Data sets by exercise

This vignette presents dataset_by_exercise, the index that links every data set in sta310r to the worked examples in Collett (2023) that use it. The same index is available as a data set, so you can filter and sort it in R rather than reading it here.

The `dX.Y` aliases

Each example that uses a data set gives that data set an alias dX.Y, where X.Y is the number of the example. For example, Example 3.7 uses the myeloma data, so d3.7 is an alias for myeloma:

identical(d3.7, myeloma)
#> [1] TRUE
dim(d3.7)
#> [1] 48 10

A data set that is used in more than one example has one alias per example. The aliases are ordinary data objects in the package, so d3.7 works after library(sta310r) just like myeloma does, and ?d3.7 opens the help page of the data set. The index below is the authoritative list of which alias belongs to which example.

Index by data set

One row per data set, with its aliases and example numbers collapsed into a single string. The full index, with one row per data set and example, is in the next section.

Data set	Title	Aliases	Examples	Rows	Variables
aortic	Survival following aortic valve replacement	d8.5, d8.6, d8.7, d8.8, d8.9	8.5, 8.6, 8.7, 8.8, 8.9	988	11
bladder	Recurrence of bladder cancer	—	—	86	6
bmt	Bone marrow transplantation in leukaemia patients	—	—	37	9
bmt_leukaemia	Bone marrow transplantation in the treatment of leukaemia	d8.2	8.2	23	8
bmt_outcome	Patient outcome following bone marrow transplantation	d13.4	13.4	2204	9
breast	Prognosis for women with breast cancer	d1.2, d2.11, d2.12, d2.13, d2.14, d3.1, d3.3, d5.5, d5.6, d5.7, d5.8, d5.13, d5.14, d5.17, d10.1, d10.2, d16.4, d16.5, d16.6	1.2, 2.11, 2.12, 2.13, 2.14, 3.1, 3.3, 5.5, 5.6, 5.7, 5.8, 5.13, 5.14, 5.17, 10.1, 10.2, 16.4, 16.5, 16.6	45	3
breast_rfs	Recurrence-free survival in breast cancer patients	d6.5, d6.6	6.5, 6.6	686	11
cgd	Chronic granulomatous disease	—	—	128	12
cirrhosis	Data from a cirrhosis study (baseline)	d8.4	8.4	12	6
cirrhosis_cp	Data from a cirrhosis study (counting process format)	—	—	54	7
cirrhosis_lbr	Data from a cirrhosis study (log-bilirubin data)	—	—	42	3
dialysis	Infection in patients on dialysis	d4.1, d4.2, d4.3, d4.4, d4.6, d4.7, d4.10, d4.11, d4.12	4.1, 4.2, 4.3, 4.4, 4.6, 4.7, 4.10, 4.11, 4.12	13	5
