| Title: | Diving Calculations and Decompression Models |
|---|---|
| Description: | Code for describing and manipulating scuba diving profiles (depth-time curves) and decompression models, for calculating the predictions of decompression models, for calculating maximum no-decompression time and decompression tables, and for performing mixed gas calculations. |
| Authors: | Adrian Baddeley [aut, cre], Vittorio Broglio [ctb, dtc], Pedro Antonio Neves [ctb, dtc], Andrew Bassom [ctb], Peter Buzzacott [ctb], Aren Leishman [ctb] |
| Maintainer: | Adrian Baddeley <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.11-1 |
| Built: | 2025-02-13 02:55:30 UTC |
| Source: | https://github.com/cran/scuba |
This is a summary of the features of
scuba, a package in R
that performs theoretical calculations
about scuba diving — dive profiles,
decompression models, gas toxicity and so on.
scuba is a package for performing
calculations in the theory of scuba diving.
The package supports
creation, manipulation and plotting of dive profiles
gas diffusion models
decompression calculations
gas toxicity calculations.
The scuba package is intended only
for use in research and education about the mathematical
and statistical basis of decompression theory. It is emphatically
not designed for actual use in scuba diving and related activities.
See the detailed disclaimer in scuba.disclaimer.
Following is a summary of the main features of the package. For a more detailed explanation, with illustrations, see the vignette Introduction to the Scuba package which accompanies the package.
A dive profile gives the diver's depth as a function of elapsed
time during a scuba dive. The command dive creates an
object representing a dive profile.
A dive profile is piecewise linear: it is a series of stages that join successive waypoints. Each waypoint is specified by the depth and elapsed time when it is reached. The stage between two waypoints is either a sojourn at a fixed depth, or an ascent or descent at a constant rate.
The function dive interprets its arguments
as a sequence of actions or events occurring during the dive.
If an argument is a vector of length 2, it is interpreted
as c(depth,time) specifying the depth and duration
of a stage of the dive. If the argument is a single number,
it is interpreted as a depth, meaning that the diver ascends or
descends to this depth.
For example, the command
d <- dive(c(18, 45)) specifies a dive to 18 metres
for 45 minutes. The command d <- dive(c(18, 45), c(5,3))
specifies a dive to 18 metres for 45 minutes followed by a safety stop
at 5 metres for 3 minutes. Multilevel dives with any number of stages
are specified in the same way. A dive object may include
periods spent at the surface (depth zero) and may therefore represent
a succession of dives separated by surface intervals. For example,
d <- dive(c(30,15),c(9,1),c(5,5),c(0,60),c(12,60),c(5,5))
represents two dives (with safety stops)
separated by a one-hour surface interval.
The resulting object d is an object of class "dive".
It can be plotted as a conventional dive profile graph by executing
the command plot(d). It can be printed as a table of depths and times
by typing its name d, or by executing
print(d,seconds=FALSE) to print times to the nearest minute.
A summary of the dive (with such information as the average depth,
maximum depth and the main stages of the dive) can be printed
by typing summary(d).
By default, the function dive fills in some details
about the dive. It assumes that the diver breathes compressed air;
the dive starts and ends at the surface
(depth zero); the diver descends
at the default descent rate of 30 metres per minute; and the diver
ascends at the default ascent rate of 18 metres per minute.
These defaults can be changed by giving extra arguments to the
function dive.
Dive profiles can also be modified after they are created: see below.
Dive profiles may also be uploaded from your dive computer
and studied in the scuba package. First convert the
uploaded profile data to a data.frame with two columns,
the first column containing the elapsed time and the second column
containing the depth (in metres) recorded at each time. The elapsed
times can be either a vector of character strings
in minutes-and-seconds format
mm:ss or hours-minutes seconds hh:mm:ss,
or a vector of integer times measured in seconds
of elapsed time, or an object of class difftime
containing the elapsed times in any time unit. Then pass this data
frame as an argument to the function dive.
An example of such a data frame, uploaded from a dive computer,
is provided in the baron dataset supplied with the
package. See the help file for
baron for an example of how to convert a data frame
to a "dive" object.
The package also provides 12 real dive profiles that have already been
converted to "dive" objects.
See the help files for pedro and deepmine.
The scuba package performs the mathematical calculations of decompression theory:
the theoretical No Decompression Limit (maximum duration of a
no-decompression dive to a specified depth) can be computed by
ndl(depth)
the quantity of nitrogen dissolved in the diver's body
after a dive d can be computed by haldane(d)
the quantity of nitrogen dissolved in the diver's body
at each instant during a dive d can be computed by
haldane(d, progressive=TRUE)
or plotted interactively by showstates(d).
These calculations are based on the classical theory of decompression originated by Haldane (Boycott et al, 1908). The diver's body is idealised as a set of independent compartments, each connected directly to the breathing gas, and governed by classical (exponential) diffusion.
The model parameters (the number of compartments, their diffusion
rates, and the maximum tolerated nitrogen tension in each compartment)
may be chosen by the user.
By default, the model parameters are taken from the DSAT model
which is the basis of the PADI Recreational Dive Planner.
Alternatively, the user can choose from a variety of standard compartment
models using the command pickmodel, or
construct a new model using hm.
No-decompression limits (the maximum duration of a no-decompression
dive to a given depth) can be calculated using the function
ndl. For example ndl(30) gives the
theoretical NDL for a dive to 30 metres,
predicted by the DSAT model. To use the classical US Navy model instead,
type ndl(30, model="USN") or ndl(30, model=pickmodel("USN")).
The ‘best’
double no-decompression dive to given depths d1 and d2
can be calculated by bestdoubledive according to
the algorithm of Baddeley and Bassom (2012).
The nitrogen tension (the quantity of dissolved nitrogen,
in atmospheres absolute) in the diver's body after
a dive, can be calculated using the function
haldane. If d is a dive object
then haldane(d) returns a data frame containing the
nitrogen tissue tensions (ata) at the end of the dive,
in each of the 8 tissue compartments
of the DSAT model.
To use the US Navy model instead,
type haldane(d, "USN") or haldane(d, pickmodel("USN")).
To compute the nitrogen tissue tensions at each waypoint during the
dive, use haldane(d, progressive=TRUE).
To visualise the nitrogen tissue tensions during the dive,
use the interactive function showstates.
This plots the dive and waits for you to click on
a position in the graph. The tissue tensions at that
instant are displayed as a bar plot.
The total oxygen toxicity incurred during a dive can be computed
by oxtox.
Oxygen partial pressure at each stage of a dive is computed
by ppO2.
Bubble theory calculations are not yet implemented.
A breathing gas is represented by an object of class "gas".
The object air is a representation of compressed air
(21% oxygen, 79% nitrogen) as an object of this class.
(Don't reassign another value to this object!!!)
Nitrox mixtures (mixtures of oxygen and nitrogen) can be
represented using the function nitrox.
For example, EAN 32 is represented by nitrox(0.32).
Trimix (a mixture of oxygen, nitrogen and helium) can also be
represented, using the command trimix.
For example, Trimix 15/50
(containing 15% oxygen, 50% helium and 35% nitrogen)
is represented by trimix(0.15, 0.5).
There are methods for print and summary
for gas objects.
Decompression calculations (haldane,
ndl, showstates)
also work with nitrox and trimix.
Decompression calculations with trimix require a Haldane model
that includes parameters for Helium diffusion.
Use pickmodel("Z") to select the Buehlmann ZH-L16A model,
or hm to create a new model that includes
Helium diffusion.
Standard nitrox calculations are also available, for example
ead |
equivalent air depth |
mod |
maximum operating depth |
maxmix |
richest nitrox mix for a given depth |
The total oxygen toxicity incurred during a nitrox or trimix dive
can be computed by oxtox.
Oxygen partial pressure at each stage of a dive is computed
by ppO2.
Every "dive" object contains information
about the breathing gas or gases used in the dive.
This information is determined when the "dive" object is
created (by the function dive). The default
breathing gas is air.
The function dive interprets its arguments
as a sequence of actions or events occurring during the dive.
If an argument is a vector of length 2, it is interpreted
as c(depth,time) specifying the depth and duration
of a stage of the dive. If the argument is a single number,
it is interpreted as a depth, meaning that the diver ascends or
descends to this depth.
Each argument to dive may also be a "gas" object,
like nitrox(0.32),
which means that the diver switches to this gas.
So, for example,
dive(nitrox(0.32), c(30,20))
means a dive to 30 metres for 20 minutes conducted on EAN 32
(Nitrox 0.32) from start to finish.
The command
dive(c(30,20), 5, nitrox(0.36), c(5,3)) means
a dive on air to 30 metres for 20 minutes, ascending to 5 metres
while breathing air, then switching to EAN 36 for a safety stop
at 5 metres for 3 minutes.
Alternatively you can use the argument tanklist to
specify a list of tanks of breathing gas (with optional names
like "travel" and "deco") and change between tanks at different
stages of the dive using an argument of the form tank=number
or tank=name. The tank list of a dive object can be extracted
using tanklist and modified using
tanklist<-.
Dive profiles can also be manipulated after they are created. This allows you, for example, to modify the deepest portion of a dive (diving to a deeper depth or for a longer duration), to abort a dive prematurely, to cut-and-paste several dives together, or to consider the tissue saturation incurred by a particular segment of a dive.
The commands depths.dive and times.dive
extract the depths and elapsed times at each waypoint during the dive.
The depths can be modified using depths.dive<-. For
example d <- dive(c(30,20)) creates a dive to 30 metres for 20
minutes, starting and finishing at the surface;
to change the depth to 35 metres, type depths.dive(d)[2:3] <- 35.
Similarly the elapsed times can be modified using
times.dive<-. It may be more convenient to use the
functions durations.dive and
durations.dive<- which give the duration of each stage
(the time between two successive waypoints).
For example durations.dive(d)[2] <- 25 would mean that the
diver now spends 25 minutes at the bottom instead of 20 minutes.
To extract only part of a dive profile, use chop.dive.
To paste together two dive profiles or fragments of dive profiles,
simply give them as arguments to dive.
A dive object has a tank list which is a list of the
tanks of breathing gas that were used (or were available to be used)
during the dive. The function tanklist returns
this list, and the function tanklist<- changes the list.
For example,
d <- dive(c(30,20), c(5,5)) is a dive conducted using air.
To modify it to a dive that used nitrox EANx 32, simply type
tanklist(d) <- list(nitrox(0.32)).
Again d <- dive(air, c(30,40), 6, nitrox(0.5), c(6,3), c(3,3)) is a
dive conducted using air (tank 1) for the deep section and EANx 50
(tank 2) for the decompression stops at 6 metres and 3 metres.
To change the contents of tank 1 to EANx 32, type
tanklist(d) <- list(nitrox(0.32), nitrox(0.5)) or
just tanklist(d)[[1]] <- nitrox(0.32).
To associate a name which
each tank, give names to the entries in the tank list, for example
tanklist(d) <- list(deep=nitrox(0.32), deco=nitrox(0.5))
or just assign names(tanklist(d)) <- c("deep", "deco").
