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Merge pull request #57 from nlmixr2/more-braces
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add more braces
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@mattfidler
mattfidler authored Jun 1, 2023
2 parents 46d6ea2 + ceb6e48 commit ca808c2
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Showing 2 changed files with 54 additions and 42 deletions.
23 changes: 13 additions & 10 deletions R/knit_printEquation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -166,16 +166,16 @@ extractEqHelperAssign <- function(x, ..., inModel, alignment = "&", name) {
latexOpMap <-
list(
"<"="<",
"<="="\\leq",
"=="="\\equiv",
">="="\\geq",
"<="="{\\leq}",
"=="="{\\equiv}",
">="="{\\geq}",
">"=">",
"&"="\\land",
"&&"="\\land",
"|"="\\lor",
"||"="\\lor",
"!="="\\ne",
"!"="\\lnot"
"&"="{\\land}",
"&&"="{\\land}",
"|"="{\\lor}",
"||"="{\\lor}",
"!="="{\\ne}",
"!"="{\\lnot}"
)

extractEqHelper.call <- function(x, ..., inModel, name) {
Expand Down Expand Up @@ -285,6 +285,7 @@ extractEqHelper.name <- function(x, ..., inModel, underscoreToSubscript = FALSE,
# Otherwise underscores are protected from LaTeX interpretation
ret <- gsub(x = ret, pattern = "_", replacement = "\\_", fixed = TRUE)
}
ret <- paste0("{", ret, "}")
} else {
ret <- character()
}
Expand All @@ -300,12 +301,14 @@ extractEqHelper.numeric <- function(x, ..., inModel, name = NULL) {
base <- gsub(x = ret, pattern = patternSi, replacement = "\\1")
# as.numeric will remove the leading zeros
exponent <- as.numeric(gsub(x = ret, pattern = patternSi, replacement = "\\2"))
ret <- sprintf("{%s \\times 10^{%d}}", base, exponent)
ret <- sprintf("%s \\times 10^{%d}", base, exponent)
}
if (!is.null(name) && !(name == "")) {
# Hopefully this is right; it occurs in named arguments to calls
ret <- sprintf("%s=%s", name, ret)
}
# Add braces to protect from combination with the prior command
ret <- paste0("{", ret, "}")
} else {
ret <- character()
}
Expand Down
73 changes: 41 additions & 32 deletions tests/testthat/test-knit_printEquation.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,15 @@ test_that("knit_print, simple version", {
ui <- rxode2::rxode(mod)
expect_equal(
knit_print(ui),
knitr::asis_output("\\begin{align*}\nka & = \\exp\\left(lka\\right) \\\\\ncl & = \\exp\\left(lcl\\right) \\\\\nvc & = \\exp\\left(lvc\\right) \\\\\ncp & = linCmt() \\\\\ncp & \\sim prop(propSd)\n\\end{align*}\n")
knitr::asis_output("\\begin{align*}\n{ka} & = \\exp\\left({lka}\\right) \\\\\n{cl} & = \\exp\\left({lcl}\\right) \\\\\n{vc} & = \\exp\\left({lvc}\\right) \\\\\n{cp} & = linCmt() \\\\\n{cp} & \\sim prop({propSd})\n\\end{align*}\n")
)

suppressMessages(
fit <- nlmixr2est::nlmixr(mod, data = nlmixr2data::theo_sd, est = "focei", control = nlmixr2est::foceiControl(eval.max = 1, print = 0))
)
expect_equal(
knit_print(fit),
knitr::asis_output("\\begin{align*}\nka & = \\exp\\left(lka\\right) \\\\\ncl & = \\exp\\left(lcl\\right) \\\\\nvc & = \\exp\\left(lvc\\right) \\\\\ncp & = linCmt() \\\\\ncp & \\sim prop(propSd)\n\\end{align*}\n")
knitr::asis_output("\\begin{align*}\n{ka} & = \\exp\\left({lka}\\right) \\\\\n{cl} & = \\exp\\left({lcl}\\right) \\\\\n{vc} & = \\exp\\left({lvc}\\right) \\\\\n{cp} & = linCmt() \\\\\n{cp} & \\sim prop({propSd})\n\\end{align*}\n")
)
})

