survival | Survival package for R
kandi X-RAY | survival Summary
kandi X-RAY | survival Summary
This is the source code for the "survival" package in R. It gets posted to the comprehensive R archive (CRAN) at intervals, each such posting preceded a throrough test. (I run the test suite for all 800+ packages that depend on survival.) In general, each new push to CRAN will update the second term of the version number, e.g. 2.40-5 to 2.41-0. Updates only to the github source increment after the dash. (If an error is found in the process of CRAN submission then the published CRAN version may be x.yy-1 or even x.yy-2 or 3.) This directory is a shadow of the 'real' respository, which is in mercurial on my own machine. As such I don't use git for pull requests. I will often copy code from a suggestion, however; they don't get ignored!. The vignette2 directory contains material that is not posted to CRAN. The file "tutorial.Rnw", for instance, requires data from the mstate package. Survival is a recommended package, and such packages can only depend on other recommended packages. (This allows for a consistent distribution bundle.) The sas.Rnw vignette has a discussion of compute time and takes too long to run, etc. A large portion of the source is found in the noweb directory, and is based on the literate programming ideas of Knuth. The reason is that it allows more complete documentation of the methods. I can have things like blocks of equations, and find having the "real" equations side by side with the code makes it much easier to get it right. Anyone who wants to study the methods is advised to perform "make code.pdf" in the noweb directory and then look at the relevant portion of that pdf file. Any file in the R or src directories that starts with an "automatically generated ..." comment should NOT be modified directly, instead work with the noweb source. (You will need to have the noweb package loaded in order to run the Makefile.). You should be able to install this using the following R code: library(devtools); install_github("therneau/survival"). Note that good practice would be to make derived files such as R/tmerge.R "on the fly" using a configure script; that way there would not be a danger of someone trying to modify the derived file rather than the actual source (noweb/tmerge.Rnw). However, I was not able to create a configure file that worked reliably on all platforms, and voted for usability rather than purity.
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survival Key Features
survival Examples and Code Snippets
def _survival_function(self, y):
if self._is_maybe_event_override:
raise NotImplementedError("survival_function is not implemented when "
"overriding event_shape")
if not self.bijector._is_injective: # p
def _log_survival_function(self, y):
if self._is_maybe_event_override:
raise NotImplementedError("log_survival_function is not implemented when "
"overriding event_shape")
if not self.bijector._is_injecti
Community Discussions
Trending Discussions on survival
QUESTION
I'm trying to produce a cumulative incidence plot for a competing hazards survival analysis using plot() in R. For some reason, the plot that is produced has a legend that I have not called. The legend is intersecting with the lines on my graph and I can't figure out how to get rid of it. Please help!
My code is as follows:
...ANSWER
Answered 2021-Jun-09 at 13:28You are using the cuminc
function from the cmprsk
package. This produces an object of class cuminc
, which has an S3 plot method. ?plot.cuminc
shows you the documentation and typing plot.cuminc
shows you the code.
There is some slightly obscure code that suggests a workaround:
QUESTION
Is there a way to add the greater than symbol ">" in ggsurvplot? in the figure legend?
Here is my sample dataset and code for this problem:
...ANSWER
Answered 2021-Jun-08 at 16:51It's worth reviewing what's actually happening. The ggtext
function attempts to parse the labels using tags and the blockquote tag (>
) is not supported. So we need some way to escape the tag. I couldn't find a documented way.
It's a bit of a hack, but I've added a zero width space unicode character (\u200B
) before the >
to break the tag:
QUESTION
I was trying to obtain the expected utility for each individual using R's survival
package (clogit
function) and I was not able to find a simple solution such as mlogit's logsum
.
Below I set an example of how one would do it using the mlogit
package. It is pretty straight forward: it just requires regressing the variables with the mlogit
function, save the output and use it as an argument in the logsum
function -- if needed, there is a short explanation in this vignette. And what I want is to know the similar method for clogit
. I've read the package's manual but I have failed to grasp what would be the most adequate function to perform the analsysis.
