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Fix blog build (#891)
* add instruction to build blog locally with personal api key * fix quidel #887 by removing r chunk result + warn readers * upgrade python covidcast version + add api key to python chunk in blog * more api key visibility + instruction link * every R chunk that import library(covidcast) will have an associated API key + instruction link code line in that chunk * fix visuals not showing up due to warning messages * workaround render python chunk plot * generated files from rmd with changes * remove warning in blog 2021-01-15-causal-effect-mobility * remove warning 2020-12-10-masks-public --------- Co-authored-by: melange396 <[email protected]>
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‎README.md

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@@ -83,6 +83,7 @@ As an alternative you can use Docker and Docker Compose:
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1. `docker-compose up -d` to create a docker container for the current environment.
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1. `docker-compose exec r bash` to jump into the container.
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1. `micromamba activate www-main` to activate the environment
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2. `export API_KEY=y0urAp1kEy` to add your own api key as env variable.
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Now you have the environment ready to start converting .Rmd blog files to html.
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#### Commands

‎content/blog/2020-08-26-fb-survey.Rmd

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toc: true
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---
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```{r, echo=FALSE}
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options(covidcast.auth = Sys.getenv("API_KEY"))
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```
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Since April 2020, in collaboration with Facebook,
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partner universities, and public health officials,
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library(dplyr)
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library(gridExtra)
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options(covidcast.auth = Sys.getenv("API_KEY")) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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# Fetch Facebook % CLI signal and JHU confirmed case incidence proportion at
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# the state level
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start_day = "2020-06-15"

‎content/blog/2020-08-26-fb-survey.html

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toc: true
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---
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#short-background">Short Background</a></li>
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<li><a href="#why-run-these-surveys">Why Run These Surveys?</a></li>
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<li><a href="#whats-in-the-survey">What’s in the Survey?</a></li>
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<li><a href="#some-interesting-examples">Some Interesting Examples</a></li>
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<li><a href="#basic-correlation-analysis">Basic Correlation Analysis</a>
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<li><a href="#short-background" id="toc-short-background">Short Background</a></li>
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<li><a href="#why-run-these-surveys" id="toc-why-run-these-surveys">Why Run These Surveys?</a></li>
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<li><a href="#whats-in-the-survey" id="toc-whats-in-the-survey">What’s in the Survey?</a></li>
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<li><a href="#some-interesting-examples" id="toc-some-interesting-examples">Some Interesting Examples</a></li>
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<li><a href="#basic-correlation-analysis" id="toc-basic-correlation-analysis">Basic Correlation Analysis</a>
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<ul>
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<li><a href="#correlations-sliced-by-time">Correlations Sliced by Time</a></li>
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<li><a href="#correlations-sliced-by-county">Correlations Sliced by County</a></li>
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<li><a href="#correlations-sliced-by-time" id="toc-correlations-sliced-by-time">Correlations Sliced by Time</a></li>
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<li><a href="#correlations-sliced-by-county" id="toc-correlations-sliced-by-county">Correlations Sliced by County</a></li>
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</ul></li>
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<li><a href="#whats-next-with-the-surveys">What’s Next with the Surveys</a></li>
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<li><a href="#whats-next-with-the-surveys" id="toc-whats-next-with-the-surveys">What’s Next with the Surveys</a></li>
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</ul>
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</div>
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library(dplyr)
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library(gridExtra)
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options(covidcast.auth = Sys.getenv(&quot;API_KEY&quot;)) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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# Fetch Facebook % CLI signal and JHU confirmed case incidence proportion at
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# the state level
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start_day = &quot;2020-06-15&quot;

‎content/blog/2020-08-28-api.Rmd

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This is important because estimates
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can change for _weeks_ as new data arrives:
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```{r q-versioning, warning=FALSE, message=FALSE, cache=TRUE}
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```{r q-versioning, warning=FALSE, message=FALSE, cache=TRUE, eval=FALSE}
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library(covidcast)
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library(dplyr)
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options(covidcast.auth = Sys.getenv("API_KEY")) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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query_date <- "2020-08-01"
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covidcast_signal(
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data_source = "quidel",
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col.names = c("Test date", "Positivity rate (%)", "Sample size",
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"Issued on", "Lag (days)"))
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```
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*November 2023 update: Quidel data is no longer publicly available, so the table generated by the code chunk above has been removed.*
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Many data sources are subject to revisions:
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```{r dv-graph, message=FALSE, cache=TRUE}
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library(covidcast)
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options(covidcast.auth = Sys.getenv("API_KEY")) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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hosp <- covidcast_signal(
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data_source = "hospital-admissions", signal = "smoothed_adj_covid19_from_claims",
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start_day = "2020-03-01", end_day = "2020-08-30",
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(Click the "Code" button to see the Python code used to produce this example.)
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```{python python-data, dev='svg'}
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import matplotlib.pyplot as plt
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import covidcast
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from datetime import date
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import matplotlib.pyplot as plt
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import os
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covidcast.use_api_key(os.environ['API_KEY']) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
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date(2020, 9, 8), date(2020, 9, 8),
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geo_type="state")
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covidcast.plot_choropleth(data, figsize=(7, 5))
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covidcast.plot(data, plot_type="choropleth", figsize=(7, 5))
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plt.title("% who know someone who is sick, Sept 8, 2020")
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```
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‎content/blog/2020-08-28-api.html