Expand Down Expand Up @@ -66,7 +66,7 @@ test_that("knit_print, less common models", {
ui <- rxode2::rxode(mod)
expect_equal(
knit_print(ui),
knitr::asis_output("\\begin{align*}\nka & = \\exp\\left(lka\\right)<1 \\\\\ncl & = \\exp\\left(lcl\\right)\\leq2 \\\\\nvc & = \\exp\\left(lvc\\right)\\equiv3 \\\\\nvc4 & = vc\\geq4 \\\\\nvc5 & = vc>5 \\\\\nvc6 & = vc\\land6 \\\\\nvc7 & = vc\\land7 \\\\\nvc8 & = vc\\lor8 \\\\\nvc9 & = vc\\lor9 \\\\\nvc10 & = vc\\ne10 \\\\\nvc11 & = \\lnot vc \\\\\n\\mathrm{if} & \\left(vc>11\\right) \\{ \\\\\n & cl = 12 \\\\\n\\} \\quad & \\mathrm{else} \\: \\mathrm{if} \\left(vc>13\\right) \\{ \\\\\n & cl = 14 \\\\\n & cl = 15 \\\\\n\\} \\quad & \\mathrm{else} \\: cl = 16 \\\\\ncp & = linCmt() \\\\\ncp & \\sim c(p0=0, p1=1, p2=2, 3)\n\\end{align*}\n")
knitr::asis_output("\\begin{align*}\n{ka} & = \\exp\\left({lka}\\right)<{1} \\\\\n{cl} & = \\exp\\left({lcl}\\right){\\leq}{2} \\\\\n{vc} & = \\exp\\left({lvc}\\right){\\equiv}{3} \\\\\n{vc4} & = {vc}{\\geq}{4} \\\\\n{vc5} & = {vc}>{5} \\\\\n{vc6} & = {vc}{\\land}{6} \\\\\n{vc7} & = {vc}{\\land}{7} \\\\\n{vc8} & = {vc}{\\lor}{8} \\\\\n{vc9} & = {vc}{\\lor}{9} \\\\\n{vc10} & = {vc}{\\ne}{10} \\\\\n{vc11} & = {\\lnot} {vc} \\\\\n\\mathrm{if} & \\left({vc}>{11}\\right) \\{ \\\\\n & {cl} = {12} \\\\\n\\} \\quad & \\mathrm{else} \\: \\mathrm{if} \\left({vc}>{13}\\right) \\{ \\\\\n & {cl} = {14} \\\\\n & {cl} = {15} \\\\\n\\} \\quad & \\mathrm{else} \\: {cl} = {16} \\\\\n{cp} & = linCmt() \\\\\n{cp} & \\sim c({p0=0}, {p1=1}, {p2=2}, {3})\n\\end{align*}\n")
)
})

Expand Down Expand Up @@ -95,19 +95,21 @@ test_that("knit_print, model with 'if' and a character string", {
ui <- rxode2::rxode(mod)
expect_equal(
knit_print(ui),
knitr::asis_output("\\begin{align*}\nka & = \\exp\\left(lka\\right)<1 \\\\\ncl & = \\exp\\left(lcl\\right)\\leq2 \\\\\nvc & = \\exp\\left(lvc\\right)\\equiv3 \\\\\n\\mathrm{if} & \\left(vc\\equiv\\text{\"a\"}\\right) \\{ \\\\\n & cl = 12 \\\\\n\\} \\quad & \\mathrm{else} \\: cl = 16 \\\\\ncp & = linCmt() \\\\\ncp & \\sim c(p0=0, p1=1, p2=2, 3)\n\\end{align*}\n")
knitr::asis_output("\\begin{align*}\n{ka} & = \\exp\\left({lka}\\right)<{1} \\\\\n{cl} & = \\exp\\left({lcl}\\right){\\leq}{2} \\\\\n{vc} & = \\exp\\left({lvc}\\right){\\equiv}{3} \\\\\n\\mathrm{if} & \\left({vc}{\\equiv}\\text{\"a\"}\\right) \\{ \\\\\n & {cl} = {12} \\\\\n\\} \\quad & \\mathrm{else} \\: {cl} = {16} \\\\\n{cp} & = linCmt() \\\\\n{cp} & \\sim c({p0=0}, {p1=1}, {p2=2}, {3})\n\\end{align*}\n")
)
})

