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johnmackintosh/caseload.R

Created September 25, 2022 22:22
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as per Chris Beeley caseload question from NHSR demo and how-to
Raw
caseload.R
teams <- c("Apple", "Banana", "Clementine")
dates <- seq(as.Date("2017-01-01"), as.Date("2021-01-01"), "days")
# 5 columns- client id, referral id, team_desc, referral_date, discharge_date
test_frame <- purrr::map_dfr(1 : 100, function(x){
rnum <- sample(1 : 5, 1)
team_name <- sample(teams, rnum, replace = TRUE)
ran_date <- sample(dates, rnum)
tibble::tibble("client_id" = rep(x, rnum),
"referral_id" = 1 : rnum,
"team_desc" = team_name,
"referral_date" = ran_date,
"discharge_date" = ran_date + sample(7 : 365, 1))
})
test_frame[sample(nrow(test_frame), 100), "discharge_date"] = NA
library(data.table)
library(patientcounter)
setDT(test_frame)
test_frame[,`:=`(unique_id = paste0(test_frame$client_id,
"_", test_frame$referral_id),
referral_date = as.POSIXct(referral_date),
discharge_date = as.POSIXct(discharge_date))
]
discharged <- test_frame[!is.na(discharge_date)]
current <- test_frame[is.na(discharge_date)]
res_dis <- interval_census(discharged,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
results = "patient")
res_cur <- interval_census(current,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
results = "patient")
combined <- rbindlist(l =list(res_cur,res_dis))
# aggregate results by date and team
combined[, .N, .(base_date, team_desc)]
# alternatively, grouped by team
res_dis_g <- interval_census(discharged,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
group_var = "team_desc",
results = "group",
uniques = FALSE)
res_cur_g <- interval_census(current,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
group_var = "team_desc",
results = "group",
uniques = FALSE)
combined2 <- rbindlist(l =list(res_cur_g, res_dis_g))
combined2[,.(total = sum(N)), .(base_date, team_desc)]
# go for totals from the off
res_dis_t <- interval_census(discharged,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
group_var = "team_desc",
results = "total",
uniques = FALSE)
res_cur_t <- interval_census(current,
identifier = "unique_id",
admit = "referral_date",
discharge = "discharge_date",
time_unit = "1 day",
group_var = "team_desc",
results = "total",
uniques = FALSE)
combined3 <- rbindlist(l =list(res_cur_t, res_dis_t))
# checks
combined[base_date == '2022-09-25'] # 100 rows
combined[base_date == '2022-09-25', .N, team_desc] # tally by team (33 + 33 + 34)
combined2[base_date == '2022-09-25'] # N = 33 + 33 + 34 = 100
combined3[base_date == '2022-09-25'] # N = 100
@johnmackintosh
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Author 

dput(test_frame)
structure(list(client_id = c(1L, 2L, 2L, 3L, 4L, 4L, 4L, 4L, 
                             5L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 11L, 
                             12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 15L, 
                             15L, 15L, 16L, 17L, 17L, 17L, 18L, 19L, 19L, 20L, 21L, 21L, 21L, 
                             21L, 21L, 22L, 22L, 23L, 23L, 23L, 24L, 24L, 25L, 25L, 25L, 25L, 
                             26L, 27L, 27L, 28L, 28L, 28L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 
                             31L, 31L, 32L, 33L, 33L, 33L, 33L, 34L, 34L, 35L, 35L, 35L, 35L, 
                             35L, 36L, 36L, 36L, 36L, 37L, 37L, 37L, 37L, 38L, 38L, 39L, 39L, 
                             39L, 39L, 39L, 40L, 40L, 40L, 40L, 41L, 41L, 41L, 41L, 42L, 43L, 
                             44L, 44L, 44L, 44L, 44L, 45L, 45L, 45L, 45L, 45L, 46L, 47L, 47L, 
                             47L, 47L, 48L, 48L, 48L, 48L, 48L, 49L, 49L, 50L, 50L, 50L, 51L, 
                             51L, 52L, 52L, 52L, 52L, 52L, 53L, 53L, 53L, 53L, 54L, 55L, 55L, 
                             55L, 55L, 55L, 56L, 56L, 56L, 56L, 57L, 57L, 57L, 58L, 58L, 58L, 
                             58L, 58L, 59L, 59L, 59L, 59L, 60L, 60L, 60L, 61L, 62L, 62L, 62L, 
                             62L, 63L, 63L, 63L, 63L, 64L, 65L, 65L, 65L, 65L, 65L, 66L, 66L, 
                             66L, 66L, 67L, 68L, 68L, 68L, 68L, 68L, 69L, 69L, 69L, 70L, 70L, 
                             70L, 70L, 70L, 71L, 71L, 72L, 72L, 73L, 73L, 74L, 74L, 74L, 74L, 
                             74L, 75L, 75L, 76L, 77L, 77L, 77L, 77L, 77L, 78L, 78L, 78L, 79L, 
                             79L, 79L, 80L, 80L, 80L, 80L, 81L, 81L, 81L, 81L, 81L, 82L, 82L, 
                             82L, 82L, 83L, 83L, 84L, 84L, 84L, 85L, 86L, 86L, 86L, 86L, 86L, 
                             87L, 88L, 88L, 88L, 88L, 88L, 89L, 89L, 90L, 90L, 90L, 91L, 91L, 
                             92L, 93L, 93L, 93L, 93L, 94L, 94L, 94L, 94L, 95L, 95L, 95L, 95L, 
                             95L, 96L, 96L, 96L, 97L, 97L, 98L, 98L, 98L, 98L, 99L, 99L, 99L, 
                             99L, 100L), referral_id = c(1L, 1L, 2L, 1L, 1L, 2L, 3L, 4L, 1L, 
                                                         2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 1L, 2L, 
                                                         3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 1L, 2L, 
                                                         3L, 1L, 1L, 2L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 1L, 2L, 3L, 1L, 
                                                         2L, 1L, 2L, 3L, 4L, 1L, 1L, 2L, 1L, 2L, 3L, 1L, 1L, 2L, 3L, 4L, 
                                                         1L, 2L, 3L, 4L, 1L, 1L, 2L, 3L, 4L, 1L, 2L, 1L, 2L, 3L, 4L, 5L, 
                                                         1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 1L, 2L, 3L, 4L, 5L, 1L, 
                                                         2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 
                                                         3L, 4L, 5L, 1L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 1L, 
                                                         2L, 3L, 1L, 2L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 1L, 2L, 
                                                         3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 1L, 2L, 3L, 4L, 5L, 1L, 
                                                         2L, 3L, 4L, 1L, 2L, 3L, 1L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 
                                                         1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 
                                                         2L, 3L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 3L, 
                                                         4L, 5L, 1L, 2L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 1L, 2L, 3L, 
                                                         1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 1L, 
                                                         2L, 3L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 
