add tasks

Signed-off-by: Daena Rys <[email protected]>
NCBI-Codeathons · Sep 24, 2024 · f590cb8 · f590cb8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,14 @@
 Package: teamlahti
-Title: What the Package Does (One Line, Title Case)
+Title: Resistome data analysis
 Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+Authors@R:
+        person("Team", "Lahti", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
-License: MIT + file LICENSE
+Description: Contains a reproducible tutorial on how to analyse and visualize 
+             variation in a large resistome profiling data set and associate it 
+             with various background factors by using the latest R/Bioconductor 
+             methods.
+License: MIT
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

diff --git a/README.Rmd b/README.Rmd
@@ -1,6 +1,6 @@
 ---
 output: github_document
----
+--- 
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -34,7 +34,7 @@ pak::pak("NCBI-Codeathons/amr-2024-team-lahti")
 This is a basic example which shows you how to solve a common problem:
 
 ```{r example}
-library(teamlahti)
+# library(teamlahti)
 ## basic example code
 ```
 

diff --git a/README.md b/README.md
@@ -1,19 +1,52 @@
-# Team Project Name
 
-List of participants and affiliations:
-- Participant, Affiliation (Team Leader)
-- Participant, Affiliation
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
-## Project Goals
+# teamlahti
 
-## Approach
+<!-- badges: start -->
+<!-- badges: end -->
 
-## Results
+The goal of teamlahti is to …
 
-## Future Work
+## Installation
 
-## NCBI Codeathon Disclaimer
-This software was created as part of an NCBI codeathon, a hackathon-style event focused on rapid innovation. While we encourage you to explore and adapt this code, please be aware that NCBI does not provide ongoing support for it.
+You can install the development version of teamlahti from
+[GitHub](https://github.com/) with:
 
-For general questions about NCBI software and tools, please visit: [NCBI Contact Page](https://www.ncbi.nlm.nih.gov/home/about/contact/)
+``` r
+# install.packages("pak")
+pak::pak("NCBI-Codeathons/amr-2024-team-lahti")
+```
 
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+# library(teamlahti)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`?
+You can include R chunks like so:
+
+``` r
+summary(cars)
+#>      speed           dist       
+#>  Min.   : 4.0   Min.   :  2.00  
+#>  1st Qu.:12.0   1st Qu.: 26.00  
+#>  Median :15.0   Median : 36.00  
+#>  Mean   :15.4   Mean   : 42.98  
+#>  3rd Qu.:19.0   3rd Qu.: 56.00  
+#>  Max.   :25.0   Max.   :120.00
+```
+
+You’ll still need to render `README.Rmd` regularly, to keep `README.md`
+up-to-date. `devtools::build_readme()` is handy for this.
+
+You can also embed plots, for example:
+
+<img src="man/figures/README-pressure-1.png" width="100%" />
+
+In that case, don’t forget to commit and push the resulting figure
+files, so they display on GitHub and CRAN.
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/teamlahti.html b/docs/articles/teamlahti.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   teamlahti: teamlahti.html
-last_built: 2024-09-24T10:13Z
+last_built: 2024-09-24T11:29Z
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/man/figures/README-pressure-1.png b/man/figures/README-pressure-1.png