diff --git a/data-raw/US/CSO/1980 CSO/USA_1980_CSO-CET.xlsx b/data-raw/US/CSO/1980 CSO/USA_1980_CSO-CET.xlsx
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diff --git a/data-raw/US/CSO/2001 CSO Preferred/2001 CSO Preferred Class Structure Mortality Tables.xls b/data-raw/US/CSO/2001 CSO Preferred/2001 CSO Preferred Class Structure Mortality Tables.xls
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diff --git a/data-raw/US/CSO/2001 CSO/CSO_taskforce_appendix_j3_june2002.xls b/data-raw/US/CSO/2001 CSO/CSO_taskforce_appendix_j3_june2002.xls
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diff --git a/data-raw/US/CSO/2001 CSO/Table 2001 VBT CSO.xls b/data-raw/US/CSO/2001 CSO/Table 2001 VBT CSO.xls
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diff --git a/data-raw/US/create_MortalityTables_US_CSO.R b/data-raw/US/create_MortalityTables_US_CSO.R
index 5b20779436d0b33d718d84bcfded9ccf265df973..1d3e6edfb27cad87a7f26001c8cb8ae50062c7f0 100644
--- a/data-raw/US/create_MortalityTables_US_CSO.R
+++ b/data-raw/US/create_MortalityTables_US_CSO.R
@@ -52,6 +52,320 @@ createUSSelectTable = function(
+#############################################################################h#
+# USA 1980 CSO Tables ####
+#############################################################################h#
+
+CSO1980.file = here::here("data-raw", "US", "CSO", "1980 CSO", "USA_1980_CSO-CET.xlsx")
+CSO1980.file.out = here::here("data", "CSO1980.RData")
+
+CSO1980 = array(
+ data = c(mortalityTable.NA),
+ dim = c(7, 2, 3),
+ dimnames = list(
+ sex = c("m", "80% Male", "60% Male", "50% Male", "40% Male", "20% Male", "f"),
+ age = c("ANB", "ALB"),
+ type = c("Composite", "Non-Smoker", "Smoker")
+ )
+)
+CET1980 = CSO1980
+
+CSO1980.basic = array(
+ data = c(mortalityTable.NA),
+ dim = c(2, 1, 3),
+ dimnames = list(
+ sex = c("m", "f"),
+ age = c("ANB"),
+ type = c("Composite", "Non-Smoker", "Smoker")
+ )
+)
+
+createCSO1980 = function(
+ data, col, age.col = "Age",
+ sex = "Male", collar = "Composite", ageType = "ANB",
+ table = "1980 CSO", baseYear = 1980, ...
+) {
+ qx = data %>%
+ select(age = !!age.col, qx = !!col) %>%
+ filter(!is.na(qx))
+
+ name = ifelse(collar == "Composite",
+ sprintf("%s %s %s", table, sex, ageType),
+ sprintf("%s %s %s %s", table, sex, collar, ageType))
+
+ mortalityTable.period(
+ name = name, ages = qx$age, deathProbs = qx$qx, baseYear = baseYear,
+ selectInitialAge = TRUE,
+ data = list(
+ dim = list(table = table, sex = sex, collar = collar, country = "USA", ageType = ageType, data = "official", year = baseYear, ...)