                                                         1L, 2L, 3L, 1L, 2L, 1L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 
                                                         3L, 4L, 5L, 1L, 2L, 3L, 1L, 2L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 
                                                         1L), team_desc = c("Apple", "Banana", "Apple", "Banana", "Apple", 
                                                                            "Apple", "Clementine", "Clementine", "Banana", "Banana", "Clementine", 
                                                                            "Apple", "Banana", "Clementine", "Clementine", "Clementine", 
                                                                            "Banana", "Banana", "Banana", "Apple", "Apple", "Banana", "Banana", 
                                                                            "Banana", "Apple", "Banana", "Clementine", "Banana", "Apple", 
                                                                            "Clementine", "Clementine", "Apple", "Banana", "Apple", "Apple", 
                                                                            "Clementine", "Apple", "Apple", "Banana", "Banana", "Apple", 
                                                                            "Banana", "Clementine", "Clementine", "Clementine", "Apple", 
                                                                            "Apple", "Banana", "Banana", "Clementine", "Banana", "Banana", 
                                                                            "Clementine", "Apple", "Apple", "Banana", "Apple", "Banana", 
                                                                            "Clementine", "Clementine", "Clementine", "Banana", "Apple", 
                                                                            "Apple", "Apple", "Clementine", "Banana", "Clementine", "Clementine", 
                                                                            "Apple", "Banana", "Banana", "Apple", "Apple", "Apple", "Clementine", 
                                                                            "Banana", "Clementine", "Apple", "Clementine", "Clementine", 
                                                                            "Banana", "Banana", "Apple", "Clementine", "Banana", "Clementine", 
                                                                            "Clementine", "Apple", "Clementine", "Banana", "Banana", "Apple", 
                                                                            "Banana", "Apple", "Apple", "Apple", "Banana", "Banana", "Clementine", 
                                                                            "Banana", "Apple", "Apple", "Apple", "Clementine", "Apple", "Clementine", 
                                                                            "Banana", "Clementine", "Apple", "Clementine", "Banana", "Clementine", 
                                                                            "Clementine", "Clementine", "Banana", "Apple", "Clementine", 
                                                                            "Apple", "Apple", "Apple", "Clementine", "Clementine", "Clementine", 
                                                                            "Clementine", "Apple", "Apple", "Apple", "Apple", "Clementine", 
                                                                            "Clementine", "Clementine", "Apple", "Banana", "Banana", "Banana", 
                                                                            "Apple", "Apple", "Apple", "Apple", "Clementine", "Apple", "Apple", 
                                                                            "Clementine", "Clementine", "Banana", "Clementine", "Apple", 
                                                                            "Banana", "Apple", "Banana", "Banana", "Apple", "Banana", "Clementine", 
                                                                            "Apple", "Clementine", "Apple", "Banana", "Clementine", "Apple", 
                                                                            "Apple", "Clementine", "Clementine", "Apple", "Clementine", "Banana", 
                                                                            "Clementine", "Apple", "Clementine", "Apple", "Apple", "Apple", 
                                                                            "Clementine", "Clementine", "Apple", "Banana", "Banana", "Clementine", 
                                                                            "Banana", "Apple", "Clementine", "Apple", "Apple", "Clementine", 
                                                                            "Apple", "Banana", "Apple", "Clementine", "Banana", "Apple", 
                                                                            "Clementine", "Apple", "Banana", "Banana", "Clementine", "Apple", 
                                                                            "Banana", "Apple", "Clementine", "Banana", "Apple", "Apple", 
                                                                            "Clementine", "Banana", "Banana", "Banana", "Clementine", "Apple", 
                                                                            "Clementine", "Apple", "Apple", "Apple", "Clementine", "Apple", 
                                                                            "Apple", "Clementine", "Clementine", "Banana", "Banana", "Apple", 
                                                                            "Banana", "Clementine", "Banana", "Apple", "Apple", "Clementine", 
                                                                            "Clementine", "Banana", "Apple", "Apple", "Banana", "Banana", 
                                                                            "Banana", "Apple", "Apple", "Banana", "Banana", "Apple", "Apple", 
                                                                            "Clementine", "Apple", "Apple", "Apple", "Apple", "Apple", "Banana", 
                                                                            "Banana", "Banana", "Clementine", "Clementine", "Apple", "Apple", 
                                                                            "Banana", "Clementine", "Apple", "Apple", "Apple", "Clementine", 
                                                                            "Banana", "Banana", "Banana", "Clementine", "Banana", "Apple", 
                                                                            "Banana", "Clementine", "Clementine", "Apple", "Banana", "Apple", 
                                                                            "Clementine", "Banana", "Banana", "Clementine", "Banana", "Banana", 
                                                                            "Apple", "Apple", "Apple", "Banana", "Clementine", "Apple", "Apple", 
