From 1b99c3d0dd49b95ae89cd76fe7dda57317489760 Mon Sep 17 00:00:00 2001 From: Ryan Tibshirani Date: Tue, 10 Nov 2020 22:44:29 -0500 Subject: [PATCH 1/9] Rename vignettes to number them --- R-packages/covidcast/vignettes/correlation-utils.Rmd | 4 ++-- R-packages/covidcast/vignettes/multi-signals.Rmd | 2 +- R-packages/covidcast/vignettes/plotting-signals.Rmd | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R-packages/covidcast/vignettes/correlation-utils.Rmd b/R-packages/covidcast/vignettes/correlation-utils.Rmd index 723775f4..a45d5c6a 100644 --- a/R-packages/covidcast/vignettes/correlation-utils.Rmd +++ b/R-packages/covidcast/vignettes/correlation-utils.Rmd @@ -1,8 +1,8 @@ --- -title: Correlation utilities +title: 2. Computing signal correlations output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{2. Correlation utilities} + %\VignetteIndexEntry{2. Computing signal correlations} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/R-packages/covidcast/vignettes/multi-signals.Rmd b/R-packages/covidcast/vignettes/multi-signals.Rmd index 6fa2fd4f..cbb5a78a 100644 --- a/R-packages/covidcast/vignettes/multi-signals.Rmd +++ b/R-packages/covidcast/vignettes/multi-signals.Rmd @@ -1,5 +1,5 @@ --- -title: Manipulating multiple signals +title: 3. Manipulating multiple signals output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{3. Manipulating multiple signals} diff --git a/R-packages/covidcast/vignettes/plotting-signals.Rmd b/R-packages/covidcast/vignettes/plotting-signals.Rmd index 3ac7b456..5ce6f550 100644 --- a/R-packages/covidcast/vignettes/plotting-signals.Rmd +++ b/R-packages/covidcast/vignettes/plotting-signals.Rmd @@ -1,5 +1,5 @@ --- -title: Plotting and mapping signals +title: 1. Plotting and mapping signals output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{1. Plotting and mapping signals} From e5b241f816dce373849d93bd3ababba0d78159b5 Mon Sep 17 00:00:00 2001 From: Ryan Tibshirani Date: Sat, 14 Nov 2020 15:44:14 -0500 Subject: [PATCH 2/9] Fix correlation vignette --- .../covidcast/vignettes/correlation-utils.Rmd | 112 +++++++----------- 1 file changed, 46 insertions(+), 66 deletions(-) diff --git a/R-packages/covidcast/vignettes/correlation-utils.Rmd b/R-packages/covidcast/vignettes/correlation-utils.Rmd index a45d5c6a..e6277891 100644 --- a/R-packages/covidcast/vignettes/correlation-utils.Rmd +++ b/R-packages/covidcast/vignettes/correlation-utils.Rmd @@ -11,9 +11,8 @@ The covidcast package provides some simple utilities for exploring the correlations between two signals, over space or time, which may be helpful for simple analyses and explorations of data. -For these examples, we'll load confirmed cases and deaths to compare against, -and restrict our analysis to counties with at least 500 total cases by August -15th. +For these examples, we'll load confirmed case and death rates. and restrict our +analysis to counties with at least 500 total cases by August 15th. ```{r, message = FALSE} library(covidcast) @@ -22,27 +21,27 @@ library(dplyr) start_day <- "2020-03-01" end_day <- "2020-08-15" -inum <- suppressMessages( +iprop <- suppressMessages( covidcast_signal(data_source = "jhu-csse", - signal = "confirmed_7dav_incidence_num", + signal = "confirmed_7dav_incidence_prop", start_day = start_day, end_day = end_day) ) -summary(inum) +summary(iprop) -dnum <- suppressMessages( +dprop <- suppressMessages( covidcast_signal(data_source = "jhu-csse", - signal = "deaths_7dav_incidence_num", + signal = "deaths_7dav_incidence_prop", start_day = start_day, end_day = end_day) ) -summary(dnum) +summary(dprop) # Restrict attention to "active" counties with at least 500 total cases case_num <- 500 -geo_values <- inum %>% group_by(geo_value) %>% +geo_values <- iprop %>% group_by(geo_value) %>% summarize(total = sum(value)) %>% filter(total >= case_num) %>% pull(geo_value) -inum_act <- inum %>% filter(geo_value %in% geo_values) -dnum_act <- dnum %>% filter(geo_value %in% geo_values) +iprop_act <- iprop %>% filter(geo_value %in% geo_values) +dprop_act <- dprop %>% filter(geo_value %in% geo_values) ``` ## Correlations sliced by time @@ -60,55 +59,35 @@ by setting `by = "time_value"`: library(ggplot2) # Compute correlation per time, over all counties -df_cor1 <- covidcast_cor(inum_act, dnum_act, by = "time_value") +df_cor <- covidcast_cor(iprop_act, dprop_act, by = "time_value") # Plot the correlation time series -ggplot(df_cor1, aes(x = time_value, y = value)) + geom_line() + - labs(title = "Correlation between cases and deaths", +ggplot(df_cor, aes(x = time_value, y = value)) + geom_line() + + labs(title = "Correlation between case and death rates", subtitle = sprintf("Per day, over counties with at least %i cases", case_num), x = "Date", y = "Correlation") ``` - -(The sudden drop on July 25th is due to a [sudden change in how New Jersey -reported deaths](https://github.com/CSSEGISandData/COVID-19/issues/2763) being -reflected in our data source as large outliers; since the signal is a 7-day -average, these outliers last until the beginning of July and affect the reported -correlation.) - -We might also be interested in how cases now correlate with deaths in the -*future*. Using the `dt_x` parameter, we can lag cases back 10 days in time, -before calculating correlations: - -```{r, warning = FALSE} -# Same, but now lag incidence case numbers back 10 days in time -df_cor2 <- covidcast_cor(inum_act, dnum_act, by = "time_value", dt_x = -10) - -# Stack rowwise into one data frame, then plot time series -df_cor <- rbind(df_cor1, df_cor2) -df_cor$dt <- as.factor(c(rep(0, nrow(df_cor1)), rep(-10, nrow(df_cor2)))) -ggplot(df_cor, aes(x = time_value, y = value)) + - geom_line(aes(color = dt)) + - labs(title = "Correlation between cases and deaths", - subtitle = sprintf("Per day, over counties with at least %i cases", - case_num), - x = "Date", y = "Correlation") + - theme(legend.position = "bottom") -``` - -We can see that, for the most part, lagging the cases time series back by 10 -days improves correlations, showing that cases are better correlated with deaths -10 days from now. - -We can also look at Spearman (rank) correlation, which is a more robust measure -of correlation: it's invariant to monotone transformations, and doesn't rely on -any particular functional form for the dependence between two variables. + +The above plot addresses the question: "on any given day, are case and death +rates linearly associated, over US counties?". We might be interested in +broadening this question, instead asking: "on any given day, do higher case +rates tend to associate with higher death rates?", removing the dependence on a +linear relationship. The latter can be addressed using Spearman correlation, +accomplished by setting `method = "spearman"` in the call to `covidcast_cor()`. +Spearman correlation is highly robust and invariant to monotone transformations +(it doesn't rely on any particular functional form for the dependence between +two variables). + +We might also interested in interested in how case rates associate with death +rates in the *future*. Using the `dt_x` parameter in `covidcast_cor()`, we can +lag case rates back any number of days we want, before calculating correlations. ```{r, warning = FALSE} -# Repeat this comparison, but now using Spearman (rank) correlation -df_cor1 <- covidcast_cor(inum_act, dnum_act, by = "time_value", +# Use Spearman correlation, with case rates and 10-day lagged case rates +df_cor1 <- covidcast_cor(iprop_act, dprop_act, by = "time_value", method = "spearman") -df_cor2 <- covidcast_cor(inum_act, dnum_act, by = "time_value", dt_x = -10, +df_cor2 <- covidcast_cor(iprop_act, dprop_act, by = "time_value", dt_x = -10, method = "spearman") # Stack rowwise into one data frame, then plot time series @@ -116,35 +95,36 @@ df_cor <- rbind(df_cor1, df_cor2) df_cor$dt <- as.factor(c(rep(0, nrow(df_cor1)), rep(-10, nrow(df_cor2)))) ggplot(df_cor, aes(x = time_value, y = value)) + geom_line(aes(color = dt)) + - labs(title = "Correlation between cases and deaths", + labs(title = "Correlation between case and death rates", subtitle = sprintf("Per day, over counties with at least %i cases", case_num), x = "Date", y = "Correlation") + theme(legend.position = "bottom") ``` -The "big dip" is