diff --git a/_quarto.yml b/_quarto.yml index 9504c495..e0ba58b4 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -160,7 +160,7 @@ website: - href: r4babs2/week-5/study_after_workshop.qmd text: Consolidate! - text: --- - - section: "Week 6: Chi-squared and correlation" + - section: "Week 6: Association" contents: - href: r4babs2/week-6/overview.qmd text: About diff --git a/pgt52m/week-9/.DS_Store b/pgt52m/week-9/.DS_Store index c76eae16..39d7bcd0 100644 Binary files a/pgt52m/week-9/.DS_Store and b/pgt52m/week-9/.DS_Store differ diff --git a/r4babs2/r4babs2.qmd b/r4babs2/r4babs2.qmd index fa9685f9..29588ec5 100644 --- a/r4babs2/r4babs2.qmd +++ b/r4babs2/r4babs2.qmd @@ -59,4 +59,4 @@ Learning Data Analysis in R is like learning to speak a new language or play an ## Two-way ANOVA -## Chi-squared tests and correlation \ No newline at end of file +## Association: Correlation and Contingency \ No newline at end of file diff --git a/r4babs2/week-6/data-raw/blood_ulcers.txt 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no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no +A no diff --git a/r4babs2/week-6/data-raw/height.txt b/r4babs2/week-6/data-raw/height.txt new file mode 100644 index 00000000..d267759a --- /dev/null +++ b/r4babs2/week-6/data-raw/height.txt @@ -0,0 +1,12 @@ +older younger +180.3 175.3 +172.7 162.6 +167.6 165.1 +170.2 160.0 +177.8 165.1 +180.3 157.5 +177.8 165.1 +185.4 162.6 +182.9 167.6 +165.1 149.9 +167.6 157.5 \ No newline at end of file diff --git a/r4babs2/week-6/figures/sibling-height.png b/r4babs2/week-6/figures/sibling-height.png new file mode 100644 index 00000000..e57b5113 Binary files /dev/null and b/r4babs2/week-6/figures/sibling-height.png differ diff --git a/r4babs2/week-6/images/code-hero.gif b/r4babs2/week-6/images/code-hero.gif new file mode 100644 index 00000000..cd674c40 Binary files /dev/null and b/r4babs2/week-6/images/code-hero.gif differ diff --git a/r4babs2/week-6/images/future_you.png b/r4babs2/week-6/images/future_you.png deleted file mode 100644 index 4bf8a20c..00000000 Binary files a/r4babs2/week-6/images/future_you.png and /dev/null differ diff --git a/r4babs2/week-6/images/rainbowr.gif b/r4babs2/week-6/images/rainbowr.gif new file mode 100644 index 00000000..2b0a8c09 Binary files /dev/null and b/r4babs2/week-6/images/rainbowr.gif differ diff --git a/r4babs2/week-6/images/super-aardvark.png b/r4babs2/week-6/images/super-aardvark.png new file mode 100644 index 00000000..5764a2e5 Binary files /dev/null and b/r4babs2/week-6/images/super-aardvark.png differ diff --git a/r4babs2/week-6/overview.qmd b/r4babs2/week-6/overview.qmd index eaa9a5a9..40712ae4 100644 --- a/r4babs2/week-6/overview.qmd +++ b/r4babs2/week-6/overview.qmd @@ -1,29 +1,31 @@ --- title: "Overview" -subtitle: "Chi-squared tests and correlation" +subtitle: "Association: Chi-squared contingency and correlation" toc: true toc-location: right --- -This week you will -### Learning objectives +![Artwork by @allison_horst: ](images/code-hero.gif){fig-alt="Animated gif with pastel lines in the background. The words 'CODE HERO' in bold black text scroll across repeatedly." width="600"} -The successful student will be able to: -- +This week you will -- +### Learning objectives -- +The successful student will be able to: -- +- Explain the principles of correlation and chi-squared contingency tests +- Select, appropriately correlation and chi-squared contingency tests +- Apply and interpret a correlation and chi-squared contingency tests in R +- Appreciate the difference between statistical significance and biological significance +- Summarise and illustrate with appropriate R figures test results scientifically ### Instructions 1. [Prepare](study_before_workshop.qmd) - i. 📖 Read the book **OR** 📹 Watch two videos + i. 