1. ph250b.14 measures of disease part 1
TRANSCRIPT
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Measures of Disease Learning Objectives
Measures of Disease: Learning Objectives1. Understand different types of populations as conceptualized in epidemiology and the relevance
of population types to measures of disease2. Understand concept of disease occurrence in time a. Understand and be able to define concepts of disease occurrence in time at a population level
(age, period, cohort effects)b. Understand and be able to define concepts of disease occurrence in time at an individual level
(i.e., latent period, lead time), and their implications for measuring disease at the population level3. Understand and be able to define and contrast prevalence and incidence4. Understand and be able to define and contrast risks and rates 5. Calculate and interpret prevalence (this includes knowing the formula)6. Understand, define, calculate, and interpret cumulative incidence (this includes knowing the
formulas)a. Know different methods for calculating cumulative incidence and the assumptions and purposes
of each7. Understand, define, calculate, and interpret incidence density (knowing the formulae)a. Understand and calculate person-time8. Define and interpret a hazard rate9. Understand and be able to convert between prevalence, cumulative incidence and incidence
density (this includes knowing the formulas)10. Direct and indirect standardization` a. Perform both and understand when each is appropriate (know the formulae) b. Know what data are required for each
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Measures of disease
Module 2PH250B Epidemiologic Methods II
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Big picture
• In epidemiology, one of our major goals is to measure occurrence of disease– Tool for surveillance (the “distribution” of disease;
descriptive epidemiology)– Tool for etiologic/risk factor research (the
“determinants” of disease; analytical epidemiology)
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Big picture
• Critical part of etiologic research– We compare measurements of disease between
groups of people (e.g., exposed and unexposed) because we are interested in associations between exposures and outcomes and, ultimately, effects (causal) of exposures on outcomes
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Big picture
• Reminder: we compare disease occurrence between groups of people that have different exposures because we do not observe the counterfactual outcomes for each person in the population– Comparisons of disease occurrence covered in next
module – measures of association• Key step in etiologic research process is
accurate measurement of disease occurrence
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Big picture
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Big picture
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Disease in time• For measuring disease occurrence in a given population
there are two important components– Measuring the disease outcome– Measuring and accounting for the time over which disease
occurs• Rothman: “disease occurrence in a population reflects
two aspects of individual experiences: the amount of time the individual is at risk in the population, and whether the individual actually has the focal event (e.g., gets disease) during that time.”
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Disease in time
Modification of Szklo Fig. 2-2 – participants observed every 2 months (vs 1)
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Disease in timeSum of time all members of the population are observed is called person-time
People move through time in a study, with and without disease
People are observed for differing amounts of time
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Disease in timeHow many people were in our study?
How many got disease?
So we could say 6/10 got disease over 2 years
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Disease in time
• Any concerns about this measure?
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Disease in time
• How might you account for the time contributed by each person?
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Disease in time
• Any concerns about this measure?
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Disease in time• If interested in a rate of disease
– # Disease/person-time• If interested in a risk of disease, but want to account for
different times people were observed– ?
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Cohort from Fig 2-2 by 2-month intervals
Interval Timeperiod
Numberin at risk
population
Numberdeveloping
disease
Numberwithdrew
Proportion of at-risk population
developing disease
j (tj-1, tj) N’0j Ij Wj Rj = Ij/ (N’0j-(Wj/2))
2 (0, 2) 10 1 1 1/(10-(1/2)) = 0.11
4 (2, 4) 10 - 1 - 1 =8
1 0 1/8 = 0.125
6 (4, 6) 8 - 1 - 0 =7
0 0 0/7 = 0
Adapted from Kleinbaum, Table 6.1
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Populations
• Populations in epidemiology– Group of people for whom we are interested in the
occurrence of disease or the effect of an exposure on disease
– Defined by: geography, occupation, demographic characteristics (age, race/ethnicity, gender), time etc.
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Populations
• Populations in epidemiology– Examples:
• Residents of NYC on 9/11/2001• Women of childbearing age in Alameda County 1980-2000• Live singleton births in Bangladesh in 2005
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Populations
• Total population– Includes everyone in a particular population
• Candidate or “at risk” population – People in the total population who could get the
disease/condition of interest– Excludes those who have the disease or who are
immune (or do not have the necessary organ or physiological function, etc.)