The selection of tanks,
i.e. which tank is actually used at each stage of the
dive, is specified by the function whichtank.
The command whichtank(d)
returns a vector of integers or character strings,
identifying which tank in the tank list is in use at each
waypoint during the dive. That is, whichtank(d)[i] is the tank
in use at the ith waypoint during the dive.
The vector whichtank(d) has the same length as the vectors
depths.dive(d) and times.dive(d).
To change the selection of tanks at each stage during the dive,
use the function whichtank<-. For example,
d <- dive(air, c(30,40), 6, nitrox(0.5), c(6,3), c(3,3)) is a
dive conducted using air (tank 1) for the deep section and EANx 50
(tank 2) for the
decompression stops at 6 metres and 3 metres. To change this
so that the deco gas is only used at the 3-metre stop, type
whichtank(d) <- ifelse(depths.dive(d) < 3, 1, 2).
Alternatively whichtank(d)[depths.dive(d) > 3] <- 1
would select tank 1 for all parts of the dive deeper than 3 metres.
These manipulations are usually easier to understand if the tanks
have names. For example typing
names(tanklist(d)) <- c("deep", "deco") we could then
type whichtank(d) <- ifelse(depths.dive(d) < 3, "deep", "deco")
or whichtank(d)[depths.dive(d) > 3] <- "deep".
This library and its documentation are usable under the terms of the "GNU General Public License", a copy of which is distributed with the package.
Adrian Baddeley [email protected] with contributions from Vittorio Broglio and Pedro Antonio Neves.
Baddeley, A. (2013) Introduction to the scuba package. Vignette accompanying this package.
Baddeley, A. and Bassom, A.P. (2011) Classical theory of decompression and the design of scuba diving tables. The Mathematical Scientist 36, 75-88.
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
Boycott, A.E. Damant, G.C.C. and Haldane, J.S. (1908) The prevention of compressed air illness. Journal of Hygiene (London) 8, 342–443.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Buehlmann, A.A. (1983) Dekompression - Dekompressionskrankheit. Springer-Verlag.
Buehlmann, A.A., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5e Auflage. Springer-Verlag.
Tikvisis, P. and Gerth, W.A. (2003) Decompression Theory. In Brubakk and Neuman (2003), Chapter 10.1, pages 419-454.
Wienke, B.R. (1994) Basic diving physics and applications. Best Publishing Co.
Workman, R.D. (1965) Calculation of decompression schedules for nitrogen-oxygen and helium-oxygen dives. Research Report 6-65. US Navy Experimental Diving Unit. Washington DC.
A dataset representing air as a breathing gas, and a function which tests whether a gas is air.
air is.air(g)air is.air(g)
g |
An object of class |
An object of class "gas" represents a breathing gas.
Such objects are required for various calculations in the
scuba library.
The dataset air represents compressed air (21% oxygen,
79% nitrogen) as a breathing gas. It is equivalent to
nitrox(0.21).
The function is.air expects its argument g
to be a gas object. It returns TRUE if
g is equivalent to air, and FALSE otherwise.
Adrian Baddeley [email protected].
v <- air is.air(v) v <- nitrox(0.21) is.air(v) # both are TRUEv <- air is.air(v) v <- nitrox(0.21) is.air(v) # both are TRUE
Specify an Ascent Rate or Ascent Time.
ascent(speed=NULL, time=NULL)ascent(speed=NULL, time=NULL)
speed |
Ascent rate in metres per minute.
Incompatible with |
time |
Total ascent time in minutes.
Incompatible with |
An object of class "rate" represents a diver's
rate of ascent or descent, or the total time taken to
ascend or descend. Such objects are useful in describing
dives, especially in the function dive.
The value returned by ascent represents an ascent rate
or ascent time. Exactly one of the arguments speed and
time should be given. If speed is given, this specifies
a fixed rate of ascent, in metres per minute. If time is given,
this specifies a fixed total time of ascent, in minutes.
An object of class "rate" representing
the ascent rate or ascent time.
Adrian Baddeley [email protected].
# Ascend at 18 metres/minute ascent(18) # Ascend in exactly 3 minutes ascent(time=3)# Ascend at 18 metres/minute ascent(18) # Ascend in exactly 3 minutes ascent(time=3)
Contains the dive profile data for a scuba dive on the Baron Gautsch wreck, uploaded from a dive computer.
A data frame with the following columns:
time |
character | elapsed time (minutes:seconds) |
depth |
numeric | depth (metres) |
temp |
numeric | temperature (C) |
bar |
numeric | breathing gas pressure (bar) |
RBT |
integer | residual bottom time (min) |
WL |
integer | workload |
This dataset contains the dive profile data for a real scuba dive uploaded from a dive computer. It gives the depth, water temperature, breathing gas cylinder pressure, calculated residual bottom time, and calculated workload, recorded every 4 seconds throughout the dive.
The dive site was the wreck of the vessel Baron Gautsch in Croatia. The dive, to a maximum depth of 40 metres, with total dive time of 40 minutes, was conducted on nitrox (EAN 30) by Vittorio Broglio.
The examples show how to convert the depth-time data to a dive
object.
Vittorio Broglio
data(baron) b <- dive(nitrox(0.30), baron[,1:2])data(baron) b <- dive(nitrox(0.30), baron[,1:2])
For two no-decompression dives,
to depths d1 and d2 metres respectively,
separated by a given time interval, find the
optimal durations of the two dives.
bestdoubledive(d1, d2, surface = 30, verbose = FALSE, model = "D", asdive=TRUE)bestdoubledive(d1, d2, surface = 30, verbose = FALSE, model = "D", asdive=TRUE)
d1 |
Depth of first dive in metres. |
d2 |
Depth of second dive in metres. |
surface |
Length of surface interval between dives, in minutes. |
verbose |
Logical. If |
model |
The decompression model. Either
a character string, containing the name of a decompression model
recognised by |
asdive |
Logical. If |
This command implements the algorithm described by Baddeley and Bassom (2012) which calculates the ‘best’ double dive to two given depths separated by a given surface interval, without exceeding the no-decompression limits.
Consider a no-decompression dive to depth metres
for minutes, followed by a surface interval of
minutes, followed by a no-decompression dive to depth
for minutes.
The ‘best’ double dive is defined by Baddeley and Bassom (2012)
as the one which maximises the integral of depth
.
By default (when verbose=FALSE and asdive=TRUE)
the result is a dive object (object of class "dive").
Otherwise, the result is a data frame with
columns t1 and t2 containing the
dive durations in minutes, phi containing the value of
, and case specifying which of the cases
specified in Baddeley and Bassom (2012) provided the optimum.
If verbose=FALSE this data frame has only one
row, giving the best double dive. If verbose=TRUE then the
data frame has several rows giving the candidates for optimal dive
in each case of the algorithm.
Adrian Baddeley [email protected].
Baddeley, A. and Bassom, A.P. (2011) Classical theory of decompression and the design of scuba diving tables. The Mathematical Scientist 36, 75-88.
d <- bestdoubledive(40, 12, 15) plot(d) # Table 3 in Baddeley and Bassom (2012) bestdoubledive(40, 12, 15, verbose=TRUE) # Brief description of optimal dive summary(bestdoubledive(40, 12, 15)) # Data for optimal dive bestdoubledive(40, 12, 15, asdive=FALSE)d <- bestdoubledive(40, 12, 15) plot(d) # Table 3 in Baddeley and Bassom (2012) bestdoubledive(40, 12, 15, verbose=TRUE) # Brief description of optimal dive summary(bestdoubledive(40, 12, 15)) # Data for optimal dive bestdoubledive(40, 12, 15, asdive=FALSE)
Data for several decompression models of Haldane type, giving the tissue halftimes for Nitrogen and the M-values (maximum tolerated partial pressure of Nitrogen for surfacing).
The dataset Bookspan is a list with the following entries:
Halftimes data. A list with entries
Haldane |
halftimes for Haldane's original model |
USN |
halftimes for US Navy original model |
DSAT |
halftimes for DSAT model |
OrcaEdge |
halftimes for OrcaEdge computer |
MicroBrain |
halftimes for MicroBrain computer |
ZHL12 |
halftimes for ZH-L12 model |
surfacing M-values in ata (atmospheres absolute). A list with entries
Haldane |
M-values for Haldane's original model |
USN |
M-values for US Navy original model |
DSAT |
M-values for DSAT model |
surfacing M-values in fsw (feet of seawater).
A list with the same structure as Mvalues.fsw.
Bookspan (1995) tabulates the parameters of several different decompression models of the classical Haldane type. The basic parameters for such a model are
the Nitrogen diffusion halftime (in minutes) for each tissue in the model
the maximum partial pressure of Nitrogen in each tissue which would be tolerated without symptoms at an ambient pressure of 1 atmosphere (the “surfacing M-value”).
The data tabulated in Bookspan (1995, page 16) purportedly give the halftimes for Haldane's original model, the original US Navy model, the DSAT model (basis of PADI repetitive dive planner), the OrcaEdge, MicroBrain and Aladin dive computers, and the Buehlmann ZH-L12 model.
The data tabulated in Bookspan (1995, page 23) give the corresponding M-values (in fsw) for the US Navy and DSAT models only.
These parameters are all contained in the dataset Bookspan.
Adrian Baddeley [email protected].
Bookspan (1995), page 16 (halftime data) and page 23 (M-values).
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
data(Bookspan) Bookspan$Halftimes$DSATdata(Bookspan) Bookspan$Halftimes$DSAT
The parameters of the decompression model ZH-L16A developed by Buehlmann.
A data frame giving the following parameters for each compartment:
id |
compartment name (1, 1b, 2, ..., 16) |
halftime |
Nitrogen halftime (minutes) |
a |
parameter ata (atmospheres absolute) |
b |
parameter |
This dataset contains the tissue parameters of the decompression model ZH-L16A.
Buehlmann's decompression model ZH-L16A is a pure
diffusion (Haldane-type) model consisting of 17 tissue compartments.
Nitrogen in the breathing gas diffuses in and out of each compartment
at a rate governed by the halftime for that compartment.
The maximum tolerable nitrogen tension in a compartment,
when the ambient pressure is atmospheres absolute,
is
where and are values intrinsic to the tissue.
Thus, for a no-decompression dive at sea level, the nitrogen tension
in each compartment must not exceed the value for
that compartment.
The dataset BuehlmannL16A is a table giving the values of
and for each of the 17 tissue compartments.
The dataset BuehlmannL16A is just a table of numbers.
It cannot be used directly for decompression calculations,
because the scuba package does not recognise it
as a decompression model (object of class "hm").
To perform decompression calculations with the ZH-L16A model,
use the functions haldane or showstates
with the argument model="ZH-L16A" (or just model="Z").
To convert a table of
and values, such as the table above,
into an object of class "hm" representing a decompression model,
first calculate the M-values M0 = a + 1/b and dM = 1/b,
and then pass the values M0, dM to the function
hm.
Adrian Baddeley [email protected].
Buehlmann et al (2003), Table 25, page 158.
Buehlmann, A.B., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5th edition. Springer-Verlag, Berlin. ISBN 3-540-42979-4.
