In WetRobot/popEpi: Functions for Epidemiological Analysis using Population Data

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Changes in 0.4.11

• No changes in any functionality --- added help page for ?"popEpi-package" as requested by CRAN.

Changes in 0.4.10

• No changes for user --- "Suggests" packages now used conditionally in vignettes/tests/examples as per Writing R Extensions.

Changes in 0.4.9

• popEpi::aggre bugfix: aggre now correctly infers which stratifying variables use Lexis time scales when output is cartesian and argument by is of type character.

Changes in 0.4.8

• small internal fixes due to upcoming new package survival release
• popEpi now includes a wrapper for survival::Surv, so you don't need to do library("survival") when using Surv() in formulae (e.g. in survtab)

Changes in 0.4.7

• implemented small internal changes due to upcoming R 3.6.0

Changes in 0.4.6

• implemented small internal changes due to upcoming data.table version

Changes in 0.4.5

• fixed errors arising from new data.table version

Changes in 0.4.4

• splitLexisDT/splitMulti bug fix: splitting along multiple time scales sometimes produced duplicate transitions (e.g. alive -> dead in the last two rows). see https://github.com/FinnishCancerRegistry/popEpi/issues/138 for details.
• splitLexisDT/splitMulti now retain time.since attribute; this attribute plays a role in cutLexis
• known issue: splitLexisDT/splitMulti not guaranteed to work identically to splitLexis from Epi when there are NA values in the time scale one is splitting along.

Changes in 0.4.3

• survtab adjusting was broken with older versions of data.table (tested 1.9.6); therefore popEpi now requires the newest version of data.table!

Changes in 0.4.2

• survtab() bug fix: standard errors were mis-specified for adjusted curves, e.g. age-adjusted Ederer II estimates. This resulted in too wide confidence intervals! SEE HERE FOR EXAMPLE: #135. The standard errors and confidence intervals of non-adjusted curves have always been correct.
• survtab() bug fix: confidence level was always 95 % regardless of conf.level #134

Changes in 0.4.1

• lexpand() bug fixed (#120): observations were dropped if their entry by age was smaller than the smallest age value, though entry at exit is correct and used now.
• sir() rewrite (#118, #122). New more consistent output, updates on plotting and minor changes in arguments. Introduce very simple coef() and confint() methods for sir class.
• new functions in sir family: sir_ag(), sir_lex() and sir_exp() for extracting SMRs from aggre and Lexis objects.
• fixed issue in internal test brought by pkg survival version 2.39.5; no changes in functions were needed (#125)
• robustified aggre(); there were issues with Epi pkg dev version which are definitely avoided (#119)

Changes in 0.4.0

• removed previously deprecated shift.var (#35)
• popEpi no longer depends on package data.table but imports it - this means the user will have to do library(data.table) separately to make data.table's functions become usable. Formerly popEpi effectively did library(data.table) when you did library(popEpi).
• summary.survtab: args t and q behaviour changed
• survtab: internal weights now based on counts of subjects in follow-up at the start of follow-up (used to be sum of counts/pyrs over all of follow-up)
• new functions: rate_ratio(), sir_ratio()
• small internal changes in preparation for data.table 1.9.8

Changes in 0.3.1

This is a hotfix. survtab() was causing warnings in certain situations, which this update fixes. Also fixed plotting survtab objects so that multiple strata are plotted correctly when one or more curves end before the longest one as well other small fixes: See Github issues #89, #90, #91, and #92.

Changes in 0.3.0

Adjusting

Direct adjusting (computing weighted averages of estimates) has been generalized. Functions such as survtab and survmean allow for using adjust() mini function within formulas, or a separate adjust argument. Weights are passed separately. See the examples in the next chapter. See also ?direct_adjusting.

Estimating functions of survival time

The survtab function computes observed, net/relative and cause-specific survivals as well as cumulative incidence functions for Lexis data. Any of the supported survival time functions can be easily adjusted by any number of categorical variables if needed.

One can also use survtab_ag for aggregated data. This means the data does not have to be on the subject-level to compute survival time function estimates.

## prep data
data(sibr)
sire$cancer <- "rectal"
sibr$cancer <- "breast"
sr <- rbind(sire, sibr)

sr$cancer <- factor(sr$cancer)
sr <- sr[sr$dg_date < sr$ex_date, ]

sr$status <- factor(sr$status, levels = 0:2, 
                    labels = c("alive", "canD", "othD"))

## create Lexis object
library(Epi)
x <- Lexis(entry = list(FUT = 0, AGE = dg_age, CAL = get.yrs(dg_date)), 
           exit = list(CAL = get.yrs(ex_date)), 
           data = sr,
           exit.status = status)

## population hazards file - see ?pophaz for general instructions
data(popmort)
pm <- data.frame(popmort)
names(pm) <- c("sex", "CAL", "AGE", "haz")

## simple usage - uses lex.Xst as status variable
st <- survtab(FUT ~ cancer, data = x,
              breaks = list(FUT = seq(0, 5, 1/12)),
              surv.type = "surv.rel", pophaz = pm)

## more explicit usage
st <- survtab(Surv(FUT, event = lex.Xst) ~ cancer, data = x,
              breaks = list(FUT = seq(0, 5, 1/12)),
              surv.type = "surv.rel", pophaz = pm)


## adjusting
x$agegr <- cut(x$dg_age, c(0,55,65,75,Inf))
w <- as.numeric(table(x$agegr))
st <- survtab(Surv(FUT, event = lex.Xst) ~ cancer + adjust(agegr), 
              data = x,
              breaks = list(FUT = seq(0, 5, 1/12)),
              surv.type = "surv.rel", 
              pophaz = pm, weights = w)

Rates

The new rate function enables easy calculation of e.g. standardized incidence rates:

## dummy data

a <- merge(0:1, 1:18)
names(a) <- c("sex", "agegroup")
set.seed(1)
a$obs <- rbinom(nrow(a), 100, 0.5)
set.seed(1)
a$pyrs <- rbinom(nrow(a), 1e4, 0.75)

## so called "world" standard rates (weighted to hypothetical world pop in 2000)
r <- rate(data = a, obs = obs, pyrs = pyrs, print = sex, 
          adjust = agegroup, weights = 'world_2000_18of5')

knitr::kable(r)

WetRobot/popEpi documentation built on Aug. 29, 2023, 3:53 a.m.