[CHNOSZ-commits] r595 - in pkg/CHNOSZ: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 11 04:21:25 CEST 2020
Author: jedick
Date: 2020-08-11 04:21:24 +0200 (Tue, 11 Aug 2020)
New Revision: 595
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/man/NaCl.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/makeup.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/objective.Rd
pkg/CHNOSZ/man/taxonomy.Rd
pkg/CHNOSZ/man/util.array.Rd
pkg/CHNOSZ/man/util.blast.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/man/util.water.Rd
Log:
Remove stopifnot() from examples, round 3
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/DESCRIPTION 2020-08-11 02:21:24 UTC (rev 595)
@@ -1,6 +1,6 @@
Date: 2020-08-11
Package: CHNOSZ
-Version: 1.3.6-68
+Version: 1.3.6-69
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/man/NaCl.Rd
===================================================================
--- pkg/CHNOSZ/man/NaCl.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/NaCl.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -81,8 +81,8 @@
dprop <- describe.property(rep("T", 3), c(100, 300, 500))
legend("topleft", dprop, lty=1, pch=1, col=col)
title(main="H2O + NaCl; HCh (points) and 'NaCl()' (lines)")
+# plot activity coefficient (gamma)
plot(c(1,6), c(0,0.8), xlab="NaCl (mol/kg)", ylab=expression(gamma[Cl^"-"]), type="n")
-# plot activity coefficient (gamma)
for(i in 1:3) {
points(m.HCh, gam_Cl.HCh[[i]], col=col[i])
lines(m_tot, gam_Cl.calc[, i], col=col[i])
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/add.protein.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -49,7 +49,7 @@
# Human Gastric juice peptide 1
aa <- seq2aa("GAJU_HUMAN", "LAAGKVEDSD")
ip <- add.protein(aa)
-stopifnot(protein.length(ip)==10)
+protein.length(ip) # 10
# the chemical formula of this peptide
as.chemical.formula(protein.formula(ip)) # "C41H69N11O18"
# we can also calculate a formula without using add.protein
Modified: pkg/CHNOSZ/man/info.Rd
===================================================================
--- pkg/CHNOSZ/man/info.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/info.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -68,10 +68,10 @@
# formulas default to aqueous species, if available
i1 <- info(c("CH4", "CO2", "CS2", "MgO"))
-stopifnot(identical(info(i1)$state, c("aq", "aq", "gas", "cr")))
+info(i1)$state # aq, aq, gas, cr
# state argument overrides the default
i2 <- info(c("CH4", "CO2", "MgO"), "gas")
-stopifnot(identical(info(i2)$state, c("gas", "gas", NA)))
+info(i2)$state # gas, gas, NA
## partial name or formula searches
info("ATP")
Modified: pkg/CHNOSZ/man/makeup.Rd
===================================================================
--- pkg/CHNOSZ/man/makeup.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/makeup.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -52,9 +52,8 @@
# the formula of lawsonite, with a parenthetical part and a suffix
makeup("CaAl2Si2O7(OH)2*H2O")
# fractional coefficients are ok
-redfield <- c(106, 16, 1)
reddiv10 <- makeup("C10.6N1.6P0.1")
-stopifnot(10*reddiv10 == redfield)
+10*reddiv10 # 106, 16, 1 (Redfield ratio)
# the coefficient for charge is a number with a *preceding* sign
# e.g., ferric iron, with a charge of +3 is expressed as
@@ -78,8 +77,8 @@
# the 'sum' argument can be used to check mass and charge
# balance in a chemical reaction
formula <- c("H2O", "H+", "(Z-1)", "O2")
-(mf <- makeup(formula, c(-1, 2, 2, 0.5), sum=TRUE))
-stopifnot(all(mf==0))
+mf <- makeup(formula, c(-1, 2, 2, 0.5), sum = TRUE)
+all(mf==0) # TRUE
}
\seealso{ \code{\link{mass}}, \code{\link{entropy}}, \code{\link{basis}}, \code{\link{i2A}} }
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/nonideal.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -139,11 +139,11 @@
# (needed for replication of the values in Alberty's book)
nonideal("Alberty")
thermo("opt$ideal.H" = FALSE)
-(sres <- subcrt(c("acetate", "H+", "acetic acid"), c(-1, -1, 1),