📖 Read the 2. [Workshop](workshop.qmd) diff --git a/r4babs2/week-6/study_after_workshop.qmd b/r4babs2/week-6/study_after_workshop.qmd index ef9aaee3..49fb83bc 100644 --- a/r4babs2/week-6/study_after_workshop.qmd +++ b/r4babs2/week-6/study_after_workshop.qmd @@ -1,6 +1,6 @@ --- title: "Independent Study to consolidate this week" -subtitle: "Chi-squared tests and correlation" +subtitle: "Association: Correlation and Contingency" toc: true toc-location: right format: diff --git a/r4babs2/week-6/study_before_workshop.qmd b/r4babs2/week-6/study_before_workshop.qmd index f87a09d8..8c65f462 100644 --- a/r4babs2/week-6/study_before_workshop.qmd +++ b/r4babs2/week-6/study_before_workshop.qmd @@ -1,11 +1,11 @@ --- title: "Independent Study to prepare for workshop" -subtitle: "Chi-squared tests and correlation" +subtitle: "Association: Correlation and Contingency" toc: true toc-location: right --- -1. 📖 Read [xxxxx](https://3mmarand.github.io/comp4biosci/xx.html) +1. 📖 Read [Association](https://3mmarand.github.io/comp4biosci/association.html) diff --git a/r4babs2/week-6/workshop.qmd b/r4babs2/week-6/workshop.qmd index 2da87947..e64be1c5 100644 --- a/r4babs2/week-6/workshop.qmd +++ b/r4babs2/week-6/workshop.qmd @@ -1,19 +1,22 @@ --- title: "Workshop" -subtitle: "Chi-squared tests and correlation" +subtitle: "Association: Correlation and Contingency" toc: true toc-location: right --- ```{r} #| include: false + library(tidyverse) library(kableExtra) ``` # Introduction -![Artwork by @allison_horst: ](images/xxx.png){fig-alt="xxxxx" width="1000"} +# Introduction + +![Artwork by @allison_horst: ](images/rainbowr.gif){fig-alt="Animated gif of the R logo with a rainbow that grows over the logo repeatedly." width="600"} ## Session overview @@ -48,18 +51,336 @@ These four symbols are used at the beginning of each instruction so you know whe ![](images/do_on_your_computer.png) Start RStudio from the Start menu. -![](images/do_in_R.png) Go the Files tab in the lower right pane and click on the `...` on the right. This will open a "Go to folder" window. Navigate to a place on your computer where you keep your work. Click Open. - ![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-2` folder and name the RStudio Project `week-6`. ![](images/do_in_R.png) Make new folders called `data-raw` and `figures`. You can do this on the Files Pane by clicking New Folder and typing into the box that appears. -![](images/do_in_R.png) Make a two new scripts called `correlation.R` and `chi-squared-tests.R` to carry out the rest of the work. +![](images/do_in_R.png) Make a two new scripts called `correlation.R` and `contingency-chi-squared-tests.R` to carry out the rest of the work. -![](images/do_in_R.png) Add a comments to each script such as: `# Correlation` and `#Chi-squared tests` and load the **`tidyverse`** [@tidyverse] package in each +![](images/do_in_R.png) Add a comments to each script such as: `# Correlation` and `# Contingency Chi-squared tests` and load the **`tidyverse`** [@tidyverse] package in each # Exercises +## Pearson's Correlation + +The data given in [height.txt](data-raw/height.txt) are the heights of eleven sibling pairs. + +![R](../pics/R.png) Save a copy of [height.txt](data-raw/height.txt) to your `data-raw` folder and import it. + +```{r} +#| include: false + +#---CODING ANSWER--- +height <- read_table("data-raw/height.txt") +``` + + + +::: {.callout-tip} +## Top Tip + +Did you know you can also read a file directly from the internet instead of saving it first? + +`height <- read_table("https://3mmarand.github.io/R4BABS/r4babs2/week-6/data-raw/data-raw/height.txt")` + +::: + + +### Exploring + +![Q](../pics/Q.png) What type of variables are `older` and `sister`? What are +the implications for the test? + + + + + + + + + + + +![Q](../pics/Q.png) Do a quick plot of the data. We