gone (since the Spearman correlation uses ranks and not the -actual values, and hence is less sensitive to outliers), and we can again see -that lagging the cases time series helps correlations. +We can see that, for the most part, the Spearman measure has bolstered the +correlations; and generally, lagging the case rates time series back by 10 days +improves correlations, confirming case rates are better correlated with death +rates 10 days from now. ## Correlations sliced by county The second option we have is to "slice by location": this calculates, for each geographic location, correlation between the time series of two signals. This is obtained by setting `by = "geo_value"`. We'll again look at correlations -both for observations at the same time and for 10-day lagged cases: +both for observations at the same time and for 10-day lagged case rates: ```{r, warning = FALSE} # Compute correlation per county, over all times -df_cor1 <- covidcast_cor(inum_act, dnum_act, by = "geo_value") -df_cor2 <- covidcast_cor(inum_act, dnum_act, by = "geo_value", dt_x = -10) +df_cor1 <- covidcast_cor(iprop_act, dprop_act, by = "geo_value") +df_cor2 <- covidcast_cor(iprop_act, dprop_act, by = "geo_value", dt_x = -10) # Stack rowwise into one data frame, then plot densities df_cor <- rbind(df_cor1, df_cor2) df_cor$dt <- as.factor(c(rep(0, nrow(df_cor1)), rep(-10, nrow(df_cor2)))) ggplot(df_cor, aes(value)) + geom_density(aes(color = dt, fill = dt), alpha = 0.5) + - labs(title = "Correlation between cases and deaths", + labs(title = "Correlation between case and death rates", subtitle = "Computed separately for each county, over all times", x = "Date", y = "Density") + theme(legend.position = "bottom") @@ -162,8 +142,8 @@ attributes(df_cor2)$metadata$geo_type <- "county" class(df_cor2) <- c("covidcast_signal", "data.frame") # Plot choropleth maps, using the covidcast plotting functionality -plot(df_cor2, title = "Correlations between 10-day lagged cases and deaths", - range = c(-1, 1), choro_col = c("orange","lightblue", "purple")) +plot(df_cor2, title = "Correlations between 10-day lagged case and death rates", + range = c(-1, 1), choro_col = c("orange", "lightblue", "purple")) ``` ## More systematic lag analysis @@ -177,7 +157,7 @@ this: dt_vec <- -(0:15) df_list <- vector("list", length(dt_vec)) for (i in 1:length(dt_vec)) { - df_list[[i]] <- covidcast_cor(inum_act, dnum_act, dt_x = dt_vec[i], + df_list[[i]] <- covidcast_cor(iprop_act, dprop_act, dt_x = dt_vec[i], by = "geo_value") df_list[[i]]$dt <- dt_vec[i] } @@ -188,11 +168,11 @@ df %>% group_by(dt) %>% summarize(median = median(value, na.rm = TRUE), .groups = "drop_last") %>% ggplot(aes(x = dt, y = median)) + geom_line() + geom_point() + - labs(title = "Median correlation between cases and deaths", + labs(title = "Median correlation between case and death rates", x = "dt", y = "Correlation") + theme(legend.position = "bottom", legend.title = element_blank()) ``` -We can see that the median correlation between cases and deaths (where the +We can see that the median correlation between case and death rates (where the correlations come from slicing by location) is maximized when we lag the case -incidence numbers back 8 days in time. +incidence rates back 8 days in time. From e3d78b26d13d418c769910a00b7a89165e566e7b Mon Sep 17 00:00:00 2001 From: Ryan Tibshirani Date: Sat, 14 Nov 2020 16:17:23 -0500 Subject: [PATCH 3/9] Fix active filter --- R-packages/covidcast/vignettes/correlation-utils.Rmd | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/R-packages/covidcast/vignettes/correlation-utils.Rmd b/R-packages/covidcast/vignettes/correlation-utils.Rmd index e6277891..4f9746a0 100644 --- a/R-packages/covidcast/vignettes/correlation-utils.Rmd +++ b/R-packages/covidcast/vignettes/correlation-utils.Rmd @@ -37,9 +37,12 @@ summary(dprop) # Restrict attention to "active" counties with at least 500 total cases case_num <- 500 -geo_values <- iprop %>% group_by(geo_value) %>% - summarize(total = sum(value)) %>% - filter(total >= case_num) %>% pull(geo_value) +geo_values <- suppressMessages( + covidcast_signal(data_source = "jhu-csse", + signal = "confirmed_cumulative_num", + start_day = end_day, end_day = end_day) %>% + filter(value >= case_num) %>% pull(geo_value) +) iprop_act <- iprop %>% filter(geo_value %in% geo_values) dprop_act <- dprop %>% filter(geo_value %in% geo_values) ``` From e48d665dbcb54b3c758dc3607ce97864432e5771 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Sat, 14 Nov 2020 17:02:45 -0500 Subject: [PATCH 4/9] Use pkgdown.yml to put articles in the correct order --- R-packages/covidcast/_pkgdown.yml | 10 ++++++++++ R-packages/covidcast/vignettes/correlation-utils.Rmd | 1 + R-packages/covidcast/vignettes/covidcast.Rmd | 1 + R-packages/covidcast/vignettes/multi-signals.Rmd | 1 + R-packages/covidcast/vignettes/plotting-signals.Rmd | 3 ++- 5 files changed, 15 insertions(+), 1 deletion(-) diff --git a/R-packages/covidcast/_pkgdown.yml b/R-packages/covidcast/_pkgdown.yml index 84db97de..10eff445 100644 --- a/R-packages/covidcast/_pkgdown.yml +++ b/R-packages/covidcast/_pkgdown.yml @@ -9,6 +9,16 @@ home: - text: View the COVIDcast map href: https://covidcast.cmu.edu/ +articles: + - title: Using the package + desc: Basic usage and examples. + navbar: ~ + contents: + - covidcast + - plotting-signals + - correlation-utils + - multi-signals + reference: - title: Fetch data desc: Fetch signals and metadata from the COVIDcast API diff --git a/R-packages/covidcast/vignettes/correlation-utils.Rmd b/R-packages/covidcast/vignettes/correlation-utils.Rmd index 4f9746a0..a4bfb95b 100644 --- a/R-packages/covidcast/vignettes/correlation-utils.Rmd +++ b/R-packages/covidcast/vignettes/correlation-utils.Rmd @@ -1,5 +1,6 @@ --- title: 2. Computing signal correlations +description: Calculate correlations over space and time between multiple signals. output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{2. Computing signal correlations} diff --git a/R-packages/covidcast/vignettes/covidcast.Rmd b/R-packages/covidcast/vignettes/covidcast.Rmd index 43043951..70e90a6e 100644 --- a/R-packages/covidcast/vignettes/covidcast.Rmd +++ b/R-packages/covidcast/vignettes/covidcast.Rmd @@ -1,5 +1,6 @@ --- title: Get started with covidcast +description: An introductory tutorial with examples. output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Get started with covidcast} diff --git a/R-packages/covidcast/vignettes/multi-signals.Rmd b/R-packages/covidcast/vignettes/multi-signals.Rmd index cbb5a78a..50aad14e 100644 --- a/R-packages/covidcast/vignettes/multi-signals.Rmd +++ b/R-packages/covidcast/vignettes/multi-signals.Rmd @@ -1,5 +1,6 @@ --- title: 3. Manipulating multiple signals +description: Download multiple signals at once, and aggregate and manipulate them in various ways. output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{3. Manipulating multiple signals} diff --git a/R-packages/covidcast/vignettes/plotting-signals.Rmd b/R-packages/covidcast/vignettes/plotting-signals.Rmd index 5ce6f550..ca837c68 100644 --- a/R-packages/covidcast/vignettes/plotting-signals.Rmd +++ b/R-packages/covidcast/vignettes/plotting-signals.Rmd @@ -1,5 +1,6 @@ --- title: 1. Plotting and mapping signals +description: Make custom time series plots, choropleth maps, and bubble plots of signals. output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{1. Plotting and mapping signals} @@ -248,4 +249,4 @@ ggplot(df, aes(x = time_value, y = value)) + ``` Again, we see that the combined indicator starts rising several days before the -new COVID-19 cases do, an exciting phenomenon that Delphi is studying now. \ No newline at end of file +new COVID-19 cases do, an exciting phenomenon that Delphi is studying now. From 5cef979ecc62057f6381c2dbf8d161d361d6f260 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Tue, 10 Nov 2020 21:12:35 -0500 Subject: [PATCH 5/9] Add simple tests for latest_issue and earliest_issue --- .../covidcast/tests/testthat/test-utils.R | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 R-packages/covidcast/tests/testthat/test-utils.R diff --git a/R-packages/covidcast/tests/testthat/test-utils.R b/R-packages/covidcast/tests/testthat/test-utils.R new file mode 100644 index 