trt1

A

4

0

9.4

1.9

2.06

7.7

9.00

12.06

weight2

trt1

B

6

0

9.3

1.5

0.99

7.2

9.10

11.74

weight2

trt2

A

4

0

10.8

1.2

0.90

9.8

10.41

12.60

weight2

trt2

B

6

0

11.2

0.6

0.70

10.5

11.04

12.30

weight3

ctrl

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

ctrl

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt1

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt1

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt2

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt2

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

+

Variable

group

group2

N

Fehl

MW

StdAbw

IQA

Min

Median

Max

weight

ctrl

A

4

0

4.9

0.6

0.80

4.2

4.90

5.60

weight

ctrl

B

6

0

5.1

0.6

0.60

4.5

5.20

6.10

weight

trt1

A

4

0

4.7

1.0

1.03

3.8

4.50

6.03

weight

trt1

B

6

0

4.6

0.8

0.50

3.6

4.60

5.87

weight

trt2

A

4

0

5.4

0.6

0.50

4.9

5.20

6.30

weight

trt2

B

6

0

5.6

0.3

0.30

5.3

5.52

6.10

weight2

ctrl

A

4

0

9.8

1.2

1.50

8.3

9.80

11.20

weight2

ctrl

B

6

0

10.3

1.2

1.20

9.0

10.30

12.20

weight2

trt1

A

4

0

9.4

1.9

2.06

7.7

9.00

12.06

weight2

trt1

B

6

0

9.3

1.5

0.99

7.2

9.10

11.74

weight2

trt2

A

4

0

10.8

1.2

0.90

9.8

10.41

12.60

weight2

trt2

B

6

0

11.2

0.6

0.70

10.5

11.04

12.30

weight3

ctrl

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

ctrl

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt1

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt1

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt2

A

2

2

3.0

0.0

0.00

3.0

3.00

3.00

weight3

trt2

B

3

3

3.0

0.0

0.00

3.0

3.00

3.00

diff --git a/docs/reference/docx_tab.html b/docs/reference/docx_tab.html index 3410209..57281b0 100644 --- a/docs/reference/docx_tab.html +++ b/docs/reference/docx_tab.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -99,7 +99,7 @@

Examples

anova <- anova(lm(weight ~ group, data = PlantGrowth)) docx_tab(anova, lang = "ger") -

Term

FG

SQ

MQ

F-Wert

p-Wert

group

2

3,8

1,9

4,8

0,016*

Residuals

27

10,5

0,4

docx_tab(anova, lang = "eng", asft = FALSE) +

Term

FG

SQ

MQ

F-Wert

p-Wert

group

2

3,8

1,9

4,8

0,016*

Residuals

27

10,5

0,4

docx_tab(anova, lang = "eng", asft = FALSE) #> # A tibble: 2 × 6 #> Term df SS MS `F value` `p value` #> <chr> <int> <dbl> <dbl> <dbl> <chr> @@ -116,8 +116,8 @@

Examples

V7 = c(NA_real_, NA_real_) ) docx_tab(before) -

V1

V2

V3

V4

V5

V6

V7

123,456

-123.0

1.001

1.100

1

1,234

-0.1

0.100

0.001

0

-5.002

docx_tab(before, digits = 2) -

V1

V2

V3

V4

V5

V6

V7

123,456

-123.00

1.0

1.1

1

1,234

-0.12

0.1

0.0

0

-5

+

V1

V2

V3

V4

V5

V6

V7

123,456

-123.0

1.001

1.100

1

1,234

-0.1

0.100

0.001

0

-5.002

docx_tab(before, digits = 2) +

V1

V2

V3

V4

V5

V6

V7

123,456

-123.00

1.0

1.1

1

1,234

-0.12

0.1

0.0

0

-5

diff --git a/docs/reference/format_p.html b/docs/reference/format_p.html index 0d5f123..ecddb55 100644 --- a/docs/reference/format_p.html +++ b/docs/reference/format_p.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/get_anova.html b/docs/reference/get_anova.html index 41a2f31..79fb5df 100644 --- a/docs/reference/get_anova.html +++ b/docs/reference/get_anova.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -56,22 +56,13 @@

Obtain analysis of variance table

- 
get_anova(model, type, ...)
-
-# S3 method for lm
-get_anova(model, type = c("I", "II", "III")[3], ...)
-
-# S3 method for lmerMod
-get_anova(model, type = c("I", "II", "III")[3], ...)
-
-# S3 method for glmmTMB
-get_anova(model, type = c("I", "II", "III")[3], ...)
+ 
get_anova(model, type = "III", ..., info = FALSE)

Arguments

model
-

a fitted model object. Supported classes: "lm", "lmerMod" & "glmmTMB".

