How does it work?
-
-Natalie Elphick
Bioinformatician I
Yihang Xin (Online TA)
-Software Engineer III
Min-Gyoung Shin
+Bioinformatician III
Keep at it—progress comes with persistence!
+
.R
.Rmd10:00
What is the output of the following code?
- +dog_breeds <- c("Labrador Retriever", "Akita", "Bulldog")
-if ("Akita" %in% dog_breeds) {
- print("dog_breeds already contains Akita")
-} else {
- dog_breeds <- c("Akita", dog_breeds)
-}[1] "dog_breeds already contains Akita"Already contains this dog[1] "Already contains this dog"[1] "German Shepard" "Labrador Retriever" "Akita"
@@ -3091,11 +3110,18 @@ can continue to improve these workshops
Single -Cell ATAC-Seq Data Analysis Part 2
+Intermediate
+RNA-Seq Analysis Using R
+September 10, 2024 9am-12pm PDT
Introduction
+to Statistics, Experimental Design, and Hypothesis Testing
+September 10 - September 12, 2024 1-3pm PDT
Single
+Cell RNA-Seq Data Analysis
+September 16-September 17, 2024 9am-4pm PDT
Natalie Elphick
Bioinformatician I
Michela Traglia (Online TA)
+
Michela Traglia
Senior Statistician
Yihang Xin (Online TA)
-Software Engineer III
Ayushi Agrawal
+Bioinformatician III
ggplot(data = mpg,
mapping = aes(x = cty, y = hwy)) +
- geom_point() +
+ geom_point(color = "brown") +
geom_smooth(formula = y ~ x, method = "lm")
10:00
@@ -4686,15 +4686,18 @@ can continue to improve these workshops
Upcoming Workshops-Single -Cell ATAC-Seq Data Analysis Part 2 +Intermediate
+RNA-Seq Analysis Using R Introduction
+to Statistics, Experimental Design, and Hypothesis Testing Single
+Cell RNA-Seq Data Analysis
@@ -109,7 +122,7 @@ feature rich graphical user interface (GUI) ## File types - **Rscript** files that end in `.R` - - The most basic, a file that contains R code + - The most basic, a file that contains only R code - **RMarkdown** files that end in `.Rmd` - Let's create a blank Rscript to see how they work, open RStudio and click: - File -\> New File -\> R Script @@ -228,7 +241,7 @@ DogBreeds <- c("Labrador Retriever", "Akita", "Bulldog") ## Data Types - Integer - - Whole numbers (in R denoted with L ex. 1L,2L) + - Whole numbers (denoted with L ex. 1L,2L) - Numeric - Decimal numbers - Logical @@ -312,7 +325,7 @@ x %in% y # Is x in this vector y? **What is the output of the following code?** ```{r, eval = FALSE} -4 %in% as.character(c(1,2,3,4)) +4 %in% c(1, 2, 3, 4) ``` 1. TRUE @@ -352,10 +365,15 @@ execution of code ```{r} dog_breeds <- c("Labrador Retriever", "Akita", "Bulldog") + if ("Akita" %in% dog_breeds) { + print("dog_breeds already contains Akita") + } else { + dog_breeds <- c("Akita", dog_breeds) + } ``` @@ -372,13 +390,12 @@ perform a single action  ## Defining a function -- To define a function we use the function keyword, the output is specified with the **return** keyword: +- To define a function we use the function keyword, the output is specified with the **return** function: ```{r} -add_dog <- function(dog_to_add, - input_vector) { +add_dog <- function(dog_to_add, input_vector) { if (dog_to_add %in% input_vector) { - message("Already contains this dog") + print("Already contains this dog") } else { @@ -453,8 +470,16 @@ packages ## Upcoming Workshops -[Single Cell ATAC-Seq Data Analysis Part 2](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1) +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5) +September 10, 2024 9am-12pm PDT -- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule +[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1) +September 10 - September 12, 2024 1-3pm PDT + +[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0) +September 16-September 17, 2024 9am-4pm PDT + + +- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule diff --git a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd index e8b5026..8c963c9 100644 --- a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd +++ b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd @@ -2,7 +2,7 @@ title: "Introduction to R Data Analysis" subtitle: "Part 2" author: "Natalie Elphick" -date: "May 21st, 2024" +date: "August 27th, 2024" knit: (function(input, ...) { rmarkdown::render( input, @@ -31,11 +31,11 @@ knitr::opts_chunk$set(comment = "") **Natalie Elphick** Bioinformatician I -**Michela Traglia (Online TA)** +**Michela Traglia** Senior Statistician -**Yihang Xin (Online TA)** -Software Engineer III +**Ayushi Agrawal** +Bioinformatician III # Schedule @@ -179,7 +179,7 @@ ggplot(data = mpg, # Input dataframe ```{r, fig.dim=c(10,4)} ggplot(data = mpg, mapping = aes(x = cty, y = hwy)) + - geom_point() + + geom_point(color = "brown") + geom_smooth(formula = y ~ x, method = "lm") ``` @@ -315,11 +315,17 @@ For any bioinformatics specific questions feel free to reach out to the Gladston ## Upcoming Workshops -[Single Cell ATAC-Seq Data Analysis Part 2](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1) +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5) +September 10, 2024 9am-12pm PDT -- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule +[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1) +September 10 - September 12, 2024 1-3pm PDT -- [Gladstone Bioinformatics Workshops](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki) - workshop wiki page for all of the workshops we offer +[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0) +September 16-September 17, 2024 9am-4pm PDT + + +- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule diff --git a/intro-r-data-analysis/renv.lock b/intro-r-data-analysis/renv.lock index 6812de9..3983be6 100644 --- a/intro-r-data-analysis/renv.lock +++ b/intro-r-data-analysis/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", @@ -11,18 +11,18 @@ "Packages": { "DBI": { "Package": "DBI", - "Version": "1.2.1", + "Version": "1.2.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "9b4993e98e0e19da84c168460c032fef" + "Hash": "065ae649b05f1ff66bb0c793107508f5" }, "MASS": { "Package": "MASS", - "Version": "7.3-60.0.1", + "Version": "7.3-61", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -33,11 +33,11 @@ "stats", "utils" ], - "Hash": "b765b28387acc8ec9e9c1530713cb19c" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-5", + "Version": "1.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -50,7 +50,18 @@ "stats", "utils" ], - "Hash": "8c7115cd3a0e048bda2a7cd110549f7a" + "Hash": "1920b2f11133b12350024297d8a4ff4a" + }, + "PKI": { + "Package": "PKI", + "Version": "0.1-14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "base64enc" + ], + "Hash": "f5b9c6b2f62f1fa3dd53fd1ddccbb241" }, "R6": { "Package": "R6", @@ -74,14 +85,14 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.13", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "askpass": { "Package": "askpass", @@ -95,13 +106,13 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" + "Hash": "e1e1b9d75c37401117b636b7ae50827a" }, "base64enc": { "Package": "base64enc", @@ -151,14 +162,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -168,42 +178,44 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", - "Version": "0.5.1", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "cachem", + "fastmap", "grDevices", "htmltools", "jquerylib", "jsonlite", + "lifecycle", "memoise", "mime", "rlang", "sass" ], - "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9" + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -212,7 +224,7 @@ "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" }, "cellranger": { "Package": "cellranger", @@ -228,26 +240,26 @@ }, "checkmate": { "Package": "checkmate", - "Version": "2.3.1", + "Version": "2.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "backports", "utils" ], - "Hash": "c01cab1cb0f9125211a6fc99d540e315" + "Hash": "0e14e01ce07e7c88fd25de6d4260d26b" }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", @@ -261,7 +273,7 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.1-0", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -271,14 +283,14 @@ "methods", "stats" ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" }, "commonmark": { "Package": "commonmark", - "Version": "1.9.