datasets

lifelines.datasets.load_canadian_senators(**kwargs)

A history of Canadian senators in office.:

Size: (933,10)
Example:
    Name                                        Abbott, John Joseph Caldwell
    Political Affiliation at Appointment                Liberal-Conservative
    Province / Territory                                              Quebec
    Appointed on the advice of                     Macdonald, John Alexander
    Term (yyyy.mm.dd)                       1887.05.12 - 1893.10.30  (Death)
    start_date                                           1887-05-12 00:00:00
    end_date                                             1893-10-30 00:00:00
    reason                                                             Death
    diff_days                                                           2363
    observed                                                            True
lifelines.datasets.load_dd(**kwargs)

Classification of political regimes as democracy and dictatorship. Classification of democracies as parliamentary, semi-presidential (mixed) and presidential. Classification of dictatorships as military, civilian and royal. Coverage: 202 countries, from 1946 or year of independence to 2008.:

Size: (1808, 12)
Example:
    ctryname                                                   Afghanistan
    cowcode2                                                           700
    politycode                                                         700
    un_region_name                                           Southern Asia
    un_continent_name                                                 Asia
    ehead                                              Mohammad Zahir Shah
    leaderspellreg       Mohammad Zahir Shah.Afghanistan.1946.1952.Mona...
    democracy                                                Non-democracy
    regime                                                        Monarchy
    start_year                                                        1946
    duration                                                             7
    observed                                                             1

References

Cheibub, José Antonio, Jennifer Gandhi, and James Raymond Vreeland. 2010. “Democracy and Dictatorship Revisited.” Public Choice, vol. 143, no. 2-1, pp. 67-101.

lifelines.datasets.load_dfcv()

A toy example of a time dependent dataset.

Size: (14, 6)
Example:

 start  group  z  stop  id  event
     0    1.0  0   3.0   1   True
     0    1.0  0   5.0   2  False
     0    1.0  1   5.0   3   True
     0    1.0  0   6.0   4   True

References

From http://www.math.ucsd.edu/~rxu/math284/slect7.pdf

lifelines.datasets.load_diabetes(**kwargs)

An interval censored dataset.

References

Borch-Johnsens, K, Andersen, P and Decker, T (1985). “The effect of proteinuria on relative mortality in Type I (insulin-dependent) diabetes mellitus.” Diabetologia, 28, 590-596.

Size: (731, 3)
Example:

   left  right  gender
     24     27    male
     22     22  female
     37     39    male
     20     20    male
      1     16    male
      8     20  female
     14     14    male
lifelines.datasets.load_g3(**kwargs)
Size: (17,7)
Example:
    no.               1
    age              41
    sex          Female
    histology    Grade3
    group           RIT
    event          True
    time             53
lifelines.datasets.load_gbsg2(**kwargs)

A data frame containing the observations from the GBSG2 study of 686 women.:

Size: (686,10)
Example:
    horTh           yes
    age             56
    menostat        Post
    tsize           12
    tgrade          II
    pnodes          7
    progrec         61
    estrec          77
    time            2018
    cens            1

References

  1. Sauerbrei and P. Royston (1999). Building multivariable prognostic and diagnostic models: transformation of the predictors by using fractional polynomials. Journal of the Royal Statistics Society Series A, Volume 162(1), 71–94
  1. Schumacher, G. Basert, H. Bojar, K. Huebner, M. Olschewski, W. Sauerbrei, C. Schmoor, C. Beyerle, R.L.A. Neumann and H.F. Rauschecker for the German Breast Cancer Study Group (1994), Randomized 2 × 2 trial evaluating hormonal treatment and the duration of chemotherapy in node- positive breast cancer patients. Journal of Clinical Oncology, 12, 2086–2093
lifelines.datasets.load_holly_molly_polly(**kwargs)

From https://stat.ethz.ch/education/semesters/ss2011/seminar/contents/presentation_10.pdf Used as a toy example for CoxPH in recurrent SA.:

  ID  Status  Stratum  Start(days)  Stop(days)  tx    T
0  M       1        1            0         100   1  100
1  M       1        2          100         105   1    5
2  H       1        1            0          30   0   30
3  H       1        2           30          50   0   20
4  P       1        1            0          20   0   20
lifelines.datasets.load_kidney_transplant(**kwargs)
Size: (863,6)
Example:
    time             5
    death            0
    age             51
    black_male       0
    white_male       1
    black_female     0
lifelines.datasets.load_larynx(**kwargs)
Size: (89,6)
Example:
    time  age  death  Stage II  Stage III  Stage IV
     0.6   77      1         0          0         0
     1.3   53      1         0          0         0
     2.4   45      1         0          0         0
     2.5   57      0         0          0         0
     3.2   58      1         0          0         0
lifelines.datasets.load_lcd(**kwargs)

Copper concentrations (µg/L) in shallow groundwater samples from two different geological zones in the San Joaquin Valley, California. The alluvial fan data include four different detection limits and the basin trough data include five different detection limits.