ducks	Survival of black ducks	—	—	50	6
gastric	Survival of patients with gastric cancer	d11.2, d11.3	11.2, 11.3	90	4
help	Health evaluation and linkage to primary care	d16.7	16.7	447	7
hepatitis	Chronic active hepatitis	d15.1, d15.2, d15.3	15.1, 15.2, 15.3	44	3
hyper	Treatment of hypernephroma	d3.4, d3.10, d3.11, d3.13, d3.14, d5.10, d6.1, d6.4	3.4, 3.10, 3.11, 3.13, 3.14, 5.10, 6.1, 6.4	36	4
iud	Time to discontinuation of an intrauterine device (IUD)	d1.1, d2.3, d2.4, d2.5, d2.7, d2.8, d2.9, d2.10, d5.1, d5.2, d5.3, d5.4, d16.1, d16.2, d16.3	1.1, 2.3, 2.4, 2.5, 2.7, 2.8, 2.9, 2.10, 5.1, 5.2, 5.3, 5.4, 16.1, 16.2, 16.3	18	2
kidney	Survival following kidney transplantation	d10.4	10.4	434	7
kidney_centres	Comparisons between kidney transplant centres	d11.4, d11.5, d11.6, d11.7, d11.8	11.4, 11.5, 11.6, 11.7, 11.8	1439	9
liver	Survival of liver transplant recipients	d12.1, d12.2, d12.3, d12.4, d12.5, d12.6	12.1, 12.2, 12.3, 12.4, 12.5, 12.6	1761	7
liver_wait	Time to death while waiting for a liver transplant	d14.1, d14.3	14.1, 14.3	281	7
lung_transplant	Survival of patients registered for a lung transplant	d10.3	10.3	196	7
melanoma	Survival times of patients with melanoma	d2.15, d2.16	2.15, 2.16	30	4
mice	Survival of laboratory mice with competing causes of death	d12.7	12.7	181	3
myeloma	Survival of multiple myeloma patients	d1.3, d2.2, d2.6, d3.2, d3.5, d3.7, d3.8, d3.9, d3.15, d3.17, d3.19, d3.20, d4.5, d4.8, d4.9, d5.16	1.3, 2.2, 2.6, 3.2, 3.5, 3.7, 3.8, 3.9, 3.15, 3.17, 3.19, 3.20, 4.5, 4.8, 4.9, 5.16	48	10
numerical_illustration	A numerical illustration of two factors	d5.9	5.9	37	4
ovarian	Chemotherapy in ovarian cancer patients	d5.11, d5.12, d7.1, d7.2, d7.3, d7.4, d8.3	5.11, 5.12, 7.1, 7.2, 7.3, 7.4, 8.3	26	7
prostate	Comparison of two treatments for prostatic cancer	d1.4, d3.6, d3.12, d3.16, d5.15	1.4, 3.6, 3.12, 3.16, 5.15	38	8
pulmonary	Pulmonary metastasis in patients with osteosarcoma	d2.1	2.1	11	1
rats	Recurrence of mammary tumours in female rats	d13.2	13.2	254	4
scottish_mbc_cohort	Synthetic Scottish metastatic breast cancer cohort	—	—	850	21
tamoxifen	Clinical trial of tamoxifen in breast cancer patients	d13.3	13.3	641	18
ulcer	Recurrence of an ulcer	d9.1, d9.4, d9.5, d9.6, d9.7, d11.1	9.1, 9.4, 9.5, 9.6, 9.7, 11.1	43	6

