pclm.fit: Penalized Composite Linear Model (PCLM) for PASH object.
In MaciejDanko/pclmpash:

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/pclm_pash.r

The PCLM method is based on the composite link model, with a penalty added to ensure the smoothness of the target distribution. Estimates are obtained by maximizing a penalized likelihood. This maximization is performed efficiently by a version of the iteratively reweighted least-squares algorithm. Optimal values of the smoothing parameter are chosen by minimizing Bayesian or Akaike<e2><80><99> s Information Criterion [From Rizzi et al. 2015 abstract].

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pclm.fit(object, population.size, out.step = "auto",
  to.pash = c("aggregated", "nonaggregated"), last_open = FALSE,
  nax.method = c("udd", "cfm"), control = list())

`object`	A `pash` object.
`population.size`	Population size. If it is not given then it will be retrieved from the pash object (if possible). You may want to set it to a high value (e.g. 10000) if the data has no information about population number.
`out.step`	Age interval length in output aggregated life-table. If set to `"auto"` then the parameter is automatically set to the length of the shortest age/time interval of pash life-table.
`to.pash`	A way how the `pash` life-table is constructed: `"aggregated"` - The `pash` life-table is constructed from aggregated PCLM fit with interval length of `out.step`. `"nonaggregated"` - The `pash` life-table is constructed from nonaggregated (raw) PCLM fit with interval of length equal to the shortest original interval length divided by `x.div`. See `pclm.control`.
`last_open`	Logical determining if to construct `pash` life-table with last open interval. See `Inputlx`.
`nax.method`	A way of calculating nax in `Inputlx` if `to.pash == "nonaggregated"`. Possible values: `"udd"` (see `naxUDD`) or `"cfm"` (see `naxCFMfromnmx`).
`control`	List with additional parameters. See `pclm.control`.

The function read pash object and run pclm.general function. The new pash object is constructed from pclm.general output.

Use pclm.general for more flexible and direct PCLM fitting.

An object of classes "pclm" and "pash" with PCLM-based life-table and $pclm component. The function updates a pash object by fitting PCLM.
The new object inherits source and time_unit attributes from the original pash object as well as class "pash". The pash life-table (component $lt) contains the life-table based on the fitted PCLM (aggregated or nonaggregated depending on to.pash parameter). The newly constructed pash object contains extra $pclm component needed to run summary and plot functions.

List of $pclm sub-components:

`grouped`	Life-table based on aggregated PCLM fit defined by `out.step`.
`raw`	Life-table based on original (raw) PCLMfit.
`fit`	PCLM fit used to construct life-tables.
`warn.list`	List with warnings.
`m`	Interval multiple, see `pclm.interval.multiple`, `pclm.compmat`.
`x.div`	Value of `x.div`, see `pclm.control`.
`out.step`	Interval length of aggregated life-table, see `pclm.control`.

Maciej J. Danko <[email protected]> <[email protected]>

Rizzi S, Gampe J, Eilers PHC. Efficient estimation of smooth distributions from coarsely grouped data. Am J Epidemiol. 2015;182:138?47.
Rizzi S, Thinggaard M, Engholm G, et al. Comparison of non-parametric methods for ungrouping coarsely aggregated data. BMC Medical Research Methodology. 2016;16:59. doi:10.1186/s12874-016-0157-8.

pclm.control, plot.pclm, summary.pclm, pash

## Not run: 
# *******************************************************************
# Usage of PCLM methods for simple cases
# *******************************************************************

# *** Create pash objects with different interval lengths
AU1 <- Inputlx(x = australia_1y$x, lx = australia_1y$lx,
   nax = australia_1y$nax, nx = australia_1y$nx, last_open = TRUE)
AU10 <- Inputlx(x = australia_10y$x, lx = australia_10y$lx,
   nax = australia_10y$nax, nx = australia_10y$nx, last_open = TRUE)

# *** Use PCLM
# Ungroup AU10 with out.step equal minimal interval length
min(AU10$lt$nx[-13])
AU10p.1a <- pclm.fit(AU10)
print(AU10p.1a)
plot(AU10p.1a)

