tests/testthat/test_merge_prov.R
In choisy/poseid: Population-based Observational Studies of the Epidemiology of Infectious Diseases
library(dplyr) #for 'filter'
library(dictionary) # for 'province_year'
library(magrittr) # for '%>%'
library(gso) # for the data table
library(gdpm) # for 'getid'
library(tidyr) # for 'replace_na'
context("Test if `merge_prov` returns the correct output")
# test merge_prov sum ---------------------------------------------------------
test_that("`merge_prov` sums correcty", {
test <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
# FROM >= 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1992-01-01", to = "2015-12-31")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total)
# Can Tho
expect_equal(df %>%
filter(province == "Can Tho", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004, key == "total") %>% .$value,
test %>% filter(province == "Yen Bai", year == 2004) %>% .$total)
# FROM < 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1990-01-01", to = "2015-12-31")
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2002) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2002) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2010) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2010) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2007) %>% .$total)
# From <= 1989
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1989-01-01", to = "2015-12-31")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007, key == "total") %>%
.$value,
test %>% filter(province == "Quang Binh", year == 2007) %>% .$total +
test %>% filter(province == "Quang Tri", year == 2007) %>% .$total +
test %>% filter(province == "Thua Thien Hue", year == 2007) %>% .$total)
})
# test NA-----------------------------------------------------------------------
test_that("`merge_prov` sums correcty and returns NA when one of the province
merge back together as an NA value", {
test <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]]
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2015-12-31")
expect_equal(df %>%
filter(province == "Hau Giang", year > 1994) %>%
select(value) %>% unlist %>% as.vector,
c(138.8, 118.4, 129.3, 82.1, rep(NA, 17)))
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2016-12-31", na.rm = TRUE)
expect_equal(df %>% filter(province == "Hau Giang", year > 1994) %>%
select(value) %>% unlist %>% as.vector,
test %>% filter(province == "Can Tho", year > 1994) %>%
.$planted_area_of_winter_paddy %>% replace_na(0) +
test %>% filter(province == "Soc Trang", year > 1994) %>%
.$planted_area_of_winter_paddy %>% replace_na(0))
})
# test provinces names ---------------------------------------------------------
test_that("`merge_prov` merges back together the good provinces", {
# < 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1979-1990` %>% unique)
# 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1990-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1990-1991` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1991-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1991-1992` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1992-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`1992-1997` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1997-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`1997-2004` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "2004-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`2004-2008` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "2008-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province)) %>% sort,
dictionary::vn_admin1_year$`2008-2020` %>% unique)
})
# test merge_prov -------------------------------------------------------------
test_that("`merge_prov` applies weighted mean correcty", {
test <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]]
pop_size <- gso::content %>% filter(data_name == "demography_5") %>%
.$data %>% .[[1]] %>% dplyr::select(province, year, total) %>%
mutate(year = as.numeric(year))
# FROM >= 1992
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1992-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2007) %>% .[, 3],
test %>% filter(province == "Ha Tay", year == 2007) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Ha Tay", year == 2007) %>%
.["total"]) %>% unlist()))
