methods
from pamm
. Can be specified via ...
. Fixes #200warn_about_new_time_points
when original data not stored in model object. Fixes #203split_data
function that now accepts Surv(start, stop, event)
type inputs, e.g., to construct left-truncated data.as_ped.ped
now also works for transformations with time-dependent covariatespamm
, which is a thin wrapper
around mgcv::gam
with some arguments pre-set.predictSurvProb.pamm
pec
as_ped
changed. The vertical bar |
is no longer necessary to indicate concurrent or cumulative effectsFunctions get_hazard
and add_hazard
also gain reference
argument.
Allows to calculate (log-)hazard ratios.
Introduces breaking changes to add_term
function. Argument relative
is replaced by reference
, makes calculation of relative (log-)hazards, i.e. hazard ratios, more flexible. Argument se.fit
is replaced by ci
.
dplyr
reverse dependency (see #101)make_newdata
concurrent
now has a lag = 0
argument, can be set to positive integer valuesas_ped
accepts multiple concurrent
specials with different lag
specificationsmake-newdata.fped
gg_laglead
and gg_partial_ll
did not
calculate the lag-lead-window correctly when applied to ped
datamake_newdata
loses arguments expand
and n
and
gains ...
where arbitrary covariate specifications can be placed, i.e.
e.g. age=seq_range(age, n=20)
. Multiple such expression can be provided and
a data frame with one row for each combination of the evaluated expressions
will be returned. All variables not specified in \code{...} will be set to
respective mean or modus values. For data of class ped
or fped
make_newdata
will try to specify time-dependent variables intelligently.
te_var
argument in concurrent
and cumulative
was renamed to
tz_var
te
arguments have been replaced by tz
(time points at which z
was observed) in all functions to avoid confusion with mgcv::te
(e.g., gg_laglead
)
Overall better support for cumulative effects
Added convenience functions for work with cumulative effects, namely
gg_partial
andgg_slice
Added helper functions to calculate and visualize Lag-lead windows
get_laglead
gg_laglead
Added convenience geom
s for piece-wise constant hazards (see examples in
?geom_hazard
, cumulative hazards and survival probabilities (usually
aes(x=time, y = surv_prob)
, but data set doesn't contain extra row for
time = 0
), thus
geom_stephazard
adds row (x=0, y = y[1]) to the data before plottinggeom_hazard
adds row (x = 0, y = 0) before plotting (can also be used
for cumulative hazard)geom_surv
add row (x = 0, y = 1) before plottingAll data transformation is now handled using as_ped
(see
data transformation vignette)
Data transformation now handles
Added functionality to flexibly simulate data from PEXP including cumulative effects, see ?sim_pexp
Added functionality to calculate Aalen-model style cumulative coefficients,
see ?cumulative_coefficient
Breaking change in split_data
(as_ped
now main data trafo function):
max.end
argumentmax_time
argument to introduce administrative censoring at
max_time
when no custom interval split points are providedtidyeval
adaptationstidyeval
pamm
package to pammtools
due to naming conflicts with PAMM
package on CRANAny scripts or data that you put into this service are public.
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