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "d691c61bff84bd63c383874d2d0c3307" + "Hash": "5d8225445acb167abf7797de48b2ee3c" }, "conflicted": { "Package": "conflicted", @@ -318,7 +330,7 @@ }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -326,34 +338,34 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "5.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" }, "data.table": { "Package": "data.table", - "Version": "1.14.10", + "Version": "1.15.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "6ea17a32294d8ca00455825ab0cf71b9" + "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" }, "dbplyr": { "Package": "dbplyr", - "Version": "2.4.0", + "Version": "2.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "DBI", "R", @@ -375,18 +387,18 @@ "vctrs", "withr" ], - "Hash": "59351f28a81f0742720b85363c4fdd61" + "Hash": "39b2e002522bfd258039ee4e889e0fd1" }, "digest": { "Package": "digest", - "Version": "0.6.33", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d" + "Hash": "33698c4b3127fc9f506654607fb73676" }, "dplyr": { "Package": "dplyr", @@ -443,14 +455,14 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "0.24.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" }, "fansi": { "Package": "fansi", @@ -466,17 +478,17 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fontawesome": { "Package": "fontawesome", @@ -508,14 +520,14 @@ }, "fs": { "Package": "fs", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, "gargle": { "Package": "gargle", @@ -552,7 +564,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.4", + "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -573,18 +585,18 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" }, "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", @@ -641,7 +653,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -652,7 +664,7 @@ "lifecycle", "rlang" ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" }, "haven": { "Package": "haven", @@ -677,14 +689,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -702,20 +714,19 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.7", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -734,9 +745,9 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.13", + "Version": "1.6.15", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -745,7 +756,7 @@ "promises", "utils" ], - "Hash": "d23d2879001f3d82ee9dc38a9ef53c4c" + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" }, "httr": { "Package": "httr", @@ -796,23 +807,22 @@ }, "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": "RSPM", "Requirements": [ "R", "digest", - "glue", "grDevices", "graphics", "htmltools", @@ -820,21 +830,19 @@ "magrittr", "rmarkdown", "rstudioapi", - "rvest", "scales", "stats", "stringr", "svglite", "tools", "viridisLite", - "webshot", "xml2" ], - "Hash": "49b625e6aabe4c5f091f5850aba8ff78" + "Hash": "532d16304274c23c8563f94b79351c86" }, "knitr": { "Package": "knitr", - "Version": "1.45", + "Version": "1.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -846,7 +854,7 @@ "xfun", "yaml" ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" + "Hash": "acf380f300c721da9fde7df115a5f86f" }, "labeling": { "Package": "labeling", @@ -917,7 +925,7 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -926,7 +934,7 @@ "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" + "Hash": "b8552d117e1b808b09a832f589b79035" }, "lubridate": { "Package": "lubridate", @@ -953,16 +961,16 @@ }, "markdown": { "Package": "markdown", - "Version": "1.12", + "Version": "1.13", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "commonmark", "utils", "xfun" ], - "Hash": "765cf53992401b3b6c297b69e1edb8bd" + "Hash": "074efab766a9d6360865ad39512f2a7e" }, "memoise": { "Package": "memoise", @@ -1022,18 +1030,18 @@ }, "munsell": { "Package": "munsell", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "colorspace", "methods" ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Hash": "4fd8900853b746af55b81fda99da7695" }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-166", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1043,17 +1051,17 @@ "stats", "utils" ], - "Hash": "a623a2239e642806158bc4dc3f51565d" + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" }, "openssl": { "Package": "openssl", - "Version": "2.1.1", + "Version": "2.