From 0ba504a12ce358d533bec0ad74e4c53de6b2e7e2 Mon Sep 17 00:00:00 2001 From: seabbs Date: Tue, 22 Jan 2019 22:21:40 +0000 Subject: [PATCH] updated environment handling for render and final cran checks --- R/render_country_report.R | 5 +- _pkgdown.yml | 4 ++ docs/articles/intro.html | 60 +++++++++--------- .../figure-html/plot-incidence-1.png | Bin 102259 -> 124132 bytes .../figure-html/plot-incidence-facet-1.png | Bin 99417 -> 97297 bytes .../plot-incidence-facet-free-y-1.png | Bin 174736 -> 186000 bytes .../plot-mortality-excluding-hiv-1.png | Bin 183875 -> 198278 bytes .../plot-mortality-including-hiv-1.png | Bin 174710 -> 186978 bytes .../dev/man/figure/map-tb-incidence-eur-1.png | Bin 89144 -> 230514 bytes .../man/figure/plot-tb-incidence-eur-1.png | Bin 97220 -> 286226 bytes .../figure/plot-tb-incidence-eur-per-1.png | Bin 101732 -> 299107 bytes .../dev/man/figure/plot-tb-incidence-uk-1.png | Bin 27706 -> 63149 bytes .../figure/plot-tb-incidence-uk-compare-1.png | Bin 31991 -> 69287 bytes docs/index.html | 44 ++++++------- docs/man/figure/map-tb-incidence-eur-1.png | Bin 89144 -> 230514 bytes docs/man/figure/plot-tb-incidence-eur-1.png | Bin 97220 -> 286226 bytes .../figure/plot-tb-incidence-eur-per-1.png | Bin 101732 -> 299107 bytes docs/man/figure/plot-tb-incidence-uk-1.png | Bin 27706 -> 63149 bytes .../figure/plot-tb-incidence-uk-compare-1.png | Bin 31991 -> 69287 bytes docs/reference/get_data.html | 2 +- docs/reference/get_data_dict.html | 2 +- docs/reference/get_tb_burden.html | 2 +- docs/reference/index.html | 15 +++++ docs/reference/map_tb_burden.html | 2 +- docs/reference/plot_tb_burden.html | 2 +- docs/reference/plot_tb_burden_overview.html | 8 +-- docs/reference/prepare_df_plot.html | 2 +- docs/reference/search_data_dict.html | 6 +- docs/reference/summarise_tb_burden.html | 4 +- inst/rmarkdown/country-report.Rmd | 14 ++-- 30 files changed, 99 insertions(+), 73 deletions(-) diff --git a/R/render_country_report.R b/R/render_country_report.R index 2e3ac1c..8406af0 100644 --- a/R/render_country_report.R +++ b/R/render_country_report.R @@ -60,6 +60,9 @@ render_country_report <- function(country = "United Kingdom", format = "html_doc rmarkdown::render(report, output_format = format, output_file = filename, output_dir = save_dir, - intermediates_dir = save_dir, + intermediates_dir = save_dir, + params = list("country" = country, + "interactive" = interactive), + envir = new.env(), clean = TRUE) } diff --git a/_pkgdown.yml b/_pkgdown.yml index b5dd1a7..7c847be 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -58,6 +58,10 @@ reference: desc: Launch interactive dashboards showcasing package functionality. These dashboards require the shiny package. contents: - starts_with("run_") + - title: Reports + desc: Render parameterised reports showcasing package functionality. These reports require the rmarkdown package. + contents: + - starts_with("render_") - title: Helpers contents: - search_data_dict diff --git a/docs/articles/intro.html b/docs/articles/intro.html index f63dc36..ec757d3 100644 --- a/docs/articles/intro.html +++ b/docs/articles/intro.html @@ -148,9 +148,9 @@

Get TB burden data with a single function call. This will download the data if it has never been accessed and then save a local copy to R’s temporary directory (see tempdir()). If a local copy exists from the current session then this will be loaded instead.

