2211 darkmode

_extensions/gadenbuie/auto-dark/LICENSE

@@ -0,0 +1,37 @@
+# MODIFIED SOURCE -----------------------------------------------------------
+
+Copyright (C) 2024  Garrick Aden-Buie
+AGPL v3: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as
+published by the Free Software Foundation, either version 3 of the
+License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+
+# ORIGINAL SOURCE -----------------------------------------------------------
+# https://ar.al/2021/08/24/implementing-dark-mode-in-a-handful-of-lines-of-css-with-css-filters/
+
+Copyright (C) 2021  Aral Balkan
+AGPL v3: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as
+published by the Free Software Foundation, either version 3 of the
+License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.

_extensions/gadenbuie/auto-dark/_extension.yml

@@ -0,0 +1,8 @@
+title: Auto Dark Mode
+author: Garrick Aden-Buie
+version: 1.0.0
+quarto-required: ">=1.4.0"
+contributes:
+  filters:
+    - auto-dark.lua
+

_extensions/gadenbuie/auto-dark/auto-dark-mode.css

@@ -0,0 +1,52 @@
+/* Auto Dark Mode for Quarto
+ *
+ * https://github.com/gadenbuie/quarto-auto-dark
+ *
+ * License: Affero GPL v3, https://www.gnu.org/licenses/agpl-3.0.en.html
+ * Original: Aral Balkan
+ *           https://ar.al/2021/08/24/implementing-dark-mode-in-a-handful-of-lines-of-css-with-css-filters/
+ *
+ * Modified: Garrick Aden-Buie
+ *
+ */
+@media (prefers-color-scheme: dark) {
+  /* Invert all elements on the body while attempting to not alter the hue substantially. */
+  body {
+    filter: invert(100%) hue-rotate(180deg);
+  }
+
+  /* Workarounds and optical adjustments. */
+
+  /*
+     Firefox workaround: Set the background colour for the html
+     element separately because, unlike other browsers, Firefox
+     doesn't apply the filter to the root element's background.
+  */
+  html {
+    background-color: #111;
+  }
+
+  /* Do not invert media (revert the invert). */
+  img, video, iframe, svg:not(.bi, .fa) {
+    filter: invert(100%) hue-rotate(180deg);
+  }
+
+  /*
+    Videos running fullscreen are no longer affected by the
+    filter on the body so we need to also unset the
+    revert we applied earlier so we're left with no filter again.
+   */
+  video:fullscreen {
+    filter: none;
+  }
+
+  /* Re-enable code block backgrounds. */
+  pre {
+    filter: invert(10%);
+  }
+
+  /* Re-enable source code block backgrounds. */
+  div.sourceCode {
+    filter: invert(10%);
+  }
+}

_extensions/gadenbuie/auto-dark/auto-dark.lua

@@ -0,0 +1,9 @@
+function Pandoc()
+  if quarto.doc.is_format("html:js") then
+    quarto.doc.add_html_dependency({
+      name = "quarto-auto-dark-mode",
+      version = "1.0.0",
+      stylesheets = {"auto-dark-mode.css"}
+    })
+  end
+end

