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Gdr 2430 #142

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merged 4 commits into from
Mar 14, 2024
Merged

Gdr 2430 #142

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935cbfa
refactor: remove ::: usage
bczech Mar 7, 2024
adf73c3
chore: bump version and update NEWS.md
bczech Mar 7, 2024
708121c
ci: trigger build
bczech Mar 12, 2024
c485ed8
ci: resolve conflict
bczech Mar 14, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -2,8 +2,8 @@ Type: Package
Package: gDRcore
Title: Processing functions and interface to process and analyze drug
dose-response data
Version: 1.1.13
Date: 2024-02-26
Version: 1.1.14
Date: 2024-03-07
Authors@R: c(
person("Bartosz", "Czech", , "[email protected]", role = "aut",
comment = c(ORCID = "0000-0002-9908-3007")),
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3 changes: 3 additions & 0 deletions NEWS.md
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@@ -1,3 +1,6 @@
## gDRcore 1.1.14 - 2024-03-07
* cleanup package

## gDRcore 1.1.13 - 2024-02-26
* improve pkgdown site
* improved references
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4 changes: 2 additions & 2 deletions tests/testthat/test-codilutions.R
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Expand Up @@ -12,7 +12,7 @@ test_that("fit_combo_codilutions works as expected", {
x = vals,
normalization_type = "GR")

obs <- gDRcore:::fit_combo_codilutions(measured, nested_identifiers, "GR")
obs <- fit_combo_codilutions(measured, nested_identifiers, "GR")
expect_equal(dim(obs), c(7, 17))
expect_true("ratio" %in% colnames(obs))
expect_equal(obs$ratio, c(.04, .1, .3, 1, 3, 10, 30), tolerance = 10e-3)
Expand All @@ -38,7 +38,7 @@ test_that("fit_codilution_series works as expected", {
keep <- !is.na(ratios) & ratios == ratio
codilution <- measured[keep, ]

res <- purrr::quietly(gDRcore:::fit_codilution_series)(
res <- purrr::quietly(fit_codilution_series)(
codilution,
series_1 = "Concentration",
series_2 = "Concentration_2",
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2 changes: 1 addition & 1 deletion tests/testthat/test-combination-helpers.R
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Expand Up @@ -38,7 +38,7 @@ test_that("calculate_excess works as expected", {
test_that(".calculate_dilution_ratio works as expected", {
ratio <- 0.5
concs <- 10 ^ (seq(-3, 1, ratio))
obs <- gDRcore:::.calculate_dilution_ratio(concs)
obs <- .calculate_dilution_ratio(concs)
expect_equal(obs, ratio)
})

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4 changes: 2 additions & 2 deletions tests/testthat/test-combinations-calculate_matrix_metric.R
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Expand Up @@ -18,15 +18,15 @@ test_that(".calculate_matrix_metric works as expected", {
n <- 10
sa1 <- data.table::data.table(conc = seq(n), conc2 = rep(0, n), smooth = seq(n))
sa2 <- data.table::data.table(conc = rep(0, n), conc2 = seq(n), smooth = seq(n))
obs <- gDRcore:::.calculate_matrix_metric(sa1, series_id1 = "conc", sa2, series_id2 = "conc2",
obs <- .calculate_matrix_metric(sa1, series_id1 = "conc", sa2, series_id2 = "conc2",
"smooth", sum, measured_col = "smooth")
expect_equal(dim(obs), c(n ^ 2, 5))

# Validates data.
temp1 <- sa2
temp2 <- sa1
expect_error(
gDRcore:::.calculate_matrix_metric(temp1, series_id1 = "conc", temp2,
.calculate_matrix_metric(temp1, series_id1 = "conc", temp2,
series_id2 = "conc2", "smooth", sum, measured_col = "smooth")
)
})
4 changes: 2 additions & 2 deletions tests/testthat/test-cotreatments.R
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Expand Up @@ -11,7 +11,7 @@ test_that("fit_combo_cotreatments works as expected", {
GRvalue = vals)

obs <- suppressWarnings(# warnings are expected
gDRcore:::fit_combo_cotreatments(
fit_combo_cotreatments(
measured,
series_id = "Concentration",
cotrt_id = "Concentration_2",
Expand Down Expand Up @@ -39,7 +39,7 @@ test_that("fit_cotreatment_series works as expected", {
normalization_type = "GR")

obs <- suppressWarnings(# warnings are expected
gDRcore:::fit_cotreatment_series(
fit_cotreatment_series(
measured,
series_id = "Concentration",
cotrt_id = "Concentration_2",
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