Index by example

The full index, ordered by chapter and example. Rows without an alias are data sets that are not used in a numbered example; the note column says where they come from.

Example	Alias	Data set	Example title	Note
1.1	d1.1	iud	Time to discontinuation of the use of an IUD
1.2	d1.2	breast	Prognosis for women with breast cancer
1.3	d1.3	myeloma	Survival of multiple myeloma patients
1.4	d1.4	prostate	Comparison of two treatments for prostatic cancer
2.1	d2.1	pulmonary	Pulmonary metastasis
2.2	d2.2	myeloma	Survival of multiple myeloma patients
2.3	d2.3	iud	Time to discontinuation of the use of an IUD
2.4	d2.4	iud	Time to discontinuation of the use of an IUD
2.5	d2.5	iud	Time to discontinuation of the use of an IUD
2.6	d2.6	myeloma	Survival of multiple myeloma patients
2.7	d2.7	iud	Time to discontinuation of the use of an IUD
2.8	d2.8	iud	Time to discontinuation of the use of an IUD
2.9	d2.9	iud	Time to discontinuation of the use of an IUD
2.10	d2.10	iud	Time to discontinuation of the use of an IUD
2.11	d2.11	breast	Prognosis for women with breast cancer
2.12	d2.12	breast	Prognosis for women with breast cancer
2.13	d2.13	breast	Prognosis for women with breast cancer
2.14	d2.14	breast	Prognosis for women with breast cancer
2.15	d2.15	melanoma	Survival times of patients with melanoma
2.16	d2.16	melanoma	Survival times of patients with melanoma
3.1	d3.1	breast	Prognosis for women with breast cancer
3.2	d3.2	myeloma	Survival of multiple myeloma patients
3.3	d3.3	breast	Prognosis for women with breast cancer
3.4	d3.4	hyper	Treatment of hypernephroma
3.5	d3.5	myeloma	Survival of multiple myeloma patients
3.6	d3.6	prostate	Comparison of two treatments for prostatic cancer
3.7	d3.7	myeloma	Survival of multiple myeloma patients
3.8	d3.8	myeloma	Survival of multiple myeloma patients
3.9	d3.9	myeloma	Survival of multiple myeloma patients
3.10	d3.10	hyper	Treatment of hypernephroma
3.11	d3.11	hyper	Treatment of hypernephroma
3.12	d3.12	prostate	Comparison of two treatments for prostatic cancer
3.13	d3.13	hyper	Treatment of hypernephroma
3.14	d3.14	hyper	Treatment of hypernephroma
3.15	d3.15	myeloma	Survival of multiple myeloma patients
3.16	d3.16	prostate	Comparison of two treatments for prostatic cancer
3.17	d3.17	myeloma	Survival of multiple myeloma patients
3.19	d3.19	myeloma	Survival of multiple myeloma patients
3.20	d3.20	myeloma	Survival of multiple myeloma patients
4.1	d4.1	dialysis	Infection in patients on dialysis
4.2	d4.2	dialysis	Infection in patients on dialysis
4.3	d4.3	dialysis	Infection in patients on dialysis
4.4	d4.4	dialysis	Infection in patients on dialysis
4.5	d4.5	myeloma	Survival of multiple myeloma patients
4.6	d4.6	dialysis	Infection in patients on dialysis
4.7	d4.7	dialysis	Infection in patients on dialysis
4.8	d4.8	myeloma	Survival of multiple myeloma patients
4.9	d4.9	myeloma	Survival of multiple myeloma patients
4.10	d4.10	dialysis	Infection in patients on dialysis
4.11	d4.11	dialysis	Infection in patients on dialysis
4.12	d4.12	dialysis	Infection in patients on dialysis
5.1	d5.1	iud	Time to discontinuation of the use of an IUD
5.2	d5.2	iud	Time to discontinuation of the use of an IUD
5.3	d5.3	iud	Time to discontinuation of the use of an IUD
5.4	d5.4	iud	Time to discontinuation of the use of an IUD
5.5	d5.5	breast	Prognosis for women with breast cancer
5.6	d5.6	breast	Prognosis for women with breast cancer
5.7	d5.7	breast	Prognosis for women with breast cancer
5.8	d5.8	breast	Prognosis for women with breast cancer
5.9	d5.9	numerical_illustration	A numerical illustration
5.10	d5.10	hyper	Treatment of hypernephroma
5.11	d5.11	ovarian	Chemotherapy in ovarian cancer patients
5.12	d5.12	ovarian	Chemotherapy in ovarian cancer patients
5.13	d5.13	breast	Prognosis for women with breast cancer
5.14	d5.14	breast	Prognosis for women with breast cancer
5.15	d5.15	prostate	Comparison of two treatments for prostatic cancer
5.16	d5.16	myeloma	Survival of multiple myeloma patients
5.17	d5.17	breast	Prognosis for women with breast cancer