expect_equal(
extractEqHelper.function(function() {ini({a <- 1});model({log(foo)+exp(bar)})}, inModel = FALSE),
"\\log\\left(foo\\right)+\\exp\\left(bar\\right)"
)
test_that("function extraction works", {
expect_equal(
extractEqHelper.function(function() {ini({a <- 1});model({log(foo)+exp(bar)})}, inModel = FALSE),
"\\log\\left({foo}\\right)+\\exp\\left({bar}\\right)"
)
})

test_that("extractEqHelper.(", {
expect_equal(
"extractEqHelper.("(str2lang("(foo)"), inModel = TRUE),
"\\left(foo\\right)"
"\\left({foo}\\right)"
)
expect_equal(
"extractEqHelper.("(str2lang("(foo)"), inModel = FALSE),
Expand All @@ -119,20 +121,20 @@ test_that("extractEqHelperAssign", {
# ODE, space with multiple-character state ("abc")
expect_equal(
extractEqHelperAssign(str2lang("d/dt(abc) = d"), inModel = TRUE),
"\\frac{d \\: abc}{dt} & = d"
"\\frac{d \\: abc}{dt} & = {d}"
)
# ODE, no space with single-character state ("a")
expect_equal(
extractEqHelperAssign(str2lang("d/dt(a) = b"), inModel = TRUE),
"\\frac{da}{dt} & = b"
"\\frac{da}{dt} & = {b}"
)
expect_equal(
extractEqHelperAssign(str2lang("a = b"), inModel = TRUE),
"a & = b"
"{a} & = {b}"
)
expect_equal(
extractEqHelperAssign(str2lang("a <- b"), inModel = TRUE),
"a & = b"
"{a} & = {b}"
)
expect_equal(
extractEqHelperAssign(str2lang("a <- b"), inModel = FALSE),
Expand All @@ -144,40 +146,40 @@ test_that("extractEqHelper.call", {
# named functions are escaped
expect_equal(
extractEqHelper.call(str2lang("model({log(foo)+exp(bar)})"), inModel = FALSE),
"\\log\\left(foo\\right)+\\exp\\left(bar\\right)"
"\\log\\left({foo}\\right)+\\exp\\left({bar}\\right)"
)
# binary plus and unary minus
expect_equal(
extractEqHelper.call(str2lang("model({-foo+add(bar)})"), inModel = FALSE),
"-foo+add(bar)"
"-{foo}+add({bar})"
)
# multiplication
expect_equal(
extractEqHelper.call(str2lang("model({foo*add(bar)})"), inModel = FALSE),
"foo {\\times} add(bar)"
"{foo} {\\times} add({bar})"
)
# division
expect_equal(
extractEqHelper.call(str2lang("model({foo/add(bar)})"), inModel = FALSE),
"\\frac{foo}{add(bar)}"
"\\frac{{foo}}{add({bar})}"
)
# exponent with both operators
expect_equal(
extractEqHelper.call(str2lang("model({foo**add(bar)})"), inModel = FALSE),
"{foo}^{add(bar)}"
"{{foo}}^{add({bar})}"
)
expect_equal(
extractEqHelper.call(str2lang("model({foo^add(bar)})"), inModel = FALSE),
"{foo}^{add(bar)}"
"{{foo}}^{add({bar})}"
)
expect_equal(
extractEqHelper.call(str2lang("model({foo~add(bar)})"), inModel = FALSE),
"foo & \\sim add(bar)"
"{foo} & \\sim add({bar})"
)
# transition to inModel works
expect_equal(
extractEqHelper.call(str2lang("model({foo(bar)})"), inModel = FALSE),
"foo(bar)"
"foo({bar})"
)
expect_equal(
