c353208702
secmal/cmprsk: Change scaling to years
2021-01-17 19:02:33 +01:00
f29a5f1ef5
secmal: Get risk and CI from competing risk
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Extract risk and calculate competing risk at specific timepoint.
2021-01-17 18:53:08 +01:00
48be520bb0
secmal: Plot competing risk for SM
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Plot competing risk plot for probability of SM and death as competing
risk.
2021-01-17 18:52:06 +01:00
471ed09dca
secmal: Adjust calculation for SM incidence
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Change calculation to cause-specific aproach.
2021-01-17 17:39:34 +01:00
388e20673c
survival: Add SM survival plot
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Plot survival after SM diagnosis.
2021-01-17 15:27:15 +01:00
465ce64487
Add cox time dependend analysis for death and sm
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Simple analysis of influence of relapse and sm on death.
The SM part is not working currently (due to limited events).
2021-01-17 11:43:34 +01:00
00d96d77f2
Add risk.R
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Add file to run coxph analysis and print result to file.
2021-01-17 11:41:57 +01:00
c74321fa54
Merge branch 'coxph'
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* coxph:
data: Update data
survival/sma_plot_surv_asct: Adjust output
visualize/sma_jitt_dx_year: Adjust output
utils: Condense Ewing sarcoma
coxph: Add uni and multivariate analysis
coxph: Adjust coxph summary output
uitils: Remove global data object before reinitializing
coxph: First commit of coxph models
2021-01-17 11:39:38 +01:00
82c5e40c8b
data: Update data
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Update data to reflect competing risk in time_at_risk_status.
Death is now labeled with "2" to be distinguishable from censoring.
2021-01-17 11:37:42 +01:00
b08320bd3b
survival/sma_plot_surv_asct: Adjust output
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Change labels.
2021-01-17 11:36:21 +01:00
beedddda01
visualize/sma_jitt_dx_year: Adjust output
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Adjust labels and remove legend.
2021-01-17 11:35:12 +01:00
3e263bb400
utils: Condense Ewing sarcoma
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Condense Ewing Sarcoma with Ewing Sarcoma / PNET due to a inconsistency
in data mining.
2021-01-17 11:33:41 +01:00
b3ef8086ec
coxph: Add uni and multivariate analysis
2021-01-17 11:22:06 +01:00
a3c816ad64
coxph: Adjust coxph summary output
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Split HR and CI, print logrank values.
2021-01-17 11:21:05 +01:00
351b26368d
uitils: Remove global data object before reinitializing
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It seems that just overriding the object may not be enough to pure it.
Before loading the data, the variable "secmal" is removed.
2020-12-21 16:39:24 +01:00
9a331a2091
Merge branch 'data-update' into coxph
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Update data.
2020-12-21 11:20:36 +01:00
2460863bcb
Merge branch 'data-update'
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* data-update:
data: Use new dataset
data: Update to latest dataset
data: Reformat data
2020-12-18 15:41:52 +01:00
2db6a44fad
data: Use new dataset
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Update link to new dataset.
2020-12-18 15:38:47 +01:00
79ccaec8fc
data: Update to latest dataset
2020-12-18 15:37:32 +01:00
aa0024256b
data: Reformat data
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Sort data descendig at value uuid
2020-12-18 15:36:30 +01:00
8f07c45f63
coxph: First commit of coxph models
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First univariate with covariates coxph models.
2020-11-25 17:28:13 +01:00
dbfcca9716
Merge branch 'visualize'
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* visualize:
Visualize asct per diagnosis per age
Visualize asct per diagnosis per year
Add basic histograms
Remove unused factor levels from data after limiting
2020-11-19 19:46:44 +01:00
3c517431f6
Merge branch 'fix-library-load'
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* fix-library-load:
utils: Move library() calls to beginning of file
2020-11-19 19:46:39 +01:00
70ed15c2b8
Merge branch 'change-plot'
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* change-plot:
Change default aspect ratio for graphs
Add optional width and height arguments save plots
2020-11-19 19:46:34 +01:00
0be00652e1
Visualize asct per diagnosis per age
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This adds ggplots to visualize the number of ascts per diagnosis per
age in various methods:
* Histogram
* Density plot
* Frequency plot
* Scatter plot
2020-11-19 19:44:33 +01:00
066d6cedf4
Visualize asct per diagnosis per year
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This adds ggplots to visualize the number of ascts per diagnosis per
year in various methods:
* Histogram
* Density plot
* Frequency plot
* Scatter plot
2020-11-19 19:23:29 +01:00
e0faa24f40
Add basic histograms
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This adds some basic histograms to show the distribution of age at
transplatation and year of transplatation.