tb_burden <- get_tb_burden()
 #> Downloading data from: https://extranet.who.int/tme/generateCSV.asp?ds=estimates
-#> Saving data to: /tmp/Rtmp32uRUo/TB_burden.rds
+#> Saving data to: /tmp/Rtmp4PqMOA/TB_burden.rds
 #> Downloading data from: https://extranet.who.int/tme/generateCSV.asp?ds=mdr_rr_estimates
-#> Saving data to: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Saving data to: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
 
 tb_burden
@@ -202,7 +202,7 @@ 

                                              "e_inc_100k_lo",
                                              "e_inc_100k_hi"))
 #> Downloading data from: https://extranet.who.int/tme/generateCSV.asp?ds=dictionary
-#> Saving data to: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Saving data to: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 4 results found for your variable search for country, e_inc_100k, e_inc_100k_lo, e_inc_100k_hi
 
 knitr::kable(vars_of_interest)
@@ -242,7 +242,7 @@

We might also want to search the variable definitions for key phrases, for example mortality.

defs_of_interest <- search_data_dict(def = c("mortality"))
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 9 results found for your definition search for mortality
 
 knitr::kable(defs_of_interest)
@@ -313,7 +313,7 @@

Finally we could both search for a known variable and for key phrases in variable definitions.

vars_defs_of_interest <- search_data_dict(var = c("country"),
                                      def = c("mortality"))
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for country
 #> 9 results found for your definition search for mortality
 
@@ -394,10 +394,10 @@ 

 Mapping Global Incidence Rates

 
To start exploring the WHO TB data we map, the most recently available, global TB incidence rates. Mapping data can help identify spatial patterns.

 
getTBinR::map_tb_burden(metric = "e_inc_100k")
-#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds
-#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_100k
@@ -407,10 +407,10 @@

To showcase how quickly we can go from no data to plotting informative graphs we quickly explore incidence rates for all countries in the WHO data.

getTBinR::plot_tb_burden_overview(metric = "e_inc_100k",
                                   interactive = FALSE)
-#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds
-#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_100k

Another way to compare incidence rates in countries is to look at the annual percentage change. The plot below only shows countries with a maximum incidence rate above 5 per 100,000.

@@ -425,10 +425,10 @@

interactive = FALSE, annual_change = TRUE, countries = higher_burden_countries) -#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds -#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds +#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds #> Joining TB burden data and MDR TB data. -#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds #> 1 results found for your variable search for e_inc_100k

@@ -437,17 +437,17 @@

Summarising Regional and Global Incidence Rates

We might also be interested in getting a regional/global overview of TB incidence rates (Hint: Use search_data_dict to look up e_inc_100k to see what role this is playing here). See ?plot_tb_burden_summary for more ways to summarise TB metrics.

getTBinR::plot_tb_burden_summary(conf = NULL, metric_label = "e_inc_100k")
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_100k
-#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds
-#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_num
-#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds
-#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_num

@@ -460,14 +460,14 @@

plot_tb_burden(tb_burden, metric = "e_inc_100k", countries = sample_countries, legend = "top") -#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds #> 1 results found for your variable search for e_inc_100k

We have faceted by country so that we can more easily see what is going on. This allows us to easily explore between country variation - depending on the sample there is likely to be alot of this.

plot_tb_burden(tb_burden, metric = "e_inc_100k",
                countries = sample_countries,
                facet = "country")
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_inc_100k

To explore within country variation we need to change the scale of the y axis.

@@ -475,7 +475,7 @@

countries = sample_countries, facet = "country", scales = "free_y") -#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds #> 1 results found for your variable search for e_inc_100k

We might also be interested in mortality in both HIV negative and HIV positive cases in our sample countries. We can also look at this using plot_tb_burden as follows. Note we can do this without specifying the TB burden data, the plotting function will automatically find it either locally or remotely.

@@ -483,20 +483,20 @@

countries = sample_countries, facet = "country", scales = "free_y") -#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds -#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds +#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds #> Joining TB burden data and MDR TB data. -#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds +#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds #> 1 results found for your variable search for e_mort_exc_tbhiv_100k 

plot_tb_burden(metric = "e_mort_tbhiv_100k",
                countries = sample_countries,
                facet = "country",
                scales = "free_y")
-#> Loading data from: /tmp/Rtmp32uRUo/TB_burden.rds
-#> Loading data from: /tmp/Rtmp32uRUo/MDR_TB.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_burden.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/MDR_TB.rds
 #> Joining TB burden data and MDR TB data.
-#> Loading data from: /tmp/Rtmp32uRUo/TB_data_dict.rds
+#> Loading data from: /tmp/Rtmp4PqMOA/TB_data_dict.rds
 #> 1 results found for your variable search for e_mort_tbhiv_100k

