Added support of survfitms #177

yoursdearboy · 2017-10-11T15:42:38Z

Greetings.

This PR adds support of survfitms - multistate survival models built using Surv(..., type = 'mstate').

Here is an overview of changes to fortify:

To preserve original variable name depending on model class (surv or pstate) it is added to the end of the output data.frame;
Where necessary checks for variable name are made;
If surv.connect = T new rows are repeated according to number of states;
In the end columns are sorted to be in usual order.

To autoplot:

Added facet_grid support - argument grid. It's more convenient for 2-dim set plots;
Added support to swap order of faceting (if facets) or column with rows (if grid). By default event first, then strata. Argument strip_swap;
An argument conf.int.group = NULL was added to plot_confint. It's required to split CI ribbons by both - event and strata, because it can't be done with fill only;
such artificial column group is assembled in autoplot.

Feedback or questions are welcome.

lintr-bot · 2017-10-11T16:13:53Z

R/fortify_surv.R:72:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(strata)),]
                                                            ^

R/fortify_surv.R:79:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(events)),]
                                                            ^

R/fortify_surv.R:83:32: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                               ^

R/fortify_surv.R:83:43: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                          ^

R/fortify_surv.R:83:51: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                                  ^

R/fortify_surv.R:107:11: style: Commas should always have a space after.

  d <- d[,intersect(c(
          ^

R/fortify_surv.R:205:18: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                 ^

R/fortify_surv.R:205:41: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                                        ^

R/fortify_surv.R:207:41: style: Commas should always have a space after.

      group.levels <- lapply(plot.data[,group], levels)
                                        ^

R/fortify_surv.R:209:45: style: Commas should always have a space after.

      group.data <- factor(apply(plot.data[,group], 1, function(x) paste(x, collapse = ' ')), levels = group.levels)
                                            ^

R/fortify_surv.R:210:18: style: Commas should always have a space after.

      plot.data[,'group'] <- group.data
                 ^

R/fortify_surv.R:214:60: style: Place a space before left parenthesis, except in a function call.

      if ('event' %in% colnames(plot.data)) 'event' else if(grid) '.',
                                                           ^

R/fortify_surv.R:215:62: style: Place a space before left parenthesis, except in a function call.

      if ('strata' %in% colnames(plot.data)) 'strata' else if(grid) '.')
                                                             ^

tests/testthat/test-surv.R:170:73: style: Commas should never have a space before.

                         event = c(1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                       ~^

tests/testthat/test-surv.R:194:86: style: Commas should never have a space before.

                         event = c(1, 2, 'any', 1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                                    ~^

lintr-bot · 2017-11-14T04:39:53Z

R/fortify_surv.R:72:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(strata)),]
                                                            ^

R/fortify_surv.R:79:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(events)),]
                                                            ^

R/fortify_surv.R:83:32: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                               ^

R/fortify_surv.R:83:43: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                          ^

R/fortify_surv.R:83:51: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                                  ^

R/fortify_surv.R:107:11: style: Commas should always have a space after.

  d <- d[,intersect(c(
          ^

R/fortify_surv.R:205:18: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                 ^

R/fortify_surv.R:205:41: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                                        ^

R/fortify_surv.R:207:41: style: Commas should always have a space after.

      group.levels <- lapply(plot.data[,group], levels)
                                        ^

R/fortify_surv.R:209:45: style: Commas should always have a space after.

      group.data <- factor(apply(plot.data[,group], 1, function(x) paste(x, collapse = ' ')), levels = group.levels)
                                            ^

R/fortify_surv.R:210:18: style: Commas should always have a space after.

      plot.data[,'group'] <- group.data
                 ^

R/fortify_surv.R:214:60: style: Place a space before left parenthesis, except in a function call.

      if ('event' %in% colnames(plot.data)) 'event' else if(grid) '.',
                                                           ^

R/fortify_surv.R:215:62: style: Place a space before left parenthesis, except in a function call.

      if ('strata' %in% colnames(plot.data)) 'strata' else if(grid) '.')
                                                             ^

tests/testthat/test-surv.R:170:73: style: Commas should never have a space before.

                         event = c(1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                       ~^

tests/testthat/test-surv.R:194:86: style: Commas should never have a space before.

