Merge pull request #766 from cmu-delphi/release/v3.1.1

Release v3.1.1

Author: krivard

README.md

@@ -79,11 +79,15 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
 1. Activate the environment: `conda activate www-main`
 1. Install extra R dependencies: `Rscript ./dependencies.R`
 
-As an alternative you can use Docker and Docker Compose. Then it reduces to `docker-compose up -d` to create a docker container for the current environment. In the following you would need to jump into the container to execute the upcoming command via `docker-compose exec r bash`.
+As an alternative you can use Docker and Docker Compose:
+1. `docker-compose up -d` to create a docker container for the current environment.
+1. `docker-compose exec r bash` to jump into the container. 
+1. `micromamba activate www-main` to activate the environment
 
+Now you have the environment ready to start converting .Rmd blog files to html.
 #### Commands
 
-1. Activate the environment: `conda activate www-main`
+
 1. Run blogdown to convert the files to HTML: `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd=TRUE)'`
    - `local=TRUE` similar to `-D` to process draft files
    - `run_hugo=FALSE` to manually run hugo

content/covid19/ctis.md

@@ -57,51 +57,7 @@ Our primary description of the survey and its results over the first year of ope
   vaccination](https://doi.org/10.1073/pnas.2111454118). *Proceedings of the
   National Academy of Sciences* 118 (51) e2111454118.
 