00000000..bf125898 --- /dev/null +++ b/R-packages/covidcast/tests/testthat/test-utils.R @@ -0,0 +1,33 @@ +# Internal utility functions. + +test_that("latest_issue gives only the latest issue", { + foo <- data.frame( + geo_value = c(rep("pa", 3), rep("tx", 3)), + issue = c(3, 2, 1, 1, 2, 3), + time_value = 1, + value = c(4, 5, 6, 7, 8, 9)) + + latest <- data.frame( + geo_value = c("pa", "tx"), + issue = 3, + time_value = 1, + value = c(4, 9)) + + expect_equal(latest_issue(foo), latest) +}) + +test_that("earliest_issue gives only the earliest issue", { + foo <- data.frame( + geo_value = c(rep("pa", 3), rep("tx", 3)), + issue = c(3, 2, 1, 1, 2, 3), + time_value = 1, + value = c(4, 5, 6, 7, 8, 9)) + + earliest <- data.frame( + geo_value = c("pa", "tx"), + issue = 3, + time_value = 1, + value = c(6, 7)) + + expect_equal(earliest_issue(foo), latest) +}) From 4e22d6e100ff5e79eaf7a40d54a893e40dac8e9f Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Wed, 11 Nov 2020 08:12:53 -0500 Subject: [PATCH 6/9] Fix source links in pkgdown documentation By providing the `repo` block with a link pointing to R-packages/covidcast/, pkgdown can build the correct URLs. --- R-packages/covidcast/_pkgdown.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/R-packages/covidcast/_pkgdown.yml b/R-packages/covidcast/_pkgdown.yml index 10eff445..b8ff2e26 100644 --- a/R-packages/covidcast/_pkgdown.yml +++ b/R-packages/covidcast/_pkgdown.yml @@ -19,6 +19,13 @@ articles: - correlation-utils - multi-signals +repo: + url: + home: https://github.com/cmu-delphi/covidcast/tree/main/R-packages/covidcast + source: https://github.com/cmu-delphi/covidcast/blob/main/R-packages/covidcast/ + issue: https://github.com/cmu-delphi/covidcast/issues + user: https://github.com/ + reference: - title: Fetch data desc: Fetch signals and metadata from the COVIDcast API From e98f92495022e3757648d093f1b0c442a259d02a Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Tue, 10 Nov 2020 21:14:50 -0500 Subject: [PATCH 7/9] Use dplyr::distinct in {latest,earliest}_issue Profiling revealed that latest_issue was responsible for a large portion of the time taken in building correlation-utils.Rmd (apart from downloading the data). Much of this time was spent in dplyr::filter. Rather than grouping by geography and time, we can use dplyr::distinct, knowing that each geo_value and time_value should appear only once per issue date. By taking the first or last (after sorting by issue date), we get the desired result. dplyr does not document algorithmic details, so I can't easily give O(n) notation here. Algorithmic details notwithstanding, the results are extraordinary: > nrow(d) [1] 203360 > system.time(latest_issue_old(d)) user system elapsed 6.395 0.037 6.465 > system.time(latest_issue(d)) user system elapsed 0.025 0.003 0.027 --- R-packages/covidcast/R/utils.R | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/R-packages/covidcast/R/utils.R b/R-packages/covidcast/R/utils.R index a8070ac0..bb59444c 100644 --- a/R-packages/covidcast/R/utils.R +++ b/R-packages/covidcast/R/utils.R @@ -15,9 +15,9 @@ latest_issue <- function(df) { attrs <- attrs[!(names(attrs) %in% c("row.names", "names"))] df <- df %>% - dplyr::group_by(.data$geo_value, .data$time_value) %>% - dplyr::filter(.data$issue == max(.data$issue)) %>% - dplyr::ungroup() + dplyr::arrange(dplyr::desc(.data$issue)) %>% + dplyr::distinct(.data$geo_value, .data$time_value, + .keep_all = TRUE) attributes(df) <- c(attributes(df), attrs) @@ -41,9 +41,9 @@ earliest_issue <- function(df) { attrs <- attrs[!(names(attrs) %in% c("row.names", "names"))] df <- df %>% - dplyr::group_by(.data$geo_value, .data$time_value) %>% - dplyr::filter(.data$issue == min(.data$issue)) %>% - dplyr::ungroup() + dplyr::arrange(.data$issue) %>% + dplyr::distinct(.data$geo_value, .data$time_value, + .keep_all = TRUE) attributes(df) <- c(attributes(df), attrs) From a04c52897842937f86caba53766aed995fa07e50 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Tue, 10 Nov 2020 22:14:22 -0500 Subject: [PATCH 8/9] Fix test thinkos Always run your tests before pushing... --- R-packages/covidcast/tests/testthat/test-utils.