don't have a causal +relationship here so either variable can go on the *x*-axis. + +```{r} +ggplot(height, aes(x = younger, y = older) ) + + geom_point() + +``` + +![Q](../pics/Q.png) Remembering that one of the assumptions for parametric +correlation is that any correlation should be linear, what do you +conclude from the plot? + + + + + + + + + +### Applying, interpreting and reporting + +We will do a parametric correlation in any case. + +![R](../pics/R.png) We can carry out a Pearson's product moment correlation +with: + +```{r} +cor.test(data = height, ~ older + younger, method = "pearson") +``` + +Notice that were are not using the `response ~ explanatory` form here +because this is not a causal relationship. + +Pearson is the default correlation smethod, therefore we could +omit `method = "pearson"`. + +![Q](../pics/Q.png) What do you conclude from the test? + + + + + + + +### Illustrating + +![R](../pics/R.png) Create a better figure for our data using: + +```{r} +fig1 <- ggplot(height, aes(x = younger, y = older)) + + geom_point() + + scale_x_continuous(name = "Younger sibling height (cm)", + limits = c(120, 190), + expand = c(0, 0)) + + scale_y_continuous(name = "Older sibling height (cm)", + limits = c(120, 190), + expand = c(0, 0)) + + theme_classic() + +fig1 +``` + + +![R](../pics/R.png) Use `ggsave()` to save your figure to file in your `figures` folder. + +```{r} +#| include: false + +#---CODING ANSWER--- + +ggsave("figures/sibling-height.png", + plot = fig1, + width = 3.5, + height = 3.5, + units = "in", + dpi = 300) + +``` + + + + +## Effect of sample size on correlation + +Now we will explore the effect of sample size on the value of the correlation +coefficient and its significance. + +![R](../pics/R.png) Create a dataset with twice the number of observations +and examine it like this: + +```{r} +height2 <- rbind(height, height) +View(height2) +``` + +Each pair of values will appear twice. + +![R](../pics/R.png) Now repeat the correlation with height2 +```{r} +#| include: false + +#---CODING ANSWER--- + +cor.test(data = height2, ~ older + younger, method = "pearson") +``` + +![Q](../pics/Q.png) What do you conclude? What does this tell you about +the sensitivity of correlation to sample size? + + + + + + + + + + + + + + +## Spearman's rank Correlation + +Since our sibling dataset is so small we might very reasonably have +chosen to do a non-parametric correlation. The same function is used +but we specify a different value for the `method` argument. + +![R](../pics/R.png) Carry out a Spearman's rank correlation: + +```{r} +cor.test(data = height, ~ older + younger, method = "spearman") +``` + +![Q](../pics/Q.png) What do you conclude? + + + + + + + + +## Blood group and ulcers + +A human geneticist found that in a sample of 477 blood group O people 65 +had peptic ulcers whereas in a sample of 387 blood group A people +31 had peptic ulcers. + +![Q](../pics/Q.png) Draw a 2 x 2 table of these data (on a piece of paper). + + + + + + + + + + + + + +![Q](../pics/Q.png) What is your null hypothesis and what type of test is required? + + + + + + + + + + +### Blood group and ulcers - inbuilt test + +![R](../pics/R.png) Make a vector `obs` that holds the 4 observed numbers. +For the moment, don't worry about what order they are in. + +```{r} +#| include: false + +#---CODING ANSWER--- + +obs <- c(65, 412, 31, 356) +``` + +For a contingency chi squared test, the inbuilt chi-squared test can be +used in a straightforward way. However, we need to structure our data +as a 2 x 2 table rather than as a 1 x 4 vector. A 2 x 2 table can be created +with the `matrix()` function. We can also name the rows and columns which +helps us interpret the results. + +![R](../pics/R.png) To create a list containing two elements which are vectors +for the two