+ )
+ )
+}
+
+
+# plotMortalityTables(CSO1980) + facet_grid(.~ageType)
+#-----------------------------------------------------------------#
+### Primary Tables: M/F Comp/NS/SM ANB ####
+#-----------------------------------------------------------------#
+
+CSO.data = full_join(
+ read_excel(CSO1980.file, sheet = "1980 CSO", skip = 4),
+ read_excel(CSO1980.file, sheet = "1980 CSO gender-blended", skip = 5),
+ by = "Age"
+)
+CET.data = full_join(
+ read_excel(CSO1980.file, sheet = "1980 CET", skip = 4),
+ read_excel(CSO1980.file, sheet = "1980 CET gender-blended", skip = 5),
+ by = "Age"
+)
+for (sex in c("m", "80% Male", "60% Male", "50% Male", "40% Male", "20% Male", "f")) {
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ for (ageType in c("ANB", "ALB")) {
+ for (type in c("Composite", "Non-Smoker", "Smoker")) {
+ col = ifelse(type == "Composite", paste(Sx, ageType), paste(Sx, type, ageType))
+ CSO1980[[sex, ageType, type]] = createCSO1980(
+ data = CSO.data, col = col, age.col = "Age",
+ table = "1980 CSO", sex = Sx, collar = type, ageType = ageType
+ )
+ CET1980[[sex, ageType, type]] = createCSO1980(
+ data = CSO.data, col = col, age.col = "Age",
+ table = "1980 CSO", sex = Sx, collar = type, ageType = ageType
+ )
+ }
+ }
+}
+for (sex in c("m", "f")) {
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ for (ageType in c("ANB")) {
+ for (type in c("Composite", "Non-Smoker", "Smoker")) {
+ col = ifelse(type == "Composite", paste("Basic Table", Sx, ageType), paste("Basic Table", Sx, type, ageType))
+ CSO1980.basic[[sex, ageType, type]] = createCSO1980(
+ data = CSO.data, col = col, age.col = "Age",
+ table = "1980 CSO Basic", sex = Sx, collar = type, ageType = ageType
+ )
+ }
+ }
+}
+
+# plotMortalityTables(CSO1980, aes = aes(color = sex)) + facet_grid(ageType ~ collar)
+# plotMortalityTables(CSO1980.basic, aes = aes(color = sex)) + facet_grid(ageType ~ collar)
+# plotMortalityTables(CSO1980.basic, aes = aes(color = collar, linetype = sex))
+
+
+
+#-----------------------------------------------------------------#
+### Select tables ####
+#-----------------------------------------------------------------#
+
+CSO1980.select = CSO1980
+CET1980.select = CET1980
+
+# Add selection factors
+CSO1980.selectionFactors = list()
+
+for (sex in c("m", "80% Male", "60% Male", "50% Male", "40% Male", "20% Male", "f")) {
+ CSO1980.selectionFactors[[sex]] = read_excel(CSO1980.file, sheet = sprintf("Selection Factors %s", recode(sex, "m" = "Male", "f" = "Female")), skip = 4)
+ CSO1980.select[sex,,] = CSO1980.select[sex,,] %>%
+ mT.setSlot("selectionFactors", CSO1980.selectionFactors[[sex]]) %>%
+ mT.setDimInfo(data = "select")
+ CET1980.select[sex,,] = CET1980.select[sex,,] %>%
+ mT.setSlot("selectionFactors", CSO1980.selectionFactors[[sex]]) %>%
+ mT.setDimInfo(data = "select")
+}
+
+
+
+# plotMortalityTables(
+# CSO1980[,"ANB","Composite"] %>% mT.setDimInfo(SelectionAge = "Ultimate"),
+# CSO1980.select[,"ANB","Composite"] %>% getPeriodTable(Period = 1980, selectionAge = 20) %>% mT.setDimInfo(SelectionAge = 20),
+# CSO1980.select[,"ANB","Composite"] %>% getPeriodTable(Period = 1980, selectionAge = 40) %>% mT.setDimInfo(SelectionAge = 40),
+# CSO1980.select[,"ANB","Composite"] %>% getPeriodTable(Period = 1980, selectionAge = 60) %>% mT.setDimInfo(SelectionAge = 60),
+# CSO1980.select[,"ANB","Composite"] %>% getPeriodTable(Period = 1980, selectionAge = 80) %>% mT.setDimInfo(SelectionAge = 80),
+# aes = aes(color = as.factor(SelectionAge))
+# ) + facet_grid(sex~.)