Extracts only part of a dive profile.
chop.dive(d, t0=0, t1=max(times.dive(d)))chop.dive(d, t0=0, t1=max(times.dive(d)))
d |
The dive. An object of class |
t0, t1
|
Elapsed times (in minutes) of the start and end of the period which should be extracted. |
The argument d should be an object of class "dive"
representing a dive profile.
This command extracts the part of the dive
profile that starts at time t0 minutes and ends at
time t1 minutes, and returns it as
an object of class "dive". The clock is adjusted so that the
new dive profile starts at time 0 and ends at time t1-t0.
Note that the resulting dive profile does not start and end at the surface:
the dive profile is
simply chopped off at elapsed time t1. If you want the dive
to start and end at the surface, execute dive(chop.dive(d, t0, t1)).
An object of class "dive" starting
at time 0 and ending at time t1-t0.
Adrian Baddeley [email protected].
d <- dive(c(30,20), c(5,5)) # fragment of dive up to 10 minutes chop.dive(d, 0, 10) # dive aborted at 10 minutes dive(chop.dive(d, 0, 10))d <- dive(c(30,20), c(5,5)) # fragment of dive up to 10 minutes chop.dive(d, 0, 10) # dive aborted at 10 minutes dive(chop.dive(d, 0, 10))
Given the state of a diver's tissues, find the diver's decompression ceiling depth (minimum permissible depth) or decompression ceiling pressure (minimum permissible ambient pressure).
deco.ceiling(state, model, what = c("depth", "pressure"))deco.ceiling(state, model, what = c("depth", "pressure"))
state |
Diver's tissue saturations. See Details. |
model |
Haldane type decompression model (object of class |
what |
What to calculate. See Details. |
Given the current state of a diver's tissues, this command calculates the diver's decompression ceiling: the shallowest depth (or lowest ambient pressure) to which it is safe to ascend.
The argument state gives the diver's current state
or the diver's progressive state during a dive.
It has typically been calculated using haldane.
It should be either:
A numeric vector giving the diver's current nitrogen tensions
for each tissue.
The length of the vector matches the number of tissues in
the model.
A matrix giving the diver's current nitrogen and (if present)
helium tensions for each tissue. The rows of the matrix correspond to
tissues in the model. The first column (or the column labelled
"N2") contains the nitrogen tensions, and if present, the second
column (or column labelled "He") contains the helium
tensions.
A three-dimensional array giving the progressive states of
the diver over time. The first index corresponds to time.
The second index corresponds to tissues in the model. The third
coordinate corresponds to inert gases "N2" and "He".
Entries in the vector, matrix or array state are pressures
in atmospheres absolute (ata).
The minimum tolerated ambient pressure Pamb.tol is calculated
using the equivalent of Buehlmann's formula (Buehlmann et al, 1995,
section 6.5, page 117). If what="pressure", this minimum
tolerated ambient pressure is returned (negative pressures are reset
to zero). If what="depth" this pressure is converted to
diving depth in metres assuming that the surface pressure is 1 ata
(negative depths are reset to zero).
A numeric vector, matrix or array of the same type as state
and with the same dimensions as state,
giving the decompression ceiling for each tissue,
each inert gas, and each time point as given.
If what="pressure" the entries in the result are pressures
in ata. If what="depth" the entries are depths in metres.
Adrian Baddeley [email protected].
Buehlmann, A.B., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5th edition. Springer-Verlag, Berlin. ISBN 3-540-42979-4.
hm for decompression models.
haldane to calculate tissue tensions
during or after a dive.
# diver state after saturation diving on EANx30 at 20 metres s <- saturated.state("Z", 20, nitrox(0.30)) # decompression ceiling for each compartment depthceiling <- deco.ceiling(s, "Z") round(depthceiling, 2) round(max(depthceiling), 2) # decompress at 8 metres or deeper # flying-after-diving with cabin pressure 0.8 ata pressureceiling <- deco.ceiling(s, "Z", "pressure") round(pressureceiling, 2) any(pressureceiling > 0.8) # immediate flying-after-diving is not safe# diver state after saturation diving on EANx30 at 20 metres s <- saturated.state("Z", 20, nitrox(0.30)) # decompression ceiling for each compartment depthceiling <- deco.ceiling(s, "Z") round(depthceiling, 2) round(max(depthceiling), 2) # decompress at 8 metres or deeper # flying-after-diving with cabin pressure 0.8 ata pressureceiling <- deco.ceiling(s, "Z", "pressure") round(pressureceiling, 2) any(pressureceiling > 0.8) # immediate flying-after-diving is not safe
Contains the dive profile for a long, extremely deep, decompression dive, using mixed gases, in a flooded mine.
An object of class "dive".
This dataset contains the dive profile data for an extreme dive in a flooded mine.
This was a dive to 110 metres for 7 minutes, followed by 147 minutes of staged decompression, including 40 minutes in a dry habitat at 4 metres. Five different mixed gases (trimix and nitrox) were breathed.
The diver suffered decompression sickness after this dive. An analysis of the dive profile was presented by Buzzacott et al (2013).
The dataset is an object of class "dive"
containing the dive profile.
It can be plotted and printed (using plot.dive
and print.dive). The nitrogen saturation can be
computed using haldane and the
cumulative oxygen toxicity using oxtox.
Peter Buzzacott.
Buzzacott, P., Papadopoulou, V., Baddeley, A., Petri, N. and Lind, F. (2013) Exceptional diving exposure with deep stops and DCS (case study). Conference Poster, European Underwater and Baromedical Society/ South Pacific Underwater Medicine Society/ Southern African Underwater and Hyperbaric Medicine Association, Tricontinental Scientific Meeting on Diving and Hyperbaric Medicine, La Reunion, September 23-28, 2013.
data(deepmine) plot(deepmine, legendpos="right")data(deepmine) plot(deepmine, legendpos="right")
Extracts, or alters, the depth at each waypoint during a dive.
depths.dive(d) depths.dive(d) <- valuedepths.dive(d) depths.dive(d) <- value
d |
A dive (object of class |
value |
A numeric vector containing depths in metres. |
An object of class "dive" represents a scuba dive profile. It is
created by the function dive. A dive is defined as a
series of waypoints occurring at specified depths and times. The
depth at each waypoint is returned by depths.dive. The
assignment depths.dive(d) <- value alters these depths,
provided the new vector value has the same length as the old one.
depths.dive returns a numeric vector containing the
depths at each waypoint, in metres.
Adrian Baddeley [email protected].
times.dive,
durations.dive,
dive.
d <- dive(c(30,20), c(5,5)) d depths.dive(d) # what if we had dived to 35 metres? depths.dive(d)[2:3] <- 35 dd <- dive(c(30,20), c(5,5)) d depths.dive(d) # what if we had dived to 35 metres? depths.dive(d)[2:3] <- 35 d
Specify an Descent Rate or Descent Time.
descent(speed=NULL, time=NULL)descent(speed=NULL, time=NULL)
speed |
Descent rate in metres per minute.
Incompatible with |
time |
Total descent time in minutes.
Incompatible with |
An object of class "rate" represents a diver's
rate of ascent or descent, or the total time taken to
ascend or descend. Such objects are useful in describing
dives, especially in the function dive.
The value returned by descent represents a descent rate
or descent time. Exactly one of the arguments speed and
time should be given. If speed is given, this specifies
a fixed rate of descent, in metres per minute. If time is given,
this specifies a fixed total time of descent, in minutes.
An object of class "rate" representing
the descent rate or descent time.
Adrian Baddeley [email protected].
# Descend at 30 metres/minute descent(30) # Descend in exactly 3 minutes descent(time=3)# Descend at 30 metres/minute descent(30) # Descend in exactly 3 minutes descent(time=3)
Define a dive profile.
dive(..., begin=0, end=0, tanklist=NULL)dive(..., begin=0, end=0, tanklist=NULL)
... |
Any number of arguments, specifying a sequence of events that make up the dive. The arguments may specify depths, time spent at each depth, ascent or descent rates, and gas switches. See Details. |
begin, end
|
The depths at the start and finish of the dive (normally zero
indicating that the dive starts and finishes at the surface)
or |
tanklist |
Optional list of the gases contained in each tank, for a dive with multiple tanks. |
This function creates
an object of class "dive" which represents a scuba dive.
The dive profile is assumed to be piecewise linear, that is,
the graph of depth against time is a broken straight line.
Dives are assumed to start and finish at the surface.
The arguments ... specify a succession of events
that make up the dive. Each argument can be
interpreted as c(depth, duration)
where depth gives the depth in metres
and duration the length of stay at this depth, in minutes.
interpreted as a waypoint depth in metres. The diver will ascend or descend to this depth, at the current default rate of ascent or descent.
"gas"
specifying a breathing gas. Such objects are
created by the functions nitrox and trimix.
The diver switches to this gas.
tank=n
specifying
a switch to another tank or cylinder of breathing gas.
This is available only when the tanks used in the dive
have been specified by the argument tanklist.
The value n should be a valid index for this list
(either a serial number in the tank list or a character string
matching one of the names in the tank list).
created by the functions ascent or
descent. This resets the default
rate of ascent or descent.
containing a dive profile, usually uploaded from a dive computer. The
first column should contain the elapsed times, and the second
column contains the depths (in metres) measured at these times.
The column of elapsed times can be either a character vector
containing times in minutes-and-seconds format mm:ss,
or an integer vector containing elapsed times in seconds,
or a vector of class difftime
representing elapsed times in any time unit.
In this case you probably want to set the arguments
begin=NA and end=NA.
"dive"
representing a dive profile. This allows the user to paste dive profiles together.
Dives are assumed to start and finish at the surface. This can be changed
by specifying values for begin and end. See the
section on Start and End of Dive.
Initially the descent rate is set to 30 metres per minute,
the ascent rate is 18 metres per minute, and the breathing gas is
air. These settings may be changed during the dive
by the ... arguments.
A dive object may include periods spent at the surface (depth zero) and may therefore represent a succession of dives separated by surface intervals.
Once an object of class "dive" has been created,
it can be plotted and printed (using plot.dive
and print.dive). The nitrogen saturation can be
computed using haldane and the
cumulative oxygen toxicity using oxtox.
An object of class "dive" describing the dive profile
and the breathing gases used.
To make it easy to specify simple dive profiles,
the algorithm fills in some information.
If the diving depths specified in the arguments ... do not
start at the surface (depth zero), then by default, the algorithm
assumes that the dive did start at the surface, and it
adds an extra dive segment at the beginning of the dive.
The diver is assumed to descend from the surface, at the standard
descent rate, to the first depth specified.
Thus dive(c(10,25)) means that the diver will first descend
from the surface to 10 metres at a rate of 30 metres per minute,
remain there for 25 minutes, then ascend to the surface
at a rate of 18 metres per minute.
To change this behaviour, set a different value for the argument begin.
If the dive really started at a nonzero depth, e.g. a dry habitat at 3 metres,
set begin=3. If one of the arguments ... is a
data frame uploaded from a dive computer, then set begin=NA,
so that that the dive will start at the first depth
specified in this data frame.