extractEqHelper.call(str2lang("foo(bar)"), inModel = FALSE),
Expand All @@ -188,19 +190,19 @@ test_that("extractEqHelper.call", {
test_that("extractEqHelper.name", {
expect_equal(
extractEqHelper.name(as.name("fo_o_bar"), inModel = TRUE, underscoreToSubscript = FALSE),
"fo\\_o\\_bar"
"{fo\\_o\\_bar}"
)
expect_equal(
extractEqHelper.name(as.name("fo_o_bar"), inModel = TRUE, underscoreToSubscript = TRUE),
"fo_{o, bar}"
"{fo_{o, bar}}"
)
expect_equal(
extractEqHelper.name(as.name("fo_o"), inModel = TRUE, underscoreToSubscript = TRUE),
"fo_{o}"
"{fo_{o}}"
)
expect_equal(
extractEqHelper.name(as.name("foo"), inModel = TRUE, underscoreToSubscript = TRUE),
"foo"
"{foo}"
)
expect_equal(
extractEqHelper.name(as.name("foo"), inModel = FALSE),
Expand All @@ -211,11 +213,11 @@ test_that("extractEqHelper.name", {
test_that("extractEqHelper.numeric", {
expect_equal(
extractEqHelper.numeric(5, inModel = TRUE),
"5"
"{5}"
)
expect_equal(
extractEqHelper.numeric(pi, inModel = TRUE),
"3.141593"
"{3.141593}"
)
# test SI
expect_equal(
Expand Down Expand Up @@ -272,22 +274,29 @@ test_that("extractEqHelper.if", {
}")
expect_equal(
extractEqHelper.if(ifOnly, inModel = TRUE),
c("\\mathrm{if} & \\left(vc>11\\right) \\{", " & cl = 12", "\\} ")
c("\\mathrm{if} & \\left({vc}>{11}\\right) \\{", " & {cl} = {12}", "\\} ")
)
expect_equal(
extractEqHelper.if(ifOnlyNoBrace, inModel = TRUE),
"\\mathrm{if} & \\left(vc>11\\right) cl = 12"
"\\mathrm{if} & \\left({vc}>{11}\\right) {cl} = {12}"
)
expect_equal(
extractEqHelper.if(ifOnlyMultiline, inModel = TRUE),
c("\\mathrm{if} & \\left(vc>11\\right) \\{", " & cl = 12", " & cl2 = 13", "\\} ")
c("\\mathrm{if} & \\left({vc}>{11}\\right) \\{", " & {cl} = {12}", " & {cl2} = {13}", "\\} ")
)
expect_equal(
extractEqHelper.if(ifElse, inModel = TRUE),
c("\\mathrm{if} & \\left(vc>11\\right) \\{", " & cl = 12", "\\} \\quad & \\mathrm{else} \\: cl = 16")
c("\\mathrm{if} & \\left({vc}>{11}\\right) \\{", " & {cl} = {12}", "\\} \\quad & \\mathrm{else} \\: {cl} = {16}")
)
expect_equal(
extractEqHelper.if(ifElseIf, inModel = TRUE),
c("\\mathrm{if} & \\left(vc>11\\right) \\{", " & cl = 12", "\\} \\quad & \\mathrm{else} \\: \\mathrm{if} \\left(vc>13\\right) \\{", " & cl = 14", " & cl = 15", "\\} \\quad & \\mathrm{else} \\: cl = 16")
c("\\mathrm{if} & \\left({vc}>{11}\\right) \\{", " & {cl} = {12}", "\\} \\quad & \\mathrm{else} \\: \\mathrm{if} \\left({vc}>{13}\\right) \\{", " & {cl} = {14}", " & {cl} = {15}", "\\} \\quad & \\mathrm{else} \\: {cl} = {16}")
)
})

test_that("items are correctly braced to prevent confusion", {
expect_equal(
extractEqHelper.call(str2lang("a & b"), inModel = TRUE),
"{a}{\\land}{b}"
)
})

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