Note1: My preference for a function like mlogit's
is related to the fact that I might need to perform tons of regressions later on and being able to perform the correct estimation in different scenarios would be helpful.
Note2: I do not intend that the dataset created below be representative of how data should behave. I've set the example solely for the purpose of perfoming the function after the logit regressions.
**
...ANSWER
Answered 2021-Jun-07 at 00:20The vignette you offer says the logsum is calculated as:
To my reading that is similar to the calculation used to construct the "linear predictor". the lp is t(coef(clog)) %*% Xhat
. If I'm correct on that interpretation, then that is stored in the clog
-object:
QUESTION
I am learning about Dynamic Bayesian Network models using the R package bnlearn
. To this end, I am following this paper where they impose certain constraints in the form of 6 layers (Table 1 in the paper):
ANSWER
Answered 2021-Jun-05 at 14:47You can add domain knowledge or constraints to structure learning in a couple of ways.
If you want to specify the network structure and parameters using domain knowledge, you can build the network manually using
custom.fit
.If you want to estimate the structure of the BN from data then you can impose constraints on edge direction & edge presence using the
whitelist
andblacklist
parameters in the structure learning algorithms.A prior can be placed on the edges in structure learning (e.g.
prior="cs"
, where "If prior is cs, beta is a data frame with columns from, to and prob specifying the prior probability for a set of arcs. A uniform probability distribution is assumed for the remaining arcs."). There are other priors that can be used.
QUESTION
I'm working with PyTorch tutorial, slightly modified to use Titanic dataset. I'm using very simple network of Linear(Dense) with ReLU... I'd like to predict survival status based on age, fare and sex for example.
I experienced a strange behavior with a simple neural network (I'm experimenting on Google Colab). Sometimes when I execute training, the accuracy doesn't change at all. It's strange because I'm recreating the model...
...ANSWER
Answered 2021-Jun-04 at 17:03As this is a classification problem, your neural network's last layer should not have a relu
activation function.
Code Snippet:
QUESTION
I'm trying to convert the tick value of Y-Axis Scale from (0 .2 .4 .6 .8 1.0) to (0 .01 .02 .03 .04 .05), but failed. However, no such problem when converting viewmax
...ANSWER
Answered 2021-Jun-01 at 15:27It works fine for me.
QUESTION
SO I have a BSD server and want to host a Minecraft BungeeCoord server. The thing is the server files are in different directories EG: /home/name/bungee/servers/Survival/start.sh AND /home/name/bungee/servers/Lobby/start.sh
Is there a way to make a file that can run multiple files from different directories ?
Just to make it clear, the reason I want to do this is because the BSD server can only take 1 file at a time, like shell/terminal.
Edit: The command I ended up using was screen
ANSWER
Answered 2021-Apr-05 at 09:30somewhat sorted by least to most advanced
example 1QUESTION
I created a array of objects and I render them based on a click event. Is there any way using Vue that If I click for example the 'survival' button, if it's already set as the activeCategory, it hides itself? Like an accordion behavior.
...ANSWER
Answered 2021-May-31 at 20:00Sure, in your method you can check if the activeCategory
is already the same category
and in that case set it back to the default of ''
:
QUESTION
I have a dataframe containing results measured through Matthews correlation coefficient, F1 score, and accuracy, and I would like to generate barcharts for each of these metrics in R
using ggplot2
.
I am trying to loop over these three rates, but R
does not let me use a variable (this_rate
) to select the proper dataframe column for my plot.
Here's my (not working) code;
...ANSWER
Answered 2021-May-27 at 03:13When you are passing character values of column names use .data
to subset them. This works and creates separate pdf
for list_of_rates
.
QUESTION
I am fitting a K.M survival model on a data and the summary for model seems fine but whenever I plot it's reversed as it 0 at day 0 and 1 at day 2500 which should be the other way around?
...ANSWER
Answered 2021-May-26 at 06:10Probably your status variable death
is a factor. It shouldn't be. It should be numeric.
Run a toy example below. Here, status
is a factor, so plot will look like yours:
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