The biogas's discuss from sashahafner

Multiple elements in when argument, summBg()

The current (old) approach is within the heart of the function, complicated, and would not work for e.g., a combination of pdwhen and a numeric. Nor would new rate.crit.met column work with more than one when element. Should rewrite as recursive call as with other additions at top.

Implement gasDens

This function replaces hard-wired N2 gas density. At least mass2vol() needs to be updated.

stdVol() warning in cumBg() and cumBgMan()

cum.prodl.man <- cumBgMan(strawPressure, comp = strawComp, temp = 31,
data.struct = 'long',
id.name = "bottle", time.name = "time",
dat.name = "pres", comp.name = "xCH4",
temp.init = 21.55, pres.resid = "pres.resid", pres.init = 0.0,
headspace = strawSetup, vol.hs.name = "headspace",
pres.amb = 101.3, absolute = FALSE,
extrap = TRUE, addt0 = TRUE,
unit.pres = "kPa")

Biogas composition is interpolated.
Pressure measurements are GAUGE If this is incorrect, change 'absolute' argu
ment to TRUE.
Using a standard pressure of 101.325 kPa and standard temperature of 0 C for
standardizing volume.
Warning message:
In stdVol(dat[, vol.hs.name], temp = dat[, "temp.prev"], pres = dat$pres.res
id.prev, :
pres ranges from 101.3 kPa to 203.4356 kPa. Is this really correct?

Check calcBgGD() arguments

For example, there is no check that m.pre.name or m.post.name are actually columns in data frame -> useless errors!

summBg() when = 'end' problem

Why did I ever user 'vol.name' to sort here?

else if (length(when) == 1 && tolower(when) == "end") {
    summ1 <- data.frame(id = ids, time = NA, vol = NA)
    names(summ1) <- c(id.name, time.name, vol.name)
    vol <- vol[order(vol[, id.name], vol[, vol.name]), ]
    for (i in ids) {
        dc <- vol[vol[, id.name] == i, ]
        summ1[summ1[, id.name] == i, c(time.name, vol.name)] <- dc[nrow(

dc),
c(time.name, vol.name)]
}
}

Means time returned may not be latest time.

Time mismatch for pd duration in summBg()

If final time is selected by e.g. when = "1p3d" but not all bottles have the same final time, function will tag a bottle as pdnotyet (rate criterion not met). Can we interpolate first in the function so we have the same times for all bottles?

calcBgVol() problem with fixed xCH4/comp

dat <- calcBgVol(dat, comp = 0.65, comp.name = 'xCH4', temp = 'temp.c', pres = 'pres.hPa', data.struct = 'long',
                 id.name = 'channel', time.name = 'time.d', vol.name = 't.vol', unit.pres = 'hPa')

will not work (gives useless error) without comp.name. Although DataPrep function has default for comp.name, call in calcBg will send in NULL and so there is no place to put xCH4/comp in the returned data frame. So DataPrep has to check for null with comp exists and use a default name xCH4.

Check of class of time column, summBg()

Should accept diftime and maybe others as well but does not.

Correcting for initial conditions in cumBgMan()

temp.init, pres.init are used with assumption that bottle is not vented once warmed up. But it is in some cases.

Missing columns feedSetup

No description

summBg() show.when problems

Error when there is no subtraction of inoculum contribution with show.when = TRUE.

IMP <- summBg(cbg, setup = ds, id.name = 'id', time.name = 'time.d',

           descrip.name = 'substrate', norm.name = 'm.inoc.vs',

           show.more = TRUE, when = 'end')

Response variable (volume) is cbg$cvCH4.
Inoculum contribution not subtracted.
Response normalized by setup$m.inoc.vs.
Error in [.data.frame(summ2, , s2cols) : undefined columns selected

Document and test convertBPC

Missing check arguments in cumBgGD function

In line 14 it says 'Check arguments', but there is nothing there. Check arguments should be added similar to how it is done in cumBg function.

Description of optional output, summBg()

From Alexandre B.: When we set show.more to TRUE , we get extra columns, such as "rsd.inoc" "fv.inoc" "se1" "se2" "se3" (if show.obs = F) and "vol.mi.rsd" "cvCH4.tot" "cvCH4.inoc" "fv.inoc" "se.inoc" "cvCH4.se" (if show.obs = T). What do they mean? I could not find anything about them.

Air density function

For testing GD-BMP method

Molar volume check for gdComp()

Can use recursive call after check of molar volume to get a more precise result, if only to exactly match mass2vol(). Should be able to do by adding molar volume of biogas as gdComp() argument.

VDI 2016 method for BMP duration

New rate.crit argument in summBg() works but is not complete. Needs to be able to identify cases where net yield drops (rates are negative). Not clear how this should be handled with respect to maximum 1% gross time based on VDI report.

planBMP unit error

There seems to be an error in mass output. See example below.

planBMP(15.6, 850, isr = 2, m.tot = 250)
Parameter Unit Value

Inoc. VS conc. g/g 15.6
Substrate VS conc. g/g 850
Mix. VS conc. g/g 23.2
ISR (VS basis) g/g 2
Inoc. mass g 248
Substrate mass g 2.27
Mixture mass g 250
Sub. VS mass g 1930
Inoc. VS mass g 3860
Mix. VS mass g 5800

Biogas composition interpolation for manometric, cumBg()

When bottles are not vented and residual pressure is the same as initial pressure, missing composition data should be set to earliest following available observation, and not interpolated. Realized this when working with LeAF data.