+
+
+save(CSO1980, CET1980, CSO1980.basic, CSO1980.select, CET1980.select, file = CSO1980.file.out)
+
+
+
+
+
+
+
+#############################################################################h#
+# USA 2001 CSO Tables ####
+#############################################################################h#
+
+CSO2001.file.out = here::here("data", "CSO2001.RData")
+
+CSO2001 = array(
+ data = c(mortalityTable.NA),
+ dim = c(7, 2, 3),
+ dimnames = list(
+ sex = c("m", "80% Male", "60% Male", "50% Male", "40% Male", "20% Male", "f"),
+ age = c("ANB", "ALB"),
+ type = c("Composite", "Non-Smoker", "Smoker")
+ )
+)
+
+createCSO2001 = function(
+ file, sheet, skip = 2,
+ sex = "m", collar = "Composite", ageType,
+ age.col = "Iss. Age", rm.cols = c("Att. Age"),
+ ...
+) {
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ name = sprintf("2001 CSO %s %s %s", Sx, collar, ageType)
+ if(missing(sheet)) {
+ if (collar == "Composite") {
+ sheet = sprintf("2001 %s %s %s", Sx, collar, ageType)
+ } else {
+ sheet = sprintf("2001 %s%s %s", toupper(sex), recode(collar, "Smoker" = "SM", "Non-Smoker" = "NS"), ageType)
+ }
+ }
+ createUSSelectTable(
+ file = file, sheet = sheet, skip = skip,
+ age.col = age.col, rm.cols = rm.cols,
+ name = name, year = 2001, scale = 0.001,
+ table = sprintf("2001 CSO %s", collar), sex = sex, collar = collar, type = "CSO", country = "USA", ageType = ageType,
+ ...)
+}
+
+# plotMortalityTables(CSO2001) + facet_grid(.~ageType)
+#-----------------------------------------------------------------#
+### Primary Tables: M/F Comp/NS/SM ANB ####
+#-----------------------------------------------------------------#
+
+file = here::here("data-raw", "US", "CSO", "2001 CSO", "Table 2001 VBT CSO.xls")
+for (sex in c("m", "f")) {
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ for (ageType in c("ANB")) {
+ for (type in c("Composite", "Non-Smoker", "Smoker")) {
+ sheet = sprintf("CSO %s%s", toupper(sex), recode(type, "Composite" = "Comp", "Smoker" = "SM", "Non-Smoker" = "NS"))
+ CSO2001[[sex, ageType, type]] = createCSO2001(
+ file = file, sheet = sheet,
+ age.col = "2001 Valuation Basic Table and 2001 CSO Table", rm.cols = "Age",
+ sex = sex, collar = type, ageType = ageType
+ )
+ }
+ }
+}
+
+file = here::here("data-raw", "US", "CSO", "2001 CSO", "CSO_taskforce_appendix_j3_june2002.xls")
+for (sex in c("m", "f")) {
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ for (ageType in c("ALB")) {
+ for (type in c("Composite", "Non-Smoker", "Smoker")) {
+ sheet = sprintf("(%s) %s S&U %s", toupper(sex), type, ageType)
+ CSO2001[[sex, ageType, type]] = createCSO2001(
+ file = file, sheet = sheet, skip = 1,
+ age.col = "Issue Age", rm.cols = "Attained Age",
+ sex = sex, collar = type, ageType = ageType
+ )
+ }
+ }
+}
+
+# Gender-blended tables
+file = here::here("data-raw", "US", "CSO", "2001 CSO", "CSO_taskforce_appendix_j3_june2002.xls")
+for (sex in c("80% Male", "60% Male", "50% Male", "40% Male", "20% Male")) {
+ Sx = substr(sex, 1, 2)
+ for (ageType in c("ANB", "ALB")) {
+ for (type in c("Composite", "Non-Smoker", "Smoker")) {
+ sheet = sprintf("(%s) %s S&U %s", Sx, type, ageType)
+ CSO2001[[sex, ageType, type]] = createCSO2001(
+ file = file, sheet = sheet, skip = 1,
+ age.col = "Issue Age", rm.cols = "Attained Age",
+ sex = sex, collar = type, ageType = ageType
+ )
+ }
+ }
+}
+
+
+
+# plotMortalityTables(CSO2001) + facet_grid(ageType ~ collar) + aes(color = sex)
+# plotMortalityTables(CSO2001) + facet_grid(sex ~ ageType) + aes(color = collar)
+
+save(CSO2001, file = CSO2001.file.out)
+
+
+#-----------------------------------------------------------------#
+### Preferred 2001 CSO Tables (only loaded) ####
+#-----------------------------------------------------------------#
+
+CSO2001.Preferred = array(
+ data = c(mortalityTable.NA),
+ dim = c(3, 2, 2, 2),
+ dimnames = list(
+ preferred = c("Super Preferred", "Preferred", "Residual"),
+ sex = c("m", "f"),
+ age = c("ANB", "ALB"),
+ type = c("Non-Smoker", "Smoker")
+ )
+)
+
+createCSO2001.Preferred = function(
+ file, sheet, skip = 6,
+ sex = "m", collar = "Composite", ageType, Preferred = "Preferred",
+ age.col = "...1", rm.cols = c("Age"),
+ ...