Similarly, if the last depth specified by the arguments ...
is a depth below the surface (depth greater than zero), then by
default the diver is assumed to ascend from this last depth to
the surface, at the standard ascent rate. To suppress this altogether,
set end=NA. To specify a different final depth for the dive,
set a different value for end.
The depths and elapsed times at each waypoint during the dive
can be extracted and changed using depths.dive
and times.dive.
Dives can be cut into pieces using chop.dive
and pasted together using dive.
It is possible to alter the breathing gases used in a dive d,
yielding a new dive object.
This makes it possible to study the effect of conducting the same
dive profile with different breathing gases.
You can change the specification of the breathing gas (or gases) by
tanklist(d) <- value.
In a multiple-tank dive you can change the periods when each tank was used,
by whichtank(d) <- value.
Not suitable for representing altitude dives.
Adrian Baddeley [email protected].
nitrox,
ascent,
descent,
haldane,
plot.dive,
times.dive,
durations.dive,
depths.dive,
chop.dive,
tanklist,
whichtank.
# Dive to 25 m for 20 min followed by safety stop at 5 metres for 3 min d <- dive(c(25,20),c(5,3)) plot(d) # Bounce dive to 20 metres d <- dive(20) # Two dives separated by a one-hour surface interval d <- dive(c(30,15),c(9,2),c(5,5),c(0,60),c(12,60),c(5,5)) # ASCENT RATES # Ascent rate 18 m/min below 9 metres, 6m/min above 9 metres d <- dive(c(30, 12), ascent(18), 9, ascent(6), c(5,3)) # UPLOADED DIVE PROFILE data(baron) pro <- baron[, 1:2] d <- dive(pro) d <- dive(pro, begin=NA, end=NA) plot(d) # GAS USE # 30-metre dive on Nitrox 32 d <- dive(nitrox(0.32), c(30,20), c(5,5)) # GAS SWITCHING # Dive to 18 m for 30 min on air, # switch to Nitrox 36, ascend to 5 metres, safety stop d <- dive(c(18, 30), nitrox(0.36), c(5,3)) # Same as above, but ascend to 5 m on air, then switch gas d <- dive(c(18, 30), 5, nitrox(0.36), c(5,3)) # SWITCHING TO SPECIFIC TANKS d <- dive(tanklist=list(main=air, deco=nitrox(0.50)), tank="main", c(30, 20), 5, tank="deco", c(5,10)) # Descend to 5 metres on pure oxygen, switch to Trimix, # descend to 30 metres, remain 40 minutes, ascend to 6 metres, # switch to pure oxygen, ascend to 5 metres, decompress 10 minutes, # surface and continue breathing pure oxygen for 10 minutes d <- dive(tanklist=list(travel=trimix(0.15, 0.5), deco=nitrox(1)), tank="deco", 5, tank="travel", c(30,40), 6, tank="deco", c(5,10), c(0,10))# Dive to 25 m for 20 min followed by safety stop at 5 metres for 3 min d <- dive(c(25,20),c(5,3)) plot(d) # Bounce dive to 20 metres d <- dive(20) # Two dives separated by a one-hour surface interval d <- dive(c(30,15),c(9,2),c(5,5),c(0,60),c(12,60),c(5,5)) # ASCENT RATES # Ascent rate 18 m/min below 9 metres, 6m/min above 9 metres d <- dive(c(30, 12), ascent(18), 9, ascent(6), c(5,3)) # UPLOADED DIVE PROFILE data(baron) pro <- baron[, 1:2] d <- dive(pro) d <- dive(pro, begin=NA, end=NA) plot(d) # GAS USE # 30-metre dive on Nitrox 32 d <- dive(nitrox(0.32), c(30,20), c(5,5)) # GAS SWITCHING # Dive to 18 m for 30 min on air, # switch to Nitrox 36, ascend to 5 metres, safety stop d <- dive(c(18, 30), nitrox(0.36), c(5,3)) # Same as above, but ascend to 5 m on air, then switch gas d <- dive(c(18, 30), 5, nitrox(0.36), c(5,3)) # SWITCHING TO SPECIFIC TANKS d <- dive(tanklist=list(main=air, deco=nitrox(0.50)), tank="main", c(30, 20), 5, tank="deco", c(5,10)) # Descend to 5 metres on pure oxygen, switch to Trimix, # descend to 30 metres, remain 40 minutes, ascend to 6 metres, # switch to pure oxygen, ascend to 5 metres, decompress 10 minutes, # surface and continue breathing pure oxygen for 10 minutes d <- dive(tanklist=list(travel=trimix(0.15, 0.5), deco=nitrox(1)), tank="deco", 5, tank="travel", c(30,40), 6, tank="deco", c(5,10), c(0,10))
Extracts, or alters, the durations of each interval between waypoints during a dive.
durations.dive(d) durations.dive(d) <- valuedurations.dive(d) durations.dive(d) <- value
d |
A dive (object of class |
value |
A numeric vector containing durations in minutes. |
An object of class "dive" represents a scuba dive. It is
created by the function dive. A dive is defined as a
series of waypoints occurring at specified depths and times.
The duration of the time interval between each successive pair of
waypoints is returned by durations.dive. The
assignment durations.dive(d) <- value alters these durations,
provided the new vector value has the same length as the old one.
durations.dive returns a numeric vector containing the
durations of intervals between each waypoint, in minutes.
Adrian Baddeley [email protected].
depths.dive,
times.dive,
dive.
d <- dive(c(30,20), c(5,5)) d durations.dive(d) # what if we stayed at the bottom for 25 minutes instead of 20? durations.dive(d)[2] <- 25 dd <- dive(c(30,20), c(5,5)) d durations.dive(d) # what if we stayed at the bottom for 25 minutes instead of 20? durations.dive(d)[2] <- 25 d
Computes the Equivalent Air Depth for a Nitrox mixture at given depths.
ead(depth, g) eadtable(g, ppO2max=1.4)ead(depth, g) eadtable(g, ppO2max=1.4)
depth |
depth of dive, in metres. |
g |
The breathing gas. An object of class |
ppO2max |
maximum permitted partial pressure of oxygen in ata. |
Applies the standard formula for equivalent air depth.
For ead, the Equivalent Air Depth in metres for each
value of depth;
for eadtable, a data frame containing depths and Equivalent
Air Depth values, for a range of depths up to the maximum permitted
by ppO2max.
This function does not check whether the breathing gas would be safe (it could be hypoxic or toxic at the depth in question).
ead returns negative values for sufficiently shallow depths.
In eadtable these values are blank.
Not applicable to altitude dives. Not applicable to gas mixtures other than nitrox (oxygen-nitrogen mixtures).
Adrian Baddeley [email protected].
# Nitrox I (32% oxygen) at 20 metres ead(20, 0.32) # Nitrox I table of EAD's eadtable(0.32) # Nitrox II (36% oxygen) at a range of depths ead(10:25, 0.36)# Nitrox I (32% oxygen) at 20 metres ead(20, 0.32) # Nitrox I table of EAD's eadtable(0.32) # Nitrox II (36% oxygen) at a range of depths ead(10:25, 0.36)
Computes the Equivalent Narcotic Depth for a Trimix mixture at given depth.
END(depth, g)END(depth, g)
depth |
depth of dive, in metres. A numeric value or a vector of values. |
g |
The breathing gas. An object of class |
Applies the standard formula for equivalent narcotic depth:
the depth at which compressed air would have the same
partial pressure of narcotic gases as the specified gas g
at the specified depth
(assuming that both Nitrogen and Oxygen are narcotic).
Numeric value or vector giving the Equivalent Narcotic Depth
in metres for each value of depth.
This function does not check whether the breathing gas would be safe (it could be hypoxic or toxic at the depth in question). It is not applicable to altitude dives.
Adrian Baddeley [email protected].
# Trimix 18/50 # (18% oxygen, 50% helium) END(30, trimix(0.18, 0.5))# Trimix 18/50 # (18% oxygen, 50% helium) END(30, trimix(0.18, 0.5))
Computes a diver's tissue saturation during and after a dive, as predicted by a Haldane model.
haldane(d, model=pickmodel("DSAT"), prevstate=NULL, progressive=FALSE, relative=FALSE, deco=FALSE, derived=FALSE)haldane(d, model=pickmodel("DSAT"), prevstate=NULL, progressive=FALSE, relative=FALSE, deco=FALSE, derived=FALSE)
d |
The dive profile. An object of class |
model |
The decompression model. An object of class |
prevstate |
Optional. Initial state of the diver. A data frame containing the tissue saturations for each tissue compartment in the model, at the start of the dive. Defaults to the state of a diver with no previous dive history. |
progressive |
Logical flag. If |
relative |
Logical flag indicating whether to compute relative tissue
saturations. If |
deco |
Logical flag indicating whether to calculate relative saturations
for a decompression dive.
If |
derived |
Logical flag indicating whether to calculate additional quantities such as the decompression ceiling. |
This command computes a diver's nitrogen saturation during and after a dive, as predicted by a Haldane model (Boycott et al, 1908).
A Haldane-type decompression model describes the diver's body as a set of independent compartments connected directly to the breathing gas and governed by classical diffusion.
Henry's Law is applied to predict the on- and off-gassing of inert gas in each tissue (compartment) of the model. The resulting differential equations are solved analytically (the solution is often called the ‘Schreiner equation’ in the decompression literature).
The argument prevstate represents the tissue saturation of the
diver at the start of the dive. It should be a data frame, with one row for
each compartment of the decompression model, and one column for each
inert gas (N2 and/or He) in the model. Such data frames
are usually generated by saturated.state or
haldane.
If progressive=FALSE, the diver's tissue saturation
at the end of the dive is calculated.
If progressive=TRUE,
the tissue saturations are calculated at each
waypoint during the dive. The corresponding times
(extracted by times.dive(d))
are not equally spaced over time.
If derived=TRUE then additional quantities are
computed including the washout (the difference
between the current tissue tension of inert gas
and the partial pressure of inert gas in the breathing gas),
the decompression ceiling depth (minimum tolerable diving depth)
and decompression ceiling pressure (minimum tolerable
ambient pressure). These quantities are returned as an attribute
of the result: attr(result, "derived").
This is a list containing the components
Dceiling (depth ceiling),
Pceiling (pressure ceiling)
and washout (washout), each of which
is a vector, matrix or array of the same format as the result.
To compute the tissue saturation
at an arbitrary instant of time during the dive, tim, use
haldane(chop.dive(d, 0, tim)). To view the tissue saturation
at arbitrary instants of time using interactive graphics,
use showstates.
If relative=FALSE and progressive=FALSE, a data frame giving
the diver's inert gas saturation state at the end of the
dive. Each row of the data frame corresponds to a tissue compartment.
The column N2 gives the nitrogen tension (in atmospheres absolute) of
each compartment. The column He, if present, gives the
Helium tension (in atmospheres absolute) in each compartment.
If relative=FALSE and progressive=TRUE,
a three-dimensional array giving
the diver's inert gas saturation state at each time point during the
dive. The first dimension of the array corresponds to successive time points
during the dive (the times can be extracted by
times.dive).