# Can Tho NA
expect_equal(df %>%
filter(province == "Can Tho", year == 2005) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2005) %>% .[, 3],
test %>% filter(province == "Hau Giang", year == 2005) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Hau Giang", year == 2005) %>%
.["total"]) %>% unlist()
))
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Dak Lak", year == 2006) %>% .[, 3],
test %>% filter(province == "Dak Nong", year == 2006) %>% .[, 3]),
c(pop_size %>% filter(province == "Dak Lak", year == 2006) %>%
.["total"],
pop_size %>% filter(province == "Dak Nong", year == 2006) %>%
.["total"]) %>% unlist()
))
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004) %>% .$value,
weighted.mean(
test %>% filter(province == "Yen Bai", year == 2004) %>% .[, 3],
pop_size %>% filter(province == "Yen Bai", year == 2004) %>%
.["total"]))
# FROM < 1992
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1990-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Hau Giang NA
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2002) %>% .[, 3],
test %>% filter(province == "Soc Trang", year == 2002) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2002) %>%
.["total"],
pop_size %>% filter(province == "Soc Trang", year == 2002) %>%
.["total"]) %>% unlist()
))
# Hau Giang NA
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2005) %>% .[, 3],
test %>% filter(province == "Hau Giang", year == 2005) %>% .[, 3],
test %>% filter(province == "Soc Trang", year == 2005) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Hau Giang", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Soc Trang", year == 2005) %>%
.["total"]) %>% unlist()
))
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2010) %>% .[, 3],
test %>% filter(province == "Hoa Binh", year == 2010) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2010) %>%
.["total"],
pop_size %>% filter(province == "Hoa Binh", year == 2010) %>%
.["total"]) %>% unlist()
))
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2007) %>% .[, 3],
test %>% filter(province == "Ha Tay", year == 2007) %>% .[, 3],
test %>% filter(province == "Hoa Binh", year == 2007) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Ha Tay", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Hoa Binh", year == 2007) %>%
.["total"]) %>% unlist())
)
# From <= 1990
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1989-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Quang Binh", year == 2007) %>% .[, 3],
test %>% filter(province == "Quang Tri", year == 2007) %>% .[, 3],
test %>% filter(province == "Thua Thien Hue", year == 2007) %>%
.[, 3]),
c(pop_size %>% filter(province == "Quang Binh", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Quang Tri", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Thua Thien Hue",
year == 2007) %>% .["total"]) %>% unlist()
))
})
# test splits list in merge_prov -----------------------------------------------
test_that("`merge_prov` follow the best list", {
test <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
# FROM >= 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1992-01-01", to = "2015-12-31")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total)
# Can Tho
expect_equal(df %>%
filter(province == "Can Tho", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004, key == "total") %>% .$value,
test %>% filter(province == "Yen Bai", year == 2004) %>% .$total)
# FROM < 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2002) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2002) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2010) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2010) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2007) %>% .$total)
# From <= 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007, key == "total") %>%
.$value,
test %>% filter(province == "Quang Binh", year == 2007) %>% .$total +
test %>% filter(province == "Quang Tri", year == 2007) %>% .$total +
test %>% filter(province == "Thua Thien Hue", year == 2007) %>% .$total)
# Province
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
expect_equal(
mean(df$province %in%
dictionary::vn_admin1_year$`1979-1990`), 1)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1991-01-01", to = "2015-12-31")
expect_equal(
mean(df$province %in%
dictionary::vn_admin1_year$`1991-1992`), 1)