Vignette for planBMP()

Simple but really useful function. Needs to be advertised.

Automatic conversion of pres.std

pres.std does not seem to automatically convert to new units in mass2vol() calls.

Tests needed for calcBg* functions

Including test of different data structures.

Issue when calculating Biogas from COD on OBA

I noticed another bug on OBA. In the theoretical biogas tab, if you set COD mass, when you choose ‘More details’ or ‘Reaction’ as output, you get a wrong value, i.e. 0.001 L for 1 g COD, instead of 0.349 L for 1 g COD. Moreover, choosing one of these options does not display the reaction or extra details…

&& problem in R-devel check

Last time I tried, package did not pass CRAN tests on R-devel because of this issue. Best option would be to get rid of all of the && and || operators if possible. I am not sure which ones remain.

calcBgGD with headspace correction

With headspace correction, should be an error when temp.init is missing

Tibbles

The data processing functions should be able to handle tibbles.

cumBgMan() does not work with missing temp. Should it?

Bug in summBg() when show.rates=T and inoc.name not specified

While looking at the other summBg() problem with show.rates = TRUE, I observed an unexpected behavior with regard to rates when inoculum contribution is not subtracted. Starting from the previous example, on latest dev branch:

data(feedSetup)
data(feedVol)

cpw <- calcBgVol(feedVol, comp = 1, temp = 0, pres = 1, data.struct = "wide",
                       time.name = "time.d", vol.name = "1", dry = TRUE, interval = FALSE)

s1.noinoc <- summBg(cpw, feedSetup, id.name = 'id', time.name = 'time.d', descrip.name = 'descrip', norm.name = 'm.sub.vs', show.obs = TRUE, show.rates = TRUE)

The column rrvCH4 is now improperly sorted. Output from plot(s1.noinoc[s1.noinoc$id==4,]$rrvCH4):

Commenting out this line makes the data properly ordered again:

biogas/R/summBg.R

Line 480 in 20b2488

dd <- dd[order(dd[, time.name]), ]

It seems to me that this line may be superfluous, as the dataframe is also sorted before returning (e.g., lines 501, 660, 694-704), but maybe I am missing an edge case here?

Automatic adjusment of relative humidity in stdVol()

For a headspace pressure of 3 atm at 35 C, expanded nearly 3x when measured at 1 atm and 20C, water vapor pressure will be slightly below saturation. For measurement at 35C, error would be larger.

NULL in checkArgClassValue()

Encountered this issue in GD functions. Should be "NULL" not NULL, it seems. Must be present in other functions.

Add VDI empirical chemical formulas

The VDI 4630 doc has these values:

Seem strange for carbohydrate and protein.
If we can find them, we might add the empirical formulas to std.forms.

summBg() help file

v. 1.23.3:

If show.more = TRUE additional columns are returned: summ2 <- summ2[ , c(descrip.name, time.name,’mean’, ’se’, ’sd’, ’n’, ’rsd.inoc’, ’fv.inoc’, ’se1’, ’se2’, ’se3’)]

Oops.

Default argument values in cumBgDataPrep

Should there be any? Can we delete all of them?

summBg() when = 'end' with unequal test duration

Function picks the latest one and then cannot find matching replicates. Would be better to pick earliest final time and use that.

calcBgGD comp.sub check

> mv <- calcBgGD(mv, temp.vol = 20, temp.grav = 30, pres.vol = 1, pres.grav = 1.
5,
+                id.name = 'id', time.name = 'time.d',
+                vol.name = 'vol', m.pre.name = 'm.init', m.post.name = 'm.final
', comp.sub = 0)
Error: Expect class "logical, character" for argument comp.sub but got "numeric"
.

Check the check. Should be numeric.

Error message for comp argument, grav method, cumBg()

See Asger and Monica's code. Why is there an error message saying that comp is needed for gravimetric method in some cases?

mass2vol mole frac check needs to handle NAs

Currently does not.

Helpful error message in summBg() when no bottles with substrate are included

Update vignette

biogas_quick_start.Rnw still uses cumBg(). Should be changed to calcBgVol() etc.

Mass gain error in calcBgGD()

Should it be a warning? For very small mass gain should it be ignored?

Add to planBMP()

Would be useful to have estimates of daily biogas production and headspace pressure for planning. Would need kinetic constant input and bottle headspace.

Currently no test data for mixed interval and cumulative vol data (empty.name = TRUE)

Stange mass2vol() values at low pressure

Following code gives some negative or very large volumes for pressure close to 1 kPa:

plot(mass2vol(0.1, xCH4 = 0.65, temp = 35, pres = c(1:200)/2, unit.pres = "kPa"))

Is this correct result? And why? May not be a problem with code but would be good to clarify.

Data reshaping function

How about a single function to handle the different data structures?