groups in each variable we do: + +```{r} +# list of two elements +# the two variables are whether someone has an ulcer or not and whether +# they are blood group O or A +vars <- list(ulcer = c("yes","no"), blood = c("O", "A")) +vars + +``` + +![R](../pics/R.png) Now we can create the matrix from our vector of numbers +`obs` and use our list `vars` to give the column and row names: + +```{r} +ulcers <- matrix(obs, nrow = 2, dimnames = vars) +ulcers +``` + +![R](../pics/R.png) Check the content of `ulcers` and recreate if +the numbers are not in the correct place (*i.e.*, do not match your table) + +![R](../pics/R.png) Run a contingency chi-squared with: + +```{r} +chisq.test(ulcers, correct = FALSE) +# you should look up the command in the manual to see what correct = FALSE does +``` + +To help us discover what is the direction of any deviation from the null hypothesis it is helpful to see what the expected values were. These are accessible in the `$expected` variable in the output value of the `chisq.test()` method (See the manual!). + +![R](../pics/R.png) View the expected values with: + +```{r} +chisq.test(ulcers, correct = FALSE)$expected +``` + +![Q](../pics/Q.png) What do you conclude about the association between ABO blood group and peptic ulcers? + + + + + + + + + + +### Blood group and ulcers- alternative data format. + +The data we were given was already tabulated. There are raw data in [blood_ulcers.txt](data-raw/blood_ulcers.txt). Examine this file to understand +the format + +![W](../pics/W.png) Save a copy of [blood_ulcers.txt](data-raw/blood_ulcers.txt) +to your `data-raw` folder + +![R](../pics/R.png) Read the data in to R and check the structure. + +```{r} +#| include: false + +#---CODING ANSWER--- + +blood_ulcers <- read_table("data-raw/blood_ulcers.txt") +str(blood_ulcers) +``` + + +![R](../pics/R.png) We can tabulate the data and assign it using the `table()` command: + +```{r} +ulctab <- table(blood_ulcers$blood, blood_ulcers$ulcer) +# examine the result +ulctab + +``` + +We need to give both variables to cross tabulate. + +![R](../pics/R.png) Now carry out the contingency chi-squared like this: + +```{r} +chisq.test(ulctab, correct = FALSE) +``` You're finished! diff --git a/renv.lock b/renv.lock index ea583967..7870ec82 100644 --- a/renv.lock +++ b/renv.lock @@ -85,18 +85,18 @@ }, "DBI": { "Package": "DBI", - "Version": "1.1.3", + "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "b2866e62bab9378c3cc9476a1954226b" + "Hash": "164809cd72e1d5160b4cb3aa57f510fe" }, "FSA": { "Package": "FSA", - "Version": "0.9.4", + "Version": "0.9.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -112,32 +112,32 @@ "utils", "withr" ], - "Hash": "50eab53c1e0a13d3077c17d0ffb38287" + "Hash": "7bbf3be5bc901319e0cd0cd9528af32b" }, "GGally": { "Package": "GGally", - "Version": "2.1.2", + "Version": "2.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "RColorBrewer", "dplyr", - "forcats", "ggplot2", + "ggstats", "grDevices", "grid", "gtable", "lifecycle", + "magrittr", "plyr", "progress", - "reshape", "rlang", "scales", "tidyr", "utils" ], - "Hash": "022f78c8698724b326f1838b1a98cafa" + "Hash": "b11ac45c916608b7d1374ff87da053d5" }, "MASS": { "Package": "MASS", @@ -156,12 +156,11 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.6-0", + "Version": "1.5-4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "grDevices", "graphics", "grid", "lattice", @@ -169,11 +168,11 @@ "stats", "utils" ], - "Hash": "31262fd18481fab05c5e7258dac163ca" + "Hash": "38082d362d317745fb932e13956dccbb" }, "MatrixModels": { "Package": "MatrixModels", - "Version": "0.5-2", + "Version": "0.5-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -182,7 +181,7 @@ "methods", "stats" ], - "Hash": "26749bd5c7c4123dd23aeb9159be22d6" + "Hash": "0776bf7526869e0286b0463cb72fb211" }, "R6": { "Package": "R6", @@ -212,37 +211,37 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.11", + "Version": "1.0.