added London data, 7/jan

mbkoltai · Jan 8, 2022 · f7d0d01 · f7d0d01
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commit f7d0d01
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Showing 42 changed files with 535 additions and 47 deletions.
diff --git a/ONS_2019_midpoint_population_estim_modified.csv b/ONS_2019_midpoint_population_estim_modified.csv
@@ -1,18 +1,18 @@
-age,UK,England
-12_15,2964509,2513686
-16_17,1427406,1206160
-18_24,5647655,4746616
-25_29,4514249,3801409
-30_34,4497132,3807954
-35_39,4395667,3733642
-40_44,4019539,3414297
-45_49,4402122,3715812
-50_54,4661015,3907461
-55_59,4405908,3670651
-60_64,3755185,3111835
-65_69,3368199,2796740
-70_74,3318867,2779326
-75_79,2325296,1940686
-80_84,1715328,1439913
-85_89,1042090,879778
-90+,605181,517273
+age,UK,England,London
+12_15,2964509,2513686,409942
+16_17,1427406,1206160,188846
+18_24,5647655,4746616,747203
+25_29,4514249,3801409,784361
+30_34,4497132,3807954,849074
+35_39,4395667,3733642,783331
+40_44,4019539,3414297,646347
+45_49,4402122,3715812,596141
+50_54,4661015,3907461,564205
+55_59,4405908,3670651,479470
+60_64,3755185,3111835,378068
+65_69,3368199,2796740,309586
+70_74,3318867,2779326,265847
+75_79,2325296,1940686,189753
+80_84,1715328,1439913,147303
+85_89,1042090,879778,91993
+90+,605181,517273,54731
diff --git a/README.md b/README.md
diff --git a/datavis.R b/datavis.R
@@ -18,9 +18,10 @@ ons_all_age_groups_uk_england_2019 <- read_csv("ons_all_age_groups_uk_england_20
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 # vacc uptake
 url_data<-
-  "https://api.coronavirus.data.gov.uk/v2/data?areaType=nation&areaCode=E92000001&metric=vaccinationsAgeDemographics&format=csv"
+ "https://api.coronavirus.data.gov.uk/v2/data?areaType=nation&areaCode=E92000001&metric=vaccinationsAgeDemographics&format=csv"
 
-vacc_dose_data_eng <- left_join(read_csv(url_data),ONS_2019_population_estim %>% #  %>% select(!contains("UK"))
+
+vacc_dose_data_eng <- left_join(read_csv(url_data),ONS_2019_population_estim %>% select(!contains(c("UK","London"))) %>%
                                 rename(population=England),by="age")
 vacc_dose_data_eng <- vacc_dose_data_eng %>% group_by(age) %>% 
   mutate(daily_first_dose_perc_agegroup=1e2*roll_mean(
@@ -271,7 +272,7 @@ ggsave(paste0("england_cases_number_10_yr_agebands_y",
 ######################################################
 # RATE of CASES in 10-yr bands
 df_cases<-left_join(eng_case_age_data,ons_all_age_groups_uk_england_2019,by="age") %>% 
-  select(!c(UK,areaCode,areaType,age_categ,areaName)) %>% rename(population=England) %>% 
+  select(!c(UK,London,areaCode,areaType,age_categ,areaName)) %>% rename(population=England) %>% 
   ungroup() %>% mutate(age_num=as.numeric(factor(age)),
                        meta_age=ifelse(ceiling(age_num/2)>8,9,ceiling(age_num/2))) %>% 
   group_by(date,meta_age) %>% 
@@ -363,7 +364,7 @@ deaths_age<-read_csv(death_url) %>% group_by(age) %>%
   mutate(rolling_rate_per_alldeaths=roll_mean(deaths,n=7,align="center",fill=NA)) %>% ungroup()  
 
 # lineplots
-df_deaths <- left_join(deaths_age,ons_all_age_groups_uk_england_2019 %>% select(!UK),by="age") %>% 
+df_deaths <- left_join(deaths_age,ons_all_age_groups_uk_england_2019 %>% select(!c(UK,London)),by="age") %>% 
   rename(population=England) %>% mutate(age_uplim=as.numeric(gsub("^.*_","",age)),
             age_grp=ifelse(age_uplim<=49,"00_49",ifelse(age_uplim>=49&age_uplim<=59,"50_59",age)),
             age_grp=ifelse(grepl("\\+",age),age,age_grp)) %>% filter(!age %in% c("00_59","60+")) %>% 