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R-packages/covidcast/tests/testthat/test-utils.R b/R-packages/covidcast/tests/testthat/test-utils.R index bf125898..d108152a 100644 --- a/R-packages/covidcast/tests/testthat/test-utils.R +++ b/R-packages/covidcast/tests/testthat/test-utils.R @@ -17,7 +17,7 @@ test_that("latest_issue gives only the latest issue", { }) test_that("earliest_issue gives only the earliest issue", { - foo <- data.frame( + foo <- data.frame( geo_value = c(rep("pa", 3), rep("tx", 3)), issue = c(3, 2, 1, 1, 2, 3), time_value = 1, @@ -25,9 +25,9 @@ test_that("earliest_issue gives only the earliest issue", { earliest <- data.frame( geo_value = c("pa", "tx"), - issue = 3, + issue = 1, time_value = 1, value = c(6, 7)) - expect_equal(earliest_issue(foo), latest) + expect_equal(earliest_issue(foo), earliest) }) From 83501c0a2a86232e8568b0b923d1a1d444de9bd8 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Sat, 14 Nov 2020 17:23:07 -0500 Subject: [PATCH 9/9] Rebuild docs site --- docs/covidcastR/404.html | 8 +- docs/covidcastR/LICENSE-text.html | 8 +- .../articles/correlation-utils.html | 126 ++++----- .../figure-html/unnamed-chunk-3-1.png | Bin 133264 -> 101741 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 177268 -> 137934 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 158200 -> 94211 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 133637 -> 966386 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 1161052 -> 50925 bytes docs/covidcastR/articles/covidcast.html | 239 +++++++++++------- docs/covidcastR/articles/index.html | 26 +- docs/covidcastR/articles/multi-signals.html | 162 ++++++------ .../covidcastR/articles/plotting-signals.html | 18 +- .../figure-html/unnamed-chunk-11-1.png | Bin 355807 -> 269492 bytes .../figure-html/unnamed-chunk-14-1.png | Bin 161637 -> 125741 bytes .../figure-html/unnamed-chunk-14-2.png | Bin 133453 -> 99171 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 142385 -> 108482 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 1305565 -> 1040865 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 1041337 -> 738429 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 1172997 -> 924132 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 1008836 -> 827907 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 1383501 -> 1277906 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 1140081 -> 1043745 bytes docs/covidcastR/authors.html | 8 +- docs/covidcastR/index.html | 10 +- docs/covidcastR/news/index.html | 10 +- docs/covidcastR/pkgdown.yml | 2 +- docs/covidcastR/reference/abbr_to_fips.html | 10 +- docs/covidcastR/reference/abbr_to_name.html | 10 +- .../reference/aggregate_signals.html | 10 +- docs/covidcastR/reference/county_census.html | 10 +- docs/covidcastR/reference/county_geo.html | 10 +- docs/covidcastR/reference/covidcast.html | 10 +- docs/covidcastR/reference/covidcast_cor.html | 10 +- .../reference/covidcast_longer.html | 10 +- docs/covidcastR/reference/covidcast_meta.html | 10 +- .../reference/covidcast_signal.html | 10 +- .../reference/covidcast_signals.html | 10 +- docs/covidcastR/reference/earliest_issue.html | 10 +- docs/covidcastR/reference/fips_to_abbr.html | 10 +- docs/covidcastR/reference/fips_to_name.html | 10 +- docs/covidcastR/reference/index.html | 8 +- docs/covidcastR/reference/latest_issue.html | 10 +- docs/covidcastR/reference/msa_census.html | 10 +- docs/covidcastR/reference/name_to_abbr.html | 10 +- docs/covidcastR/reference/name_to_fips.html | 10 +- .../reference/plot.covidcast_signal.html | 10 +- .../reference/print.covidcast_meta.html | 10 +- .../reference/print.covidcast_signal.html | 10 +- docs/covidcastR/reference/state_census.html | 10 +- docs/covidcastR/reference/state_geo.html | 10 +- .../reference/summary.covidcast_meta.html | 10 +- .../reference/summary.covidcast_signal.html | 10 +- 52 files changed, 460 insertions(+), 415 deletions(-) diff --git a/docs/covidcastR/404.html b/docs/covidcastR/404.html index 04c59a41..a123e598 100644 --- a/docs/covidcastR/404.html +++ b/docs/covidcastR/404.html @@ -97,13 +97,13 @@ @@ -113,7 +113,7 @@