})
# test merge_prov with monthly data---------------------------------------------
test_that("`merge_prov` returns the correct values for monthly data", {
dyear <- seq(1989, 2009)
chickenpox <- NULL
for (i in seq_along(dyear)[-length(dyear)]){
c <- gdpm::getid(chickenpox, from = dyear[i],
to = paste0(dyear[i], "-12-01"))
chickenpox <- rbind(chickenpox, c) %>%
dplyr::filter(duplicated(.) == FALSE)
}
chickenpox0 <- tidyr::replace_na(chickenpox,
list(incidence_chickenpox = 0))
expect_equal(
merge_prov(chickenpox, from = "2000-01-01", to = "2000-12-01") %>%
dplyr::filter(province == "Cao Bang", key == "incidence_chickenpox") %>%
.$value,
c(0, 21, 0, 0, 0, 7, 0, 0, 1, 0, 0, 0))
expect_equal(
merge_prov(chickenpox, from = "1991-01-01", to = "1992-12-01") %>%
dplyr::filter(province == "Ha Nam Ninh",
key == "incidence_chickenpox") %>%
.$value,
c(75, 0, 36, 0, 57, 69, 122, 88, 98, 119, 65, 27, 21, 18, 62, 59, 74, 89,
144, 67, 59, 37, 22, 24))
expect_equal(
merge_prov(chickenpox, from = "1996-01-01", to = "1997-12-01") %>%
dplyr::filter(province == "Nam Ha",
key == "incidence_chickenpox") %>%
.$value,
c(17, 24, 57, 8, 0, 6, 7, 19, 17, 12, 39, 5, 67, 18, 35, 21, 12, 13, 31, 29,
20, 6, 22, 10))
expect_equal(
merge_prov(chickenpox, from = "1991-01-01", to = "1997-12-01") %>%
dplyr::filter(province == "Ha Nam Ninh",
key == "incidence_chickenpox") %>%
.$value,
c(75, 0, 36, 0, 57, 69, 122, 88, 98, 119, 65, 27, 21, 18, 62, 59, 74, 89,
144, 67, 59, 37, 22, 24, 17, 11, 52, 9, 34, 78, 142, 141, 131, 39, 13, 23,
82, 15, 69, 65, 54, 60, 83, 56, 21, 15, 15, 1, 7, 17, 45, 51, 31, 36, 69,
38, 35, 27, 16, 21, 22, 38, 57, 12, 6, 6, 26, 27, 17, 12, 39, 6, 70, 18,
39, 21, 18, 20, 33, 35, 25, 6, 23, 10))
expect_equal(
merge_prov(chickenpox0, from = "1989-01-01", to = "1990-12-01") %>%
dplyr::filter(province == "Binh Tri Thien",
key == "incidence_chickenpox") %>%
.$value,
c(8, 6, 4, 25, 0, 0, 0, 17, 30, 1, 3, 0, 10, 6, 3, 8, 4, 2, 0, 0, 0,
0, 0, 13))
expect_equal(
merge_prov(chickenpox, from = "2007-01-01", to = "2008-12-01") %>%
dplyr::filter(province == "Ha Noi",
key == "incidence_chickenpox") %>%
.$value,
c(273, 1315, 1569, 674, 461, 347, 244, 227, 51, 52, 143, 192, 680, 653,
1260, 988, 459, 406, 289, 84, 714, 106, 89, 85))
expect_equal(
merge_prov(chickenpox0, from = "1991-01-01", to = "2008-12-01") %>%
dplyr::filter(province == "Ha Noi",
key == "incidence_chickenpox") %>%
.$value,
c(164, 52, 107, 132, 162, 106, 58, 111, 56, 120, 30, 22, 57, 119, 134, 117,
70, 53, 32, 69, 66, 23, 21, 44, 42, 34, 39, 102, 134, 107, 38, 97, 91, 46,
33, 27, 67, 96, 130, 72, 46, 64, 44, 16, 19, 18, 51, 35, 20, 39, 38, 53,
21, 46, 57, 49, 23, 29, 18, 40, 62, 168, 92, 87, 102, 59, 92, 103, 490,
284, 58, 31, 36, 40, 61, 69, 22, 109, 14, 12, 28, 9, 5, 29, 58, 32, 30,
33, 7, 68, 39, 28, 18, 24, 19, 17, 68, 98, 79, 93, 65, 39, 31, 28, 15,
20, 18, 14, 14, 43, 3, 113, 16, 39, 24, 35, 19, 15, 24, 37, 102, 99, 205,
91, 57, 54, 57, 40, 33, 14, 21, 39, 30, 43, 193, 23, 62, 59, 17, 17, 29,
43, 46, 28, 93, 62, 11, 13, 74, 114, 61, 70, 34, 71, 31, 108, 204, 579,
995, 844, 424, 411, 235, 158, 134, 79, 184, 140, 186, 79, 235, 406, 343,
268, 167, 168, 261, 82, 97, 235, 146, 511, 644, 657, 304, 236, 127, 115,
100, 81, 56, 109, 287, 1317, 1615, 758, 472, 393, 272, 242, 63, 63, 155,
267, 773, 668, 1304, 1152, 545, 505, 307, 102, 725, 111, 99, 105))
expect_error(merge_prov(chickenpox, from = "2117-01-01", to = "2119-01-01"))
})
test_that("`merge_prov` returns the correct error", {
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
expect_error(merge_prov(df, from = "1990-01-01", df2 = "fail"), regexp = NULL)
expect_error(merge_prov(df, from = "2119-01-01"), regexp = NULL)
expect_error(merge_prov(df, from = "2017-01-01"), regexp = NULL)
expect_error(merge_prov(df, sel = "patate", from = "2007-01-01"))
df2 <- gso::content %>% filter(data_name == "demography_5") %>%
.$data %>% .[[1]] %>% dplyr::select(province, year, total) %>%
mutate(year = as.numeric(year))
expect_error(merge_prov(df, from = "1990", df2 = df2,
args = c("total", "fail")), regexp = NULL)
expect_error(merge_prov(df, from = "1990", df2 = df2, args = "Fail"),
regexp = NULL)
names(df) <- c("oups", "its", "not", "going", "to", "work")
expect_warning(merge_prov(df, from = "1990-01-01"))
})
choisy/poseid documentation built on Aug. 22, 2019, 4:45 a.m.