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See a

Examples


 ## Map raw incidence rates
-map_tb_burden()
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k
# NOT RUN {
+map_tb_burden()
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k
# NOT RUN {
 #' ## Map raw incidence rates
 map_tb_burden(year = 2014:2017, facet = "year")
 
diff --git a/docs/reference/plot_tb_burden.html b/docs/reference/plot_tb_burden.html
index 6a7cb08..1d0b27b 100644
--- a/docs/reference/plot_tb_burden.html
+++ b/docs/reference/plot_tb_burden.html
@@ -321,7 +321,7 @@ 
See a
     
Examples

     

 ## Get the WHO TB burden data and the data dictionary
-tb_burden <- get_tb_burden()
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
dict <- get_data_dict()
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds

+tb_burden <- get_tb_burden()
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
dict <- get_data_dict()
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds

 ## Get a random sample of 9 countries
 sample_countries <- sample(unique(tb_burden$country), 9)
 
diff --git a/docs/reference/plot_tb_burden_overview.html b/docs/reference/plot_tb_burden_overview.html
index cdcc2b5..3ab6609 100644
--- a/docs/reference/plot_tb_burden_overview.html
+++ b/docs/reference/plot_tb_burden_overview.html
@@ -311,15 +311,15 @@ 
Examp
     

 ## Plot incidence rates over time for both the United Kingdom and Botswana
 plot_tb_burden_overview(countries = c("United Kingdom", "Botswana"),
-                        compare_to_region = FALSE)
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

+                        compare_to_region = FALSE)
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

 ## Plot percentage annual change in incidence rates.
 plot_tb_burden_overview(countries = c("United Kingdom", "Botswana"),
-                        compare_to_region = FALSE, annual_change = TRUE)
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

+                        compare_to_region = FALSE, annual_change = TRUE)
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

 ## Compare incidence rates in the UK and Botswana to incidence rates in their regions
 plot_tb_burden_overview(countries = c("United Kingdom", "Botswana"),
-                        compare_to_region = TRUE)
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

+                        compare_to_region = TRUE)
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k

 ## Find variables relating to mortality in the WHO dataset
-search_data_dict(def = "mortality")
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
+search_data_dict(def = "mortality")
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
 #>   variable_name      dataset  code_list definition                              
 #>   <chr>              <chr>    <chr>     <chr>                                   
 #> 1 e_mort_100k        Estimat… ""        Estimated mortality of TB cases (all fo…
diff --git a/docs/reference/prepare_df_plot.html b/docs/reference/prepare_df_plot.html
index b9f5d39..e88fca9 100644
--- a/docs/reference/prepare_df_plot.html
+++ b/docs/reference/prepare_df_plot.html
@@ -279,7 +279,7 @@ 
See a
 
     
Examples

     

-prepare_df_plot(countries = "Guinea")
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k
#> $df
+prepare_df_plot(countries = "Guinea")
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_inc_100k
#> $df
 #> # A tibble: 18 x 70
 #>    country iso2  iso3  iso_numeric g_whoregion  year e_pop_num e_inc_100k
 #>    <fct>   <chr> <chr>       <int> <chr>       <int>     <int>      <dbl>
diff --git a/docs/reference/search_data_dict.html b/docs/reference/search_data_dict.html
index 81d113d..137ec4e 100644
--- a/docs/reference/search_data_dict.html
+++ b/docs/reference/search_data_dict.html
@@ -232,12 +232,12 @@ 
Examp
     

 ## Search for a known variable
 ## Download and save the dictionary if it is not available locally
-search_data_dict(var = "country")
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for country
#> # A tibble: 1 x 4
+search_data_dict(var = "country")
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for country
#> # A tibble: 1 x 4
 #>   variable_name dataset                code_list definition               
 #>   <chr>         <chr>                  <chr>     <chr>                    
 #> 1 country       Country identification ""        Country or territory name