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Populations
• Candidate or “at risk” population – Example: candidate population for pregnancy
excludes men, currently pregnant women, women with hysterectomy, and older women
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Populations
• Closed or fixed populations– Membership is permanent and defined by some life
event– Add no new members and only lose members to
death– The size of the population will eventually reach 0
because everyone ultimately dies
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Populations
• Closed or fixed populations– Examples: being born in 1975, serving in Iraq or
Afghanistan
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Populations
• Open populations – Gain members over time through immigration or birth– Lose members through emigration or death– Sometimes called dynamic, but a misnomer b/c both
open and closed populations are changing– If membership can be lost due to events other than
death, then the population is open
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Populations
• Open populations – Examples: most populations such as cities, states,
hospital populations, etc.
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Populations
• Steady state populations – a type of open population– When the number of persons entering the population
is balanced by the number exiting over a period of time
– Example: a city where the number of people moving out or dying is approximately equal to the number moving in or being born between over a given time interval
– Example: population of women in the maternity ward at Alta Bates hospital
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Populations
• Distinctions can depend on measurement of time or disease– Example: a population that starts a new drug could
be considered closed if only the population starting at a particular time is included but if new users of the drug are allowed to enter the population it could be considered open
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Populations
• Relevance– Population properties are important to consider in
study planning• Example: when studying a particular outcome (e.g.,
pregnancy) need to make sure you study a population “at-risk” of that outcome (e.g., women of certain ages)
• Example: should define your study population so that you can address your study question in that population (e.g., differences in PTSD between OEF/OIF Veterans and civilians vs differences in PTSD among OEF/OIF Veterans)
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Populations• Example: studying exposure to a fixed event (e.g., hurricane
Katrina) population of interest is fixed/closed and a study would need to be designed to capture that population appropriately
• Example: a population of interest may be open (e.g., tourists visiting a given city) and a study would need to be designed to capture that population appropriately
– Important to consider in calculation and interpretation of measures of disease (more later in relations between measures)
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Time scales
• Disease occurrence at a population level affected by different time scales– age, period and cohort effects
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Time scales
• People are conceived, born, and then move through time until death with a variety of health states and events along the way
• Time (and exposures in time) can affect health/disease in three main ways – Age effects: biological age of individuals– Period effects: calendar time– Cohort effects: year of birth
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Time scales
• Age effect• Definition: variation in health status arising from
social or biological consequences of aging• What it looks like when graphed
– Rate (of disease) changes with age– Irrespective of birth cohort and calendar time
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Time scales
• Age effect• Example: rate of heart disease increases with
age regardless of whether you examine a population born in 1900 or 1950; at the age of 50 the rate of heart disease is higher than at age 30
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Time scales
• Age effect - depiction
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Time scales
• Period effect• Definition: Variation in health status arising from
changes in physical, ecological, or social environment during a time period
• What it looks like– Change in rate (of disease) affecting an entire
population at some point in time– Irrespective of age and birth cohort
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Time scales
• Period effect• Example: DDT spraying in 1950s led to
increased risk of certain cancers for anyone living in affected areas in the 1950s, regardless of how old they were or when they were born
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Time scales
• Period effect - depiction
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Time scales
• Cohort effect • Definition: Variation in health status arising from
exposures that vary by cohort• What it looks like:
– Change in the rate (of disease) according to membership in some cohort
– Birth cohort is established by year of birth• Note that one can examine cohorts defined by any life event
which places a person permanently in a group– Irrespective of age and calendar time
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Time scales
• Cohort effect • Example: Women exposed to DES in utero
have increased risk of vaginal and cervical cancer at all ages and over all time periods
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Time scales
• Cohort effect - depiction
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Time scalesA real example• Peptic ulcer mortality
(Susser 1982, reprinted 2001) – Cohort effects – for
those born after 1900 age-specific mortality from peptic ulcer was continually declining