_freeze/materials/04-plotting/execute-results/html.json

@@ -1,8 +1,8 @@
 {
-  "hash": "d4a131e91826a1b7c0f7e8f521c61159",
+  "hash": "745894eb74ce2359bb9cfa4c3181e1cb",
   "result": {
     "engine": "knitr",
-    "markdown": "---\ntitle: Plotting data\n---\n\n\n\n\n::: {.callout-tip}\n#### Learning objectives\n\n- \n:::\n\n## Context\nWe now have a good grasp of how data is commonly structured, with variables in columns and observations in rows. This is the perfect format for visualising data.\n\n## Introducing plotting\n\nTo create a plot we'll need three things:\n\n1. data\n2. mapping aesthetics\n3. specify the type of plot\n\n::: {.panel-tabset group=\"language\"}\n## R\n\n\n\n\n::: {.cell}\n\n```{.r .cell-code  code-line-numbers=\"2\"}\nlibrary(tidyverse)\n```\n\n::: {.cell-output .cell-output-stderr}\n\n```\n── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──\n✔ dplyr     1.1.4     ✔ readr     2.1.5\n✔ forcats   1.0.0     ✔ stringr   1.5.1\n✔ ggplot2   3.5.1     ✔ tibble    3.2.1\n✔ lubridate 1.9.3     ✔ tidyr     1.3.1\n✔ purrr     1.0.2     \n── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──\n✖ dplyr::filter() masks stats::filter()\n✖ dplyr::lag()    masks stats::lag()\nℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors\n```\n\n\n:::\n\n```{.r .cell-code  code-line-numbers=\"2\"}\nsurveys <- read_csv(\"data/surveys.csv\")\n```\n\n::: {.cell-output .cell-output-stderr}\n\n```\nRows: 34786 Columns: 13\n── Column specification ────────────────────────────────────────────────────────\nDelimiter: \",\"\nchr (6): species_id, sex, genus, species, taxa, plot_type\ndbl (7): record_id, month, day, year, plot_id, hindfoot_length, weight\n\nℹ Use `spec()` to retrieve the full column specification for this data.\nℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.\n```\n\n\n:::\n\n```{.r .cell-code  code-line-numbers=\"2\"}\nggplot(data = surveys,\n       mapping = aes(x = weight, y = hindfoot_length)) +\n  geom_point()\n```\n\n::: {.cell-output .cell-output-stderr}\n\n```\nWarning: Removed 4048 rows containing missing values or values outside the scale range\n(`geom_point()`).\n```\n\n\n:::\n\n::: {.cell-output-display}\n![](04-plotting_files/figure-html/unnamed-chunk-1-1.png){width=672}\n:::\n:::\n\n\n\n\n## Python\n\n:::\n\n### Start plotting\n* LO: plotting with ggplot2\n\n### Building up plots\n* LO: layering plots\n\n### Changing plots\n* LO: changing aesthetics (colour, fill, transparency, size)\n\n\n\n## Summary\n\n::: {.callout-tip}\n#### Key points\n\n- \n:::\n",
+    "markdown": "---\ntitle: Plotting data\n---\n\n\n\n\n::: {.callout-tip}\n#### Learning objectives\n\n- \n:::\n\n## Context\nWe now have a good grasp of how data is commonly structured, with variables in columns and observations in rows. This is the perfect format for visualising data.\n\n## Introducing plotting\n\nTo create a plot we'll need three things:\n\n1. data\n2. mapping aesthetics\n3. specify the type of plot\n\n::: {.panel-tabset group=\"language\"}\n## R\n\n\n## Python\n\n:::\n\n### Start plotting\n* LO: plotting with ggplot2\n\n### Building up plots\n* LO: layering plots\n\n\n\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(tidyverse)\n\nsurveys <- read_csv(\"data/surveys.csv\")\n```\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nggplot(data = surveys,\n       mapping = aes(x = weight, y = hindfoot_length)) +\n  geom_point()\n```\n\n::: {.cell-output-display}\n![](04-plotting_files/figure-html/unnamed-chunk-2-1.png){width=672}\n:::\n:::\n\n\n\n\n### Changing plots\n* LO: changing aesthetics (colour, fill, transparency, size)\n\n\n\n## Summary\n\n::: {.callout-tip}\n#### Key points\n\n- \n:::\n",
     "supporting": [
       "04-plotting_files"
     ],

_quarto.yml

@@ -13,14 +13,17 @@ project:
     - materials/*
     - "!materials/*/no_render"
 
-format: courseformat-html
+format:
+  courseformat-html:
+    theme: flatly
 
 exercises:
   number: true
   hide-answers: false
 
 filters:
   - courseformat
+  - auto-dark
 
 execute:
   freeze: auto

materials/04-plotting.qmd

@@ -33,6 +33,22 @@ To create a plot we'll need three things:
 ### Building up plots
 * LO: layering plots
 
+```{r}
+#| message: false
+
+library(tidyverse)
+
+surveys <- read_csv("data/surveys.csv")
+```
+
+
+```{r}
+#| warning: false
+ggplot(data = surveys,
+       mapping = aes(x = weight, y = hindfoot_length)) +
+  geom_point()
+```
+
 ### Changing plots
 * LO: changing aesthetics (colour, fill, transparency, size)
 

