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fixed dependence of slides to online api; added vim swap files to git…
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@trevorcampbell
trevorcampbell committed Sep 9, 2024
1 parent 1abd192 commit eee565f
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -7,3 +7,6 @@ _site/
*_cache/

/.luarc.json

*.swp
*.swo
19 changes: 15 additions & 4 deletions schedule/slides/00-r-review.qmd
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Expand Up @@ -22,8 +22,6 @@ Things to note
1. Getting help
1. Environment, Git



## Simple stuff

:::: {.columns}
Expand Down Expand Up @@ -725,16 +723,29 @@ To be sure, prefix it like `dplyr::select()`.

## A useful data frame

<!--
Old code that breaks if you don't have an API key; replaced
this with just a covid.csv file in the data/ folder
Keeping this block here though so that later instructors can see
where the data came from
```{r}
library(epidatr)
covid <- covidcast(
covid <- pub_covidcast(
source = "jhu-csse",
signals = "confirmed_7dav_incidence_prop,deaths_7dav_incidence_prop",
time_type = "day",
geo_type = "state",
time_values = epirange(20220801, 20220821),
geo_values = "ca,wa") |>
fetch() |>
select(geo_value, time_value, signal, value)
covid
```
-->

```{r message=FALSE}
library(tidyverse)
covid <- read_csv("data/covid.csv") |>
select(geo_value, time_value, signal, value)
covid
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85 changes: 85 additions & 0 deletions schedule/slides/data/covid.csv
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@@ -0,0 +1,85 @@
geo_value,signal,source,geo_type,time_type,time_value,direction,issue,lag,missing_value,missing_stderr,missing_sample_size,value,stderr,sample_size
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-01,NA,2023-03-10,221,0,5,5,45.4113392,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-01,NA,2022-08-02,1,0,5,5,27.6537396,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-02,NA,2023-03-10,220,0,5,5,44.9011361,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-02,NA,2022-08-03,1,0,5,5,27.6537396,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-03,NA,2023-03-10,219,0,5,5,44.548421,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-03,NA,2022-08-04,1,0,5,5,26.6324842,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-04,NA,2023-03-10,218,0,5,5,42.2858918,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-04,NA,2022-08-05,1,0,5,5,26.6324842,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-05,NA,2023-03-10,217,0,5,5,40.6700068,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-05,NA,2022-08-06,1,0,5,5,34.6205583,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-06,NA,2023-03-10,216,0,5,5,40.6406139,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-06,NA,2022-08-07,1,0,5,5,34.6205583,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-07,NA,2023-03-10,215,0,5,5,40.5985203,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-07,NA,2022-08-08,1,0,5,5,34.6205583,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-08,NA,2023-03-10,214,0,5,5,37.5057317,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-08,NA,2022-08-09,1,0,5,5,14.2158753,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-09,NA,2023-03-10,213,0,5,5,32.8950345,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-09,NA,2022-08-10,1,0,5,5,14.2158753,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-10,NA,2023-03-10,212,0,5,5,34.897382,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-10,NA,2022-08-11,1,0,5,5,23.2252048,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-11,NA,2023-03-10,211,0,5,5,33.2121878,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-11,NA,2022-08-12,1,0,5,5,23.2252048,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-12,NA,2023-03-10,210,0,5,5,32.709968,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-12,NA,2022-08-13,1,0,5,5,22.2485133,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-13,NA,2023-03-10,209,0,5,5,32.6675116,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-13,NA,2022-08-14,1,0,5,5,22.2485133,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-14,NA,2023-03-10,208,0,5,5,32.6551738,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-14,NA,2022-08-15,1,0,5,5,22.2485133,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-15,NA,2023-03-10,207,0,5,5,31.070859,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-15,NA,2022-08-16,1,0,5,5,29.7556689,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-16,NA,2023-03-10,206,0,5,5,33.707513,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-16,NA,2022-08-17,1,0,5,5,29.7556689,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-17,NA,2023-03-10,205,0,5,5,30.9500214,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-17,NA,2022-08-18,1,0,5,5,19.4279915,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-18,NA,2023-03-10,204,0,5,5,29.9956586,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-18,NA,2022-08-19,1,0,5,5,19.4279915,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-19,NA,2023-03-10,203,0,5,5,28.0898361,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-19,NA,2022-08-20,1,0,5,5,18.7038286,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-20,NA,2023-03-10,202,0,5,5,28.0941906,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-20,NA,2022-08-21,1,0,5,5,18.7038286,NA,NA