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toc: true
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---
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#purpose-of-the-api">Purpose of the API</a></li>
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<li><a href="#unique-data-sources">Unique Data Sources</a></li>
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<li><a href="#tracking-observations-and-revisions">Tracking Observations and Revisions</a></li>
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<li><a href="#accessing-the-api">Accessing the API</a></li>
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<li><a href="#putting-the-api-to-work">Putting the API to Work</a></li>
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<li><a href="#purpose-of-the-api" id="toc-purpose-of-the-api">Purpose of the API</a></li>
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<li><a href="#unique-data-sources" id="toc-unique-data-sources">Unique Data Sources</a></li>
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<li><a href="#tracking-observations-and-revisions" id="toc-tracking-observations-and-revisions">Tracking Observations and Revisions</a></li>
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<li><a href="#accessing-the-api" id="toc-accessing-the-api">Accessing the API</a></li>
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<li><a href="#putting-the-api-to-work" id="toc-putting-the-api-to-work">Putting the API to Work</a></li>
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</ul>
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</div>
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can change for <em>weeks</em> as new data arrives:</p>
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<pre class="r"><code>library(covidcast)
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library(dplyr)
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options(covidcast.auth = Sys.getenv(&quot;API_KEY&quot;)) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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query_date &lt;- &quot;2020-08-01&quot;
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covidcast_signal(
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data_source = &quot;quidel&quot;,
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knitr::kable(&quot;html&quot;, digits = 2,
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col.names = c(&quot;Test date&quot;, &quot;Positivity rate (%)&quot;, &quot;Sample size&quot;,
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&quot;Issued on&quot;, &quot;Lag (days)&quot;))</code></pre>
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<table>
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<thead>
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<th style="text-align:left;">
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Test date
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Positivity rate (%)
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Sample size
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<p><em>November 2023 update: Quidel data is no longer publicly available, so the table generated by the code chunk above has been removed.</em></p>
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<p>Many data sources are subject to revisions:</p>
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<ul>
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<li>Case and death counts are frequently corrected or adjusted by authorities.</li>
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that are due to COVID-19 in several states.
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(Click the “Code” button to see the R code used to produce this example.)</p>
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<pre class="r"><code>library(covidcast)
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options(covidcast.auth = Sys.getenv(&quot;API_KEY&quot;)) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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hosp &lt;- covidcast_signal(
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data_source = &quot;hospital-admissions&quot;, signal = &quot;smoothed_adj_covid19_from_claims&quot;,
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start_day = &quot;2020-03-01&quot;, end_day = &quot;2020-08-30&quot;,
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According to the {{< apireflink "api/covidcast-signals/fb-survey.html" "relevant documentation page" >}},
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this is the <code>fb-survey</code> data source’s <code>smoothed_hh_cmnty_cli</code> signal.
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(Click the “Code” button to see the Python code used to produce this example.)</p>
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<pre class="python"><code>import covidcast
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<pre class="python"><code>import matplotlib.pyplot as plt
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import covidcast
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from datetime import date
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import matplotlib.pyplot as plt
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import os
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covidcast.use_api_key(os.environ[&#39;API_KEY&#39;]) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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data = covidcast.signal(&quot;fb-survey&quot;, &quot;smoothed_hh_cmnty_cli&quot;,
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date(2020, 9, 8), date(2020, 9, 8),
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geo_type=&quot;state&quot;)
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covidcast.plot_choropleth(data, figsize=(7, 5))
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covidcast.plot(data, plot_type=&quot;choropleth&quot;, figsize=(7, 5))
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plt.title(&quot;% who know someone who is sick, Sept 8, 2020&quot;)</code></pre>
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<p><img src="/blog/2020-08-28-api_files/figure-html/python-data-1.svg" /><!-- --></p>
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<p>Each package’s documentation gives numerous other examples of pulling, plotting,

‎content/blog/2020-09-18-google-survey.Rmd

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library(ggplot2)
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library(gridExtra)
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options(covidcast.auth = Sys.getenv("API_KEY")) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html
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# Fetch county-level Google and Facebook % CLI-in-community signals, and JHU
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# confirmed case incidence proportion
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df_go = covidcast_signal("google-survey", "smoothed_cli", geo_type = "state")

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