 ## Search for all variables mentioning mortality in their definition
-search_data_dict(def = "mortality")
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
+search_data_dict(def = "mortality")
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
 #>   variable_name      dataset  code_list definition                              
 #>   <chr>              <chr>    <chr>     <chr>                                   
 #> 1 e_mort_100k        Estimat… ""        Estimated mortality of TB cases (all fo…
@@ -251,7 +251,7 @@ 
Examp
 #> 9 e_mort_tbhiv_100k… Estimat… ""        Estimated mortality of TB cases who are…

 ## Search for both a known variable and for mortality being mentioned in there definition
 ## Duplicate entries will be omitted.
-search_data_dict(var = "e_mort_exc_tbhiv_100k", def = "mortality")
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_mort_exc_tbhiv_100k
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
+search_data_dict(var = "e_mort_exc_tbhiv_100k", def = "mortality")
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_mort_exc_tbhiv_100k
#> 9 results found for your definition search for mortality
#> # A tibble: 9 x 4
 #>   variable_name      dataset  code_list definition                              
 #>   <chr>              <chr>    <chr>     <chr>                                   
 #> 1 e_mort_exc_tbhiv_… Estimat… ""        Estimated mortality of TB cases (all fo…
diff --git a/docs/reference/summarise_tb_burden.html b/docs/reference/summarise_tb_burden.html
index e765e36..672d31d 100644
--- a/docs/reference/summarise_tb_burden.html
+++ b/docs/reference/summarise_tb_burden.html
@@ -307,7 +307,7 @@ 
Value

     
Examples

     

 ## Get the most recent year of data
-tb_burden <- get_tb_burden()
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
most_recent_year <- max(tb_burden$year)
+tb_burden <- get_tb_burden()
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
most_recent_year <- max(tb_burden$year)
 
 ## Get summary of the e_mdr_pct_rr_new cases
 summarise_tb_burden(metric = "e_mdr_pct_rr_new",
@@ -316,7 +316,7 @@ 
Examp
                     samples = 100,
                     compare_all_regions = TRUE,
                     compare_to_world = TRUE,
-                    verbose = TRUE)
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_mdr_pct_rr_new
#> Loading data from: /tmp/RtmpG9erjR/TB_burden.rds
#> Loading data from: /tmp/RtmpG9erjR/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpG9erjR/TB_data_dict.rds
#> 1 results found for your variable search for e_mdr_pct_rr_new
#> Filtering to use only data from: 2017
#> Confidence intervals were not found using your specified conf, so defaulting to estimating
+                    verbose = TRUE)
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_mdr_pct_rr_new
#> Loading data from: /tmp/RtmpiQhHV1/TB_burden.rds
#> Loading data from: /tmp/RtmpiQhHV1/MDR_TB.rds
#> Joining TB burden data and MDR TB data.
#> Loading data from: /tmp/RtmpiQhHV1/TB_data_dict.rds
#> 1 results found for your variable search for e_mdr_pct_rr_new
#> Filtering to use only data from: 2017
#> Confidence intervals were not found using your specified conf, so defaulting to estimating
 #>                 only based on the point estimate.
#> # A tibble: 7 x 5
 #>   area    year e_mdr_pct_rr_new e_mdr_pct_rr_new_lo e_mdr_pct_rr_new_hi
 #>   <fct>  <int>            <dbl>               <dbl>               <dbl>
diff --git a/inst/rmarkdown/country-report.Rmd b/inst/rmarkdown/country-report.Rmd
index e1ddc2e..5d36291 100644
--- a/inst/rmarkdown/country-report.Rmd
+++ b/inst/rmarkdown/country-report.Rmd
@@ -1,17 +1,17 @@
 ---
 title: "Tuberculosis Report"
 output: html_document
-params:
-  country: "United kingdom"
+params: 
+  country: "United Kingdom"
   interactive: FALSE
 ---
 
-```{r setup, include=FALSE}
+```{r setup, include = FALSE}
 knitr::opts_chunk$set(echo = FALSE,
-                      warnings = FALSE)
+                      warnings = FALSE,
+                      eval = TRUE)
 ```
 
-
 ```{r report-setup, include = FALSE, results = "hide"}
 ## Load the package
 library(getTBinR)
@@ -27,6 +27,10 @@ tb <- get_tb_burden(verbose = FALSE)
 
 ## Get the data dictionary
 dict <- get_data_dict(verbose = FALSE)
+
+##Assign parameters
+country <- params$country
+interactive <- params$interactive
 ```
 
 ## TB incidence rates