materials/data/patients.csv

@@ -0,0 +1,119 @@
+patient_id,systolic_pressure,heart_rate,weight_kg,age,diabetic
+N8805,113,NA,132.84,46,yes
+N6558,85,NA,137.6,61,yes
+N5556,89,48,131.66,31,yes
+N2297,67,31,129.78,37,yes
+N7318,154,118,84.78,61,yes
+N6378,78,34,78.41,52,yes
+N3615,102,75,131.97,40,yes
+N9260,95,50,83.7,42,yes
+N6710,159,124,127.76,37,yes
+N0327,124,97,82.48,39,yes
+N2729,113,82,128.07,44,yes
+N3727,NA,77,119.39,42,yes
+N4053,NA,102,126.92,57,yes
+N9763,100,66,122.34,37,yes
+N9370,86,56,88.51,52,yes
+N3105,100,71,80.02,40,yes
+N9493,147,118,122.74,34,yes
+N9740,124,86,83.47,33,yes
+N8578,118,87,106.43,36,yes
+N2269,104,77,87.71,51,yes
+N6540,104,67,124.81,34,yes
+N8825,42,3,96.7,63,yes
+N7768,82,47,118.4,44,yes
+N7594,94,60,111.8,32,yes
+N3321,103,80,106.74,44,yes
+N3908,107,67,124.19,48,yes
+N9885,97,69,81.97,58,yes
+N5679,84,52,94.88,44,yes
+N0492,136,98,96.19,57,yes
+N9240,113,85,127.16,48,yes
+N5541,107,93,126.02,43,yes
+N9229,117,77,82.82,52,yes
+N0768,93,66,124.57,41,yes
+N2449,109,72,130.75,48,yes
+N4585,NA,50,100.19,48,yes
+N1874,NA,51,101.88,54,yes
+N3514,117,86,105.35,57,yes
+N1652,107,75,NA,39,yes
+N0905,110,77,111,32,yes
+N9827,93,52,111.67,33,yes
+N0834,118,85,136.79,35,yes
+N9997,85,51,79.67,50,yes
+N9535,115,79,114.03,45,yes
+N2257,86,NA,110.88,44,yes
+N5462,135,103,96.03,42,yes
+N5239,111,68,115.97,50,yes
+N2877,79,45,117.45,39,yes
+N5530,79,45,78.17,30,yes
+N4203,110,78,108.83,48,yes
+N4969,109,55,95.98,58,yes
+N1967,127,107,113.35,38,yes
+N8417,NA,NA,79.52,32,yes
+N6410,88,48,92.52,34,yes
+N2877,97,66,NA,27,yes
+N9238,84,49,116.07,43,yes
+N7212,121,90,104.29,43,yes
+N9349,118,89,NA,59,yes
+N0467,85,57,115.35,23,yes
+N0621,104,69,116.82,33,yes
+N0205,76,59,107.79,48,no
+N6888,93,80,72.39,61,no
+N4083,90,61,96.14,54,no
+N9464,85,59,75.38,43,no
+N7081,119,80,68.97,36,no
+N3923,94,71,86.64,41,no
+N7134,103,65,62.9,55,no
+N8136,127,90,54.11,43,no
+N5784,85,55,115.02,58,no
+N5147,91,74,55.34,46,no
+N8283,70,54,57.05,42,no
+N9819,114,67,83.35,45,no
+N2010,87,64,96.96,46,no
+N2947,92,65,68.18,41,no
+N3321,68,NA,91.82,40,no
+N3918,99,NA,NA,55,no
+N0936,79,51,71.75,36,no
+N2960,69,53,106.67,41,no
+N5935,96,77,110.95,47,no
+N0142,87,72,100.01,38,no
+N3181,94,79,79.38,53,no
+N5442,92,58,75.09,43,no
+N0926,101,60,98.7,41,no
+N9785,102,81,66.85,37,no
+N8086,99,70,97.93,46,no
+N8125,134,79,52.75,31,no
+N1462,69,59,102.41,53,no
+N9748,88,46,101.17,52,no
+N3518,91,49,NA,45,no
+N2987,55,51,59.45,51,no
+N1296,117,74,65.16,42,no
+N3078,76,53,61.49,69,no
+N4111,65,58,76.66,50,no
+N9348,85,53,76.78,32,no
+N8166,102,68,115.75,51,no
+N4498,85,51,75.77,54,no
+N6176,100,51,53.03,41,no
+N9995,59,48,111.25,55,no
+N0445,102,69,NA,51,no
+N1699,126,76,58.78,37,no
+N8807,82,64,100.09,30,no
+N5871,79,54,86.5,45,no
+N8369,128,76,63.83,38,no
+N0487,94,57,53.92,40,no
+N7382,97,72,NA,33,no
+N9838,80,68,78.05,39,no
+N2303,91,55,92.81,44,no
+N7620,79,NA,64.88,47,no
+N6609,82,62,98.83,44,no
+N1186,50,46,113.33,33,no
+N9751,115,92,75.42,52,no
+N2265,NA,77,92.5,56,no
+N8156,79,47,89.68,34,no
+N7870,50,45,115.07,46,no
+N6467,NA,82,52.57,44,no
+N4159,110,84,75.99,53,no
+N4453,96,74,105.11,33,no
+N4513,71,65,59.39,50,no
+N7071,92,72,58.77,60,no