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library(dplyr) #for 'filter'
library(dictionary) # for 'province_year'
library(magrittr) # for '%>%'
library(gso) # for the data table
library(gdpm) # for 'getid'
library(tidyr) # for 'replace_na'
context("Test if `merge_prov` returns the correct output")
# test merge_prov sum ---------------------------------------------------------
test_that("`merge_prov` sums correcty", {
test <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
# FROM >= 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1992-01-01", to = "2015-12-31")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total)
# Can Tho
expect_equal(df %>%
filter(province == "Can Tho", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004, key == "total") %>% .$value,
test %>% filter(province == "Yen Bai", year == 2004) %>% .$total)
# FROM < 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1990-01-01", to = "2015-12-31")
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2002) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2002) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2010) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2010) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2007) %>% .$total)
# From <= 1989
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1989-01-01", to = "2015-12-31")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007, key == "total") %>%
.$value,
test %>% filter(province == "Quang Binh", year == 2007) %>% .$total +
test %>% filter(province == "Quang Tri", year == 2007) %>% .$total +
test %>% filter(province == "Thua Thien Hue", year == 2007) %>% .$total)
})
# test NA-----------------------------------------------------------------------
test_that("`merge_prov` sums correcty and returns NA when one of the province
merge back together as an NA value", {
test <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]]
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2015-12-31")
expect_equal(df %>%
filter(province == "Hau Giang", year > 1994) %>%
select(value) %>% unlist %>% as.vector,
c(138.8, 118.4, 129.3, 82.1, rep(NA, 17)))
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2016-12-31", na.rm = TRUE)
expect_equal(df %>% filter(province == "Hau Giang", year > 1994) %>%
select(value) %>% unlist %>% as.vector,
test %>% filter(province == "Can Tho", year > 1994) %>%
.$planted_area_of_winter_paddy %>% replace_na(0) +
test %>% filter(province == "Soc Trang", year > 1994) %>%
.$planted_area_of_winter_paddy %>% replace_na(0))
})
# test provinces names ---------------------------------------------------------
test_that("`merge_prov` merges back together the good provinces", {
# < 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1980-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1979-1990` %>% unique)
# 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1990-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1990-1991` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1991-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Son Binh") %>% sort,
dictionary::vn_admin1_year$`1991-1992` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1992-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`1992-1997` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "1997-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`1997-2004` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "2004-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province), "Ha Tay") %>% sort,
dictionary::vn_admin1_year$`2004-2008` %>% unique)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, from = "2008-01-01", to = "2015-12-31")