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" + "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.3", + "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "Matrix", "R", "Rcpp", "stats", "utils" ], - "Hash": "1e035db628cefb315c571202d70202fe" + "Hash": "df49e3306f232ec28f1604e36a202847" }, "Rhdf5lib": { "Package": "Rhdf5lib", - "Version": "1.24.1", + "Version": "1.24.2", "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", "Requirements": [ "R" ], - "Hash": "beaded2ac0f712ae3d8409f5fa470381" + "Hash": "3cf103db29d75af0221d71946509a30c" }, "S4Vectors": { "Package": "S4Vectors", @@ -364,10 +363,13 @@ }, "brio": { "Package": "brio", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "976cf154dfb043c012d87cddd8bca363" + "Requirements": [ + "R" + ], + "Hash": "68bd2b066e1fe780bbf62fc8bcc36de3" }, "broom": { "Package": "broom", @@ -390,9 +392,30 @@ ], "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" }, + "broom.helpers": { + "Package": "broom.helpers", + "Version": "1.14.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "broom", + "cli", + "dplyr", + "labelled", + "lifecycle", + "purrr", + "rlang", + "stats", + "stringr", + "tibble", + "tidyr" + ], + "Hash": "ea30eb5d9412a4a5c2740685f680cd49" + }, "bslib": { "Package": "bslib", - "Version": "0.5.0", + "Version": "0.6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -403,12 +426,13 @@ "htmltools", "jquerylib", "jsonlite", + "lifecycle", "memoise", "mime", "rlang", "sass" ], - "Hash": "1b117970533deb6d4e992c1b34e9d905" + "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" }, "cachem": { "Package": "cachem", @@ -423,7 +447,7 @@ }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -432,7 +456,7 @@ "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "9f0e4fae4963ba775a5e5c520838c87b" }, "car": { "Package": "car", @@ -495,14 +519,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" }, "clipr": { "Package": "clipr", @@ -543,10 +567,13 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.4", + "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "3f7d8664d7324406cd10cd650ad85e5f" + "Requirements": [ + "R" + ], + "Hash": "5a295d7d963cc5035284dcdbaf334f4e" }, "crayon": { "Package": "crayon", @@ -562,13 +589,13 @@ }, "curl": { "Package": "curl", - "Version": "5.0.1", + "Version": "5.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "2118af9cb164c8d2dddc7b89eaf732d9" + "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" }, "cytolib": { "Package": "cytolib", @@ -585,18 +612,18 @@ }, "data.table": { "Package": "data.table", - "Version": "1.14.8", + "Version": "1.15.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "b4c06e554f33344e044ccd7fdca750a9" + "Hash": "536dfe4ac4093b5d115caed7a1a7223b" }, "dbplyr": { "Package": "dbplyr", - "Version": "2.3.3", + "Version": "2.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -620,21 +647,20 @@ "vctrs", "withr" ], - "Hash": "d6fd1b1440c1cacc6623aaa4e9fe352b" + "Hash": "59351f28a81f0742720b85363c4fdd61" }, "desc": { "Package": "desc", - "Version": "1.4.2", + "Version": "1.4.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", "cli", - "rprojroot", "utils" ], - "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21" + "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f" }, "diffobj": { "Package": "diffobj", @@ -653,18 +679,18 @@ }, "digest": { "Package": "digest", - "Version": "0.6.33", + "Version": "0.6.34", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d" + "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" }, "dplyr": { "Package": "dplyr", - "Version": "1.1.2", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -683,7 +709,7 @@ "utils", "vctrs" ], - "Hash": "dea6970ff715ca541c387de363ff405e" + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, "dtplyr": { "Package": "dtplyr", @@ -724,7 +750,7 @@ }, "emmeans": { "Package": "emmeans", - "Version": "1.8.8", + "Version": "1.10.