STAT 602 - Logistic RegressionNonparametric Methods Assignment
1 - Swan-Ganz Catheterization and 30-Day Mortality of Heart Patients
Below is the abstract from the paper “Effectivenessof Right Heart Catheterization in Critically Ill Patients” published in JAMA, 1996, by Conners et al.
OBJECTIVE: To examine the association between the use of right heart catheterization (RHC) during the first 24 hours of care in the intensive care unit (ICU) and subsequent survival, length of stay, intensity of care, and cost of care.
DESIGN: Prospective cohort study.
SETTING: Five US teaching hospitals between 1989 and 1994.
SUBJECTS: A total of 5735 critically ill adult patients receiving care in an ICU for 1 of 9 prespecified disease categories.
MAIN OUTCOME MEASURES: Survival time, cost of care, intensity of care, and length of stay in the ICU and hospital, determined from the clinical record and from the National Death Index. A propensity score for RHC was constructed using multivariable logistic regression. Case-matching and multivariable regression modeling techniques were used to estimate the association of RHC with specific outcomes after adjusting for treatment selection using the propensity score. Sensitivity analysis was used to estimate the potential effect of an unidentified or missing covariate on the results.
RESULTS: By case-matching analysis, patients with RHC had an increased 30-day mortality (odds ratio, 1.24; 95% confidence interval, 1.03-1.49). The mean cost (25th, 50th, 75th percentiles) per hospital stay was $49 300 ($17 000, $30 500, $56 600) with RHC and $35 700 ($11 300, $20 600, $39 200) without RHC. Mean length of stay in the ICU was 14.8 (5, 9, 17) days with RHC and 13.0 (4, 7, 14) days without RHC. These findings were all confirmed by multivariable modeling techniques. Subgroup analysis did not reveal any patient group or site for which RHC was associated with improved outcomes. Patients with higher baseline probability of surviving 2 months had the highest relative risk of death following RHC. Sensitivity analysis suggested that a missing covariate would have to increase the risk of death 6-fold and the risk of RHC 6-fold for a true beneficial effect of RHC to be misrepresented as harmful.
CONCLUSION: In this observational study of critically ill patients, after adjustment for treatment selection bias, RHC was associated with increased mortality and increased utilization of resources. The cause of this apparent lack of benefit is unclear. The results of this analysis should be confirmed in other observational studies. These findings justify reconsideration of a randomized controlled trial of RHC and may guide patient selection for such a study.
Research Goal: The goal of your analysis of these data is to discuss and quantify the risk of 30-day mortality of patients that had a Swan-Ganz right heart catheter used during their treatment vs. those that did not. You will first do this marginally, that is by looking only at the relationship between 30-day mortality (Y) and right heart catheterization (X). Then you will examine this relationship adjusted for other covariates that might be related to the 30-day mortality of the patient.
DESCRIPTION OF VARIABLES (Datafile: RHC.JMP)
Response (Y)
DeathPatient died within in 30 days? (Died or Survived)
Risk Factor of Primary Interest (X1)
swang1Right Heart Catheterization (RHC vs. No RHC)
COVARIATES USED FOR ADJUSTMENT PURPOSES (X2, ... ,X38)
Demographics and Disease Category
Variable nameVariable Definition
AgeAge (yrs.)
SexSex (Female or Male)
RaceRace (white, black, other)
EduYears of education (yrs.)