ca,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-21,NA,2023-03-10,201,0,5,5,28.0836672,NA,NA
wa,confirmed_7dav_incidence_prop,jhu-csse,state,day,2022-08-21,NA,2022-08-22,1,0,5,5,18.7038286,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-01,NA,2023-03-09,220,0,5,5,0.1045082,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-01,NA,2022-08-02,1,0,5,5,0.1689713,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-02,NA,2023-03-09,219,0,5,5,0.1055968,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-02,NA,2022-08-03,1,0,5,5,0.1689713,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-03,NA,2023-03-09,218,0,5,5,0.1066854,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-03,NA,2022-08-04,1,0,5,5,0.172685,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-04,NA,2023-03-09,217,0,5,5,0.1124914,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-04,NA,2022-08-05,1,0,5,5,0.172685,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-05,NA,2023-03-09,216,0,5,5,0.1157573,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-05,NA,2022-08-06,1,0,5,5,0.2246762,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-06,NA,2023-03-09,215,0,5,5,0.1161202,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-06,NA,2022-08-07,1,0,5,5,0.2246762,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-07,NA,2023-03-09,214,0,5,5,0.1161202,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-07,NA,2022-08-08,1,0,5,5,0.2246762,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-08,NA,2023-03-09,213,0,5,5,0.1128543,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-08,NA,2022-08-09,1,0,5,5,0.1355484,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-09,NA,2023-03-09,212,0,5,5,0.1121286,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-09,NA,2022-08-10,1,0,5,5,0.1355484,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-10,NA,2022-08-11,1,0,5,5,0.1099513,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-10,NA,2022-08-11,1,0,5,5,0.1448326,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-11,NA,2022-08-12,1,0,5,5,0.1063225,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-11,NA,2022-08-12,1,0,5,5,0.1448326,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-12,NA,2022-08-13,1,0,5,5,0.1099513,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-12,NA,2022-08-13,1,0,5,5,0.183826,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-13,NA,2023-03-09,208,0,5,5,0.1095884,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-13,NA,2022-08-14,1,0,5,5,0.183826,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-14,NA,2023-03-09,207,0,5,5,0.1095884,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-14,NA,2022-08-15,1,0,5,5,0.183826,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-15,NA,2023-03-09,206,0,5,5,0.1088627,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-15,NA,2022-08-16,1,0,5,5,0.2191057,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-16,NA,2023-03-09,205,0,5,5,0.1143058,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-16,NA,2022-08-17,1,0,5,5,0.2191057,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-17,NA,2023-03-09,204,0,5,5,0.1150316,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-17,NA,2022-08-18,1,0,5,5,0.2061079,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-18,NA,2022-08-19,1,0,5,5,0.1150316,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-18,NA,2022-08-19,1,0,5,5,0.2061079,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-19,NA,2022-08-20,1,0,5,5,0.1164831,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-19,NA,2022-08-20,1,0,5,5,0.1782555,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-20,NA,2023-03-09,201,0,5,5,0.1168459,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-20,NA,2022-08-21,1,0,5,5,0.1782555,NA,NA
ca,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-21,NA,2023-03-09,200,0,5,5,0.1168459,NA,NA
wa,deaths_7dav_incidence_prop,jhu-csse,state,day,2022-08-21,NA,2022-08-22,1,0,5,5,0.1782555,NA,NA

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