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Measures – basic concepts
• Proportion• Numerator is included in the denominator (a/
(a+b))• Range: 0 to 1 (or 0% to 100%)• Example: number of students with tattoos/total
number of students in class (number with tattoos + number without tattoos)
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Measures – basic concepts
• Ratio• Numerator is NOT included in the denominator
(a/b)• Range: 0-infinity• Example: number with tattoos/number without
tattoos (odds of tattoo)• Example: number of hospital beds/number of
patients• In epidemiology, you will see ratios of
probabilities, rates, and odds (to be elaborated later)
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Measures – basic concepts
• Odds– A ratio with wide application in epidemiology (more in
measures of association, study designs, analysis of epidemiologic data)
• Odds of disease: number with disease/number without disease
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Measures – basic concepts
• Rate• Time is in the denominator• Range: 0-infinity• Examples: cases of flu/month, miles per hour• Dimension is always 1/time or time-1
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Measures – measuring diseases
• Disease process and measuring disease– Induction period = time from causal action to
biological onset– Latent period = time from biological onset to disease
detection
Biologic onset Detectable by screening
Symptoms develop
DeathCausal action
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Measures – measuring diseases
• Disease process and measuring disease– Timing of disease process may differ between
individuals– Timing of detection may differ between individuals
Biologic onset Detectable by screening
Symptoms develop
DeathCausal action
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Measures – measuring diseases
• Disease process and measuring disease– Timing of disease process may differ between
individuals
Biologic onset Detectable by screening
Symptoms develop
DeathCausal action
Biologic onset
Detectable by screening
Symptoms develop
Death
Causal action
A
B
JC: mention length bias
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Measures – measuring diseases
• Disease process and measuring disease– Timing of detection may differ between individuals
Biologic onset Detectable by screening
Symptoms develop
DeathCausal action
Biologic onset Detectable by screening
Symptoms develop
DeathCausal action
A
B
JC: mention lead time bias
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Measures – measuring diseases
• Defining disease outcome for a study– Have to consider underlying disease process and
potential variations in that process– Have to consider how disease is being detected
• This will influence what your measure of disease is capturing
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Measures – measuring diseases
• Example: prevalence of cancer (proportion with disease at a particular time) will miss cases of aggressive cancers
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Epidemiologic measures
• Prevalence vs. incidence– Prevalence = proportion of the population with a
disease– Incidence = frequency of development of new cases
of disease in a population • New case is usually the first occurrence of a
disease for a non-diseased person
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Epidemiologic measures• Risk vs. rate• Risk = the probability of developing disease over a
specified time period– Population measure that is often interpreted at the individual
level– Must specify the time period for the risk to be meaningfully
interpreted (X-year risk)– Example: 10 year risk of mortality among men diagnosed with
prostate cancer is 0.1 or 1/10 men diagnosed with prostate cancer die within 10 years
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Epidemiologic measures• Risk vs. rate• Rate (average) = average change in disease status per
unit of time over a time period relative to the size of the candidate population (incidence density)
• Example: There are 78 new cases of lyme disease per 100,000 population per year in CT (estimated in 2008)
• Interpreted at population level• A rate, so time is in the denominator
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Epidemiologic measures• Risk vs. rate• Rate (instantaneous) = the instantaneous potential for
change in disease status per unit of time at time t relative to the size of the candidate (i.e., disease-free) population at time t (hazard)
• The instantaneous rate (hazard) of lyme disease on August 31, 2008 in CT is ?– Instantaneous rates cannot be directly calculated from
epidemiologic data because they are defined for an infinitely small time interval
– We can estimate average rates for smaller time intervals when we have sufficient data
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Measures - prevalence
Prevalence• Proportion of existing disease in the total population,
without regard to when cases developed • Numerator: number of existing cases of disease in the
population• Denominator: number of all persons in the population of
interest• A proportion• Range is 0-1 - dimensionless• Prevalence odds = prevalence of outcome/prevalence
of no outcome = P/(1-P)
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Measures - prevalence
Two types of prevalence measures:• Point prevalence: the proportion of subjects who have
disease at a specified point in time– Example: proportion of population that is HIV positive on July 1,
2010
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Measures - prevalence
Two types of prevalence measures:• Period prevalence: the proportion of subjects in a
population who have disease during a certain period of time– Uncommon - used when exact time of onset difficult to
determine– Example: proportion of population with an episode of
depression over the past 12 months
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Measures - prevalence
Uses and limitations of prevalence• A disease that has high incidence but is rapidly fatal or