                         event = c(1, 2, 'any', 1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                                    ~^

lintr-bot · 2017-11-14T06:09:57Z

R/fortify_surv.R:72:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(strata)),]
                                                            ^

R/fortify_surv.R:79:61: style: Commas should always have a space after.

      base <- base[rep(seq_len(nrow(base)), length(events)),]
                                                            ^

R/fortify_surv.R:83:32: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                               ^

R/fortify_surv.R:83:43: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                          ^

R/fortify_surv.R:83:51: style: Commas should always have a space after.

      base[base$event == 'any',c('pstate','upper','lower')] <- 1.0
                                                  ^

R/fortify_surv.R:107:11: style: Commas should always have a space after.

  d <- d[,intersect(c(
          ^

R/fortify_surv.R:205:18: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                 ^

R/fortify_surv.R:205:41: style: Commas should always have a space after.

      plot.data[,'group'] <- plot.data[,group]
                                        ^

R/fortify_surv.R:207:41: style: Commas should always have a space after.

      group.levels <- lapply(plot.data[,group], levels)
                                        ^

R/fortify_surv.R:209:45: style: Commas should always have a space after.

      group.data <- factor(apply(plot.data[,group], 1, function(x) paste(x, collapse = ' ')), levels = group.levels)
                                            ^

R/fortify_surv.R:210:18: style: Commas should always have a space after.

      plot.data[,'group'] <- group.data
                 ^

R/fortify_surv.R:214:60: style: Place a space before left parenthesis, except in a function call.

      if ('event' %in% colnames(plot.data)) 'event' else if(grid) '.',
                                                           ^

R/fortify_surv.R:215:62: style: Place a space before left parenthesis, except in a function call.

      if ('strata' %in% colnames(plot.data)) 'strata' else if(grid) '.')
                                                             ^

tests/testthat/test-surv.R:170:73: style: Commas should never have a space before.

                         event = c(1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                       ~^

tests/testthat/test-surv.R:194:86: style: Commas should never have a space before.

                         event = c(1, 2, 'any', 1, 1, 1, 1, 2, 2, 2, 2, 'any', 'any' , 'any', 'any'))
                                                                                    ~^

sinhrks · 2017-11-14T09:10:32Z

Thanks for the PR. Could you fix the Travis failure?

yoursdearboy · 2017-12-01T13:04:35Z

@sinhrks Everything should be ok now. I don't understand why Travis build failed, there's 0 warnings and errors.

sinhrks · 2017-12-02T05:56:17Z

Thx! A warning is raised because of a doc issue.

sinhrks · 2017-12-02T05:57:35Z

R/fortify_surv.R

@@ -114,7 +159,9 @@ autoplot.survfit <- function(object, fun = NULL,
                             conf.int.fill = '#000000', conf.int.alpha = 0.3,
                             censor = TRUE, censor.colour = NULL, censor.size = 3,
                             censor.alpha = NULL, censor.shape = '+',
-                             facets = FALSE, nrow = NULL, ncol = 1, scales = 'free_y',
+                             facets = FALSE, nrow = NULL, ncol = 1,
+                             grid = FALSE, strip_swap = FALSE,


can u add docs for grid and strip_swap?

sinhrks · 2017-12-23T01:14:15Z

Thanks! I'll fix the doc issue.

yoursdearboy added 2 commits October 11, 2017 15:24

Added support of survfitms to fortify.

1ff6913

Added support of survfitms to autoplot.

e405a75

sinhrks added 2 commits November 14, 2017 12:44

Merge branch 'master' into survfitms

77cf083

Merge branch 'master' into survfitms

7dad9be

yoursdearboy added 2 commits December 1, 2017 11:08

Fix codestyle issues

d11b85f

Fix nevent for survfitms.

389ace8

sinhrks requested changes Dec 2, 2017

View reviewed changes

sinhrks approved these changes Dec 23, 2017

View reviewed changes

sinhrks merged commit f2f68ae into sinhrks:master Dec 23, 2017

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Added support of survfitms #177

Added support of survfitms #177

yoursdearboy commented Oct 11, 2017

lintr-bot commented Oct 11, 2017

lintr-bot commented Nov 14, 2017

lintr-bot commented Nov 14, 2017

sinhrks commented Nov 14, 2017

yoursdearboy commented Dec 1, 2017

sinhrks commented Dec 2, 2017 •

edited

sinhrks Dec 2, 2017

sinhrks commented Dec 23, 2017

Added support of survfitms #177

Added support of survfitms #177

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yoursdearboy commented Oct 11, 2017

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lintr-bot commented Nov 14, 2017

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sinhrks commented Nov 14, 2017

yoursdearboy commented Dec 1, 2017

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edited