-Other research publications using the survey data include:
-
-- Rader, B., Astley, C.M., Sewalk, K. et al (2022). [Spatial modeling of vaccine deserts as barriers to controlling SARS-CoV-2](https://doi.org/10.1038/s43856-022-00183-8). Communications Medicine 2, 141.
-- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K. Grabowski & E. A. Stuart (2022). [Consistency between Household and County Measures of Onsite Schooling during the COVID-19 Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research on Educational Effectiveness*.
-- Nguyen, Q.C., Yardi, I., Gutierrez, F.X.M. et al. (2022). [Leveraging 13 million responses to the U.S. COVID-19 Trends and Impact Survey to examine vaccine hesitancy, vaccination, and mask wearing, January 2021-February 2022](https://doi.org/10.1186/s12889-022-14286-3). *BMC Public Health* 22, 1911. 
-- J. G. Lu (2022). [Two large-scale global studies on COVID-19 vaccine hesitancy over time: Culture, uncertainty avoidance, and vaccine side-effect concerns](https://doi.org/10.1037/pspa0000320). *Journal of Personality and Social Psychology*.
-- J. M. Cox-Ganser, P. K. Henneberger, D. N. Weissman, G. Guthrie, and C. P. Groth (2022). [COVID-19 test positivity by occupation using the Delphi US COVID-19 Trends and Impact Survey, September–November 2020](https://doi.org/10.1002/ajim.23410). *American Journal of Industrial Medicine* 65 (9), 721-730.
-- M. Jahja, A. Chin, and R.J. Tibshirani (2022). [Real-Time Estimation of COVID-19 Infections: Deconvolution and Sensor Fusion](https://doi.org/10.1214/22-STS856). *Statistical Science* 37 (2), 207-228.
-- Henneberger, PK, Cox-Ganser, JM, Guthrie, GM, Groth, CP (2022). [Estimates of COVID-19 vaccine uptake in major occupational groups and detailed occupational categories in the United States, April–May 2021](https://doi.org/10.1002/ajim.23370). *American Journal of Industrial Medicine* 65 (7), 525-536.
-- K. E. Wiens, C. P. Smith, E. Badillo-Goicoechea, K. H. Grantz, M. K. Grabowski, A. S. Azman, E. A. Stuart, and J. Lessler (2022). [In-person schooling and associated COVID-19 risk in the United States over spring semester 2021](https://doi.org/10.1126/sciadv.abm9128). *Science Advances* 8, eabm9128.
-- F. Petersen, A. Errore, and P. Karaca-Mandic (2022). [Lifting statewide mask mandates and COVID-19 cases: A synthetic control study](https://doi.org/10.1097/MLR.0000000000001725). *Medical Care* 60 (7), 538-544.
-- F. Pierri, B. L. Perry, M. R. DeVerna, et al. (2022). [Online misinformation is linked to early COVID-19 vaccination hesitancy and refusal](https://doi.org/10.1038/s41598-022-10070-w). *Scientific Reports* 12, 5966.
-- A. Pilehvari, J. Ton, M. R. Mohan, A. Marathe, and A. Vullikanti (2022). [Drivers and Predictors of COVID-19 Vaccine Hesitancy in Virginia](https://doi.org/10.1007/978-3-030-96188-6_8). In: Yang, Z., von Briesen, E. (eds), *Proceedings of the 2021 Conference of The Computational Social Science Society of the Americas*. CSSSA 2021.
-- L. S. Flor, J. Friedman, C. N. Spencer, et al. (2022). [Quantifying the effects of the COVID-19 pandemic on gender equality on health, social, and economic indicators: a comprehensive review of data from March, 2020, to September, 2021](https://doi.org/10.1016/S0140-6736(22)00008-3). *The Lancet* 399 (10344), 2381-2397.
-- D. P. Do and R. Frank (2022). [Prior COVID-19 infection: an underappreciated factor in vaccine hesitancy in the USA](https://doi.org/10.1093/pubmed/fdab404). *Journal of Public Health* 44 (2), 471-474.
-- W. C. King, M. Rubinstein, A. Reinhart, and R. J. Mejia (2021). [Time trends, factors associated with, and reasons for COVID-19 vaccine hesitancy: A massive online survey of US adults from January-May 2021](https://doi.org/10.1371/journal.pone.0260731). *PLoS ONE* 16 (12), e0260731.
-- C. Lupton-Smith, E. Badillo-Goicochea, T.-H. Chang, H. Maniates, K. E. Riehm, I. Schmid, and E. A. Stuart (2021). [Factors associated with county-level mental health during the COVID-19 pandemic](https://doi.org/10.1002/jcop.22785). *Journal of Community Psychology* 50 (5), 2431-2442.
-- D. P. Do and R. Frank (2021). [U.S. frontline workers and COVID-19 inequities](https://doi.org/10.1016/j.ypmed.2021.106833). *Preventive Medicine* 153, 106833.
-- W. C. King, M. Rubinstein, A. Reinhart, and R. J. Mejia (2021). [COVID-19 vaccine hesitancy January-May 2021 among 18–64 year old US adults by employment and occupation](https://doi.org/10.1016/j.pmedr.2021.101569). *Preventive Medicine Reports* 24, 101569.
-- C. H. Sudre, A. Keshet, M. S. Graham, A. D. Joshi, S. Shilo, H. Rossman, B. Murray, E. Molteni, K. Klaser, L. D. Canas, M. Antonelli, L. H. Nguyen, D. A. Drew, M. Modat, J. Capdevila Pujol, S. Ganesh, J. Wolf, T. Meir, A. T. Chan, C. J. Steves, T. D. Spector, J. S. Brownstein, E. Segal, S. Ourselin, and C. M. Astley (2021). [Anosmia, ageusia, and other COVID-19-like symptoms in association with a positive SARS-CoV-2 test, across six national digital surveillance platforms: an observational study](https://doi.org/10.1016/S2589-7500(21)00115-1). *The Lancet Digital Health* 3 (9), e577-e586.
-- R. Sukumaran, P. Patwa, S. T V, S. Shankar, R. Kanaparti, J. Bae, Y. Mathur, A. Singh, A. Chopra, M. Kang, P. Ramaswamy, and R. Raskar (2021). [COVID-19 outbreak prediction and analysis using self reported symptoms](https://doi.org/10.35566/jbds/v1n1/p8). *Journal of Behavioral Data Science* 1 (1), 154–169.