Millard, S.P. and Deverel, S.J. (1988). Nonparametric statistical methods for comparing two sites based on data with multiple non-detect limits. Water Resources Research 24: doi: 10.1029/88WR03412. issn: 0043-1397.

Size: (104,3)
Example:
    C  T         group
    0  1  alluvial_fan
    0  1  alluvial_fan
    0  1  alluvial_fan
    0  1  alluvial_fan
    1  1  alluvial_fan
lifelines.datasets.load_leukemia(**kwargs)

Leukemia dataset.:

Size: (42,5)
Example:
        t  status  sex  logWBC  Rx
    0  35       0    1    1.45   0
    1  34       0    1    1.47   0
    2  32       0    1    2.20   0
    3  32       0    1    2.53   0
    4  25       0    1    1.78   0

References

From http://web1.sph.emory.edu/dkleinb/allDatasets/surv2datasets/anderson.dat

lifelines.datasets.load_lung(**kwargs)

Survival in patients with advanced lung cancer from the North Central Cancer Treatment Group. Performance scores rate how well the patient can perform usual daily activities.:

Size: (288,10)
Example:
 inst  time  status  age  sex  ph.ecog  ph.karno  pat.karno  meal.cal  wt.loss
  3.0   306       2   74    1      1.0      90.0      100.0    1175.0      NaN
  3.0   455       2   68    1      0.0      90.0       90.0    1225.0     15.0
  3.0  1010       1   56    1      0.0      90.0       90.0       NaN     15.0
  5.0   210       2   57    1      1.0      90.0       60.0    1150.0     11.0
  1.0   883       2   60    1      0.0     100.0       90.0       NaN      0.0

References

Loprinzi CL. Laurie JA. Wieand HS. Krook JE. Novotny PJ. Kugler JW. Bartel J. Law M. Bateman M. Klatt NE. et al. Prospective evaluation of prognostic variables from patient-completed questionnaires. North Central Cancer Treatment Group. Journal of Clinical Oncology. 12(3):601-7, 1994.

lifelines.datasets.load_lupus(**kwargs)

See https://projecteuclid.org/download/pdf_1/euclid.aos/1176345693

Note

I transcribed this from the original paper, and highly suspect there are differences.

References

Merrell, M., & Shulman, L. E. (1955). Determination of prognosis in chronic disease, illustrated by systemic lupus erythematosus. Journal of Chronic Diseases, 1(1), 12–32. doi:10.1016/0021-9681(55)90018-7

lifelines.datasets.load_lymphoma(**kwargs)
Size: (80, 3)
Example:

  Stage_group  Time  Censor
            1     6       1
            1    19       1
            1    32       1
            1    42       1
            1    42       1

References

From https://www.statsdirect.com/help/content/survival_analysis/logrank.htm

lifelines.datasets.load_multicenter_aids_cohort_study(**kwargs)

Originally in [1]:

Siz: (78, 4)

AIDSY: date of AIDS diagnosis
W: years from AIDS diagnosis to study entry
T: years from AIDS diagnosis to minimum of death or censoring
D: indicator of death during follow up


i   AIDSY       W      T        D
1   1990.425    4.575   7.575   0
2   1991.250    3.750   6.750   0
3   1992.014    2.986   5.986   0
4   1992.030    2.970   5.970   0
5   1992.072    2.928   5.928   0
6   1992.220    2.780   4.688   1

References

[1] Cole SR, Hudgens MG. Survival analysis in infectious disease research: describing events in time. AIDS. 2010;24(16):2423-31.

lifelines.datasets.load_nh4(**kwargs)

Ammonium (NH4) concentration (mg/L) in precipitation measured at Olympic National Park, Hoh Ranger Station (WA14), weekly or every other week from January 6, 2009 through December 20, 2011.