Create leak() function

Function needed for calculating leakage from mass measurements.

Something like:

leakBg(
dat,
time.name,
m.pre.name,
m.post.name,
...
)

Output should include:
Interval
Leak mass
Total mass
Venting mass
Cumulative
Leak mass
Total mass
Venting mass

New release

The CRAN and master versions of biogas are almost 2 years old. Let's try to sort out the remaining important open issues and merge with master, create a release on GitHub, and submit a new version to CRAN.

Initial conditions for headspace corrections

In mass2vol() and probably others, there is no pres.init, it is assumed to be 1 atm. Should be argument.

cumBgVol() and cumBgMan() do not work without comp argument

But they should

summBg() 'when' argument bugs (with/without 'show.rates' = TRUE)

From Alex B. (see message below)

library(biogas)
data(vol2)
data(comp2)
data(setup2)

cbg <- cumBg(vol2, comp = comp2, temp = 20, pres = 1,
id.name = "bottle", time.name = "days",
dat.name = "meas.vol", comp.name = "CH4.conc",
extrap = TRUE)

s1 <- summBg(vol = cbg, setup = setup2, id.name = "bottle",
time.name = "days", descrip.name = "description",
inoc.name = "Inoculum", inoc.m.name = "inoc.mass",
norm.name = "sub.vs", show.obs = TRUE, show.rates = TRUE)

s2 <- summBg(vol = cbg, setup = setup2, id.name = "bottle",
time.name = "days", descrip.name = "description",
inoc.name = "Inoculum", inoc.m.name = "inoc.mass",
norm.name = "sub.vs", show.obs = TRUE, when = "meas", show.rates = FALSE)

Problems:

Gives warning on ignoring 'when' for s1 (even though no when is given.
s1 seems to normalize CH4 volume but s2 does not.
Observation in output differ between s1 and s2.

Package check problems

These are from R CMD check --as-cran with a76aaff

Nothing too difficult, just needs some time.

* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component 14: 'is.NA' value mismatch: 6 in current 1 in target
  ── Failure (test_LowLevelFunctions.R:126:3): mass2vol non vectorised result is correct ──
  mass2vol(...) not equal to `stdVCH4`.
  1/1 mismatches
  [1] 1673 - 1676 == -2.56
  ── Failure (test_LowLevelFunctions.R:131:5): planBMP works ─────────────────────
  planBMP(...) not equal to c(...).
  3/10 mismatches (average diff: 2)
  [8]  0.001 - 1 == -0.999
  [9]  0.002 - 2 == -1.998
  [10] 0.003 - 3 == -2.997
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted

* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mass2vol':
mass2vol
  Code: function(mass, xCH4, xCO2 = 1 - xCH4 - xN2, xN2 = 0, temp,
                 pres, temp.std = getOption("temp.std",
                 as.numeric(NA)), pres.std = getOption("pres.std",
                 as.numeric(NA)), unit.temp = getOption("unit.temp",
                 "C"), unit.pres = getOption("unit.pres", "atm"), value
                 = "CH4", headspace = NULL, headcomp = "N2", temp.init
                 = NULL, std.message = TRUE)
  Docs: function(mass, xCH4, temp, pres, temp.std =
                 getOption("temp.std", as.numeric(NA)), pres.std =
                 getOption("pres.std", as.numeric(NA)), unit.temp =
                 getOption("unit.temp", "C"), unit.pres =
                 getOption("unit.pres", "atm"), value = "CH4",
                 headspace = NULL, headcomp = "N2", temp.init = NULL,
                 std.message = TRUE)
  Argument names in code not in docs:
    xCO2 xN2
  Mismatches in argument names (first 3):
    Position: 3 Code: xCO2 Docs: temp
    Position: 4 Code: xN2 Docs: pres
    Position: 5 Code: temp Docs: temp.std

Codoc mismatches from documentation object 'planBMP':
planBMP
  Code: function(vs.inoc, vs.sub, isr = NA, m.inoc = NA, m.sub = NA,
                 m.tot = m.inoc + m.sub, m.vs.sub = vs.sub *
                 m.sub/1000, digits = 3, warn = TRUE, nice = TRUE)
  Docs: function(vs.inoc, vs.sub, isr = NA, m.inoc = NA, m.sub = NA,
                 m.tot = NA, m.vs.sub = vs.sub * m.sub, digits = 3,
                 warn = TRUE, nice = TRUE)
  Mismatches in argument default values:
    Name: 'm.tot' Code: m.inoc + m.sub Docs: NA
    Name: 'm.vs.sub' Code: vs.sub * m.sub/1000 Docs: vs.sub * m.sub

Data codoc mismatches from documentation object 'feedSetup':
Variables in data frame 'feedSetup'
  Code: descrip id m.inoc m.sub.vs
  Docs: id m.inoc m.sub.vs

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biogas's Issues

If show.more = TRUE additional columns are returned: summ2 <- summ2[ , c(descrip.name, time.name,’mean’, ’se’, ’sd’, ’n’, ’rsd.inoc’, ’fv.inoc’, ’se1’, ’se2’, ’se3’)]

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