quickly cured would have low prevalence• An exposure that increases survival with the disease will
increase prevalence• Useful for resource planning• Can estimate the rate under certain conditions (more to
come)
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Measures - prevalence
Uses and limitations of prevalence• In measuring congenital anomalies we use prevalence
out of necessity (many incident cases are lost, as are others in the denominator)– Cannot measure the population at-risk (conceptions)
or person-time contributed by the population, so we necessarily take a point prevalence—the point being birth
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Measures - prevalence
Side note: Szklo and “prevalence rate”• Szklo uses the term “prevalence rate” for prevalence• Although you will see this in other places in the literature
as well, you should not use this term• Use the term prevalence• Prevalence is not a rate and thus the term “prevalence
rate” is incorrect and potentially confusing
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Measures - incidence
Incidence time• Not sufficient to just record proportion of population
affected by disease• Necessary to account for the time elapsed before
disease occurs and the period of time during which the disease events take place
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Measures - incidenceA
B
P(DA) = 0.6
P(DB) = 0.6
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Measures - incidence
Incidence time• Incidence time is time from referent or zero time (e.g.,
birth, start of treatment or exposure, start of measurement period) until the time at which the outcome event occurs
• Also called event time, failure time, occurrence time
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Measures - incidence
Incidence time• “Censoring” occurs if the time of event is not known
because something happens before the outcome occurs – Examples: lost to follow-up, death, surgery to make outcome
impossible like hysterectomy, end of measurement period
• Average incidence time = average time until an event occurs
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Measures – incidence densityIncidence density (ID) - aka incidence rate (IR)• The rate of occurrence of new cases of disease during
person-time of observation in a population at risk of developing disease
• Numerator: number of new cases of disease– Only count cases in the numerator that are contributing to
person-time in the denominator• Denominator: person-time of observation in population
at risk– Only count contributions to the denominator that could yield
cases for the numerator• A rate• Units are “inverse time” (1/time, time-1)• Range is 0-infinity
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Measures – incidence density
Incidence density• What is “person-time”?• Person-time at risk: length of time for each individual
that they are in the population at risk– Sum over population is total person time at risk
• When a person is no longer “at risk” they cease contributing to person-time, this includes when they get the outcome of interest
• One person year could be 2 people x 6 months each, 1 person x 12 months, 3 people x 4 months, etc.
• Helps account for censoring and different observation periods
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Measures – incidence density“Figure 2 suggests that ID may be viewed as theconcentration or 'density' of new case occurrencesin a sea of population time. The more dots per unit area under the curve, the greater is the ID.”
Morgenstern et al. 1980
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Measures – incidence density
Person-time calculations for individual level data
1) If exact time contribution of each individual is known:– Sum the disease-free observation time
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Measures – incidence density
Person-time calculations for individual level data
2) If data on each individual is collected at regular intervals:– Estimate the disease-free observation time in each
interval
– Note: variants of this formula also subtract Ij/2 from N’0j
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Measures – incidence densityPerson-time estimation from group level data1) If the population is in steady state can estimate based on
population size (N’) and duration of follow-up (Δt)
2) If the population is not in steady state can estimate based on mid-interval population (N’1/2) and duration of follow-up (Δt)
– Note: mid-interval population size can be estimated as: (Nt0 + Nt1)/2
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Measures – incidence density
Uses and limitations of incidence density• Appropriate for fixed or dynamic populations; does not
assume that everyone is followed for specified time period
• Does not distinguish between people who do not contribute to disease incidence because they were not in the study population long enough for disease to develop and those who do not contribute because they never got the disease (relates to next point)
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Measures – incidence density
Uses and limitations of incidence density• 100 person-years could come from following 100 people
for one year or two people for 50 years – no way to tell the difference without knowing the incidence time– Have to consider whether study design allowed appropriate time
to elapse to plausibly consider an exposure disease relation– Disease process is important to consider in developing
appropriate study design and disease measures– Example: disease free cohort of 50 exposed and 50 unexposed
followed for 1 year might not allow sufficient time to elapse for exposure to cause disease
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Measures – incidence density
• In class exercise
– Study population observed monthly for 6 months– What is the person-time contributed by this
population?– What is the incidence density?