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -737,32 +763,33 @@ "stats", "utils" ], - "Hash": "1f74dbb608b24135dde896f84a2d117b" + "Hash": "fa6dcc3b50ce8c6ad148786ea82fccbe" }, "estimability": { "Package": "estimability", - "Version": "1.4.1", + "Version": "1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "stats" ], - "Hash": "1a78288c1188772070240b89ffe33579" + "Hash": "0d5f495f1edc281fca2510d8dabcba0f" }, "evaluate": { "Package": "evaluate", - "Version": "0.21", + "Version": "0.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "d59f3b464e8da1aef82dc04b588b8dfb" + "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" }, "fansi": { "Package": "fansi", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -770,7 +797,7 @@ "grDevices", "utils" ], - "Hash": "3e8583a60163b4bc1a80016e63b9959e" + "Hash": "962174cf2aeb5b9eea581522286a911f" }, "farver": { "Package": "farver", @@ -835,7 +862,7 @@ }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -843,7 +870,7 @@ "htmltools", "rlang" ], - "Hash": "1e22b8cabbad1eae951a75e9f8b52378" + "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" }, "forcats": { "Package": "forcats", @@ -863,18 +890,18 @@ }, "fs": { "Package": "fs", - "Version": "1.6.2", + "Version": "1.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "94af08e0aa9675a16fadbb3aaaa90d2a" + "Hash": "47b5f30c720c23999b913a1a635cf0bb" }, "gargle": { "Package": "gargle", - "Version": "1.5.1", + "Version": "1.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -892,7 +919,7 @@ "utils", "withr" ], - "Hash": "d3a3cb2fefea5b3d4f8e0ea33c948406" + "Hash": "fc0b272e5847c58cd5da9b20eedbd026" }, "generics": { "Package": "generics", @@ -907,7 +934,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.2", + "Version": "3.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -928,18 +955,41 @@ "vctrs", "withr" ], - "Hash": "3a147ee02e85a8941aad9909f1b43b7b" + "Hash": "52ef83f93f74833007f193b2d4c159a2" + }, + "ggstats": { + "Package": "ggstats", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "broom.helpers", + "cli", + "dplyr", + "forcats", + "ggplot2", + "lifecycle", + "magrittr", + "patchwork", + "purrr", + "rlang", + "scales", + "stats", + "stringr", + "tidyr" + ], + "Hash": "006a64911e79a7dc7cbf839a57baaff4" }, "glue": { "Package": "glue", - "Version": "1.6.2", + "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" + "Hash": "e0b3a53876554bd45879e596cdb10a52" }, "googledrive": { "Package": "googledrive", @@ -996,7 +1046,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.3", + "Version": "0.3.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1007,11 +1057,11 @@ "lifecycle", "rlang" ], - "Hash": "b44addadb528a0d227794121c00572a0" + "Hash": "b29cf3031f49b04ab9c852c912547eef" }, "haven": { "Package": "haven", - "Version": "2.5.3", + "Version": "2.5.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1028,7 +1078,7 @@ "tidyselect", "vctrs" ], - "Hash": "9b302fe352f9cfc5dcf0a4139af3a565" + "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1" }, "hexbin": { "Package": "hexbin", @@ -1074,7 +1124,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.5", + "Version": "0.5.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1087,11 +1137,11 @@ "rlang", "utils" ], - "Hash": "ba0240784ad50a62165058a27459304a" + "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" }, "httr": { "Package": "httr", - "Version": "1.4.6", + "Version": "1.4.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1102,7 +1152,7 @@ "mime", "openssl" ], - "Hash": "7e5e3cbd2a7bc07880c94e22348fb661" + "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" }, "ids": { "Package": "ids", @@ -1160,23 +1210,22 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.7", + "Version": "1.8.