+

a fitted model object. Supported classes: "lm", "lmerModLmerTest", "glmmTMB", "gls", "lme".

type
@@ -81,16 +72,59 @@

Arguments

...

additional arguments to be passed to the specific anova function.

+ +
info
+

Logical, if TRUE, information about the type of ANOVA and +test statistic used is printed to the console. Default is FALSE.

+

Details

-

The function utilizes car::Anova() for all supported model classes. For models of class 'lm' and 'lmerMod', the F-test is employed. In contrast, for models of the 'glmmTMB' class, the Chi-Square test is used since the F-test is currently unavailable. It's worth noting that only the 'lmerMod' models support (and default to) the Kenward-Roger method as a degrees of freedom method.

+

The function utilizes car::Anova() for all supported model +classes and defaults to type III of sum of squares. For models of class +'lm' and 'lmerModLmerTest', the F-test is employed. In contrast, for models of the +'glmmTMB', 'gls', and 'lme' class, the Chi-Square test is used since the +F-test is +currently +unavailable. It's worth noting that only the 'lmerModLmerTest' models support (and +default to) the Kenward-Roger method as a degrees of freedom method.

+

The type argument specifies the type of sum of squares to be used in the analysis:

Kenward-Roger Degrees of Freedom: The Kenward-Roger (KR) method is +a sophisticated approach to approximating the degrees of freedom in mixed +models, particularly in the presence of small sample sizes or unbalanced +data. It is not applicable to non-mixed models. Unlike the classical +degrees of freedom methods which may overestimate the significance of +effects, the KR approximation tends to provide a more conservative and +accurate estimation. This method adjusts the degrees of freedom to account +for the complexity of the mixed model structure, thereby enhancing the +robustness of the resulting inference. The Kenward-Roger method is +especially beneficial when working with complex models that include +multiple random effects and/or nested structures, as it helps to mitigate +the risk of Type I errors, offering a more reliable foundation for +hypothesis testing. Importantly, employing the KR method is never +disadvantageous when compared to using the default method; it provides a +more accurate reflection of the model's complexity and the data structure, +thus leading to more reliable statistical inferences.

See also

-

[car::Anova()], - [lmerTest::lmer()], - [glmmTMB::glmmTMB()]

+

car::Anova(), +lmerTest::lmer(), +glmmTMB::glmmTMB(), +nlme::gls(), +nlme::lme()

diff --git a/docs/reference/get_d3_colourScale.html b/docs/reference/get_d3_colourScale.html index 1506fb6..f9f4a20 100644 --- a/docs/reference/get_d3_colourScale.html +++ b/docs/reference/get_d3_colourScale.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/get_residual_plots.html b/docs/reference/get_residual_plots.html index b8b984f..2358b10 100644 --- a/docs/reference/get_residual_plots.html +++ b/docs/reference/get_residual_plots.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/get_unique_references.html b/docs/reference/get_unique_references.html index e1768b2..8b050a6 100644 --- a/docs/reference/get_unique_references.html +++ b/docs/reference/get_unique_references.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/get_varcomp.html b/docs/reference/get_varcomp.html index 6c5e9cb..3f497e5 100644 --- a/docs/reference/get_varcomp.html +++ b/docs/reference/get_varcomp.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -77,9 +77,9 @@

Arguments

See also

-

[lme4::VarCorr()], - [glmmTMB::VarCorr()], - [mixedup::extract_vc()]

+

lme4::VarCorr(), +glmmTMB::VarCorr(), +mixedup::extract_vc()

diff --git a/docs/reference/gg_export.html b/docs/reference/gg_export.html index 78a400e..222a9dc 100644 --- a/docs/reference/gg_export.html +++ b/docs/reference/gg_export.html @@ -20,7 +20,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/grapes-not_in-grapes.html b/docs/reference/grapes-not_in-grapes.html index 9153c79..8e1afc2 100644 --- a/docs/reference/grapes-not_in-grapes.html +++ b/docs/reference/grapes-not_in-grapes.html @@ -18,7 +18,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 1db82a7..3ba2543 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -168,12 +168,16 @@

string manipulation

str_wrap_br()