6.1	d6.1	hyper	Treatment of hypernephroma
6.4	d6.4	hyper	Treatment of hypernephroma
6.5	d6.5	breast_rfs	Recurrence-free survival in breast cancer patients
6.6	d6.6	breast_rfs	Recurrence-free survival in breast cancer patients
7.1	d7.1	ovarian	Chemotherapy in ovarian cancer patients
7.2	d7.2	ovarian	Chemotherapy in ovarian cancer patients
7.3	d7.3	ovarian	Chemotherapy in ovarian cancer patients
7.4	d7.4	ovarian	Chemotherapy in ovarian cancer patients
8.2	d8.2	bmt_leukaemia	Bone marrow transplantation in the treatment of leukaemia
8.3	d8.3	ovarian	Chemotherapy in ovarian cancer patients
8.4	d8.4	cirrhosis	Data from a cirrhosis study
8.4	NA	cirrhosis_cp	Data from a cirrhosis study	Counting process form of the cirrhosis study; used with Example 8.4, whose alias d8.4 is the baseline data.
8.4	NA	cirrhosis_lbr	Data from a cirrhosis study	Long-format log-bilirubin measurements for the cirrhosis study; used with Example 8.4, whose alias d8.4 is the baseline data.
8.5	d8.5	aortic	Survival following aortic valve replacement
8.6	d8.6	aortic	Survival following aortic valve replacement
8.7	d8.7	aortic	Survival following aortic valve replacement
8.8	d8.8	aortic	Survival following aortic valve replacement
8.9	d8.9	aortic	Survival following aortic valve replacement
9.1	d9.1	ulcer	Recurrence of an ulcer
9.4	d9.4	ulcer	Recurrence of an ulcer
9.5	d9.5	ulcer	Recurrence of an ulcer
9.6	d9.6	ulcer	Recurrence of an ulcer
9.7	d9.7	ulcer	Recurrence of an ulcer
10.1	d10.1	breast	Prognosis for women with breast cancer
10.2	d10.2	breast	Prognosis for women with breast cancer
10.3	d10.3	lung_transplant	Survival of patients registered for a lung transplant
10.4	d10.4	kidney	Survival following kidney transplantation
11.1	d11.1	ulcer	Recurrence of an ulcer
11.2	d11.2	gastric	Survival of patients with gastric cancer
11.3	d11.3	gastric	Survival of patients with gastric cancer
11.4	d11.4	kidney_centres	Comparisons between kidney transplant centres
11.5	d11.5	kidney_centres	Comparisons between kidney transplant centres
11.6	d11.6	kidney_centres	Comparisons between kidney transplant centres
11.7	d11.7	kidney_centres	Comparisons between kidney transplant centres
11.8	d11.8	kidney_centres	Comparisons between kidney transplant centres
12.1	d12.1	liver	Survival of liver transplant recipients
12.2	d12.2	liver	Survival of liver transplant recipients
12.3	d12.3	liver	Survival of liver transplant recipients
12.4	d12.4	liver	Survival of liver transplant recipients
12.5	d12.5	liver	Survival of liver transplant recipients
12.6	d12.6	liver	Survival of liver transplant recipients
12.7	d12.7	mice	Survival of laboratory mice
13.2	d13.2	rats	Recurrence of mammary tumours in female rats
13.3	d13.3	tamoxifen	Clinical trial of tamoxifen in breast cancer patients
13.4	d13.4	bmt_outcome	Patient outcome following bone marrow transplantation
14.1	d14.1	liver_wait	Time to death while waiting for a liver transplant
14.3	d14.3	liver_wait	Time to death while waiting for a liver transplant
15.1	d15.1	hepatitis	Survival from chronic active hepatitis
15.2	d15.2	hepatitis	Survival from chronic active hepatitis
15.3	d15.3	hepatitis	Survival from chronic active hepatitis
16.1	d16.1	iud	Time to discontinuation of the use of an IUD
16.2	d16.2	iud	Time to discontinuation of the use of an IUD
16.3	d16.3	iud	Time to discontinuation of the use of an IUD
16.4	d16.4	breast	Prognosis for women with breast cancer
16.5	d16.5	breast	Prognosis for women with breast cancer
16.6	d16.6	breast	Prognosis for women with breast cancer
16.7	d16.7	help	Health evaluation and linkage to primary care
NA	NA	bladder	NA	Collett (2023), Appendix B.2; no numbered example.
NA	NA	bmt	NA	Collett (2023), Appendix B.4; no numbered example.
NA	NA	cgd	NA	Collett (2023), Appendix B.5; no numbered example.
NA	NA	ducks	NA	Collett (2023), Appendix B.3; no numbered example.
NA	NA	scottish_mbc_cohort	NA	Course data set from the Edinburgh Cancer Informatics group; not from Collett (2023) and not used in a numbered example.