# Ungroup AU10 with out.step equal minimal interval length
# and get good estimates of nax
AU10p.1b <- pclm.fit(AU10, control = list(x.div = 10))
print(AU10p.1b)
plot(AU10p.1b)
# This time number of internal (raw) PCLM classes was high
# and automatically P-splines were used to prevent long computations

# This number can be estimated before performing
# PCLM calclualtions:
pclm.nclasses(AU10$lt$x, control = list(x.div = 10))
# which is the same as in the fitted model
length(AU10p.1b$pclm$raw$x)
# whereas number of classes in the pash life-table
# depends on out.step
length(AU10p.1b$lt$x)
length(AU10p.1b$pclm$grouped$x) # equivalently

# To speed-up computations we can decrease the number of P-sline knots
AU10p.1c <- pclm.fit(AU10, control = list(x.div = 10,
                     bs.use = TRUE, bs.df.max = 100))

# We can also use raw (nonaggregated) PCLM life-table
# as the default pash life-table:
AU10p.1d <- pclm.fit(AU10, control = list(x.div = 10),
                     to.pash = "nonaggregated")
print(AU10p.1d)
length(AU10p.1d$lt$x) # the number of raw PCLM classes =
# = number of pash life-table classes

# *** Pace measures sorted (ascending order) by
#     potential precision of computation
GetPace(AU10)
GetPace(AU10p.1a)
GetPace(AU10p.1b)
GetPace(AU10p.1c)
GetPace(AU10p.1d)
GetPace(AU1)

# The same for shappe
GetShape(AU10)
GetShape(AU10p.1a)
GetShape(AU10p.1b)
GetShape(AU10p.1c)
GetShape(AU10p.1d)
GetShape(AU1)

# *** Diagnostic plots for fitted PCLM model
# Aggregated PCLM fit:
plot(AU10p.1b, type = 'aggregated')
# Raw PCLM fit before aggregation:
plot(AU10p.1b, type = 'nonaggregated')

# In this PCLM fit aggregated life-table is identical
# with nonaggregated
plot(AU10p.1a, type = 'aggregated')
plot(AU10p.1a, type = 'nonaggregated')

# *** Combined summary of pash and pclm objects
summary(AU10p.1a)
summary(AU10p.1b)
summary(AU10p.1c)
summary(AU10p.1d)
# Summary if pclm object is not present
summary(AU10)

# *** Smooth and aggregate data into 12-year interval
AU10p.2 <- pclm.fit(AU10, out.step = 12)
print(AU10p.2)
print(AU10p.2, type = 'aggregated') # grouped PCLM life-table
print(AU10p.2, type = 'nonaggregated') # raw PCLM life-table
plot(AU10p.2)

# *** Effect of the smaller sample size on the estimate.
#     Forced change of population size.
AU10p.3 <- pclm.fit(AU10, population.size = 20, out.step = 1,
                    control = list(x.div = 1))
plot(AU10p.3)

# *** Plotting mortality
AU10p.4a <- pclm.fit(AU10, population.size=1e6, control = list(x.div = 5))
plot(AU10p.4a$lt$x, log10(AU10p.4a$lt$nmx), type='l', lwd = 2,
     xlim=c(0,130), xlab='Age', ylab='log_10 mortality', col = 2)
lines(AU1$lt$x, log10(AU1$lt$nmx), type = 'p')
tail(AU10p.4a, n = 10)
#note that lx has standardized values

# Improving the plot to cover more age classes
AU10p.4b <- pclm.fit(AU10, control = list(zero.class.end = 150,
                     x.div = 4))
plot(AU10p.4b$lt$x, log10(AU10p.4b$lt$nmx), type='l', lwd = 2,
     xlim=c(0,130), xlab='Age', ylab='log_10 mortality', col = 2)
lines(AU1$lt$x, log10(AU1$lt$nmx), type = 'p')
print(AU10p.4b$lt[111:120,])

# The change of the order of the difference in pclm algorithm may
# affect hte interpretation of the tail.
# But try to check also pclm.deg = 4 and 5.
AU10p.4c <- pclm.fit(AU10, control = list(zero.class.end = 150,
                     x.div = 4, pclm.deg = 4))
plot(AU10p.4c$lt$x, log10(AU10p.4c$lt$nmx), type='l', lwd = 2,
     xlim=c(0,130), xlab='Age', ylab='log_10 mortality', col = 2)
lines(AU1$lt$x, log10(AU1$lt$nmx), type = 'p')