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "266a20443ca13c65688b2116d5220f76" + "Hash": "e1b9c55281c5adc4dd113652d9e26768" }, "kableExtra": { "Package": "kableExtra", - "Version": "1.3.4", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "digest", - "glue", "grDevices", "graphics", "htmltools", @@ -1184,21 +1233,19 @@ "magrittr", "rmarkdown", "rstudioapi", - "rvest", "scales", "stats", "stringr", "svglite", "tools", "viridisLite", - "webshot", "xml2" ], - "Hash": "49b625e6aabe4c5f091f5850aba8ff78" + "Hash": "532d16304274c23c8563f94b79351c86" }, "knitr": { "Package": "knitr", - "Version": "1.43", + "Version": "1.45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1210,7 +1257,7 @@ "xfun", "yaml" ], - "Hash": "9775eb076713f627c07ce41d8199d8f6" + "Hash": "1ec462871063897135c1bcbe0fc8f07d" }, "labeling": { "Package": "labeling", @@ -1223,6 +1270,23 @@ ], "Hash": "b64ec208ac5bc1852b285f665d6368b3" }, + "labelled": { + "Package": "labelled", + "Version": "2.12.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "dplyr", + "haven", + "lifecycle", + "rlang", + "stringr", + "tidyr", + "vctrs" + ], + "Hash": "1ec27c624ece6c20431e9249bd232797" + }, "lattice": { "Package": "lattice", "Version": "0.21-8", @@ -1240,7 +1304,7 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1249,11 +1313,11 @@ "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" + "Hash": "b8552d117e1b808b09a832f589b79035" }, "lme4": { "Package": "lme4", - "Version": "1.1-34", + "Version": "1.1-35.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1275,7 +1339,7 @@ "stats", "utils" ], - "Hash": "73ed88b282d27d4cf3d89b744aa21217" + "Hash": "07fb0c5b727b15b0ce40feb641498e4e" }, "lmtest": { "Package": "lmtest", @@ -1363,13 +1427,13 @@ }, "minqa": { "Package": "minqa", - "Version": "1.2.5", + "Version": "1.2.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp" ], - "Hash": "587ce77fd3c7bada7eadb2d18b62930d" + "Hash": "f48238f8d4740426ca12f53f27d004dd" }, "modelr": { "Package": "modelr", @@ -1402,14 +1466,14 @@ }, "mvtnorm": { "Package": "mvtnorm", - "Version": "1.2-3", + "Version": "1.2-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "463b268710930f7bffef33147400966a" + "Hash": "17e96668f44a28aef0981d9e17c49b59" }, "nlme": { "Package": "nlme", @@ -1459,13 +1523,31 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.6", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" + "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" + }, + "patchwork": { + "Package": "patchwork", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "cli", + "ggplot2", + "grDevices", + "graphics", + "grid", + "gtable", + "rlang", + "stats", + "utils" + ], + "Hash": "9c8ab14c00ac07e9e04d1664c0b74486" }, "pbkrtest": { "Package": "pbkrtest", @@ -1502,6 +1584,21 @@ ], "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, + "pkgbuild": { + "Package": "pkgbuild", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "callr", + "cli", + "desc", + "processx" + ], + "Hash": "c0143443203205e6a2760ce553dafc24" + }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", @@ -1514,7 +1611,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2.1", + "Version": "1.3.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1525,16 +1622,17 @@ "fs", "glue", "methods", + "pkgbuild", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "a7f498a1b2a4a6816148e498509f6e1d" + "Hash": "876c618df5ae610be84356d5d7a5d124" }, "plotrix": { "Package": "plotrix", - "Version": "3.8-2", + "Version": "3.8-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1544,18 +1642,18 @@ "stats", "utils" ], - "Hash": "2ebe8c2ec200da649738b0fc35a9b1a1" + "Hash": "d47fdfc45aeba360ce9db50643de3fbd" }, "plyr": { "Package": "plyr", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "Rcpp" ], - "Hash": "d744387aef9047b0b48be2933d78e862" + "Hash": "6b8177fd19982f0020743fadbfdbd933" }, "praise": { "Package": "praise", @@ -1576,7 +1674,7 @@ }, "processx": { "Package": "processx", - "Version": "3.8.2", + "Version": "3.8.