expect_identical(c(unique(df$province)) %>% sort,
dictionary::vn_admin1_year$`2008-2020` %>% unique)
})
# test merge_prov -------------------------------------------------------------
test_that("`merge_prov` applies weighted mean correcty", {
test <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]]
pop_size <- gso::content %>% filter(data_name == "demography_5") %>%
.$data %>% .[[1]] %>% dplyr::select(province, year, total) %>%
mutate(year = as.numeric(year))
# FROM >= 1992
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1992-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2007) %>% .[, 3],
test %>% filter(province == "Ha Tay", year == 2007) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Ha Tay", year == 2007) %>%
.["total"]) %>% unlist()))
# Can Tho NA
expect_equal(df %>%
filter(province == "Can Tho", year == 2005) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2005) %>% .[, 3],
test %>% filter(province == "Hau Giang", year == 2005) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Hau Giang", year == 2005) %>%
.["total"]) %>% unlist()
))
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Dak Lak", year == 2006) %>% .[, 3],
test %>% filter(province == "Dak Nong", year == 2006) %>% .[, 3]),
c(pop_size %>% filter(province == "Dak Lak", year == 2006) %>%
.["total"],
pop_size %>% filter(province == "Dak Nong", year == 2006) %>%
.["total"]) %>% unlist()
))
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004) %>% .$value,
weighted.mean(
test %>% filter(province == "Yen Bai", year == 2004) %>% .[, 3],
pop_size %>% filter(province == "Yen Bai", year == 2004) %>%
.["total"]))
# FROM < 1992
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1990-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Hau Giang NA
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2002) %>% .[, 3],
test %>% filter(province == "Soc Trang", year == 2002) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2002) %>%
.["total"],
pop_size %>% filter(province == "Soc Trang", year == 2002) %>%
.["total"]) %>% unlist()
))
# Hau Giang NA
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Can Tho", year == 2005) %>% .[, 3],
test %>% filter(province == "Hau Giang", year == 2005) %>% .[, 3],
test %>% filter(province == "Soc Trang", year == 2005) %>% .[, 3]),
c(pop_size %>% filter(province == "Can Tho", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Hau Giang", year == 2005) %>%
.["total"],
pop_size %>% filter(province == "Soc Trang", year == 2005) %>%
.["total"]) %>% unlist()
))
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2010) %>% .[, 3],
test %>% filter(province == "Hoa Binh", year == 2010) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2010) %>%
.["total"],
pop_size %>% filter(province == "Hoa Binh", year == 2010) %>%
.["total"]) %>% unlist()
))
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Ha Noi", year == 2007) %>% .[, 3],
test %>% filter(province == "Ha Tay", year == 2007) %>% .[, 3],
test %>% filter(province == "Hoa Binh", year == 2007) %>% .[, 3]),
c(pop_size %>% filter(province == "Ha Noi", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Ha Tay", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Hoa Binh", year == 2007) %>%
.["total"]) %>% unlist())
)
# From <= 1990
df <- gso::content %>% filter(data_name == "agriculture_22") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = weighted.mean,
from = "1989-01-01", to = "2015-12-31",
df2 = pop_size, args = "total")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007) %>% .$value,
weighted.mean(c(
test %>% filter(province == "Quang Binh", year == 2007) %>% .[, 3],
test %>% filter(province == "Quang Tri", year == 2007) %>% .[, 3],