-- D. Adjodah, K. Dinakar, M. Chinazzi, S. P. Fraiberger, A. Pentland, S. Bates, K. Staller, A. Vespignani, and D. L. Bhatt (2021). [Association between COVID-19 outcomes and mask mandates, adherence, and attitudes](https://doi.org/10.1371/journal.pone.0252315). *PLoS ONE* 16 (6), e0252315.
-- C. M. Zipfel, V. Colizza, and S. Bansal (2021). [The missing season: The impacts of the COVID-19 pandemic on influenza](https://doi.org/10.1016/j.vaccine.2021.05.049). *Vaccine* 39 (28), 3645-3648.
-- J. Lessler, M. K. Grabowski, K. H. Grantz, E. Badillo-Goicoechea, C. J. E. Metcalf, C. Lupton-Smith, A. S. Azman, and E. A. Stuart (2021). [Household COVID-19 risk and in-person schooling](https://doi.org/10.1126/science.abh2939). *Science* 372 (6545), 1092-1097.
-- Doerr, A.J. (2021). [Locked (Down) and Loaded (Language): Effect of Policy and Speech on COVID-19 Outcomes](https://doi.org/10.1177/15480518211012404). *Journal of Leadership & Organizational Studies* 28 (3), 340-348.
-- Fischer CB, Adrien N, Silguero JJ, Hopper JJ, Chowdhury AI, Werler MM (2021). [Mask adherence and rate of COVID-19 across the United States](https://doi.org/10.1371/journal.pone.0249891). *PLoS ONE* 16 (4), e0249891.
-- Bilinski, A., Emanuel, E., Salomon, J.A. and Venkataramani, A. (2021). [Better Late Than Never: Trends in COVID-19 Infection Rates, Risk Perceptions, and Behavioral Responses in the USA](https://doi.org/10.1007/s11606-021-06633-8). *Journal of General Internal Medicine* 36, 1825-1828.
-- Molteni, E., Astley, C.M., Ma, W. et al. (2021). [Symptoms and syndromes associated with SARS-CoV-2 infection and severity in pregnant women from two community cohorts](https://doi.org/10.1038/s41598-021-86452-3). *Scientific Reports* 11, 6928.
-- Rebeiro, P., Aronoff, D, and Smith, M.K. (2021). [The Impact of State Mask-Wearing Requirements on the Growth of COVID-19 Cases, Hospitalizations, and Deaths in the United States](https://doi.org/10.1093/cid/ciab101). *Clinical Infectious Diseases* 73 (9), 1703–1706.
-- Rader, White, Burns, Chen, Brilliant, Cohen, Shaman, Brilliant, Kraemer, Moritz, Hawkins, Scarpino, Astley, and Brownstein (2021). [Mask-wearing and control of SARS-CoV-2 transmission in the USA: a cross-sectional study](https://doi.org/10.1016/S2589-7500(20)30293-4). *Lancet Digital Health* 3 (3), e148-e157.
-- Flaxman AD, Henning DJ and Duber HC (2020). [The relative incidence of COVID-19 in healthcare workers versus non-healthcare workers: evidence from a web-based survey of Facebook users in the United States](https://doi.org/10.12688/gatesopenres.13202.2). *Gates Open Research*, 4:174.
-- Kreuter, F., Barkay, N., Bilinski, A., Bradford, A., Chiu, S., Eliat, R., Fan, J., Galili, T., Haimovich, D., Kim, B., LaRocca, S., Li, Y., Morris, K., Presser, S., Sarig, T., Salomon, J. A., Stewart, K., Stuart, E. A., & Tibshirani, R. J. (2020). [Partnering with a global platform to inform research and public policy making](https://doi.org/10.18148/srm/2020.v14i2.7761). *Survey Research Methods*, 14 (2), 159-163.
-
-If you have used the survey data, or the aggregate data available in the COVIDcast API, to publish research results, please [contact us](#who-can-i-contact) so we can include your work here.
-
-### Blog posts and reports
-
-- Surgo Ventures, Resolve to Save Lives (2021). [COVID-19 Vaccine Precision Response Toolkit: An End-to-End Vaccination Improvement Framework to Improve COVID-19 Vaccine Uptake](https://surgoventures.org/resource-library/increasing-covid-19vaccine-uptake-a-four-step-framework-to-promote-access-acceptance-and-equity).
-- Alejandra Arrieta, Emmanuela Gakidou, Heidi Larson, Erin Mullany, and Christopher Troeger, April 1, 2021. [Through Understanding and Empathy, We Can Convince Women to Get the COVID-19 Vaccine](https://www.thinkglobalhealth.org/article/through-understanding-and-empathy-we-can-convince-women-get-covid-19-vaccine). Think Global Health.
-- Joseph Friedman, Silvia Montoya and Emmanuela Gakidou, March 8, 2021. [Gender Equality in the Global Return to School](https://www.thinkglobalhealth.org/article/gender-equality-global-return-school). Think Global Health.
-- Leanna Morinishi, Kris Barkume, Esther Kim, and Alex Reinhart, February 2, 2021. [Home for the Holidays? The Impact of US Holidays on Social Behaviors and Preventative Measures]({{< relref "2021-01-22-holiday-surveys" >}}). Delphi blog.
-- Alex Reinhart, Esther Kim, Andy Garcia, and Sarah LaRocca, January 28, 2021. [Using the COVID-19 Symptom Survey to Track Vaccination Uptake and Sentiment in the United States]({{< relref "2021-01-28-survey-vaccines" >}}). Delphi blog.
-- Alex Reinhart, October 12, 2020. [New and Improved COVID Symptom Survey Tracks Testing and Mask-Wearing]({{< relref "2020-10-06-survey-wave-4" >}}). Delphi blog.
-- Ryan Tibshirani, September 21, 2020. [Can Symptom Surveys Improve COVID-19 Forecasts?]({{< relref "2020-09-21-forecast-demo" >}}) Delphi blog.
-- Alex Reinhart and Ryan Tibshirani, August 26, 2020. [COVID-19 Symptom Surveys through Facebook]({{< relref "2020-08-26-fb-survey" >}}). Delphi blog.
+Dozens of other peer-reviewed publications and reports have used CTIS data to study important questions in public health, epidemiology, forecasting, and related fields. A [full list is available on our survey documentation site](https://cmu-delphi.github.io/delphi-epidata/symptom-survey/publications.html).
 