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1585,31 +1683,32 @@ "ps", "utils" ], - "Hash": "3efbd8ac1be0296a46c55387aeace0f3" + "Hash": "82d48b1aec56084d9438dbf98087a7e9" }, "progress": { "Package": "progress", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ + "R", "R6", "crayon", "hms", "prettyunits" ], - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + "Hash": "f4625e061cb2865f111b47ff163a5ca6" }, "ps": { "Package": "ps", - "Version": "1.7.5", + "Version": "1.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "709d852d33178db54b17c722e5b1e594" + "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" }, "purrr": { "Package": "purrr", @@ -1628,7 +1727,7 @@ }, "quantreg": { "Package": "quantreg", - "Version": "5.95", + "Version": "5.97", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1642,18 +1741,18 @@ "stats", "survival" ], - "Hash": "6cdf5a3dc958f55529b0401a8e5869e3" + "Hash": "1bbc97f7d637ab3917c514a69047b2c1" }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" + "Hash": "90a1b8b7e518d7f90480d56453b4d062" }, "rappdirs": { "Package": "rappdirs", @@ -1667,9 +1766,9 @@ }, "readr": { "Package": "readr", - "Version": "2.1.4", + "Version": "2.1.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -1686,7 +1785,7 @@ "utils", "vroom" ], - "Hash": "b5047343b3825f37ad9d3b5d89aa1078" + "Hash": "9de96463d2117f6ac49980577939dfb3" }, "readxl": { "Package": "readxl", @@ -1732,9 +1831,9 @@ }, "reprex": { "Package": "reprex", - "Version": "2.0.2", + "Version": "2.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "callr", @@ -1750,18 +1849,7 @@ "utils", "withr" ], - "Hash": "d66fe009d4c20b7ab1927eb405db9ee2" - }, - "reshape": { - "Package": "reshape", - "Version": "0.8.9", - "Source": "Repository", - 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"Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1843,14 +1931,13 @@ "rlang", "selectr", "tibble", - "withr", "xml2" ], - "Hash": "a4a5ac819a467808c60e36e92ddf195e" + "Hash": "0bcf0c6f274e90ea314b812a6d19a519" }, "sass": { "Package": "sass", - "Version": "0.4.6", + "Version": "0.4.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1860,25 +1947,27 @@ "rappdirs", "rlang" ], - "Hash": "cc3ec7dd33982ef56570229b62d6388e" + "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" }, "scales": { "Package": "scales", - "Version": "1.2.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "R6", "RColorBrewer", + "cli", "farver", + "glue", "labeling", "lifecycle", "munsell", "rlang", "viridisLite" ], - "Hash": "906cb23d2f1c5680b8ce439b44c6fa63" + "Hash": "c19df082ba346b0ffa6f833e92de34d1" }, "selectr": { "Package": "selectr", @@ -1907,7 +1996,7 @@ }, "stringi": { "Package": "stringi", - 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"Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "8548b44f79a35ba1791308b61e6012d7" + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" }, "tinytex": { "Package": "tinytex", - "Version": "0.45", + "Version": "0.49", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "e4e357f28c2edff493936b6cb30c3d65" + "Hash": "5ac22900ae0f386e54f1c307eca7d843" }, "tzdb": { "Package": "tzdb", @@ -2155,27 +2243,27 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "uuid": { "Package": "uuid", - "Version": "1.1-1", + "Version": "1.2-0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "3d78edfb977a69fc7a0341bee25e163f" + "Hash": "303c19bfd970bece872f93a824e323d9" }, "vctrs": { "Package": "vctrs", - 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