test %>% filter(province == "Thua Thien Hue", year == 2007) %>%
.[, 3]),
c(pop_size %>% filter(province == "Quang Binh", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Quang Tri", year == 2007) %>%
.["total"],
pop_size %>% filter(province == "Thua Thien Hue",
year == 2007) %>% .["total"]) %>% unlist()
))
})
# test splits list in merge_prov -----------------------------------------------
test_that("`merge_prov` follow the best list", {
test <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
# FROM >= 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1992-01-01", to = "2015-12-31")
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total)
# Can Tho
expect_equal(df %>%
filter(province == "Can Tho", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Yen Bai
expect_equal(df %>%
filter(province == "Yen Bai", year == 2004, key == "total") %>% .$value,
test %>% filter(province == "Yen Bai", year == 2004) %>% .$total)
# FROM < 1992
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
# Dack Lak
expect_equal(df %>%
filter(province == "Dack Lak", year == 2006, key == "total") %>% .$value,
test %>% filter(province == "Dak Lak", year == 2006) %>% .$total +
test %>% filter(province == "Dak Nong", year == 2006) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2002, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2002) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2002) %>% .$total)
# Hau Giang
expect_equal(df %>%
filter(province == "Hau Giang", year == 2005, key == "total") %>% .$value,
test %>% filter(province == "Can Tho", year == 2005) %>% .$total +
test %>% filter(province == "Soc Trang", year == 2005) %>% .$total +
test %>% filter(province == "Hau Giang", year == 2005) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2010, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2010) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2010) %>% .$total)
# Ha Noi
expect_equal(df %>%
filter(province == "Ha Noi", year == 2007, key == "total") %>% .$value,
test %>% filter(province == "Ha Noi", year == 2007) %>% .$total +
test %>% filter(province == "Ha Tay", year == 2007) %>% .$total +
test %>% filter(province == "Hoa Binh", year == 2007) %>% .$total)
# From <= 1990
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
# Binh Tri Thien
expect_equal(df %>%
filter(province == "Binh Tri Thien", year == 2007, key == "total") %>%
.$value,
test %>% filter(province == "Quang Binh", year == 2007) %>% .$total +
test %>% filter(province == "Quang Tri", year == 2007) %>% .$total +
test %>% filter(province == "Thua Thien Hue", year == 2007) %>% .$total)
# Province
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1990-01-01", to = "2015-12-31")
expect_equal(
mean(df$province %in%
dictionary::vn_admin1_year$`1979-1990`), 1)
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]] %>%
merge_prov(FUN = sum, diseases = c("hepatitis", "cholera", "ili"),
from = "1991-01-01", to = "2015-12-31")
expect_equal(
mean(df$province %in%
dictionary::vn_admin1_year$`1991-1992`), 1)
})
# test merge_prov with monthly data---------------------------------------------
test_that("`merge_prov` returns the correct values for monthly data", {
dyear <- seq(1989, 2009)
chickenpox <- NULL
for (i in seq_along(dyear)[-length(dyear)]){
c <- gdpm::getid(chickenpox, from = dyear[i],
to = paste0(dyear[i], "-12-01"))
chickenpox <- rbind(chickenpox, c) %>%
dplyr::filter(duplicated(.) == FALSE)
}
chickenpox0 <- tidyr::replace_na(chickenpox,
list(incidence_chickenpox = 0))
expect_equal(
merge_prov(chickenpox, from = "2000-01-01", to = "2000-12-01") %>%
dplyr::filter(province == "Cao Bang", key == "incidence_chickenpox") %>%
.$value,
c(0, 21, 0, 0, 0, 7, 0, 0, 1, 0, 0, 0))