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Measures – incidence
Hazard rate• The instantaneous potential for change in disease
status per unit of time at time t relative to the size of the candidate (i.e., disease-free) population at time t
• Instantaneous rate in contrast to incidence density which is an average rate
• Cannot be directly calculated because it is defined for an infinitely small time interval
• Hazard function over time can be estimated using modeling techniques (more in the analyzing epidemiologic data section)
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Measures – incidence
Hazard rate
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Measures – incidence
Survival function
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Measures of disease outline– Big picture– Illustration/discussion of measuring disease in time– Populations– Time scales affecting disease in populations– Epidemiologic measures
• Basic concepts• Measuring diseases• Prevalence• Incidence density (incidence rate)• Cumulative incidence (risk)• Relations among measures
– Standardization– Summary– Appendix: specific measures of disease
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Measures – cumulative incidence
Cumulative incidence (CI) – aka risk, incidence proportion (IP – Rothman)
• The proportion of a closed population at risk that becomes diseased within a given period of time
• Numerator: number of new cases of a disease or a condition (Rothman calls this A)
• Denominator: number of persons in population at risk (Rothman calls this N)
• A proportion• Range is 0-1 – dimensionless
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Measures – cumulative incidence
Cumulative incidence• Calculated for a fixed time period
– Only interpretable with information on time period over which it was measured
• Population measure that translates most readily to individual– Interpreted as capturing individual risk of disease
• Different methods for calculating– Variations depending on how time at risk is handled– Option for calculating from rate measure
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Measures – cumulative incidence
• Different methods for calculating– Simple cumulative– Actuarial– Kaplan-Meier– Density
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Measures – cumulative incidence
• Subscript notation– R(t0,tj) – risk of disease over the time interval t0
(baseline) to tj (time j)– R(tj-1,tj) – risk of disease over the time interval tj-1
(time before time j) to tj (time j)
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Measures – cumulative incidence
• Subscript notation– N’0 – number at risk of disease at t0 (baseline)– N’0j – number at risk of disease at the beginning of
interval j
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Measures – cumulative incidence
• Subscript notation– Ij – incident cases during the interval j– Wj – withdrawals during the interval j
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Measures – cumulative incidence
Simple cumulative method: R(t0,tj) = CI(t0,tj) = I
N'0
• Risk calculated across entire study period assuming all study participants followed for the entire study period, or until disease onset– Assumes no death from competing causes, no withdrawals
• Only appropriate for short time frame
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Measures – cumulative incidence
Simple cumulative method:• Example: incidence of a foodborne illness if all those
potentially exposed are identified
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Measures – cumulative incidenceActuarial method:
R(tj-1, tj) = CI(tj-1, tj) =____Ij____ N'0j - Wj/2
• Risk calculated accounting for fact that some observations will be censored or will withdraw
• Assume withdrawals occur halfway through each observation period on average
• Can be calculated over an entire study period– R(t0,tj) = CI(t0, tj) = I/(N’0-W/2)
• Typically calculated over shorter time frames and risks accumulated
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Measures – cumulative incidence
Modification of Szklo Fig. 2-2 – participants observed every 2 months (vs 1)
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• Where to start – set up table with time intervals• Fill incident disease cases and withdrawals into appropriate
intervals• Fill in population at risk
Measures – cumulative incidenceActuarial Method
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• Calculate interval risk• R(tj-1, tj) = Ij/(N’0j-(Wj/2))
• R(0,2)=1/(10-(1/2)) = 0.11
Measures – cumulative incidenceActuarial Method
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• Calculate interval survival• S(tj-1,tj) = 1-R(tj-1,tj)
Measures – cumulative incidenceActuarial Method
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• Calculate cumulative risk – example of time 0 to 10• R(t0, tj) = 1 - Π (1 – R(tj-1,tj)) = 1 - Π (S(tj-1,tj))• R(0, 10) = 1 – (0.89 x 0.88 x 1.0 x 1.0 x 0.85) = 0.34
Measures – cumulative incidenceActuarial Method
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• Calculate cumulative survival • S(t0,tj) = 1-R(t0,tj)
Measures – cumulative incidenceActuarial Method
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• Intuition for why R(t0, tj) = 1 - Π (Sj) using conditional probabilities
• Example of 5 time intervals:– Π (Sj) = P(S1)*P(S2|S1)*P(S3|S2)*P(S4|S3)*P(S5|S4)
= P(S5)– Product first two terms: P(S2|S1)*P(S1) = P(S2) – Multiplying conditional probabilities gives you
unconditional probability of surviving up to any given time point
– the value (1 - survival) up to (or at) a given time point is then the probability of not surviving up to that time point
Measures – cumulative incidence
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Measures – cumulative incidence
• Exercise for home (discuss in lab)
– Study population observed monthly for 6 months– Calculate the cumulative incidence of disease from
month 0 to 6