Data sets without a numbered example

Four of the data sets from the book are used in the appendices rather than in a numbered example, and the Scottish cohort is course material rather than book data. They have no dX.Y alias:

	Data set	Title	Note
80	cirrhosis_cp	Data from a cirrhosis study (counting process format)	Counting process form of the cirrhosis study; used with Example 8.4, whose alias d8.4 is the baseline data.
81	cirrhosis_lbr	Data from a cirrhosis study (log-bilirubin data)	Long-format log-bilirubin measurements for the cirrhosis study; used with Example 8.4, whose alias d8.4 is the baseline data.
126	bladder	Recurrence of bladder cancer	Collett (2023), Appendix B.2; no numbered example.
127	bmt	Bone marrow transplantation in leukaemia patients	Collett (2023), Appendix B.4; no numbered example.
128	cgd	Chronic granulomatous disease	Collett (2023), Appendix B.5; no numbered example.
129	ducks	Survival of black ducks	Collett (2023), Appendix B.3; no numbered example.
130	scottish_mbc_cohort	Synthetic Scottish metastatic breast cancer cohort	Course data set from the Edinburgh Cancer Informatics group; not from Collett (2023) and not used in a numbered example.

The cirrhosis study is a special case. Example 8.4 uses three forms of the same data: cirrhosis (the baseline values, alias d8.4), cirrhosis_lbr (the log-bilirubin measurements in long format) and cirrhosis_cp (the counting process format). Only the baseline object has the alias; the other two are listed with the same example but without an alias.

Using the index in R

Because the index is a data frame, you can query it directly:

# Which data set does Example 8.3 use?
dataset_by_exercise$dataset[dataset_by_exercise$example == "8.3"]
#> [1] "ovarian" NA        NA        NA        NA        NA

# Which examples use the myeloma data?
subset(dataset_by_exercise, dataset == "myeloma", c("alias", "example"))
#>    alias example
#> 3   d1.3     1.3
#> 6   d2.2     2.2
#> 10  d2.6     2.6
#> 22  d3.2     3.2
#> 25  d3.5     3.5
#> 27  d3.7     3.7
#> 28  d3.8     3.8
#> 29  d3.9     3.9
#> 35 d3.15    3.15
#> 37 d3.17    3.17
#> 38 d3.19    3.19
#> 39 d3.20    3.20
#> 44  d4.5     4.5
#> 47  d4.8     4.8
#> 48  d4.9     4.9
#> 67 d5.16    5.16

# All data sets used in Chapter 3
unique(dataset_by_exercise$dataset[dataset_by_exercise$chapter == 3])
#> [1] "breast"   "myeloma"  "hyper"    "prostate" NA

The index is generated by data-raw/dataset_by_exercise.R. If a new data set is added, or the example mapping changes, update that script and re-run it; it recreates both dataset_by_exercise and the dX.Y aliases.

Reproducing the book’s analyses

The help page of every data set shows how the analyses in Collett (2023) are carried out in R, with a comment for each example number. Each page has two parts:

Collett (2023), Chapter 17 style uses the functions and packages of the book’s own R chapter: survival::survfit(), survival::coxph(), survival::survdiff(), survival::survreg(), survival::cox.zph(), survival::tmerge(), survival::survSplit(), penalized::penalized(), eha::pchreg() and cmprsk::cuminc() / cmprsk::crr().
Modern tools repeats the same analysis with newer packages: ggsurvfit, flexsurv, coxme, icenReg, tidycmprsk, broom, rms and glmnet.