The second dimension corresponds to the tissue compartments.
The third dimension corresponds to the inert gases
(N2 and/or He).
The entries are gas tensions (in atmospheres absolute).
If relative=TRUE and progressive=FALSE, a vector
giving the diver's relative saturation of inert gas at the end of the
dive. Entries in the vector correspond to tissue compartments.
The entries are relative gas tensions, that is,
the total inert gas (Nitrogen plus Helium) tissue saturation
divided by the appropriate M-value for that compartment: either
the surfacing M-value (if deco=FALSE) or the
M-value at current depth (if deco=TRUE).
If relative=TRUE and progressive=TRUE,
a matrix giving the diver's relative saturation
at each time point during the
dive. Rows of the array correspond to successive time points
during the dive. Columns correspond to the tissue compartments.
The entries are relative gas tensions, that is,
the total inert gas (Nitrogen plus Helium) tissue saturation
divided by the appropriate M-value for that compartment: either
the surfacing M-value (if deco=FALSE) or the
M-value at current depth (if deco=TRUE).
If derived=TRUE then additional quantities are
returned as an attribute
of the result. This is extracted by: attr(result, "derived").
It is a list containing the components
Dceiling (depth ceiling),
Pceiling (pressure ceiling)
and washout (washout), each of which
is a vector, matrix or array of the same format as the result.
Not applicable to altitude dives. Not suitable for dive planning.
No constraints of any kind are checked. In particular it is not guaranteed that the model accepts the dive profile as a no-decompression dive.
Adrian Baddeley [email protected].
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
Boycott, A.E. Damant, G.C.C. and Haldane, J.B. (1908) The prevention of compressed air illness. Journal of Hygiene (London) 8, 342–443.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Buehlmann, A.A. (1983) Dekompression - Dekompressionskrankheit. Springer-Verlag.
Buehlmann, A.A., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5e Auflage. Springer-Verlag.
Tikvisis, P. and Gerth, W.A. (2003) Decompression Theory. In Brubakk and Neuman (2003), Chapter 10.1, pages 419-454.
Wienke, B.R. (1994) Basic diving physics and applications. Best Publishing Co.
Workman, R.D. (1965) Calculation of decompression schedules for nitrogen-oxygen and helium-oxygen dives. Research Report 6-65. US Navy Experimental Diving Unit. Washington DC.
dive,
oxtox,
pickmodel,
showstates,
Mmix,
M0mix.
# First dive to 25 m for 20 min with safety stop d1 <- dive(c(25,20),c(5,5)) # Evaluate saturation according to DSAT model s1 <- haldane(d1) s1 # Look at saturation (in ata) barplot(s1$N2, ylab="Saturation (ata)") # Look at relative saturation M0 <- param(pickmodel("D"), "N2", "M0") barplot(100 * s1$N2/M0, ylab="Saturation (percent)") # Evaluate saturation after 2 hour surface interval s2 <- haldane(dive(c(0,120)), prevstate=s1) # Then after another dive to 18 m for 30 min with safety stop s3 <- haldane(dive(c(18, 30),c(5,3)), prevstate=s2) # Assess effect of breathing 80% oxygen at safety stop s3o <- haldane(dive(c(18, 30),5, nitrox(0.8), c(5,3)), prevstate=s2) # Inspect saturation during dive d1 at time 10 minutes s10 <- haldane(chop.dive(d1, 0, 10)) # Progressive saturation during dive # A real dive plot(deepmine, col=1, key.gases="none") # compute saturations during dive hmine <- haldane(deepmine, model="Z", progressive=TRUE) # show N2 saturations during dive # Image plot image(x=times.dive(deepmine), y=1:17, z=hmine[,,"N2"], xlab="Time (min)", ylab="Compartment", axes=FALSE) axis(1) axis(2, at=1:17, labels=dimnames(hmine)[[2]]) # Perspective plot persp(x=times.dive(deepmine), y=1:17, z=hmine[,,"N2"], xlab="Time (min)", ylab="Compartment", zlab="Saturation (atm)", col="green3", shade=0.6, border=NA, theta=20, phi=30, ltheta=120, lphi=20) #.... Derived quantities ..... hmine <- haldane(deepmine, model="Z", progressive=TRUE, derived=TRUE) der <- attr(hmine, "derived") names(der) # Decompression ceiling depth (time x compartment x gas) dcd <- der$Dceiling # Overall decompression ceiling at each time point dc <- apply(dcd, 1, max) # plot dive with deco ceiling plot(deepmine, key.gases="none", col=1) lines(times.dive(deepmine), -dc, lty=3, lwd=2) legend(100, -60, lty=c(1,3), lwd=2, legend=c("dive profile", "deco ceiling")) # Nitrogen washout for tissue 1b (positive values indicate off-gassing) plot(times.dive(deepmine), der$washout[,"1b", "N2"], type="l", xlab="Time (min)", ylab="Washout")# First dive to 25 m for 20 min with safety stop d1 <- dive(c(25,20),c(5,5)) # Evaluate saturation according to DSAT model s1 <- haldane(d1) s1 # Look at saturation (in ata) barplot(s1$N2, ylab="Saturation (ata)") # Look at relative saturation M0 <- param(pickmodel("D"), "N2", "M0") barplot(100 * s1$N2/M0, ylab="Saturation (percent)") # Evaluate saturation after 2 hour surface interval s2 <- haldane(dive(c(0,120)), prevstate=s1) # Then after another dive to 18 m for 30 min with safety stop s3 <- haldane(dive(c(18, 30),c(5,3)), prevstate=s2) # Assess effect of breathing 80% oxygen at safety stop s3o <- haldane(dive(c(18, 30),5, nitrox(0.8), c(5,3)), prevstate=s2) # Inspect saturation during dive d1 at time 10 minutes s10 <- haldane(chop.dive(d1, 0, 10)) # Progressive saturation during dive # A real dive plot(deepmine, col=1, key.gases="none") # compute saturations during dive hmine <- haldane(deepmine, model="Z", progressive=TRUE) # show N2 saturations during dive # Image plot image(x=times.dive(deepmine), y=1:17, z=hmine[,,"N2"], xlab="Time (min)", ylab="Compartment", axes=FALSE) axis(1) axis(2, at=1:17, labels=dimnames(hmine)[[2]]) # Perspective plot persp(x=times.dive(deepmine), y=1:17, z=hmine[,,"N2"], xlab="Time (min)", ylab="Compartment", zlab="Saturation (atm)", col="green3", shade=0.6, border=NA, theta=20, phi=30, ltheta=120, lphi=20) #.... Derived quantities ..... hmine <- haldane(deepmine, model="Z", progressive=TRUE, derived=TRUE) der <- attr(hmine, "derived") names(der) # Decompression ceiling depth (time x compartment x gas) dcd <- der$Dceiling # Overall decompression ceiling at each time point dc <- apply(dcd, 1, max) # plot dive with deco ceiling plot(deepmine, key.gases="none", col=1) lines(times.dive(deepmine), -dc, lty=3, lwd=2) legend(100, -60, lty=c(1,3), lwd=2, legend=c("dive profile", "deco ceiling")) # Nitrogen washout for tissue 1b (positive values indicate off-gassing) plot(times.dive(deepmine), der$washout[,"1b", "N2"], type="l", xlab="Time (min)", ylab="Washout")
Creates a Haldane-type decompression model.
hm(HalfT, M0=NULL, dM=NULL, ..., N2 = list(HalfT=HalfT, M0=M0, dM=dM), He = NULL, title="user-defined model", cnames=NULL, mixrule=NULL)hm(HalfT, M0=NULL, dM=NULL, ..., N2 = list(HalfT=HalfT, M0=M0, dM=dM), He = NULL, title="user-defined model", cnames=NULL, mixrule=NULL)
HalfT |
Vector of nitrogen halftimes (in minutes) for each compartment. |
M0 |
Optional vector of surfacing M-values (in ata) of nitrogen for each compartment. |
dM |
Optional vector of gradients for M-values (dimensionless) for each nitrogen compartment. |
... |
Ignored. |
N2 |
An alternative way of specifying all the data for
Nitrogen. A list with elements labelled
|
He |
Data for Helium, if available.
A list with elements labelled
|
title |
Optional name of model. A character string. |
cnames |
Optional names of compartments. A vector of character strings. |
mixrule |
Mixing rule for M-values.
Either |
This function creates an object of class "hm",
which represents a Haldane-type decompression model.
Objects of this class are needed by the commands ndl,
haldane and others.
A Haldane-type decompression model describes the diver's body as a set of independent compartments connected directly to the breathing gas and governed by classical diffusion.
The argument halfT specifies the half-times of the
nitrogen compartments, in minutes. The length of halfT implicitly
determines the number of nitrogen compartments.
The argument M0, if present, specifies the surfacing M-values
for the nitrogen compartments. These are the maximum values of
nitrogen tissue tension that are tolerated at the surface.
These values are required in order to plan a no-decompression dive.
The argument dM, if present, specifies the rate of increase
in nitrogen M-values with pressure. The maximum nitrogen tissue
tension tolerated at a pressure P atmospheres is M0 + (P-1) * dM.
These values are required in order to plan a decompression dive.
Optionally the model may also allow calculation with Helium diffusion.
In that case, the argument He should be a list, with
components halfT, M0 and dM, specifying the
Helium halftimes, maximum surfacing Helium tensions, and
Helium gradients, respectively.
If Helium parameters are included, so that diving with
trimix (Oxygen/Nitrogen/Helium mixture) is permitted,
then the model must also specify a rule for combining the
parameters for Helium and Nitrogen to obtain the parameters
for any trimix gas. This rule is specified by the argument mixrule.
Current options are:
"N2"Ignore the Helium parameters; pretend that Helium is Nitrogen.
Combine Nitrogen and Helium into a single inert gas,
and take the parameters M0, dM for this gas
to be the parameters M0, dM for Nitrogen.
"interpolate"Apply Buehlmann's (1983, 2002) interpolation rule. Convert the
parameters M0, dM to the Buehlmann parameters
a = M0 - dM and b = 1/dM. For a mixture of
Nitrogen and Helium, calculate the a,b values by
linear interpolation between the values for Nitrogen and Helium
according to the gas fractions. Then convert from a,b
back to M0, dM.
The default is mixrule="interpolate" whenever the Helium
parameters are specified.
Note that this mixture calculation applies only to the saturation
parameters M0, dM which tell us whether a dive is
staying within the no-decompression limits. This mixture calculation
does not affect the Haldane calculations of the gas tensions in the
diver's body.
The class "hm" has methods for print and
as.data.frame.
An object of class "hm", representing the decompression model.
Adrian Baddeley [email protected].
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
Boycott, A.E. Damant, G.C.C. and Haldane, J.B. (1908) The prevention of compressed air illness. Journal of Hygiene (London) 8, 342–443.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Buehlmann, A.A. (1983) Dekompression - Dekompressionskrankheit. Springer-Verlag.
Buehlmann, A.A., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5e Auflage. Springer-Verlag.
Tikvisis, P. and Gerth, W.A. (2003) Decompression Theory. In Brubakk and Neuman (2003), Chapter 10.1, pages 419-454.