National Atmospheric Deposition Program, National Trends Network (NADP/NTN). http://nadp.slh.wisc.edu/data/sites/siteDetails.aspx?net=NTN&id=WA14 http://nadp.isws.illinois.edu/NTN/

Size: (104,3)
lifelines.datasets.load_panel_test(**kwargs)
Size: (28,5)
Example:
    id  t  E  var1  var2
     1  1  0   0.0     1
     1  2  0   0.0     1
     1  3  0   4.0     3
     1  4  1   8.0     4
     2  1  0   1.2     1
lifelines.datasets.load_psychiatric_patients(**kwargs)
Size: (26,4)
Example:
    Age   T  C  sex
     51   1  1    2
     58   1  1    2
     55   2  1    2
     28  22  1    2
     21  30  0    1
lifelines.datasets.load_recur(**kwargs)

From ftp://ftp.wiley.com/public/sci_tech_med/survival/, first published in “Applied Survival Analysis: Regression Modeling of Time to Event Data, Second Edition”:

ID          Subject Identification        1 - 400
AGE         Age                           years
TREAT       Treatment Assignment          0 = New
                                          1 = Old
TIME0       Day of Previous Episode       Days
TIME1       Day of New Episode            Days
              or censoring
CENSOR      Indicator for Soreness        1 = Episode Occurred
              Episode or Censoring            at TIME1
                                          0 = Censored
EVENT       Soreness Episode Number       0 to at most 4

Size: (1296, 7)
Example:
    ID,AGE,TREAT,TIME0,TIME1,CENSOR,EVENT
    1,43,0,9,56,1,3
    1,43,0,56,88,1,4
    1,43,0,0,6,1,1
    1,43,0,6,9,1,2
lifelines.datasets.load_regression_dataset(**kwargs)

Artificial regression dataset. Useful since there are no ties in this dataset. Slightly edit in v0.15.0 to achieve this, however.:

Size: (200,5)
Example:
        var1      var2      var3          T  E
    0.595170  1.143472  1.571079  14.785479  1
    0.209325  0.184677  0.356980   7.336734  1
    0.693919  0.071893  0.557960   5.271527  1
    0.443804  1.364646  0.374221  11.684168  1
    1.613324  0.125566  1.921325   7.637764  1
lifelines.datasets.load_rossi(**kwargs)

This data set is originally from Rossi et al. (1980), and is used as an example in Allison (1995). The data pertain to 432 convicts who were released from Maryland state prisons in the 1970s and who were followed up for one year after release. Half the released convicts were assigned at random to an experimental treatment in which they were given financial aid; half did not receive aid.:

Size: (432,9)
Example:
    week      20
    arrest     1
    fin        0
    age       27
    race       1
    wexp       0
    mar        0
    paro       1
    prio       3

References

Rossi, P.H., R.A. Berk, and K.J. Lenihan (1980). Money, Work, and Crime: Some Experimental Results. New York: Academic Press. John Fox, Marilia Sa Carvalho (2012). The RcmdrPlugin.survival Package: Extending the R Commander Interface to Survival Analysis. Journal of Statistical Software, 49(7), 1-32.

lifelines.datasets.load_stanford_heart_transplants(**kwargs)

This is a classic dataset for survival regression with time varying covariates. The original dataset is from [1], and this dataset is from R’s survival library.:

Size: (172, 8)
Example:
    start  stop  event        age      year  surgery  transplant  id
      0.0  50.0      1 -17.155373  0.123203        0           0   1
      0.0   6.0      1   3.835729  0.254620        0           0   2
      0.0   1.0      0   6.297057  0.265572        0           0   3
      1.0  16.0      1   6.297057  0.265572        0           1   3
      0.0  36.0      0  -7.737166  0.490075        0           0   4

References

[1] J Crowley and M Hu. Covariance analysis of heart transplant survival data. J American
Statistical Assoc, 72:27–36, 1977.
lifelines.datasets.load_static_test(**kwargs)
Size: (7,5)
Example:
    id  t  E  var1  var2
     1  4  1    -1    -1
     2  3  1    -2    -2
     3  3  0    -3    -3
     4  4  1    -4    -4
     5  2  1    -5    -5
     6  0  1    -6    -6
     7  2  1    -7    -7
lifelines.datasets.load_waltons(**kwargs)

Genotypes and number of days survived in Drosophila. Since we work with flies, we don’t need to worry about left-censoring. We know the birth date of all flies. We do have issues with accidentally killing some or if some escape. These would be right-censored as we do not actually observe their death due to “natural” causes.:

Size: (163,3)
Example:
     T  E    group
     6  1  miR-137
    13  1  miR-137
    13  1  miR-137
    13  1  miR-137
    19  1  miR-137