-

str_wrap() with <br> instead

+

str_wrap() with
instead

utility

+

add_group_column()

+ +

Add Group Column

+

project_setup()

Intitiate an R-project

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b/docs/reference/partial_block_pour_docx.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/project_setup.html b/docs/reference/project_setup.html index a7d742e..8f34002 100644 --- a/docs/reference/project_setup.html +++ b/docs/reference/project_setup.html @@ -18,7 +18,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/round_smart.html b/docs/reference/round_smart.html index bd83096..24bb3f3 100644 --- a/docs/reference/round_smart.html +++ b/docs/reference/round_smart.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/save_wb.html b/docs/reference/save_wb.html index 6bf41f3..09454d1 100644 --- a/docs/reference/save_wb.html +++ b/docs/reference/save_wb.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/smart_fit.html b/docs/reference/smart_fit.html index 57069c3..880251b 100644 --- a/docs/reference/smart_fit.html +++ b/docs/reference/smart_fit.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/str_unGer.html b/docs/reference/str_unGer.html index c06b54a..10cbb34 100644 --- a/docs/reference/str_unGer.html +++ b/docs/reference/str_unGer.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/reference/str_wrap_br.html b/docs/reference/str_wrap_br.html index ed6f5c5..76576ef 100644 --- a/docs/reference/str_wrap_br.html +++ b/docs/reference/str_wrap_br.html @@ -1,5 +1,5 @@ -str_wrap() with <br> instead — str_wrap_br • BioMathRstr_wrap() with instead — str_wrap_br • BioMathR @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0 @@ -46,13 +46,13 @@
-