Wienke, B.R. (1994) Basic diving physics and applications. Best Publishing Co.
Workman, R.D. (1965) Calculation of decompression schedules for nitrogen-oxygen and helium-oxygen dives. Research Report 6-65. US Navy Experimental Diving Unit. Washington DC.
pickmodel for some standard models of Haldane type;
ndl,
haldane,
showstates
hm(c(10,20,60), rep(2 * 0.79, 3)) hm(c(10,20,60), rep(2 * 0.79, 3), rep(2 * 0.79, 3)) hm(c(10,20,60), rep(2 * 0.79, 3), rep(2 * 0.79, 3), He=list(HalfT=c(5,10,30), M0=c(1,1,1), dM=c(1,1,1)))hm(c(10,20,60), rep(2 * 0.79, 3)) hm(c(10,20,60), rep(2 * 0.79, 3), rep(2 * 0.79, 3)) hm(c(10,20,60), rep(2 * 0.79, 3), rep(2 * 0.79, 3), He=list(HalfT=c(5,10,30), M0=c(1,1,1), dM=c(1,1,1)))
Determines whether a given gas is nitrox.
is.nitrox(g)is.nitrox(g)
g |
An object of class |
An object of class "gas" represents a breathing gas.
Such objects are required for various calculations in the
scuba library.
The function is.nitrox expects its argument g
to be a gas object. It returns TRUE if
g is a nitrox gas (a mixture of oxygen and nitrogen),
and FALSE otherwise.
Adrian Baddeley [email protected].
v <- nitrox(0.50) is.nitrox(v) is.nitrox(air)v <- nitrox(0.50) is.nitrox(v) is.nitrox(air)
Computes the optimal nitrox mixture for a given maximum depth.
maxmix(depth, ppO2max=1.4)maxmix(depth, ppO2max=1.4)
depth |
the maximum depth, in metres |
ppO2max |
maximum permitted partial pressure of oxygen in atmospheres absolute |
Computes the maximum fraction of oxygen in a nitrox mixture
subject to the constraint that the partial pressure of oxygen
does not exceed ppO2max atmospheres.
The optimal nitrox mixture. An object of class "gas".
Not applicable to altitude dives. Not applicable to gas mixtures other than nitrox (oxygen-nitrogen mixtures).
Adrian Baddeley [email protected].
# 30 metres maxmix(30)# 30 metres maxmix(30)
Computes the maximum tolerated inert gas tension at depth
(M-value) or at the surface (surfacing M-value, M0)
for a given gas.
M0mix(model, fN2, fHe, mixrule=NULL) Mmix(model, depth, fN2, fHe, mixrule=NULL)M0mix(model, fN2, fHe, mixrule=NULL) Mmix(model, depth, fN2, fHe, mixrule=NULL)
model |
The decompression model.
Either an object of class |
depth |
Numeric value or numeric vector giving the depth or depths in metres of seawater. |
fN2 |
Fraction of nitrogen in the breathing gas.
Number between 0 and 1.
Alternatively this can be a |
fHe |
Fraction of helium in the breathing gas. Number between 0 and 1. |
mixrule |
Optional string specifying the mixture rule:
either |
M0mix computes the maximum tolerated inert gas tension,
in each tissue compartment, for a diver returning to the surface
(known as the surfacing M-value M0). This is used for
planning no-decompression dives.
Mmix computes the maximum tolerated inert gas tension,
in each tissue compartment, for a diver at a specified depth,
called the M-value. This is used for planning decompression dives.
A Haldane-type decompression model only specifies these M-values for a single inert gas (i.e. only nitrogen or only helium). When the breathing gas is trimix, the inert gas is a mixture of nitrogen and helium, and the M-values for nitrogen and helium must somehow be combined to obtain M-values relevant to the mixed gas.
The rule for combining the M-values is specified
by the argument mixrule. Current options are:
"N2"Ignore the Helium parameters; pretend that Helium is Nitrogen.
Combine Nitrogen and Helium into a single inert gas,
and take the parameters M0, dM for this gas
to be the parameters M0, dM for Nitrogen.
"interpolate"Apply Buehlmann's (1983, 2002) interpolation rule. Convert the
parameters M0, dM to the Buehlmann parameters
a = M0 - dM and b = 1/dM. For a mixture of
Nitrogen and Helium, calculate the a,b values by
linear interpolation between the values for Nitrogen and Helium
according to the gas fractions. Then convert from a,b
back to M0, dM.
If the argument mixrule is missing or NULL, then the
default mixture rule is taken from the model
(since every Haldane model has a mixture rule,
as explained in hm).
A matrix, with one column for each compartment in the model,
and one row for each entry of fN2 (and fHe and
depth).
Entries in the matrix are M-values in atmospheres absolute (ata).
Adrian Baddeley [email protected].
hm,
pickmodel for specifying models.
haldane for computing tissue saturations.
# Trimix 18/50, surfacing M-values M0mix("Z", trimix(0.18, 0.5)) # Trimix 18/50, M-values at 0, 10, 20 metres Mmix("Z", c(0,10,20), trimix(0.18, 0.5))# Trimix 18/50, surfacing M-values M0mix("Z", trimix(0.18, 0.5)) # Trimix 18/50, M-values at 0, 10, 20 metres Mmix("Z", c(0,10,20), trimix(0.18, 0.5))
Computes the Maximum Operating Depth for a given gas mixture.
mod(g, ppO2max=1.4)mod(g, ppO2max=1.4)
g |
Breathing gas. An object of class |
ppO2max |
maximum permitted partial pressure of oxygen in atmospheres absolute |
Computes the maximum depth at which the
partial pressure of oxygen does not exceed ppO2max.
The maximum operating depth for this gas.
Not applicable to altitude dives. Does not check whether the gas would be hypoxic at the surface.
Adrian Baddeley [email protected].
# Nitrox I (32% oxygen) mod(0.32) # Nitrox II (36% oxygen) mod(nitrox(0.36)) # Trimix 15/50 mod(trimix(0.15, 0.5))# Nitrox I (32% oxygen) mod(0.32) # Nitrox II (36% oxygen) mod(nitrox(0.36)) # Trimix 15/50 mod(trimix(0.15, 0.5))
Compute the No-Decompression Limit (NDL) for a dive to a specified depth, under a Haldane-type decompression model.
ndl(depth, g=air, prevstate=NULL, model = "DSAT")ndl(depth, g=air, prevstate=NULL, model = "DSAT")
depth |
Depth (in metres) for which the NDL should be computed. A single number or a numeric vector. |
g |
Breathing gas for the dive. An object of class |
prevstate |
Optional. Initial state of the diver. A data frame containing the tissue saturations for each tissue compartment in the model, at the start of the dive. Defaults to the state of a diver with no previous dive history. |
model |
The decompression model. Either an object of class |
The No-Decompression Limit (NDL) for a given depth is the
maximum duration of a No-Decompression dive to depth .
A No-Decompression dive is one which can (theoretically) be aborted at any time without requiring staged decompression. Equivalently, in a No-Decompression Dive, the Nitrogen saturation in each of the diver's tissue compartments never exceeds the maximum Nitrogen saturation tolerated at sea level (known as the surfacing M-value for that compartment).
This algorithm computes the NDL for a dive to the given depth, or for several possible alternative dives to the given depths, based on the specified decompression model. The NDL is determined by the halftimes and the surfacing M-values for all the compartments in the model.
If the breathing gas g contains Helium, then model
must include compartments for Helium. Similar calculations apply in
this case.
The argument prevstate represents the tissue saturation of the
diver at the start of the dive. It should be a data frame, with one row for
each compartment of the decompression model, and one column for each
inert gas (N2 and/or He). Such data frames
are usually generated by saturated.state or
haldane.
Numeric vector, of the same length as depth,
giving the No-Decompression Limit in minutes for each depth.
Infinite values are possible.
The value also has an attribute called "controlling" which
identifies the controlling tissue (the tissue for which the M-value
is reached).
This is not intended for use as a scuba diving table! The NDL calculated here is not the same as the NDL indicated in any published scuba diving table. For example, the NDL calculated by this algorithm using the halftimes and M-values of the DSAT model, may be longer than the NDL published in the DSAT Recreational Dive Planner. Infinite values of NDL may be returned in some cases.
Adrian Baddeley [email protected].
scuba.disclaimer,
haldane,
showstates,
saturated.state
# NDL for a dive to 15 metres ndl(15) # NDL for a dive to 24 metres on EANx 32 ndl(15, g=nitrox(0.32)) # NDL for a dive to 60 metres on Trimix 15/50 under ZH-L16A model ndl(70, g=trimix(0.15, 0.5), model="Z") # NDL for a repetitive dive on air to 15 metres, following an # 18-minute air dive to 30 metres and half-hour surface interval firstdive <- dive(c(30,18), c(5,3), c(0,30)) ndl(15, prevstate=haldane(firstdive))# NDL for a dive to 15 metres ndl(15) # NDL for a dive to 24 metres on EANx 32 ndl(15, g=nitrox(0.32)) # NDL for a dive to 60 metres on Trimix 15/50 under ZH-L16A model ndl(70, g=trimix(0.15, 0.5), model="Z") # NDL for a repetitive dive on air to 15 metres, following an # 18-minute air dive to 30 metres and half-hour surface interval firstdive <- dive(c(30,18), c(5,3), c(0,30)) ndl(15, prevstate=haldane(firstdive))
Create a Nitrox gas mixture.
nitrox(fO2)nitrox(fO2)
fO2 |
Fraction (between 0 and 1) of oxygen in the nitrox mixture. |
An object of class "gas" represents a breathing gas.
Such objects are required for various calculations in the
scuba library.
The value returned by nitrox represents Nitrox
(oxygen-nitrogen mixture) with the fraction of oxygen
specified by the argument fO2.
For the standard Nitrox calculations, see ead
and mod.
To determine whether a gas is nitrox, use is.nitrox.
There are methods for print and summary
for objects of class "gas".
An object of class "gas" representing
Nitrox with the specified fraction of oxygen.
Adrian Baddeley [email protected].
dive,
ead,
mod,
air,
is.nitrox
# Nitrox I (32% oxygen) nitrox(0.32) # Nitrox II (36% oxygen) nitrox(0.36) # g <- nitrox(0.50) is.nitrox(g)# Nitrox I (32% oxygen) nitrox(0.32) # Nitrox II (36% oxygen) nitrox(0.36) # g <- nitrox(0.50) is.nitrox(g)
Computes pulmonary oxygen toxicity dose for a given dive profile and breathing gas.
oxtox(d, progressive=FALSE, warn=TRUE)oxtox(d, progressive=FALSE, warn=TRUE)
d |
The dive profile. An object of class |
progressive |
Logical flag. If |
warn |
Logical flag indicating whether to issue a warning if the partial pressure of oxygen exceeds a threshold (1.4, 1.5 or 1.6 ata). |
Computes the total dose of pulmonary oxygen toxicity from the given dive profile, by
The maximum tolerable dose per day is usually reckoned as 1500 OTU. Allowing 650 OTU for recompression therapy implies a working maximum of 850 OTU per day.