- IS=c(0, 0.1, 0.25), T=25, property="logK"))
-# we're within 0.01 log of Alberty's pK values
+sres <- subcrt(c("acetate", "H+", "acetic acid"), c(-1, -1, 1),
+ IS=c(0, 0.1, 0.25), T=25, property="logK")
+# we're within 0.01 of Alberty's pK values
Alberty_logK <- c(4.75, 4.54, 4.47)
-stopifnot(maxdiff(sres$out$logK, Alberty_logK) < 0.01)
+maxdiff(sres$out$logK, Alberty_logK) # 0.0072
# reset option to default
thermo("opt$ideal.H" = TRUE)
@@ -181,11 +181,9 @@
sres <- subcrt("Na+", T = 700, P = 10000, IS = IS)
water(oldwat)
# compare the calculated activity coefficient to values from Manning's figure
+gamma <- 10^sres$out[[1]]$loggam
Manning_gamma <- c(0.93, 0.82, 0.65, 0.76, 1.28, 2)
-gamma <- 10^sres$out[[1]]$loggam
-# the error is larger at higher IS
-stopifnot(maxdiff(gamma[1], Manning_gamma[1]) < 0.01)
-stopifnot(maxdiff(gamma, Manning_gamma) < 0.2)
+gamma - Manning_gamma
## Plot the data and splines used for calculating b_gamma
## (extended term parameter)
Modified: pkg/CHNOSZ/man/objective.Rd
===================================================================
--- pkg/CHNOSZ/man/objective.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/objective.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -107,8 +107,8 @@
title(main=paste("Transformation between metastable equilibrium\n",
"assemblages of n-alkanes"))
# DGtr but not DDGmix is positive (or zero) everywhere
-stopifnot(all(DGtr.out >= 0))
-stopifnot(!all(DDGmix.out >= 0))
+all(DGtr.out >= 0) # TRUE
+all(DDGmix.out >= 0) # FALSE
}
\references{
Modified: pkg/CHNOSZ/man/taxonomy.Rd
===================================================================
--- pkg/CHNOSZ/man/taxonomy.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/taxonomy.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -73,7 +73,7 @@
getrank(id5,taxdir)
# find the species for each of these
id6 <- sapply(id5,function(x) parent(x,taxdir=taxdir,rank="species"))
-stopifnot(unique(getrank(id6,taxdir))=="species")
+unique(getrank(id6, taxdir)) # "species"
# note that the K-12 is dropped
sciname(id6,taxdir)
Modified: pkg/CHNOSZ/man/util.array.Rd
===================================================================
--- pkg/CHNOSZ/man/util.array.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/util.array.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -81,7 +81,7 @@
a2 <- affinity(O2 = c(-80, -60), pH = c(0, 14, 7))
# in the 2nd dimension (pH) get the 4th slice (pH=7)
a3 <- slice.affinity(a2, 2, 4)
-stopifnot(all.equal(a1$values, a3$values))
+all.equal(a1$values, a3$values) # TRUE
}
\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.blast.Rd
===================================================================
--- pkg/CHNOSZ/man/util.blast.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/util.blast.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -63,7 +63,7 @@
\examples{
## using def2gi
def <- "gi|218295810|ref|ZP_03496590.1|"
-stopifnot(all.equal(def2gi(def), "218295810"))
+def2gi(def) # "218295810"
## process some of the BLAST output for proteins
## from Bison Pool metagenome (JGI, 2007)
Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/util.fasta.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -94,7 +94,7 @@
# warnings are issued for unrecognized characters
atest <- count.aa("WhatAmIMadeOf?")
# there are 3 "A" (alanine)
-stopifnot(atest[, "A"]==3)
+atest[, "A"]
}
}
Modified: pkg/CHNOSZ/man/util.water.Rd
===================================================================
--- pkg/CHNOSZ/man/util.water.Rd 2020-08-11 01:24:46 UTC (rev 594)
+++ pkg/CHNOSZ/man/util.water.Rd 2020-08-11 02:21:24 UTC (rev 595)
@@ -68,7 +68,7 @@
V.vapor <- subcrt("water", T=convert(445:455, "C"))$out[[1]]$V
thermo("opt$IAPWS.sat" = "liquid") # the default
V.liquid <- subcrt("water", T=convert(445:455, "C"))$out[[1]]$V
-stopifnot(all(V.vapor > V.liquid))
+all(V.vapor > V.liquid) # TRUE
water(oldwat)
}
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