+) {
+ # browser()
+ Sx = recode(sex, "m" = "Male", "f" = "Female")
+ name = sprintf("2001 CSO %s %s - %s %s", Preferred, ageType, Sx, collar)
+ if(missing(sheet)) {
+ if (collar == "Non-Smoker") {
+ prf = recode(Preferred, "Super Preferred" = 1, "Preferred" = 2, "Residual" = 3)
+ } else {
+ prf = recode(Preferred, "Preferred" = 1, "Residual" = 2)
+ }
+ sheet = sprintf("%s%s%s %s", toupper(sex), Sm.short, prf, ageType)
+ }
+ createUSSelectTable(
+ file = file, sheet = sheet, skip = skip,
+ age.col = age.col, rm.cols = rm.cols,
+ name = name, year = 2001, scale = 0.001,
+ table = sprintf("2001 CSO %s", collar), sex = sex, collar = collar, type = "CSO", country = "USA", ageType = ageType, Preferred = Preferred,
+ ...)
+}
+
+
+file = here::here("data-raw", "US", "CSO", "2001 CSO Preferred", "2001 CSO Preferred Class Structure Mortality Tables.xls")
+for (preferred in c("Super Preferred", "Preferred", "Residual")) {
+ for (sex in c("m", "f")) {
+ for (ageType in c("ANB", "ALB")) {
+ for (type in c("Smoker", "Non-Smoker")) {
+ # There are no super-preferred smokers => skip that case
+ if (preferred != "Super Preferred" || type != "Smoker") {
+ # Sheet naming is defined in the tab "Table of Contents": A.[1234].[ab].{i,ii,iii,iv,v}
+ sheet = sprintf("A.%d.%s.%s", recode(ageType, "ANB" = 1, "ALB" = 3), recode(sex, "m" = "a", "f" = "b"), recode(
+ paste(preferred, type),
+ "Super Preferred Non-Smoker" = "i",
+ "Preferred Non-Smoker" = "ii",
+ "Residual Non-Smoker" = "iii",
+ "Preferred Smoker" = "iv",
+ "Residual Smoker" = "v"))
+ CSO2001.Preferred[[preferred, sex, ageType, type]] = createCSO2001.Preferred(
+ file = file, sheet = sheet,
+ sex = sex, collar = type, ageType = ageType, Preferred = preferred
+ )
+ }
+ }
+ }
+ }
+}
+
+
+# plotMortalityTables(CSO2001.Preferred[,,"ANB",], legend.position = "bottom") + facet_grid(sex ~ collar) + aes(color = Preferred)
+
+save(CSO2001.Preferred, file = CSO2001Pref.file.out)
+
+
+
+
+
#############################################################################h#
# USA 2017 CSO Tables ####
#############################################################################h#
@@ -205,6 +519,7 @@ save(CSO2017, file = CSO2017file.out)
# plotMortalityTables(CSO2017) + facet_grid(ageType ~ collar) + aes(linetype = loaded, color = sex)
# plotMortalityTables(CSO2017) + facet_grid(sex ~ ageType) + aes(linetype = loaded, color = collar)
+# plotMortalityTables(CSO2017.Preferred[,,"ANB",,]) + facet_grid(sex ~ collar) + aes(linetype = loaded, color = Preferred)
#-----------------------------------------------------------------#
diff --git a/data/CSO1980.RData b/data/CSO1980.RData
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