expect_equal(
merge_prov(chickenpox, from = "1991-01-01", to = "1992-12-01") %>%
dplyr::filter(province == "Ha Nam Ninh",
key == "incidence_chickenpox") %>%
.$value,
c(75, 0, 36, 0, 57, 69, 122, 88, 98, 119, 65, 27, 21, 18, 62, 59, 74, 89,
144, 67, 59, 37, 22, 24))
expect_equal(
merge_prov(chickenpox, from = "1996-01-01", to = "1997-12-01") %>%
dplyr::filter(province == "Nam Ha",
key == "incidence_chickenpox") %>%
.$value,
c(17, 24, 57, 8, 0, 6, 7, 19, 17, 12, 39, 5, 67, 18, 35, 21, 12, 13, 31, 29,
20, 6, 22, 10))
expect_equal(
merge_prov(chickenpox, from = "1991-01-01", to = "1997-12-01") %>%
dplyr::filter(province == "Ha Nam Ninh",
key == "incidence_chickenpox") %>%
.$value,
c(75, 0, 36, 0, 57, 69, 122, 88, 98, 119, 65, 27, 21, 18, 62, 59, 74, 89,
144, 67, 59, 37, 22, 24, 17, 11, 52, 9, 34, 78, 142, 141, 131, 39, 13, 23,
82, 15, 69, 65, 54, 60, 83, 56, 21, 15, 15, 1, 7, 17, 45, 51, 31, 36, 69,
38, 35, 27, 16, 21, 22, 38, 57, 12, 6, 6, 26, 27, 17, 12, 39, 6, 70, 18,
39, 21, 18, 20, 33, 35, 25, 6, 23, 10))
expect_equal(
merge_prov(chickenpox0, from = "1989-01-01", to = "1990-12-01") %>%
dplyr::filter(province == "Binh Tri Thien",
key == "incidence_chickenpox") %>%
.$value,
c(8, 6, 4, 25, 0, 0, 0, 17, 30, 1, 3, 0, 10, 6, 3, 8, 4, 2, 0, 0, 0,
0, 0, 13))
expect_equal(
merge_prov(chickenpox, from = "2007-01-01", to = "2008-12-01") %>%
dplyr::filter(province == "Ha Noi",
key == "incidence_chickenpox") %>%
.$value,
c(273, 1315, 1569, 674, 461, 347, 244, 227, 51, 52, 143, 192, 680, 653,
1260, 988, 459, 406, 289, 84, 714, 106, 89, 85))
expect_equal(
merge_prov(chickenpox0, from = "1991-01-01", to = "2008-12-01") %>%
dplyr::filter(province == "Ha Noi",
key == "incidence_chickenpox") %>%
.$value,
c(164, 52, 107, 132, 162, 106, 58, 111, 56, 120, 30, 22, 57, 119, 134, 117,
70, 53, 32, 69, 66, 23, 21, 44, 42, 34, 39, 102, 134, 107, 38, 97, 91, 46,
33, 27, 67, 96, 130, 72, 46, 64, 44, 16, 19, 18, 51, 35, 20, 39, 38, 53,
21, 46, 57, 49, 23, 29, 18, 40, 62, 168, 92, 87, 102, 59, 92, 103, 490,
284, 58, 31, 36, 40, 61, 69, 22, 109, 14, 12, 28, 9, 5, 29, 58, 32, 30,
33, 7, 68, 39, 28, 18, 24, 19, 17, 68, 98, 79, 93, 65, 39, 31, 28, 15,
20, 18, 14, 14, 43, 3, 113, 16, 39, 24, 35, 19, 15, 24, 37, 102, 99, 205,
91, 57, 54, 57, 40, 33, 14, 21, 39, 30, 43, 193, 23, 62, 59, 17, 17, 29,
43, 46, 28, 93, 62, 11, 13, 74, 114, 61, 70, 34, 71, 31, 108, 204, 579,
995, 844, 424, 411, 235, 158, 134, 79, 184, 140, 186, 79, 235, 406, 343,
268, 167, 168, 261, 82, 97, 235, 146, 511, 644, 657, 304, 236, 127, 115,
100, 81, 56, 109, 287, 1317, 1615, 758, 472, 393, 272, 242, 63, 63, 155,
267, 773, 668, 1304, 1152, 545, 505, 307, 102, 725, 111, 99, 105))
expect_error(merge_prov(chickenpox, from = "2117-01-01", to = "2119-01-01"))
})
test_that("`merge_prov` returns the correct error", {
df <- gso::content %>% filter(data_name == "education_3") %>%
.$data %>% .[[1]]
expect_error(merge_prov(df, from = "1990-01-01", df2 = "fail"), regexp = NULL)
expect_error(merge_prov(df, from = "2119-01-01"), regexp = NULL)
expect_error(merge_prov(df, from = "2017-01-01"), regexp = NULL)
expect_error(merge_prov(df, sel = "patate", from = "2007-01-01"))
df2 <- gso::content %>% filter(data_name == "demography_5") %>%
.$data %>% .[[1]] %>% dplyr::select(province, year, total) %>%
mutate(year = as.numeric(year))
expect_error(merge_prov(df, from = "1990", df2 = df2,
args = c("total", "fail")), regexp = NULL)
expect_error(merge_prov(df, from = "1990", df2 = df2, args = "Fail"),
regexp = NULL)
names(df) <- c("oups", "its", "not", "going", "to", "work")
expect_warning(merge_prov(df, from = "1990-01-01"))
})
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