                                                                            "Banana", "Banana", "Clementine", "Banana", "Apple", "Clementine", 
                                                                            "Banana", "Clementine", "Clementine", "Clementine", "Banana", 
                                                                            "Clementine", "Clementine", "Banana"), referral_date = structure(c(1541548800, 
                                                                                                                                               1522368000, 1584144000, 1484697600, 1599004800, 1497916800, 1502668800, 
                                                                                                                                               1555113600, 1574294400, 1572393600, 1578614400, 1526256000, 1518998400, 
                                                                                                                                               1543363200, 1604966400, 1483574400, 1488067200, 1569283200, 1523318400, 
                                                                                                                                               1598313600, 1512950400, 1548720000, 1565395200, 1544832000, 1496966400, 
                                                                                                                                               1512864000, 1563494400, 1562112000, 1501200000, 1528761600, 1491523200, 
                                                                                                                                               1537660800, 1495670400, 1591401600, 1488240000, 1504224000, 1566432000, 
                                                                                                                                               1541289600, 1496707200, 1553990400, 1540339200, 1529625600, 1548115200, 
                                                                                                                                               1535241600, 1499644800, 1510099200, 1567296000, 1599004800, 1591574400, 
                                                                                                                                               1549584000, 1519344000, 1561939200, 1507680000, 1581465600, 1494460800, 
                                                                                                                                               1522195200, 1599436800, 1582070400, 1549152000, 1607385600, 1576540800, 
                                                                                                                                               1548806400, 1592006400, 1598140800, 1564531200, 1508112000, 1566691200, 
                                                                                                                                               1534291200, 1539043200, 1573776000, 1601251200, 1601510400, 1583884800, 
                                                                                                                                               1591056000, 1510272000, 1585180800, 1500249600, 1549843200, 1531440000, 
                                                                                                                                               1559433600, 1590105600, 1604966400, 1533513600, 1525219200, 1569974400, 
                                                                                                                                               1518912000, 1506729600, 1569456000, 1581379200, 1531094400, 1522627200, 
                                                                                                                                               1509408000, 1538092800, 1528070400, 1559088000, 1585785600, 1526428800, 
                                                                                                                                               1561075200, 1529452800, 1558396800, 1494374400, 1505260800, 1517011200, 
                                                                                                                                               1501200000, 1527379200, 1548633600, 1579651200, 1557273600, 1525651200, 
                                                                                                                                               1557964800, 1538784000, 1586304000, 1546992000, 1606348800, 1545350400, 
                                                                                                                                               1555891200, 1604880000, 1540512000, 1572220800, 1553040000, 1525737600, 
                                                                                                                                               1515888000, 1526169600, 1556236800, 1510617600, 1581465600, 1592265600, 
                                                                                                                                               1555545600, 1498867200, 1562457600, 1605312000, 1561248000, 1538438400, 
                                                                                                                                               1521331200, 1596585600, 1513987200, 1584835200, 1497830400, 1511568000, 
                                                                                                                                               1555632000, 1504396800, 1519689600, 1563494400, 1608681600, 1553817600, 
                                                                                                                                               1537574400, 1560816000, 1532995200, 1593648000, 1519344000, 1490832000, 
                                                                                                                                               1579910400, 1609286400, 1591056000, 1566518400, 1534896000, 1599091200, 
                                                                                                                                               1507852800, 1580256000, 1585699200, 1502755200, 1580428800, 1522627200, 
                                                                                                                                               1602288000, 1519171200, 1569801600, 1512604800, 1512777600, 1606608000, 
                                                                                                                                               1514937600, 1532476800, 1560816000, 1576195200, 1553212800, 1592352000, 
                                                                                                                                               1533859200, 1577059200, 1547942400, 1548374400, 1527811200, 1531094400, 