IncomeIncome (Under $11k, $11k - < $25k, $25k - $50k, > $50k )
NinsclasMedical insurance (No Insurance, Medicaid, Medicare, Medicare &
Medicaid, Private, or Private & Medicare)
CaCancer status (Yes, No, or Metastatic)
Categories of Admission Diagnosis
Diagnosis variables are all coded as (Yes or No)
RespRespiratory Diagnosis
CardCardiovascular Diagnosis
NeuroNeurological Diagnosis
GastrGastrointestinal Diagnosis
RenalRenal Diagnosis
MetaMetabolic Diagnosis
HemaHematologic Diagnosis
SepsSepsis Diagnosis
TraumaTrauma Diagnosis
OrthoOrthopedic Diagnosis
Dnr1DNR status on day1 (Yes or No)
Aps1APACHE score
Scoma1Glasgow Coma Score
Wtkilo1Weight
Temp1Temperature
Meanbp1Mean blood pressure
Resp1Respiratory rate
Hrt1Heart rate
Pafi1PaO2/FIO2 ratio
Paco21PaCo2
Ph1PH
Wblc1WBC
Hema1Hematocrit
Sod1Sodium
Pot1Potassium
Crea1Creatinine
Bili1Bilirubin
Alb1Albumin
wtkilo1Weight (kg)
QUESTIONS AND ANALYSES
a) Use appropriate methods to examine the relationship between right heart catheterization (swang1) and 30-day mortality (Death). The methods you use should provide achieve the following analysis goals:
- Determine if a significant relationship between right heart catheterization and 30-day mortality exists.
- Estimate the risk difference associated with right heart catheterization
- Estimate the risk in multiplicative terms.
Summarize all your findings in regards to these three analysis goals. (10 pts.)
b) Now consider adjusting for all of the covariates listed above. Use backward elimination or forward selection (using the default settings in JMP) to develop a logistic regression model that contains the most important covariates along with the right heart catheterization predictor (swang1), then calculate the OR for 30-day mortality associated with the Swan-Ganz right heart catheterization procedure adjusted for the other included covariates. Summarize your findings and be sure to explain how you arrived at your final multiple logistic regression model. (25 pts.)
2 - Effect of Fire on Germination of Banksia Serrata
In order for Banksiaserrata to germinate, fire is required
to open its seed cones. In order to understand the effect
of fire on these trees, two neighboring sites were surveyed.
Site A has been burned frequently during the last 80 years,
while fire at Site B has been infrequent during this same
period. It is hypothesized that the different frequency of fire will result in larger median DBH for B. serrata(in cm) at location B than at location A. Perform an appropriate nonparametric test to see if the research hypothesis is supported by the data below:
Site A1216202630323646
Site B283444484850
Summarize the test results and state your conclusion. You may use JMP to perform the test or do it “by hand”. (6 pts.)
3 – Beak Color and Length of Song
A study of the courtship behavior of domesticated zebra finches is run to determine the effect of beak color in the female on the number of song patterns sung during courtship. It is thought that the red, a sign of maturity, will elicit more patterns than the black beak, which is found in juvenile birds. Each of the 10 mature males is presented separately with a live red-beaked and live black-beaked female bird. The male's behavior is observed in each case. The measured response is the mean number of song patterns over three-10 minute observation periods with each female:
Mean Number of Song Patterns
Male Number / Red Beak Female / Black Beak Female1 / 11.24 / 2.19
2 / 12.21 / 1.69
3 / 11.7 / 9.85
4 / 14.09 / 13.98
5 / 15.7 / 12.66
6 / 17.08 / 14.78
7 / 11.17 / 15.66
8 / 15.18 / 11.06
9 / 16.9 / 7.90
10 / 14.72 / 20.08
Test the hypothesis of interest using an appropriate nonparametric test. Be sure to state your conclusion. You may enter these data into JMP or do the test “by hand”. (6 pts.)
4–Primer Dependent Polymerase Labeling Index and Tumor Type
A study evaluated the accuracy of a primer-dependent polymerase labeling index (PDP-LI) as measure of the proliferative activity of human solid tumors (Alama, et al. 1986).
These data contain the PDP-LI values for 13 patients with epithelial carcinoma of the ovary and 25 patients with nonmetastatic breast carcinoma. Do these data provide evidence that the “typical or average” PDP-LI values differ significantly between these two populations of patients? Data File: Tumor Comparison PDPLI
Conduct an appropriate test to answer this question. Include any computer supporting computer output. Summarize your findings. (8 pts.)