add pages and updates output-dir

mjxstowe · Aug 17, 2022 · c026c2f · c026c2f
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diff --git a/_freeze/posts/2022-08-03-colour-dataViz/2022-08-03-colour-dataViz/execute-results/html.json b/_freeze/posts/2022-08-03-colour-dataViz/2022-08-03-colour-dataViz/execute-results/html.json
@@ -0,0 +1,16 @@
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+  "hash": "4744f3a13931f4f76f2ec23eb9c5c920",
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+    "markdown": "---\ntitle: \"Colour related resources\"\ndescription: |\n  Synthesis of links and resources on colours & data visualization\nauthor: \"Siobhon Egan\"\ndate: \"2022-08-02\"\ncategories: [rstudio, rstats, colour]\n---\n\n\nAs I need to reach for this information often I have decided to dedicate a solo post on all things coloour related.\n\nFigures are an important part of any publication. They are often the first thing readers look at and will help usually are the deciders as to whether non-specialists are going to read on...a good figure goes a long way! If you can spend the time it is well worth it (within reason of course). A good read on some do and don’ts for figures by [Rougier et al. 2014 PLOS comp biol](https://doi.org/10.1371/journal.pcbi.1003833), while your at it check out this one by [Mensh and Kording 2017](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619).\n\n:link: General colour resources\n\n-   [GeoDataViz Toolkit](https://github.com/OrdnanceSurvey/GeoDataViz-Toolkit/tree/master/Colours)\n-   [Your Friendly Guide to Colors in Data Visualisation](https://blog.datawrapper.de/colorguide/) by Lisa Charlotte Rost\n-   [Colorbrewer2](https://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3)\n-   [Color-hex](https://www.color-hex.com/)\n-   [Coloring for colorblindness](https://davidmathlogic.com/colorblind/#%23D81B60-%231E88E5-%23FFC107-%23004D40)\n-   [Viz palette](https://projects.susielu.com/viz-palette) - love this resource!\n-   [CSS Colours](https://www.w3schools.com/cssref/css_colors.asp)\n-   [HTML colour names](https://www.w3schools.com/colors/colors_names.asp)\n-   [HTML colour codes](https://htmlcolorcodes.com/)\n\n\n:link: R packages and resources\n\n- [Viridis](https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html): One of my favourite colour palettes at the moment.\n    - [Viridis Color Palette Generator](https://waldyrious.net/viridis-palette-generator/)\n    - [ggplot2 and viridis](https://ggplot2.tidyverse.org/reference/scale_viridis.html)\n\n\n**Examples**\n\nExample for viridis to get 8 colours \n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(viridis)\n```\n\n::: {.cell-output .cell-output-stderr}\n```\nLoading required package: viridisLite\n```\n:::\n\n```{.r .cell-code}\n# get certain number of colours from viridis palette\nnewcols = viridis(8, option = \"B\")\n```\n:::\n\n\n\nRColour brewer - display colours and get their hex numbers\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(RColorBrewer)\n\n# View a single RColorBrewer palette by specifying its name\ndisplay.brewer.pal(n = 8, name = 'Dark2')\n```\n\n::: {.cell-output-display}\n![](2022-08-03-colour-dataViz_files/figure-html/unnamed-chunk-2-1.png){width=672}\n:::\n\n```{.r .cell-code}\n# Hexadecimal color specification \nbrewer.pal(n = 8, name = \"Dark2\")\n```\n\n::: {.cell-output .cell-output-stdout}\n```\n[1] \"#1B9E77\" \"#D95F02\" \"#7570B3\" \"#E7298A\" \"#66A61E\" \"#E6AB02\" \"#A6761D\"\n[8] \"#666666\"\n```\n:::\n:::\n",
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diff --git a/...8-03-colour-dataViz/2022-08-03-colour-dataViz/figure-html/unnamed-chunk-2-1.png b/...8-03-colour-dataViz/2022-08-03-colour-dataViz/figure-html/unnamed-chunk-2-1.png