                                                                                                                                               1585180800, 1518912000, 1488672000, 1499731200, 1590019200, 1598918400, 
                                                                                                                                               1514246400, 1487376000, 1592438400, 1597017600, 1564531200, 1606348800, 
                                                                                                                                               1565049600, 1549411200, 1496707200, 1508284800, 1539734400, 1.566e+09, 
                                                                                                                                               1553385600, 1539388800, 1534464000, 1518307200, 1539043200, 1501891200, 
                                                                                                                                               1487289600, 1535155200, 1498089600, 1582848000, 1555113600, 1489276800, 
                                                                                                                                               1572566400, 1555200000, 1517184000, 1490054400, 1539043200, 1565654400, 
                                                                                                                                               1516060800, 1519344000, 1589500800, 1590278400, 1498521600, 1554249600, 
                                                                                                                                               1496361600, 1587600000, 1543017600, 1564617600, 1532563200, 1488499200, 
                                                                                                                                               1564531200, 1548288000, 1517788800, 1509321600, 1545264000, 1498003200, 
                                                                                                                                               1556928000, 1587427200, 1572998400, 1514505600, 1607817600, 1491782400, 
                                                                                                                                               1528070400, 1580947200, 1576800000, 1605657600, 1542844800, 1524009600, 
                                                                                                                                               1572912000, 1576454400, 1533081600, 1491782400, 1489190400, 1501113600, 
                                                                                                                                               1591401600, 1596585600, 1515715200, 1533168000, 1526342400, 1523750400, 
                                                                                                                                               1516579200, 1504224000, 1591920000, 1542326400, 1528588800, 1574035200, 
                                                                                                                                               1561852800, 1566777600, 1550707200, 1550793600, 1591920000, 1539820800, 
                                                                                                                                               1529884800, 1484697600, 1573603200, 1496620800, 1518307200, 1544400000, 
                                                                                                                                               1511654400, 1579219200, 1536883200, 1548460800, 1506470400, 1523750400, 
                                                                                                                                               1493337600, 1538870400, 1576281600, 1508544000, 1584489600, 1549497600, 
                                                                                                                                               1501113600, 1587427200, 1509753600, 1488672000, 1486598400, 1555372800, 
                                                                                                                                               1486771200, 1561161600, 1500768000), class = c("POSIXct", "POSIXt"
                                                                                                                                               )), discharge_date = structure(c(1572307200, NA, 1613088000, 
                                                                                                                                                                                1501372800, 1612828800, 1511740800, NA, NA, 1588982400, 1587081600, 
                                                                                                                                                                                NA, 1532131200, 1524873600, NA, NA, 1486598400, 1495065600, NA, 
                                                                                                                                                                                1530316800, 1603756800, 1518393600, 1554163200, NA, 1546300800, 
                                                                                                                                                                                1498435200, 1514332800, 1564963200, 1563580800, 1527552000, 1555113600, 
                                                                                                                                                                                1517875200, NA, 1496620800, NA, 1489190400, NA, 1581897600, 1556755200, 
                                                                                                                                                                                NA, 1583452800, 1569801600, 1559088000, 1571961600, 1552608000, 
                                                                                                                                                                                1517011200, NA, NA, 1622764800, 1615334400, NA, NA, 1590796800, 
                                                                                                                                                                                1536537600, NA, 1514160000, 1541894400, 1625356800, NA, NA, NA, 
                                                                                                                                                                                NA, 1576195200, 1592784000, 1607040000, 1573430400, NA, NA, 1548201600, 
                                                                                                                                                                                NA, 1598227200, NA, NA, 1608336000, 1596758400, 1515974400, 1590883200, 