str_wrap() with <br> instead

+

str_wrap() with
instead

-

str_wrap() with <br> instead

+

str_wrap() with
instead

diff --git a/docs/reference/theme_BioMath.html b/docs/reference/theme_BioMath.html index ce365d7..6292938 100644 --- a/docs/reference/theme_BioMath.html +++ b/docs/reference/theme_BioMath.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0
diff --git a/docs/reference/theme_UBA.html b/docs/reference/theme_UBA.html index 94ca723..04c7c4d 100644 --- a/docs/reference/theme_UBA.html +++ b/docs/reference/theme_UBA.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0
diff --git a/docs/reference/tidy_reg.html b/docs/reference/tidy_reg.html index 0af0bbf..2cf5fc3 100644 --- a/docs/reference/tidy_reg.html +++ b/docs/reference/tidy_reg.html @@ -17,7 +17,7 @@ BioMathR - 0.6.0 + 0.7.0
diff --git a/docs/reference/write_ascii.html b/docs/reference/write_ascii.html index 5f5aa85..b76e95f 100644 --- a/docs/reference/write_ascii.html +++ b/docs/reference/write_ascii.html @@ -20,7 +20,7 @@ BioMathR - 0.6.0 + 0.7.0 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 67321fb..09b0680 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -9,6 +9,9 @@ schmidtpaul.github.io/BioMathR/index.html + + schmidtpaul.github.io/BioMathR/reference/add_group_column.html + schmidtpaul.github.io/BioMathR/reference/add_sheet.html diff --git a/man/add_group_column.Rd b/man/add_group_column.Rd new file mode 100644 index 0000000..ad0da58 --- /dev/null +++ b/man/add_group_column.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/add_group_column.R +\name{add_group_column} +\alias{add_group_column} +\title{Add Group Column} +\usage{ +add_group_column(data, name, group_by = NULL) +} +\arguments{ +\item{data}{A data frame.} + +\item{name}{The name of the new column to be added.} + +\item{group_by}{A vector of strings specifying the column names used for grouping. Default is NULL.} +} +\value{ +A data frame with the new column added. +} +\description{ +This function adds a new column to a data frame with a specified name. The new column indicates groups based on the grouping variables provided. When no grouping variable is provided, a default value is assigned to the new column. +} +\examples{ +\dontrun{ +data <- data.frame(x = c(1,2,3,1,2,3), y = c("a","b","c","a","b","c")) +data \%>\% add_group_column(name = "group_id", group_by = c("x", "y")) +} + +} diff --git a/man/get_anova.Rd b/man/get_anova.Rd index 45a18ae..aa88728 100644 --- a/man/get_anova.Rd +++ b/man/get_anova.Rd @@ -2,34 +2,79 @@ % Please edit documentation in R/get_anova.R \name{get_anova} \alias{get_anova} -\alias{get_anova.lm} -\alias{get_anova.lmerMod} -\alias{get_anova.glmmTMB} \title{Obtain analysis of variance table} \usage{ -get_anova(model, type, ...) - -\method{get_anova}{lm}(model, type = c("I", "II", "III")[3], ...) - -\method{get_anova}{lmerMod}(model, type = c("I", "II", "III")[3], ...) - -\method{get_anova}{glmmTMB}(model, type = c("I", "II", "III")[3], ...) +get_anova(model, type = "III", ..., info = FALSE) } \arguments{ -\item{model}{a fitted model object. Supported classes: \code{"lm"}, \code{"lmerMod"} & \code{"glmmTMB"}.} +\item{model}{a fitted model object. Supported classes: \code{"lm"}, \code{"lmerModLmerTest"}, \code{"glmmTMB"}, \code{"gls"}, \code{"lme"}.} \item{type}{Type of ANOVA test: \code{"I"}, \code{"II"} or \code{"III"} (default).} \item{...}{additional arguments to be passed to the specific anova function.} + +\item{info}{Logical, if \code{TRUE}, information about the type of ANOVA and +test statistic used is printed to the console. Default is \code{FALSE}.} } \description{ This function obtains the ANOVA table for a model. } \details{ -The function utilizes \code{car::Anova()} for all supported model classes. For models of class 'lm' and 'lmerMod', the F-test is employed. In contrast, for models of the 'glmmTMB' class, the Chi-Square test is used since the F-test is \href{https://github.com/glmmTMB/glmmTMB/blob/bd1932addbfb4edf2ce933675f5a8bf72abc0e7c/glmmTMB/R/Anova.R#L73C8-L73C8}{currently unavailable}. It's worth noting that only the 'lmerMod' models support (and default to) the Kenward-Roger method as a degrees of freedom method. +The function utilizes \code{car::Anova()} for all supported model +classes and defaults to type III of sum of squares. For models of class +'lm' and 'lmerModLmerTest', the F-test is employed. In contrast, for models of the +'glmmTMB', 'gls', and 'lme' class, the Chi-Square test is used since the +F-test is +\href{https://github.com/glmmTMB/glmmTMB/blob/bd1932addbfb4edf2ce933675f5a8bf72abc0e7c/glmmTMB/R/Anova.R#L73C8-L73C8}{currently +unavailable}. It's worth noting that only the 'lmerModLmerTest' models support (and +default to) the Kenward-Roger method as a degrees of freedom method. + +\itemize{ +\item{\code{lm} (Package: stats):} {Types I/II/III; F-Test; Standard df.} +\item{\code{lmer/lmerTest} (Packages: lme4/lmerTest):} {Types I/II/III; F-Test; Kenward-Roger (KR) df.} +\item{\code{lme} (Package: nlme):} {Types I/II/III; Chi-Square Test (Chisq*); Standard df.} +\item{\code{gls} (Package: nlme):} {Types I/II/III; Chi-Square Test (Chisq*); Standard df.} +\item{\code{glmmTMB} (Package: glmmTMB):} {Types I/II/III; Chi-Square Test; Standard df.