If progressive=FALSE, a single numeric value,
the total pulmonary oxygen toxicity dose in OTU.
If progressive=TRUE, a numeric vector containing the
cumulative pulmonary oxygen toxicity dose in OTU at each
time point during the dive. The corresponding time points can be
extracted by times.dive.
Not applicable to altitude dives.
Adrian Baddeley [email protected].
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Buehlmann, A.A., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5e Auflage. Springer-Verlag.
Wienke, B.R. (1994) Basic diving physics and applications. Best Publishing Co.
ppO2,
ead, eadtable,
mod,
maxmix
# Nitrox II (36% oxygen) at 30 metres for 27 minutes d <- dive(nitrox(0.36), c(30,27)) oxtox(d) # Same as above, followed by safety stop on 100% oxygen d <- dive(nitrox(0.36), c(30,27),5, nitrox(1), c(5,5)) oxtox(d)# Nitrox II (36% oxygen) at 30 metres for 27 minutes d <- dive(nitrox(0.36), c(30,27)) oxtox(d) # Same as above, followed by safety stop on 100% oxygen d <- dive(nitrox(0.36), c(30,27),5, nitrox(1), c(5,5)) oxtox(d)
Extracts the tissue compartment parameters from a Haldane type decompression model.
param(model, species = "N2", what = "HalfT")param(model, species = "N2", what = "HalfT")
model |
The decompression model. An object of class |
species |
Character string.
The inert gas for which parameters are required:
|
what |
Character string.
The parameter required: |
This command extracts the tissue compartment parameters from a Haldane-type decompression model.
The argument model should be an object of class "hm"
(created by hm or obtained using
pickmodel).
See hm for explanation of the parameters.
A vector containing the values of the specified parameter for
each tissue compartment. If the model does not contain this data,
NULL is returned.
Adrian Baddeley [email protected].
# halftimes for the DSAT model param(pickmodel("DSAT"), "N2", "HalfT")# halftimes for the DSAT model param(pickmodel("DSAT"), "N2", "HalfT")
Dive profiles for 11 different scuba dives.
Each of the datasets pedro902,
pedro903, etc, is an object of class "dive".
The command data(pedro)
gives access to 11 datasets named
pedro902,
pedro903,
pedro904,
pedro922,
pedro943,
pedro944,
pedro945,
pedro946,
pedro948,
pedro949 and
pedro950. These are the dive profiles for 11 real scuba dives,
uploaded from a dive computer.
Each of the datasets is an object of class "dive"
containing the dive profile for one dive.
It can be plotted and printed (using plot.dive
and print.dive). The nitrogen saturation can be
computed using haldane and the
cumulative oxygen toxicity using oxtox.
The dives were conducted by Pedro Antonio Neves. Details are as follows:
| Dive | Max depth | Gases | Type | Location |
| 902 | 19 m | EAN 32 | single | Armacao de Pera, Portugal |
| 903 | 27 m | EAN 32 | single | Farilhoes, Portugal |
| 904 | 30 m | EAN 32 | single | Berlenga, Portugal |
| 922 | 15 m | EAN 32 | multiple | Sines, Portugal |
| 943 | 21 m | EAN 32 | single | Armacao de Pera, Portugal |
| 944 | 19 m | EAN 32 | single | Armacao de Pera, Portugal |
| 945 | 22 m | EAN 32 | single | Armacao de Pera, Portugal |
| 946 | 20 m | EAN 32 | single | Armacao de Pera, Portugal |
| 949 | 16 m | EAN 32 | single | Finisterra,Galicia,Spain |
| 950 | 40 m | EAN 50, Trimix | single | Finisterra,Galicia,Spain |
All dives were conducted on Nitrox 32, except pedro950 which was
conducted using Trimix 18/45 and Nitrox 50.
All dive profiles consist of a single descent and ascent,
except for pedro922 which consists of 5 short bounce dives separated
by short surface intervals.
Pedro Antonio Neves
data(pedro) summary(pedro950) plot(pedro950)data(pedro) summary(pedro950) plot(pedro950)
Selects one of a list of standard Haldane-type decompression models, identified by the name of the model.
pickmodel(model)pickmodel(model)
model |
The name of the model. A character string. |
A Haldane-type decompression model describes the diver's body as a set of independent compartments connected directly to the breathing gas and governed by classical diffusion.
This function is a convenient way to select one of the commonly used decompression models of Haldane type.
The argument model is partially matched to
one of the following:
The original Haldane (1908) model with 5 compartments.
The first model used by the US Navy, with 6 compartments.
The DSAT model, with 8 compartments, underlying the PADI recreational dive planner tables.
The model of Workman (1965) with 9 compartments.
The ‘theoretical’ model ZH-L16A of Buehlmann with 17 compartments.
The result is an object (of class "hm")
in the format required for use by commands such as
haldane, ndl and showstates.
The data for the USN and Haldane models are taken from Wienke (1994), page 127 ff. The DSAT model is taken from Bookspan (1995), pp 16 and 23. The Workman 65 model is taken from Tikvisis and Gerth (2003), Table 10.1.1, page 440. The ZH-L16A parameters were taken from Buehlmann et al (2002) Table 25, page 158.
An object of class "hm" representing a Haldane-type
decompression model.
If the argument model is missing, then the list of available
options for model is printed.
Adrian Baddeley [email protected].
Bookspan, J. (1995) Diving physiology in plain English. Undersea and Hyperbaric Medicine Society, Kensington, Maryland (USA). ISBN 0-930406-13-3.
Boycott, A.E. Damant, G.C.C. and Haldane, J.B. (1908) The prevention of compressed air illness. Journal of Hygiene (London) 8, 342–443.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Buehlmann, A.A. (1983) Dekompression - Dekompressionskrankheit. Springer-Verlag.
Buehlmann, A.A., Voellm, E.B. and Nussberger, P. (2002) Tauchmedizin. 5e Auflage. Springer-Verlag.
Tikvisis, P. and Gerth, W.A. (2003) Decompression Theory. In Brubakk and Neuman (2003), Chapter 10.1, pages 419-454.
Wienke, B.R. (1994) Basic diving physics and applications. Best Publishing Co.
Workman, R.D. (1965) Calculation of decompression schedules for nitrogen-oxygen and helium-oxygen dives. Research Report 6-65. US Navy Experimental Diving Unit. Washington DC.
pickmodel("Z") ndl(30, model=pickmodel("Z"))pickmodel("Z") ndl(30, model=pickmodel("Z"))
Plot a dive profile.
## S3 method for class 'dive' plot(x, ..., main=deparse(substitute(x)), key.gases=c("text", "legend", "none"), text.cex=1, text.verticals=TRUE, col.gases=1:length(tanklist(x)), legendpos=c("top","bottom", "left", "right", "topleft", "topright", "bottomleft", "bottomright", "center"))## S3 method for class 'dive' plot(x, ..., main=deparse(substitute(x)), key.gases=c("text", "legend", "none"), text.cex=1, text.verticals=TRUE, col.gases=1:length(tanklist(x)), legendpos=c("top","bottom", "left", "right", "topleft", "topright", "bottomleft", "bottomright", "center"))
x |
The dive profile. An object of class |
... |
Arguments passed to |
main |
Overall label for plot. |
key.gases |
String indicating whether the plot should be annotated with labels indicating what gas is breathed, and how to do the annotation. |
text.cex |
Numeric value controlling the size of text when |
text.verticals |
Logical flag indicating whether the plot should indicate what gas is breathed during ascent and descent between stages, as well as during the main stages of the dive. |
col.gases |
Colours to be used to represent each of the breathing gases used in the dive. Either a numeric vector of colour codes, or a vector of character strings identifying colours. |
legendpos |
Character string determining the position of the
legend, when |
A representation of the dive profile is plotted.
NULL.
Adrian Baddeley [email protected].
# Dive to 25 m for 20 min with safety stop d1 <- dive(c(25,20),c(5,5)) # plot it plot.dive(d1) # Dive to 18 m for 30 min with safety stop, on Nitrox EANx 36 d3 <- dive(nitrox(0.36), c(18,30), c(5,3)) plot.dive(d3) # Real dive profile data(baron) d4 <- dive(nitrox(0.30), baron[, 1:2]) plot(d4, main="Baron Gautsch dive")# Dive to 25 m for 20 min with safety stop d1 <- dive(c(25,20),c(5,5)) # plot it plot.dive(d1) # Dive to 18 m for 30 min with safety stop, on Nitrox EANx 36 d3 <- dive(nitrox(0.36), c(18,30), c(5,3)) plot.dive(d3) # Real dive profile data(baron) d4 <- dive(nitrox(0.30), baron[, 1:2]) plot(d4, main="Baron Gautsch dive")
Computes the partial pressure of oxygen at each stage during a dive.
ppO2(d)ppO2(d)
d |
The dive profile. An object of class |
This function computes the partial pressure of oxygen at each stage of the
dive profile. The result is a data frame with two columns: time
giving the elapsed time, and ppO2 giving the partial pressure
of oxygen (in atmospheres) in the current breathing gas at the current depth.
A data frame with columns time and ppO2.
Adrian Baddeley [email protected].
data(pedro) plot(ppO2(pedro902), type="l")data(pedro) plot(ppO2(pedro902), type="l")
Print a dive profile.
## S3 method for class 'dive' print(x, ..., seconds=TRUE)## S3 method for class 'dive' print(x, ..., seconds=TRUE)
x |
The dive profile. An object of class |
... |
Arguments passed to |
seconds |
Flag indicating whether to print elapsed time to the
nearest second (if |
A representation of the dive profile is printed.
NULL.
Adrian Baddeley [email protected].
# Dive to 25 m for 20 min with safety stop dive(c(25,20),c(5,5)) # Dive to 18 m for 30 min with safety stop, on Nitrox EANx 36 dive(nitrox(0.36), c(18,30), c(5,3))# Dive to 25 m for 20 min with safety stop dive(c(25,20),c(5,5)) # Dive to 18 m for 30 min with safety stop, on Nitrox EANx 36 dive(nitrox(0.36), c(18,30), c(5,3))
Computes the amount of inert gas in each compartment of a diver who has reached equilibrium with the breathing gas at the specified depth. The default is a fresh diver with no diving history.
saturated.state(model="D", depth = 0, g = air)saturated.state(model="D", depth = 0, g = air)
model |
The decompression model. An object of class |
depth |
The diving depth at which saturation is achieved. A single number. |
g |
The breathing gas. An object of class |
A Haldane-type decompression model describes the diver's body as a set of independent compartments connected directly to the breathing gas and governed by classical diffusion.
This command computes the amount of inert gas in each compartment of a diver who has reached equilibrium with the breathing gas at the specified depth.
The default is a fresh diver (in equilibrium with air at the surface at sea level).
A data frame, with one row for each compartment of the model,
and one column for each inert gas in the model (N2 and/or
He). Entries in the data frame are tissue tensions in ata.