                                                                                                                                                                                NA, 1574380800, NA, 1574035200, 1604707200, NA, 1536883200, NA, 
                                                                                                                                                                                1594598400, NA, NA, 1594080000, NA, 1532563200, NA, NA, 1539561600, 
                                                                                                                                                                                1557878400, 1588896000, NA, 1556236800, 1587600000, 1555977600, 
                                                                                                                                                                                NA, 1515801600, NA, 1538438400, NA, 1549584000, NA, 1601856000, 
                                                                                                                                                                                1579478400, 1533945600, 1566259200, 1547078400, 1594598400, 1576108800, 
                                                                                                                                                                                NA, 1556496000, NA, NA, NA, 1583366400, 1557792000, 1530489600, 
                                                                                                                                                                                1520640000, 1530921600, NA, NA, 1606694400, 1617494400, NA, NA, 
                                                                                                                                                                                1581811200, 1624665600, NA, NA, NA, NA, 1517788800, 1616371200, 
                                                                                                                                                                                1529366400, 1543104000, 1559001600, NA, 1520812800, 1564617600, 
                                                                                                                                                                                NA, 1554940800, 1538697600, NA, 1548979200, 1609632000, NA, 1501200000, 
                                                                                                                                                                                1599955200, 1629331200, 1611100800, 1586563200, NA, 1627689600, 
                                                                                                                                                                                1536451200, NA, 1614297600, 1518307200, 1595980800, 1538179200, 
                                                                                                                                                                                1603152000, 1520035200, 1570665600, 1513468800, 1513641600, NA, 
                                                                                                                                                                                NA, 1556755200, 1585094400, 1583020800, NA, 1599177600, NA, NA, 
                                                                                                                                                                                1554768000, 1555200000, NA, 1555891200, 1609977600, 1543708800, 
                                                                                                                                                                                NA, 1501113600, 1606953600, NA, NA, 1504310400, 1609372800, NA, 
                                                                                                                                                                                1592179200, 1633996800, NA, NA, NA, 1515283200, 1546732800, 1572998400, 
                                                                                                                                                                                NA, NA, NA, NA, 1539820800, 1502668800, 1488067200, 1535932800, 
                                                                                                                                                                                1498867200, 1597708800, 1569974400, 1493942400, NA, 1562198400, 
                                                                                                                                                                                1524182400, 1515110400, 1564099200, 1590710400, 1541116800, 1544400000, 
                                                                                                                                                                                1616630400, NA, NA, 1564531200, 1506643200, 1597881600, NA, 1574899200, 
                                                                                                                                                                                1562112000, NA, 1594080000, NA, NA, 1539734400, NA, NA, 1579737600, 
                                                                                                                                                                                1610236800, 1591488000, 1532995200, 1626307200, 1510272000, 1546560000, 
                                                                                                                                                                                1604361600, 1600214400, 1629072000, 1566259200, 1548806400, 1597708800, 
                                                                                                                                                                                1584835200, NA, NA, 1491004800, NA, 1615248000, NA, 1539561600, 
                                                                                                                                                                                1557014400, NA, 1525651200, 1518480000, 1506124800, 1593820800, 
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                                                                                                                                                                                                                                        "94_1", "94_2", "94_3", "94_4", "95_1", "95_2", "95_3", "95_4", 
                                                                                                                                                                                                                                        "95_5", "96_1", "96_2", "96_3", "97_1", "97_2", "98_1", "98_2", 
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