2020-11-19 19:21:52 +01:00
2175d46379
Change default aspect ratio for graphs
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This adds a 4:3 default aspect ratio.
2020-11-19 16:20:20 +01:00
4762523c20
Add optional width and height arguments save plots
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Sometimes the graphs must have a special size. This adds optional
arguments for width and height.
2020-11-19 16:14:21 +01:00
30c03f01d0
Remove unused factor levels from data after limiting
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After limiting the data there may be factors with empty levels. This can
be confusing and should be avoided.
2020-11-19 13:16:34 +01:00
d96e3c5ed8
utils: Move library() calls to beginning of file
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It seems that calling library() within a function may fail silently.
Moving them out of the function at the beginning of utils.R fixes this.
One particular place, where all necessary libraries are loaded, seem to
be a much easier way than inside a function.
2020-11-18 10:26:45 +01:00
792b42373e
Merge branch 'data'
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* data:
Use data from repository
Add data to repository
2020-11-17 19:50:01 +01:00
2a67cecf0a
Use data from repository
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Starting with this commit, all calculation will base on data/data.csv.
2020-11-17 19:49:22 +01:00
6d99d0a825
Add data to repository
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Add the study data into repository.
2020-11-17 19:49:08 +01:00
27942f784a
secmal: Fix median survival line warning
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Median survival lines are not allowed with "cumhaz" function in
ggsurvplot().
2020-11-17 19:45:18 +01:00
6c4f717793
Merge branch 'secmal'
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* secmal:
Rename plot_survival.R
Add secondary malignancy plots
Introduce initialization function
2020-11-17 18:22:18 +01:00
08f9ddfc23
Rename plot_survival.R
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This scripts is now used to create all plots in this project.
2020-11-17 18:21:54 +01:00
fcd2d330aa
Add secondary malignancy plots
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This adds some plots to show data for the secondary malignacies.
2020-11-17 18:21:54 +01:00
5e7b6007f1
Introduce initialization function
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sma_init() can now be used to load all libraries and the data.
It is safe to call sma_init() multiple times. To forcefully reload the
data call sma_init_force().
2020-11-17 18:17:40 +01:00
a6b5292890
Update README.md
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Add a much more precise description how this repo can be used.
2020-11-17 18:16:57 +01:00
57165dd6d1
Merge branch 'limit-data'
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* limit-data:
utils: Filter all hematologic patients
utils: Filter patient by age
2020-11-17 15:20:21 +01:00
5c26e4100e
Merge branch 'plots-per-dx'
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* plots-per-dx:
survival: Add plots per diagnosis
2020-11-17 15:20:15 +01:00
b81756310b
utils: Filter all hematologic patients
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At this time only solid tumors are important. This is a hard coded
switch, not very useful. But it get the job done and we can decide later
how this can be made better.
2020-11-17 15:12:58 +01:00
c68e536861
utils: Filter patient by age
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The minimum age for this study is 16.0 years or older at time of
transplantation.
2020-11-17 15:05:31 +01:00
95be046985
survival: Add plots per diagnosis
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This adds survival curves per diagnosis. They still look a bit
overloaded.
2020-11-17 14:33:56 +01:00
3c160c37bb
Set global break.time.by value for ggsurvplot
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Substitute manual "break.time.by" values with global which can be used
by all plots.
2020-11-17 14:32:59 +01:00
c087b40f5c
Merge branch 'survminer'
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* survminer:
survival: Improve plots
survival: Change plot function to ggsurvplot
2020-11-17 14:04:07 +01:00
c0c890c78c
survival: Improve plots
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Display a risk table, median survival line and adjust theme.
2020-11-17 13:28:06 +01:00
12ffcd4e38
survival: Change plot function to ggsurvplot
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This will create the plot using the ggsurvplot from "survminer" package.
survminer user ggplot for plotting and comes with some powerful and nice
looking features.
2020-11-17 12:58:51 +01:00
b5634b7f8f
survival: Remove excessive newlines
2020-11-16 22:52:14 +01:00