# *******************************************************************
# Usage of PCLM methods for more complicated dataset
# - understanding the out.step, x.div, and interval multiple
# *******************************************************************

# *** Generate a dataset with varying and fractional interval lengths
x <- c(0, 0.6, 1, 1.4, 3, 5.2, 6.4, 8.6, 11, 15,
       17.2, 19, 20.8, 23, 25, 30)
ndx <- ceiling(10000*diff(pgamma(x, shape = 3.8, rate = .4)))
barplot(ndx/diff(x), width = c(diff(x), 2)) # preview

# *** Create pash object
(B <- Inputlx(x = x, lx = 10000-c(0, cumsum(ndx)), last_open = TRUE))

# *** Fit PCLM with automatic out.step
Bp1 <- pclm.fit(B)
# Output interval length (out.step) is automatically set to 0.4
# which is the minimal interval length in original data.
min(B$lt$nx, na.rm = T)
summary(Bp1) #new out.step can be also read from summary
plot(Bp1)

# *** Setting manually out.step
Bp2 <- pclm.fit(B, out.step = 1)
plot(Bp2, type = 'aggregated') # The fit with out.step = 1
plot(Bp2, type = 'nonaggregated') # It is clear that
# PCLM extended internal interval length even without changing x.div
# It was done because of the fractional parts in x vector.
# This is also a case for Bp1
summary(Bp2) #PCLM interval length = 0.2
Bp2$pclm$raw$n[1:10]

# *** Setting manually out.step to a smaller value than
#     the smallest original interval length
Bp3 <- pclm.fit(B, out.step = 0.1)
summary(Bp3)
# We got a warning as out.step cannot be smaller than
# smallest age class if x.div = 1

# We can change x.div to make it possible
Bp3 <- pclm.fit(B, out.step = 0.1, control = list(x.div = 2))
#0.1 is two times smaller than minimal interval length
summary(Bp3) # We were able to change the interval
plot(Bp3)
# NOTE: In this case x.div has not sufficient value to
#       get good axn estimates
Bp3$pclm$grouped$ax[1:10]
Bp3$lt$nax[1:10] #equivalently

# This can be changed by the further increase of x.div
Bp4 <- pclm.fit(B, out.step = 0.1, control = list(x.div = 20))
Bp4$pclm$grouped$ax[1:10]
# NOTE: This time P-spline approximation was used because
# the composition matrix was huge

# Finally, we were able to get our assumed out.step
Bp4$pclm$grouped$n[1:10]
Bp4$lt$nx[1:10] #equivalently

In the fitted model the interval multiple (m) is 5.
(m <- pclm.interval.multiple(B$lt$x, control = list(x.div = 20)))
summary(Bp4)
# Interval multiple determines
# the maximal interval length in raw PCLM life-table,
(K <- 1 / m)
# which is further divided by x.div.
K / 20
# Simply: 1 / (m * x.div) = 1 / (5 * 20) = 0.01
# The interval in the raw PCLM life-table is 10 times shorter than
# in the grouped life-table
#interval length in aggregated PCLM life-table:
Bp4$pclm$grouped$n[1:10]/ # divided by
# interval length in nonaggregated PCLM life-table:
Bp4$pclm$raw$n[1:10]
# REMEBER: The interval for the raw PCLM life-table depends
# on original interval, m, and x.div,
# whereas the grouped PCLM interval length is set by out.step,
# which could be eventually increased if out.step < raw PCLM
# interval length.

# *** Setting nonaggregated PCLM life-table as pash life-table #2
Bp5 <- pclm.fit(B, out.step = 0.1, control = list(x.div = 20),
                to.pash = "nonaggregated", nax.method = "cfm")
# NOTE: For the very small interval length the "cfm" method
#       may not give realistic nax values
Bp5
Bp4
GetShape(Bp4)
GetShape(Bp5)

# **** See more examples in the help for pclm.nclasses() function.

## End(Not run)