} +} +\itemize{ +\item You can obtain the F-Test only for type I/II via \code{stats::anova()} +} + +The \code{type} argument specifies the type of sum of squares to be used in the analysis: +\itemize{ +\item{Type I (Sequential) sum of squares:}{ +The order in which factors are entered into the model does matter. Each factor is adjusted for the factors listed before it. +} +\item{Type II (Marginal) sum of squares:}{ +The order in which factors are entered into the model does not matter. Each factor is adjusted for all of the other factors in the model. +} +\item{Type III sum of squares:}{ +The order in which factors are entered into the model does not matter, similar to Type II. However, each factor is adjusted for all +of the other factors as well as for itself, which allows for the testing of each factor in the presence of interactions. +} +} + +Kenward-Roger Degrees of Freedom: The Kenward-Roger (KR) method is +a sophisticated approach to approximating the degrees of freedom in mixed +models, particularly in the presence of small sample sizes or unbalanced +data. It is not applicable to non-mixed models. Unlike the classical +degrees of freedom methods which may overestimate the significance of +effects, the KR approximation tends to provide a more conservative and +accurate estimation. This method adjusts the degrees of freedom to account +for the complexity of the mixed model structure, thereby enhancing the +robustness of the resulting inference. The Kenward-Roger method is +especially beneficial when working with complex models that include +multiple random effects and/or nested structures, as it helps to mitigate +the risk of Type I errors, offering a more reliable foundation for +hypothesis testing. Importantly, employing the KR method is never +disadvantageous when compared to using the default method; it provides a +more accurate reflection of the model's complexity and the data structure, +thus leading to more reliable statistical inferences. } \seealso{ -[car::Anova()], - [lmerTest::lmer()], - [glmmTMB::glmmTMB()] +\code{\link[car:Anova]{car::Anova()}}, +\code{\link[lmerTest:lmer]{lmerTest::lmer()}}, +\code{\link[glmmTMB:glmmTMB]{glmmTMB::glmmTMB()}}, +\code{\link[nlme:gls]{nlme::gls()}}, +\code{\link[nlme:lme]{nlme::lme()}} } diff --git a/man/get_varcomp.Rd b/man/get_varcomp.Rd index 8e0c24e..d409401 100644 --- a/man/get_varcomp.Rd +++ b/man/get_varcomp.Rd @@ -21,7 +21,7 @@ get_varcomp(model, digits = 3) This function extracts the estimated variance components of the random-effects terms in a linear mixed model. It is very heavily based on \href{https://m-clark.github.io/mixedup/reference/extract_vc.html}{\code{mixedup::extract_vc()}}. } \seealso{ -[lme4::VarCorr()], - [glmmTMB::VarCorr()], - [mixedup::extract_vc()] +\code{\link[lme4:VarCorr]{lme4::VarCorr()}}, +\code{\link[glmmTMB:VarCorr.glmmTMB]{glmmTMB::VarCorr()}}, +\href{https://github.com/m-clark/mixedup}{mixedup::extract_vc()} } diff --git a/man/str_wrap_br.Rd b/man/str_wrap_br.Rd index 626dfd8..91b7367 100644 --- a/man/str_wrap_br.Rd +++ b/man/str_wrap_br.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/str_wrap_br.R \name{str_wrap_br} \alias{str_wrap_br} -\title{\code{str_wrap()} with
instead} +\title{\code{str_wrap()} with \if{html}{\out{
}} instead} \usage{ str_wrap_br(string, whitespace_only = FALSE, ...) } @@ -14,5 +14,5 @@ str_wrap_br(string, whitespace_only = FALSE, ...) \item{...}{other arguments passed to \code{stringr::str_wrap()}} } \description{ -\code{str_wrap()} with
instead +\code{str_wrap()} with \if{html}{\out{
}} instead } diff --git a/tests/testthat/test-get_anova.R b/tests/testthat/test-get_anova.R new file mode 100644 index 0000000..165b4af --- /dev/null +++ b/tests/testthat/test-get_anova.R @@ -0,0 +1,50 @@ +# Load necessary libraries +library(testthat) + +# lm test +test_that("get_anova does not throw an error for lm class", { + lm_model <- lm(mpg ~ wt + hp, data = mtcars) + expect_error(get_anova(lm_model), NA) +}) + +# lmerTest test +test_that("get_anova does not throw an error for lmerTest class", { + if (requireNamespace("lmerTest", quietly = TRUE)) { + lmerTest_model <- lmerTest::lmer(mpg ~ wt + hp + (1 | cyl), data = mtcars) + expect_error(get_anova(lmerTest_model), NA) + } else { + skip() + } +}) + +# glmmTMB test +test_that("get_anova does not throw an error for glmmTMB class", { + if (suppressWarnings(requireNamespace("glmmTMB", quietly = TRUE))) { + fabricated_data <- mtcars + fabricated_data$Response <- ifelse(fabricated_data$mpg > 20, 1, 0) + glmmTMB_model <- suppressWarnings(glmmTMB::glmmTMB(Response ~ wt + hp + (1 | cyl), data = fabricated_data, family = binomial())) + expect_error(get_anova(glmmTMB_model), NA) + } else { + skip() + } +}) + +# gls test +test_that("get_anova does not throw an error for gls class", { + if (requireNamespace("nlme", quietly = TRUE)) { + gls_model <- nlme::gls(mpg ~ wt + hp, data = mtcars) + expect_error(get_anova(gls_model), NA) + } else { + skip() + } +}) + +# lme test +test_that("get_anova does not throw an error for lme class", { + if (requireNamespace("nlme", quietly = TRUE)) { + lme_model <- nlme::lme(mpg ~ wt + hp, random = ~ 1 | cyl, data = mtcars) + expect_error(get_anova(lme_model), NA) + } else { + skip() + } +})