 ## Can I use the surveys in my research?
 

dependencies.R

@@ -3,6 +3,8 @@
 
 # blogdown::install_hugo()
 
+install.packages("ggrepel", repo="http://cran.rstudio.com/")
+install.packages("base64url", repo="http://cran.rstudio.com/")
 install.packages("covidcast", repo="http://cran.rstudio.com/")
 # devtools::install_github("cmu-delphi/covidcast", ref = "main",
 #                          upgrade = 'never',

devops/r.dockerfile

@@ -1,13 +1,12 @@
 # docker image for setting up an R environment
-FROM continuumio/miniconda
-
-RUN conda install --name base --channel conda-forge mamba=*
+FROM mambaorg/micromamba
 
 ADD ./environment.yml .
-RUN mamba env create -f environment.yml
 
+RUN micromamba env create -f environment.yml
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 ADD ./dependencies.R .
 
-RUN conda run -n www-main Rscript ./dependencies.R
+RUN micromamba run -n www-main Rscript ./dependencies.R
 
-ENV PATH /opt/conda/envs/www-main/bin:$PATH
+ENV PATH /opt/conda/envs/www-main/bin:$PATH

environment.yml

@@ -2,6 +2,7 @@ name: www-main
 channels:
   - conda-forge
   - defaults
+  - conda-forge/linux-64
 dependencies:
   - gdal
   - python=3.9.1
@@ -13,7 +14,7 @@ dependencies:
   - r-devtools
   - r-directlabels
   - r-gridextra
-  - r-reticulate
+  - r-reticulate==1.22
   - r-blogdown
   - r-svglite
   - r-dplyr

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "www-main",
-  "version": "3.1.0",
+  "version": "3.1.1",
   "private": true,
   "dependencies": {
     "@fortawesome/fontawesome-free": "^6.2.1",