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" + "Hash": "c62edf62de70cadf40553e10c739049d" }, "packrat": { "Package": "packrat", @@ -1106,7 +1114,7 @@ }, "prismatic": { "Package": "prismatic", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1115,20 +1123,20 @@ "grDevices", "graphics" ], - "Hash": "faa2193fdec94a45b4390aefc1280a62" + "Hash": "51967d2e55a523791ae22832e86209ae" }, "processx": { "Package": "processx", - "Version": "3.8.3", + "Version": "3.8.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", "ps", "utils" ], - "Hash": "82d48b1aec56084d9438dbf98087a7e9" + "Hash": "0c90a7d71988856bad2a2a45dd871bb9" }, "progress": { "Package": "progress", @@ -1146,7 +1154,7 @@ }, "promises": { "Package": "promises", - "Version": "1.2.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1158,18 +1166,18 @@ "rlang", "stats" ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" + "Hash": "434cd5388a3979e74be5c219bcd6e77d" }, "ps": { "Package": "ps", - "Version": "1.7.5", + "Version": "1.7.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "709d852d33178db54b17c722e5b1e594" + "Hash": "878b467580097e9c383acbb16adab57a" }, "purrr": { "Package": "purrr", @@ -1188,14 +1196,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.2.7", + "Version": "1.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "90a1b8b7e518d7f90480d56453b4d062" + "Hash": "e3087db406e079a8a2fd87f413918ed3" }, "rappdirs": { "Package": "rappdirs", @@ -1274,9 +1282,9 @@ }, "reprex": { "Package": "reprex", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "callr", @@ -1292,13 +1300,13 @@ "utils", "withr" ], - "Hash": "1425f91b4d5d9a8f25352c44a3d914ed" + "Hash": "97b1d5361a24d9fb588db7afe3e5bcbf" }, "revealjs": { "Package": "revealjs", "Version": "0.9", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "rmarkdown" @@ -1307,18 +1315,18 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.1", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb" + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.25", + "Version": "2.28", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1331,14 +1339,13 @@ "jsonlite", "knitr", "methods", - "stringr", "tinytex", "tools", "utils", "xfun", "yaml" ], - "Hash": "d65e35823c817f09f4de424fcdfa812a" + "Hash": "062470668513dcda416927085ee9bdc7" }, "rprojroot": { "Package": "rprojroot", @@ -1352,10 +1359,11 @@ }, "rsconnect": { "Package": "rsconnect", - "Version": "1.2.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "PKI", "R", "cli", "curl", @@ -1370,18 +1378,18 @@ "tools", "yaml" ], - "Hash": "c064d4993aedbf6c383041d1606aabeb" + "Hash": "90dc9ac04cec50f25657b077d4aaca57" }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.15.0", + "Version": "0.16.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "5564500e25cffad9e22244ced1379887" + "Hash": "96710351d642b70e8f02ddeb237c46a7" }, "rvest": { "Package": "rvest", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1394,14 +1402,13 @@ "rlang", "selectr", "tibble", - "withr", "xml2" ], - "Hash": "a4a5ac819a467808c60e36e92ddf195e" + "Hash": "0bcf0c6f274e90ea314b812a6d19a519" }, "sass": { "Package": "sass", - "Version": "0.4.7", + "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1411,7 +1418,7 @@ "rappdirs", "rlang" ], - "Hash": "6bd4d33b50ff927191ec9acbf52fd056" + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" }, "scales": { "Package": "scales", @@ -1448,9 +1455,9 @@ }, "shiny": { "Package": "shiny", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -1458,7 +1465,6 @@ "cachem", "commonmark", "crayon", - "ellipsis", "fastmap", "fontawesome", "glue", @@ -1478,7 +1484,7 @@ "withr", "xtable" ], - "Hash": "3a1f41807d648a908e3c7f0334bf85e6" + "Hash": "6a293995a66e12c48d13aa1f957d09c7" }, "sourcetools": { "Package": "sourcetools", @@ -1492,7 +1498,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1501,11 +1507,11 @@ "tools", "utils" ], - "Hash": "ca8bd84263c77310739d2cf64d84d7c9" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1518,7 +1524,7 @@ "stringi", "vctrs" ], - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" + "Hash": "960e2ae9e09656611e0b8214ad543207" }, "svglite": { "Package": "svglite", @@ -1541,26 +1547,28 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "15b594369e70b975ba9f064295983499" - }, - "textshaping": { - "Package": "textshaping", - "Version": "0.3.7", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle" + ], + "Hash": "213b6b8ed5afbf934843e6c3b090d418" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", @@ -1583,7 +1591,7 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1602,11 +1610,11 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1618,7 +1626,7 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tidyverse": { "Package": "tidyverse", @@ -1662,24 +1670,24 @@ }, "timechange": { "Package": "timechange", - "Version": "0.2.0", + "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "8548b44f79a35ba1791308b61e6012d7" + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" }, "tinytex": { "Package": "tinytex", - "Version": "0.48", + "Version": "0.52", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "8f96d229b7311beb32b94cf413b13f84" + "Hash": "cfbad971a71f0e27cec22e544a08bc3b" }, "tzdb": { "Package": "tzdb", @@ -1704,17 +1712,17 @@ }, "uuid": { "Package": "uuid", - "Version": "1.2-0", + "Version": "1.2-1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "303c19bfd970bece872f93a824e323d9" + "Hash": "34e965e62a41fcafb1ca60e9b142085b" }, "vctrs": { "Package": "vctrs", - "Version": "0.6.4", + "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1724,7 +1732,7 @@ "lifecycle", "rlang" ], - "Hash": "266c1ca411266ba8f365fcc726444b87" + "Hash": "c03fa420630029418f7e6da3667aac4a" }, "viridisLite": { "Package": "viridisLite", @@ -1762,19 +1770,6 @@ ], "Hash": "390f9315bc0025be03012054103d227c" }, - "webshot": { - "Package": "webshot", - "Version": "0.5.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "callr", - "jsonlite", - "magrittr" - ], - "Hash": "16858ee1aba97f902d24049d4a44ef16" - }, "whisker": { "Package": "whisker", "Version": "0.4.1", @@ -1784,27 +1779,28 @@ }, "withr": { "Package": "withr", - "Version": "2.5.2", + "Version": "3.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "grDevices", - "graphics", - "stats" + "graphics" ], - "Hash": "4b25e70111b7d644322e9513f403a272" + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" }, "xfun": { "Package": "xfun", - "Version": "0.41", + "Version": "0.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", + "grDevices", "stats", "tools" ], - "Hash": "460a5e0fe46a80ef87424ad216028014" + "Hash": "36ab21660e2d095fef0d83f689e0477c" }, "xml2": { "Package": "xml2", @@ -1833,10 +1829,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" } } } diff --git a/intro-r-data-analysis/style.css b/intro-r-data-analysis/style.css index 9928aff..825123c 100644 --- a/intro-r-data-analysis/style.css +++ b/intro-r-data-analysis/style.css @@ -22,7 +22,6 @@ } - /* Add horizontal scrolling to all code outputs */ .reveal pre code.output { @@ -43,12 +42,12 @@ pre, code, kbd, samp { /* Bold slide titles and change color */ .reveal h2 { font-weight: bold !important; - color: #9c0366; + color: #0072B2; } /* Bold slide titles and change color */ .reveal h1 { font-weight: bold !important; - color: #9c0366; + color: #0072B2; } .reveal .slides>section:first-child h2 { color: #333; @@ -57,7 +56,7 @@ pre, code, kbd, samp { /* Custom slide title */ .my-title-slide h1 { font-weight: bold; - color: #9c0366; + color: #0072B2; } .my-title-slide h2 { color: #333; @@ -68,7 +67,7 @@ font-weight: normal !important; .reveal .slides>section:first-child h1 { font-weight: bold !important; - color: #9c0366; + color: #0072B2; } /* Increase the spacing between list items */ @@ -136,7 +135,7 @@ small { color: #0c74dc; } -/* Change link color to magenta on hover */ +/* Change link color to darker blue on hover */ .reveal a:hover { - color: #9c0366 !important; + color: #0072B2 !important; } |
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