diff --git a/...sts/2022-08-03-rstats-dataframes/2022-08-03-rstats-dataframes/execute-results/html 2.json b/...sts/2022-08-03-rstats-dataframes/2022-08-03-rstats-dataframes/execute-results/html 2.json
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+    "markdown": "---\ntitle: \"Data frames in R\"\ndescription: |\n Quick bits for manipulating data frames in R.\nauthor: \"Siobhon Egan\"\ndate: \"22-08-02\"\ncategories: [rstudio, rstats]\n---\n\n::: {.cell}\n\n```{.r .cell-code}\nproducers <- data.frame(\n  surname =  c(\"Tarantino\", \"Scorsese\", \"Spielberg\", \"Hitchcock\", \"Polanski\"),\n  nationality = c(\"US\", \"US\", \"US\", \"UK\", \"Poland\"),\n  stringsAsFactors = FALSE\n)\n\nmovies <- data.frame(\n  surname = c(\"Spielberg\",\n              \"Scorsese\",\n              \"Hitchcock\",\n              \"Tarantino\",\n              \"Polanski\"),\n  title = c(\"Super 8\",\n            \"Taxi Driver\",\n            \"Psycho\",\n            \"Reservoir Dogs\",\n            \"Chinatown\"),\n  stringsAsFactors = FALSE\n)\n```\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nidx <- match(producers$surname, movies$surname)\nmovies_matched <- movies[idx, ]\n```\n:::\n\n\nUsing dplyr to rename a column with specific name we can call.\n```\ndf <- df %>%\n  dplyr::rename(newName = oldName)\n```\n\nAlternative way without using dylyr we cal call the specific column number\n```\ncolnames(df)[1] <- \"newName\"\n```\n\nSay you have a vector with the names we can use\n```\ncolnames(df) <- vector\n```\n\nMaybe col names are contained within a row 2 of the data frame\n```\ncolnames(df) <- df[2,]\n```\n",
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diff --git a/...posts/2022-08-03-rstats-dataframes/2022-08-03-rstats-dataframes/execute-results/html.json b/...posts/2022-08-03-rstats-dataframes/2022-08-03-rstats-dataframes/execute-results/html.json
@@ -0,0 +1,14 @@
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+    "markdown": "---\ntitle: \"Data frames in R\"\ndescription: |\n Quick bits for manipulating data frames in R.\nauthor: \"Siobhon Egan\"\ndate: \"2022-08-02\"\ncategories: [rstudio, rstats]\n---\n\n::: {.cell}\n\n```{.r .cell-code}\nproducers <- data.frame(\n  surname =  c(\"Tarantino\", \"Scorsese\", \"Spielberg\", \"Hitchcock\", \"Polanski\"),\n  nationality = c(\"US\", \"US\", \"US\", \"UK\", \"Poland\"),\n  stringsAsFactors = FALSE\n)\n\nmovies <- data.frame(\n  surname = c(\"Spielberg\",\n              \"Scorsese\",\n              \"Hitchcock\",\n              \"Tarantino\",\n              \"Polanski\"),\n  title = c(\"Super 8\",\n            \"Taxi Driver\",\n            \"Psycho\",\n            \"Reservoir Dogs\",\n            \"Chinatown\"),\n  stringsAsFactors = FALSE\n)\n```\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nidx <- match(producers$surname, movies$surname)\nmovies_matched <- movies[idx, ]\n```\n:::\n\n\nUsing dplyr to rename a column with specific name we can call.\n```r\ndf <- df %>%\n  dplyr::rename(newName = oldName)\n```\n\nAlternative way without using dylyr we cal call the specific column number\n```r\ncolnames(df)[1] <- \"newName\"\n```\n\nSay you have a vector with the names we can use\n```r\ncolnames(df) <- vector\n```\n\nMaybe col names are contained within a row 2 of the data frame\n```r\ncolnames(df) <- df[2,]\n```\n",
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+      "rmarkdown/pagebreak.lua"
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diff --git a/_quarto.yml b/_quarto.yml
@@ -1,5 +1,6 @@
 project:
   type: website
+  output-dir: docs
 website:
   title: "Siobhon Egan"
   site-url: https://www.siobhon-egan.github.io/