diff --git a/london/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear.png b/london/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear.png
diff --git a/...ses_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear_nofacet.png b/...ses_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear_nofacet.png
diff --git a/...ases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear_yfixed.png b/...ases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_linear_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log.png b/london/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log.png
diff --git a/.../cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log_nofacet.png b/.../cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log_nofacet.png
diff --git a/...n/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log_yfixed.png b/...n/cases_hosp_deaths_from_2020_12_01/london_cases_by_age_lineplot_log_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear.png b/london/cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear.png
diff --git a/...es_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear_nofacet.png b/...es_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear_nofacet.png
diff --git a/...ses_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear_yfixed.png b/...ses_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_linear_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log.png b/london/cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log.png
diff --git a/...cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log_nofacet.png b/...cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log_nofacet.png
diff --git a/.../cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log_yfixed.png b/.../cases_hosp_deaths_from_2020_12_01/london_deaths_by_age_lineplot_log_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear.png b/london/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear.png
diff --git a/...ses_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear_nofacet.png b/...ses_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear_nofacet.png
diff --git a/...ases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear_yfixed.png b/...ases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_linear_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log.png b/london/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log.png
diff --git a/.../cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log_nofacet.png b/.../cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log_nofacet.png
diff --git a/...n/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log_yfixed.png b/...n/cases_hosp_deaths_from_2021_07_01/london_cases_by_age_lineplot_log_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear.png b/london/cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear.png
diff --git a/...es_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear_nofacet.png b/...es_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear_nofacet.png
diff --git a/...ses_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear_yfixed.png b/...ses_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_linear_yfixed.png
diff --git a/london/cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log.png b/london/cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log.png
diff --git a/...cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log_nofacet.png b/...cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log_nofacet.png
diff --git a/.../cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log_yfixed.png b/.../cases_hosp_deaths_from_2021_07_01/london_deaths_by_age_lineplot_log_yfixed.png
diff --git a/london/cumul_deaths_by_age.png b/london/cumul_deaths_by_age.png
diff --git a/london/london_cases_age_4groups_rollingsum_change.png b/london/london_cases_age_4groups_rollingsum_change.png
diff --git a/london/london_cases_number_10_yr_agebands_y_lin_fixed.png b/london/london_cases_number_10_yr_agebands_y_lin_fixed.png
diff --git a/london/london_cases_number_10_yr_agebands_y_log_fixed.png b/london/london_cases_number_10_yr_agebands_y_log_fixed.png
diff --git a/london/london_cases_number_10_yr_agebands_y_log_free.png b/london/london_cases_number_10_yr_agebands_y_log_free.png
diff --git a/london/ons_all_age_groups_london_2019.csv b/london/ons_all_age_groups_london_2019.csv
@@ -0,0 +1,20 @@
+age,London
+0-4,"615,881"
+5-9,"599,855"
+10-14,"524,126"
+15-19,"464,768"
+20-24,"563,241"
+25-29,"784,361"
+30-34,"849,074"
+35-39,"783,331"
+40-44,"646,347"
+45-49,"596,141"
+50-54,"564,205"
+55-59,"479,470"
+60-64,"378,068"
+65-69,"309,586"
+70-74,"265,847"
+75-79,"189,753"
+80-84,"147,303"
+85-89,"91,993"
+90+,"54,731"
diff --git a/london/vaccine_data/vaccine_allage_phaseportrait_3rows.png b/london/vaccine_data/vaccine_allage_phaseportrait_3rows.png
diff --git a/london/vaccine_data/vaccine_by_age_cumul.png b/london/vaccine_data/vaccine_by_age_cumul.png
diff --git a/london/vaccine_data/vaccine_by_age_phaseportrait_both_doses_line_log.png b/london/vaccine_data/vaccine_by_age_phaseportrait_both_doses_line_log.png
diff --git a/london/vaccine_data/vaccine_by_age_rate_absnum_lin.png b/london/vaccine_data/vaccine_by_age_rate_absnum_lin.png
diff --git a/london/vaccine_data/vaccine_by_age_rate_absnum_log.png b/london/vaccine_data/vaccine_by_age_rate_absnum_log.png
diff --git a/london/vaccine_data/vaccine_by_age_rate_lin.png b/london/vaccine_data/vaccine_by_age_rate_lin.png
diff --git a/london/vaccine_data/vaccine_by_age_rate_log.png b/london/vaccine_data/vaccine_by_age_rate_log.png
diff --git a/london_datavis.R b/london_datavis.R
diff --git a/ons_all_age_groups_uk_england_2019.csv b/ons_all_age_groups_uk_england_2019.csv
@@ -1,21 +1,20 @@
-age,UK,England
-00_04,3857263,3299637
-05_09,4149852,3538206
-10_14,3953866,3354246
-15_19,3656968,3090232
-20_24,4153080,3487863
-25_29,4514249,3801409
-30_34,4497132,3807954
-35_39,4395667,3733642
-40_44,4019539,3414297
-45_49,4402122,3715812
-50_54,4661015,3907461
-55_59,4405908,3670651
-60_64,3755185,3111835
-65_69,3368199,2796740
-70_74,3318867,2779326
-75_79,2325296,1940686
-80_84,1715328,1439913
-85_89,1042090,879778
-90+,605181,517273
-
+age,UK,England,London
+00_04,3857263,3299637,615881
+05_09,4149852,3538206,599855
+10_14,3953866,3354246,524126
+15_19,3656968,3090232,464768
+20_24,4153080,3487863,563241
+25_29,4514249,3801409,784361
+30_34,4497132,3807954,849074
+35_39,4395667,3733642,783331
+40_44,4019539,3414297,646347
+45_49,4402122,3715812,596141
+50_54,4661015,3907461,564205
+55_59,4405908,3670651,479470
+60_64,3755185,3111835,378068
+65_69,3368199,2796740,309586
+70_74,3318867,2779326,265847
+75_79,2325296,1940686,189753
+80_84,1715328,1439913,147303
+85_89,1042090,879778,91993
+90+,605181,517273,54731