Adrian Baddeley [email protected].
fresh <- saturated.state() deep <- saturated.state("ZH", 80, trimix(0.15, 0.5))fresh <- saturated.state() deep <- saturated.state("ZH", 80, trimix(0.15, 0.5))
A list of various useful physical constants needed in calculations in the scuba package.
scuba.constants is a list containing the following entries:
fsw.per.atm |
factor to convert atm (atmospheres absolute) |
| to fsw (feet of seawater) | |
fO2air |
the fraction of oxygen in dry air at 25 C |
fN2air |
the fraction of nitrogen plus argon in dry air at 25 C |
Adrian Baddeley [email protected].
This page contains important warnings.
The scuba software library is intended
for use in research and education about the mathematical
and statistical basis of decompression theory. It is
not designed for actual use in scuba diving and related activities.
It is emphatically not suitable for use in actual diving.
Scuba diving is a dangerous activity with inherent risks of death and serious injury. No-one should attempt scuba diving without professional training, certification, supervision and regular medical assessment.
It is also dangerous for trained scuba divers to exceed the limitations of their training. Diving at altitudes above sea level, and breathing mixed gases other than air, carry increased risk and additional types of risk. Divers should seek additional, professional training and certification for such activities.
This software is not suitable for use in actual scuba diving.
The software will yield numerical results for any diving activity,
without giving any warning if the activity would be dangerous or fatal.
Each function in the scuba library calculates
the predictions of one theoretical model (a law of physics,
a decompression model or another empirical relationship).
In doing so, it does not take account of safety restrictions,
other physical laws, or other important information.
The software is provided for academic interest only. It should not be used to generate diving tables or protocols related to diving. No output from this software should be misconstrued as a diving table. Only persons qualified to supervise diving activities or qualified in hyperbaric medicine should attempt to design diving tables. Although existing published diving tables are based on theoretical models, such tables have been extensively field-tested and modified before approval. Existing tables are more conservative than the models from which they were originally derived.
The author does not warrant that the software is correct in any sense whatsoever. Even if correctly computed, the predictions of a theoretical physical model may not be correct predictions.
Adrian Baddeley [email protected].
Plots a dive profile and interactively displays the diver's nitrogen saturation state at any intermediate stage indicated by the mouse.
showstates(d, model="DSAT", relative=TRUE, deco=FALSE, ...)showstates(d, model="DSAT", relative=TRUE, deco=FALSE, ...)
d |
The dive. An object of class |
model |
The decompression model. Either an object of class |
relative |
Logical flag indicating whether to compute relative tissue
saturations. If |
deco |
Logical flag indicating whether to calculate relative saturations
for a decompression dive.
If |
... |
Arguments passed to |
An object of class "dive" represents a scuba dive.
It is created by the command dive.
This function plots the dive using plot.dive
then waits for the user to click on the plot. This click selects
a time during the dive. The algorithm computes the nitrogen tensions
in the tissues at the indicated time, using haldane,
and plots them as a bar graph. The cumulative oxygen toxicity is also
computed using oxtox.
Note that (by default) the bar graph shows the relative nitrogen tensions in each compartment, that is, the tissue nitrogen tension divided by the "surfacing M-value" (tissue maximum nitrogen tension for a no-decompression dive at sea level).
The argument model determines the decompression model.
It should be either an object of class "hm" (created by
hm) or a character string matching one of the
options in pickmodel.
The vector of absolute nitrogen tensions (in ata) in the most recently clicked stage.
Adrian Baddeley [email protected].
## Not run: showstates(dive(c(30,20), c(5,3)), "ZH") ## End(Not run)## Not run: showstates(dive(c(30,20), c(5,3)), "ZH") ## End(Not run)
Extracts or modifies the list of breathing gases in a dive object.
tanklist(d) tanklist(d) <- valuetanklist(d) tanklist(d) <- value
d |
The dive (an object of class |
value |
The new tank list. A list, whose entries are gases
(objects of class |
An object of class "dive" represents a scuba dive,
including information about depth, time and gas breathed at each
stage of the dive. These objects are created by the function
dive.
The tank list of a dive object is a list of the tanks of breathing gas
that were used (or available to be used) during the dive.
The function tanklist returns this list.
If a new value is assigned to the tank list of a dive d,
then d is changed. The new dive d is conducted
to the same depths and times as the old d, but with different
gases.
The value of tanklist(d) is a list whose elements are
gases (objects of class "gas").
Adrian Baddeley [email protected].
d <- dive(air, c(30,4), 5, nitrox(0.5), c(5,10)) d tanklist(d) tanklist(d) <- list(air, nitrox(0.8)) d tanklist(d) <- list(travel=air, deco=nitrox(0.8)) dd <- dive(air, c(30,4), 5, nitrox(0.5), c(5,10)) d tanklist(d) tanklist(d) <- list(air, nitrox(0.8)) d tanklist(d) <- list(travel=air, deco=nitrox(0.8)) d
Extracts, or alters, the elapsed time at each waypoint during a dive.
times.dive(d) times.dive(d) <- valuetimes.dive(d) times.dive(d) <- value
d |
A dive (object of class |
value |
A numeric vector containing elapsed times in minutes. |
An object of class "dive" represents a scuba dive. It is
created by the function dive. A dive is defined as a
series of waypoints occurring at specified depths and times. The
elapsed time at each waypoint is returned by times.dive. The
assignment times.dive(d) <- value alters these elapsed times,
provided the new vector value has the same length as the old one.
times.dive returns a numeric vector containing the elapsed
times at each waypoint, in minutes.
Adrian Baddeley [email protected].
depths.dive,
durations.dive,
dive.
d <- dive(c(30,20), c(5,5)) d times.dive(d) # stretch time by 10 percent times.dive(d) <- 1.1 * times.dive(d) dd <- dive(c(30,20), c(5,5)) d times.dive(d) # stretch time by 10 percent times.dive(d) <- 1.1 * times.dive(d) d
Create a Trimix gas.
trimix(fO2, fHe, fN2)trimix(fO2, fHe, fN2)
fO2, fHe, fN2
|
Fractions (between 0 and 1) of oxygen, helium and nitrogen, respectively, in the trimix gas. |
An object of class "gas" represents a breathing gas.
Such objects are required for various calculations in the
scuba library.
The value returned by trimix represents Trimix
(oxygen-nitrogen-helium mixture) with the fractions of oxygen,
nitrogen and helium specified by the arguments fO2, fN2,
fHe respectively. These fractions should sum to 1.
If only two of the gas fractions are given, the missing fraction will be calculated so that the three values sum to 1.
There are methods for print and summary
for objects of class "gas".
An object of class "gas" representing
Trimix with the specified composition.
Adrian Baddeley [email protected].
# Trimix 18/50 # (18% oxygen, 50% helium) trimix(0.18, 0.5)# Trimix 18/50 # (18% oxygen, 50% helium) trimix(0.18, 0.5)
Determine which tank of breathing gas is used at each time point during a dive.
whichtank(d) whichtank(d) <- valuewhichtank(d) whichtank(d) <- value
d |
The dive (an object of class |
value |
Vector of integers or character strings identifying which tank of breathing gas is used at each time point. |
An object of class "dive" represents a scuba dive,
including information about depth, time and gas breathed at each
stage of the dive. These objects are created by the function
dive.
A dive object has a tank list which is a list of the
tanks of breathing gas that were used (or were available to be used)
during the dive. The function tanklist returns
this list.
The selection of tanks, i.e. which tank is actually used at each stage of the
dive, is specified by whichtank. The command whichtank(d)
returns a vector of integers or character strings,
identifying which tank in the tank list is in use at each
waypoint during the dive. That is, whichtank(d)[i] is the tank
in use at the ith waypoint during the dive.
The command whichtank(d) <- value will change the selection of
tanks used at each stage during the dive. Here value should be
a vector of integers or character strings identifying tanks in the
tank list, and the length of value should be
equal to the length of the vectors depths.dive(d) and
depths.dive(d).
A common use of whichtank is to specify that a particular
gas should be used only in a particular range of depths. This is done
by applying ifelse to depths.dive as shown
in the Examples.
The value of whichtank(d) is a vector of integers or
character strings.
Adrian Baddeley [email protected].
# tanks are numbered d <- dive(air, c(30,40), 6, nitrox(0.5), c(6,3), c(3,3)) d tanklist(d) whichtank(d) # change choice of tank at 6 metre deco stop # The Hard Way: whichtank(d) <- c(1,1,1,1,1,2,2,2) d # The Snazzy Way: # if shallower than 3 metres, then tank 2, else tank 1 whichtank(d) <- ifelse(depths.dive(d) <= 3, 2, 1) d # tanks with names dd <- dive(tanklist=list(travel=trimix(0.18, 0.5), deco=nitrox(0.8)), tank="travel", c(30,40), c(20, 10), 9, tank="deco", c(9,10), c(6,5), c(3,5)) dd # if shallower than 6 metres, then deco gas, else travel gas whichtank(dd) <- ifelse(depths.dive(dd) <= 6, "deco", "travel") dd# tanks are numbered d <- dive(air, c(30,40), 6, nitrox(0.5), c(6,3), c(3,3)) d tanklist(d) whichtank(d) # change choice of tank at 6 metre deco stop # The Hard Way: whichtank(d) <- c(1,1,1,1,1,2,2,2) d # The Snazzy Way: # if shallower than 3 metres, then tank 2, else tank 1 whichtank(d) <- ifelse(depths.dive(d) <= 3, 2, 1) d # tanks with names dd <- dive(tanklist=list(travel=trimix(0.18, 0.5), deco=nitrox(0.8)), tank="travel", c(30,40), c(20, 10), 9, tank="deco", c(9,10), c(6,5), c(3,5)) dd # if shallower than 6 metres, then deco gas, else travel gas whichtank(dd) <- ifelse(depths.dive(dd) <= 6, "deco", "travel") dd
The parameters of the decompression model due to Workman, 1965.
A data frame giving the following parameters for each compartment:
halftime |
Nitrogen halftime (minutes) |
M0 |
surfacing M-value parameter |
A |
slope parameter |
The decompression model developed for the US Navy by Workman (1965)
is a pure diffusion (Haldane-type) model consisting of 9 tissue compartments.
Nitrogen in the breathing gas diffuses in and out of each compartment
at a rate governed by the halftime for that compartment.
The maximum tolerable nitrogen tension in a compartment,
when the diver is at depth msw (metres of sea water), is
msw, where and are values intrinsic to the tissue.
The value is called the ‘surfacing M-value’
since it is the maximum nitrogen tension that is allowed
in each compartment during a no-decompression dive at sea level.
Adrian Baddeley [email protected].
Tikvisis and Gerth (2003), Table 10.1.1, page 440.
Brubakk, A.O. and Neuman, T.S. (eds.) (2003) Bennett and Elliott's Physiology and Medicine of Diving. 5th Edition. Saunders. ISBN 0-7020-2571-2
Tikvisis, P. and Gerth, W.A. (2003) Decompression Theory. In Brubakk and Neuman (2003), Chapter 10.1, pages 419-454.
Workman, R.D. (1965) Calculation of decompression schedules for nitrogen-oxygen and helium-oxygen dives. Research Report 6-65. US Navy Experimental Diving Unit. Washington DC.