diff --git a/about.qmd b/about.qmd
@@ -15,7 +15,7 @@ about:
       href: https://twitter.com/siobhon_egan
     - icon: linkedin
       text: LinkedIn
-      href: https://linkedin.com
+      href: https://www.linkedin.com/in/siobhon-egan/
     - icon: google
       text: GoogleScholar
       href: https://scholar.google.com/citations?user=BrX5o08AAAAJ&hl=en&oi=ao
@@ -33,25 +33,23 @@ from: markdown+emoji
 
 ## Welcome!
 
-I am a research fellow at Murdoch University based at the [Centre for Computational and Systems Medicine](https://www.murdoch.edu.au/research/hfi/our-centres/centre-for-computational-and-systems-medicine) and the [Australian National Phenome Centre](https://www.murdoch.edu.au/research/anpc). I begun working under the direction of [Prof. Elaine Holmes](https://www.researchgate.net/profile/Elaine-Holmes), Centre Director Computational and Systems Medicine, in March 2021. Prof. Holmes was awarded an Australian Laureate Fellowship (FL200100220) titled [*Understanding host-microbiome signalling axes in ageing*](https://www.arc.gov.au/news-publications/media/funding-announcement-kits/australian-laureate-fellowships-2020/2020-laureate-profile-professor-elaine-holmes). The project aims to deepen the understanding of host-microbiome signalling in ageing by: (i) bringing together next generation sequencing technologies to characterise age-associated change in gut bacterial composition, (ii) metabolic profiling to identify changes in functionality of the ageing microbiome, and (iii) a combination of in vitro and in vivo screening approaches to establish molecular mechanisms. The new knowledge will facilitate development of improved models of health care.
+I am an early career researcher at Murdoch University, Western Australia. I am currently employed as a post‐doctoral research fellow within the [Centre for Computational and Systems Medicine](https://www.murdoch.edu.au/research/hfi/our-centres/centre-for-computational-and-systems-medicine). This research is focused on understand‐ ing the interactions at the host‐microbe axis using a range of ‐omic technologies. My recent PhD research was foc‐ sued on ticks (Ixodida) and associated vector‐borne microbes (bacteria and protozoa) in Australian wildlife
 
+I am currently working on a project in conjunction with the [Australian National Phenome Centre](https://www.murdoch.edu.au/research/anpc) titled [*Understanding host-microbiome signalling axes in ageing*](https://www.arc.gov.au/news-publications/media/funding-announcement-kits/australian-laureate-fellowships-2020/2020-laureate-profile-professor-elaine-holmes) under the direction of [Prof. Elaine Holmes](https://www.researchgate.net/profile/Elaine-Holmes). The research aims to deepen the understanding of host-microbiome signalling in ageing by: (i) bringing together next generation sequencing technologies to characterise age-associated change in gut bacterial composition, (ii) metabolic profiling to identify changes in functionality of the ageing microbiome, and (iii) a combination of in vitro and in vivo screening approaches to establish molecular mechanisms. The new knowledge will facilitate development of improved models of health care.
 
 ```{r echo = FALSE, out.width = "100%", fig.align='center'}
 knitr::include_graphics("images/IMG_6695.JPG")
 ```
 
-I recently completed by PhD thesis titled *Tiresome ticks: Ecology and transmission of tick-borne disease in Australia* . This was part of an ARC linkage grant (LP160100200) by the [Vector and Waterborne Pathogens Research Group](http://www.murdoch.edu.au/Research-capabilities/Vector-and-Waterborne-Pathogens-Group/Meet-the-Team/) at Murdoch University. It aimed to identify and characterise the microbial biodiversity in ticks and wildlife reservoir hosts, providing important insights into potential causative agent(s) of zoonotic tick-borne pathogens.        
-
-I completed a Bachelor of Science in Animal Health and Wildlife & Conservation Biology (2014--2016). Durng my undergraduate studies I developed a strong passion for wildlife health which evolved into my fascination with the interconnection of the health of the environment, animals and people. I spent time volunteering on a number of projects, and was heavily involved as a volunteer field and lab assistant into the woylie decline as part of [Dr. Amy Northover's](https://www.researchgate.net/profile/Amy_Northover) PhD. My interests expand to other areas of wildlife conservation, including the completion of an independent project on camera trapping of small mammals in Dryandra woodlands under the supervision of [A/Prof Peter Spencer](http://profiles.murdoch.edu.au/myprofile/peter-spencer/) (Murdoch University) and [Mark Cowan](https://www.researchgate.net/profile/Mark_Cowan5) (Parks and Wildlife, Western Australia).
-
-My undertook my honours in Molecular Biology and completed with first class in 2017. My thesis was titled 'Profiling the bacterial microbiome of ticks that parasitise bandicoots in Australia', under the supervision of [Dr. Charlotte Oksam](http://profiles.murdoch.edu.au/myprofile/charlotte-oskam/) and [Prof. Peter Irwin,](http://profiles.murdoch.edu.au/myprofile/peter-irwin/) and is available for download [here](http://researchrepository.murdoch.edu.au/id/eprint/40003/). During my project I identified a number of recently described and novel candidate tick-borne pathogens in ticks parasitsing bandicoots (Order: Peramelemorphia).
-
-With no time to rest, I undertook a paid summer internship with [Pawsey Supercomputing Centre](https://www.pawsey.org.au/) in November 2017, diving into all things coding and bioinformatics.
+I recently completed by PhD thesis titled *Tiresome ticks: Ecology and transmission of tick-borne disease in Australia* . This was part of an ARC linkage grant (LP160100200) by the [Vector and Waterborne Pathogens Research Group](http://www.murdoch.edu.au/Research-capabilities/Vector-and-Waterborne-Pathogens-Group/Meet-the-Team/) at Murdoch University. It aimed to identify and characterise the microbial biodiversity in ticks and wildlife reservoir hosts, providing important insights into potential causative agent(s) of zoonotic tick-borne pathogens.  
+I started my PhD in 2018, as a continuation of the number of questions that arose from my honours project. Under the supervision of [Dr. Charlotte Oksam](http://profiles.murdoch.edu.au/myprofile/charlotte-oskam/), [Prof. Peter Irwin,](http://profiles.murdoch.edu.au/myprofile/peter-irwin/), [Prof. Una Ryan](http://profiles.murdoch.edu.au/myprofile/una-ryan/) and [Prof. Peter Banks](http://sydney.edu.au/science/people/peter.banks.php) (University of Sydney). My project is titled *Ecology of ticks and microbes in Australia*. I hope to uncover patterns in the life cycle of ticks and their related microbes in Australian wildlife and investigate the overlap with cases of human tick-borne illnesses.      
 