materials/data/plots.csv

@@ -0,0 +1,25 @@
+plot_id,plot_type
+1,Spectab exclosure
+2,Control
+3,Long-term Krat Exclosure
+4,Control
+5,Rodent Exclosure
+6,Short-term Krat Exclosure
+7,Rodent Exclosure
+8,Control
+9,Spectab exclosure
+10,Rodent Exclosure
+11,Control
+12,Control
+13,Short-term Krat Exclosure
+14,Control
+15,Long-term Krat Exclosure
+16,Rodent Exclosure
+17,Control
+18,Short-term Krat Exclosure
+19,Long-term Krat Exclosure
+20,Short-term Krat Exclosure
+21,Long-term Krat Exclosure
+22,Control
+23,Rodent Exclosure
+24,Rodent Exclosure

materials/data/species.csv

@@ -0,0 +1,55 @@
+species_id,genus,species,taxa
+AB,Amphispiza,bilineata,Bird
+AH,Ammospermophilus,harrisi,Rodent
+AS,Ammodramus,savannarum,Bird
+BA,Baiomys,taylori,Rodent
+CB,Campylorhynchus,brunneicapillus,Bird
+CM,Calamospiza,melanocorys,Bird
+CQ,Callipepla,squamata,Bird
+CS,Crotalus,scutalatus,Reptile
+CT,Cnemidophorus,tigris,Reptile
+CU,Cnemidophorus,uniparens,Reptile
+CV,Crotalus,viridis,Reptile
+DM,Dipodomys,merriami,Rodent
+DO,Dipodomys,ordii,Rodent
+DS,Dipodomys,spectabilis,Rodent
+DX,Dipodomys,sp.,Rodent
+EO,Eumeces,obsoletus,Reptile
+GS,Gambelia,silus,Reptile
+NL,Neotoma,albigula,Rodent
+NX,Neotoma,sp.,Rodent
+OL,Onychomys,leucogaster,Rodent
+OT,Onychomys,torridus,Rodent
+OX,Onychomys,sp.,Rodent
+PB,Chaetodipus,baileyi,Rodent
+PC,Pipilo,chlorurus,Bird
+PE,Peromyscus,eremicus,Rodent
+PF,Perognathus,flavus,Rodent
+PG,Pooecetes,gramineus,Bird
+PH,Perognathus,hispidus,Rodent
+PI,Chaetodipus,intermedius,Rodent
+PL,Peromyscus,leucopus,Rodent
+PM,Peromyscus,maniculatus,Rodent
+PP,Chaetodipus,penicillatus,Rodent
+PU,Pipilo,fuscus,Bird
+PX,Chaetodipus,sp.,Rodent
+RF,Reithrodontomys,fulvescens,Rodent
+RM,Reithrodontomys,megalotis,Rodent
+RO,Reithrodontomys,montanus,Rodent
+RX,Reithrodontomys,sp.,Rodent
+SA,Sylvilagus,audubonii,Rabbit
+SB,Spizella,breweri,Bird
+SC,Sceloporus,clarki,Reptile
+SF,Sigmodon,fulviventer,Rodent
+SH,Sigmodon,hispidus,Rodent
+SO,Sigmodon,ochrognathus,Rodent
+SS,Spermophilus,spilosoma,Rodent
+ST,Spermophilus,tereticaudus,Rodent
+SU,Sceloporus,undulatus,Reptile
+SX,Sigmodon,sp.,Rodent
+UL,Lizard,sp.,Reptile
+UP,Pipilo,sp.,Bird
+UR,Rodent,sp.,Rodent
+US,Sparrow,sp.,Bird
+ZL,Zonotrichia,leucophrys,Bird
+ZM,Zenaida,macroura,Bird