 ::: {style="float:left;"}
 ![](images/am_triguttatum_SEa.png)
 :::
 
-I started my PhD in 2018, as a continuation of the number of questions that arose from my honours project. Under the supervision of Dr. Charlotte Oksam, Prof. Peter Irwin, [Prof. Una Ryan](http://profiles.murdoch.edu.au/myprofile/una-ryan/) and [Prof. Peter Banks](http://sydney.edu.au/science/people/peter.banks.php) (University of Sydney). My project is titled *Ecology of ticks and microbes in Australia*. I hope to uncover patterns in the life cycle of ticks and their related microbes in Australian wildlife and investigate the overlap with cases of human tick-borne illnesses.
+In 2017 I undertook an honours research project in Molecular Biology (first class). My thesis was titled 'Profiling the bacterial microbiome of ticks that parasitise bandicoots in Australia', under the supervision of [Dr. Charlotte Oksam](http://profiles.murdoch.edu.au/myprofile/charlotte-oskam/) and [Prof. Peter Irwin,](http://profiles.murdoch.edu.au/myprofile/peter-irwin/) and is available for download [here](http://researchrepository.murdoch.edu.au/id/eprint/40003/). During my project I identified a number of recently described and novel candidate tick-borne pathogens in ticks parasitsing bandicoots (Order: Peramelemorphia). After finishing my honours research I undertook a paid summer internship with [Pawsey Supercomputing Centre](https://www.pawsey.org.au/) in November 2017, diving into all things coding and bioinformatics.
+
+I completed a Bachelor of Science in Animal Health and Wildlife & Conservation Biology (2014--2016). Durng my undergraduate studies I developed a strong passion for wildlife health which evolved into my fascination with the interconnection of the health of the environment, animals and people. I spent time volunteering on a number of projects, and was heavily involved as a volunteer field and lab assistant into the woylie decline as part of [Dr. Amy Northover's](https://www.researchgate.net/profile/Amy_Northover) PhD. My interests expand to other areas of wildlife conservation, including the completion of an independent project on camera trapping of small mammals in Dryandra woodlands under the supervision of [A/Prof Peter Spencer](http://profiles.murdoch.edu.au/myprofile/peter-spencer/) (Murdoch University) and [Mark Cowan](https://www.researchgate.net/profile/Mark_Cowan5) (Parks and Wildlife, Western Australia).
 
 ![](images/IMG_9093.JPG){width="500"}
diff --git a/contact.qmd b/contact.qmd
@@ -7,14 +7,12 @@ format:
 from: markdown+emoji
 ---
 
-**Contact details**
+:pushpin: Australian National Phenome Centre     
+*Murdoch University*
 
-
-:pushpin: Australian National Phenome Centre. 
-*Murdoch University*.       
-Level 3, Harry Perkins Institute.     
-5 Robin Warren Drive.     
-Murdoch, 6150, Western Australia.
+Harry Perkins Institute of Medical Research     
+Level 3, 5 Robin Warren Drive    
+Murdoch, 6150, Western Australia
 
 
 :envelope: [siobhon.egan\@murdoch.edu.au](mailto:siobhon.egan@murdoch.edu.au){.email}