version 0.1.7

DESCRIPTION

@@ -1,21 +1,20 @@
 Package: interactionR
 Type: Package
 Title: Full Reporting of Interaction Analyses
-Version: 0.1.6
+Version: 0.1.7
 Author: Babatunde Alli
 Maintainer: Babatunde Alli <babatunde.alli@mail.mcgill.ca>
-Description: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>].
-    It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]). 
+Description: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>]. It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]). 
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Imports: msm, car, officer, flextable
-RoxygenNote: 7.1.2
-URL: https://github.com/epi-zen/interactionR
-BugReports: https://github.com/epi-zen/interactionR/issues
+RoxygenNote: 7.2.3
+URL: https://github.com/tunsmart/interactionR
+BugReports: https://github.com/tunsmart/interactionR/issues
 Suggests: testthat (>= 2.1.0)
 Depends: R (>= 2.10)
 NeedsCompilation: no
-Packaged: 2022-06-04 18:14:14 UTC; tunsm
+Packaged: 2023-12-03 22:43:43 UTC; tunsm
 Repository: CRAN
-Date/Publication: 2022-06-04 18:30:02 UTC
+Date/Publication: 2023-12-03 23:00:03 UTC

MD5

@@ -1,20 +1,20 @@
-ab67ae9e15919bebf8f6e28963924f7d *DESCRIPTION
+850013e1f9eb67e9c4448d98334e500d *DESCRIPTION
 edc81ef3b426a176e280f83a20b9841b *NAMESPACE
-b5febf648d39e924ac7be2e6a191b09b *NEWS.md
+8cfbca5f277d89e9b2278fcc7ba92abc *NEWS.md
 8da546be75587747de5eeb415091373b *R/HDiscdata.R
 05746067aaaebe75ddd7520c860d0e12 *R/OCdata.R
-01dca54da04e82749c353c1d831ae153 *R/global.R
-9380da78eb96b449035ff9367a43927e *R/helpers.R
-e6f11c93a778933fafe9aab9025eb6da *R/interactionR.R
+5695b49a67cb6e1ad9e56733733b8912 *R/global.R
+125e51bee7806ba357ec4110e80d5530 *R/helpers.R
+67b0368bd93de47ca47f5a51cd817552 *R/interactionR.R
 1a50059080b0fffc141a65562d48ff4e *R/interactionR_boot.R
-ff439e4c562ce80d12e0cef37ceb5741 *R/interactionR_delta.R
+5349b0fc8571892d7ebefe51ebaae30d *R/interactionR_delta.R
 5df8de12ac83201579bf2249613fb5fc *R/interactionR_mover.R
 68cedcaf25a1443daa713de8e115f904 *R/interactionR_table.R
-5297ce6113a2e27dbeaf5d58f3fef206 *README.md
-720388527841511fb0ab138d7bf95dbd *build/partial.rdb
+ebd98b1f9c4604edfbafdd5298af1fa0 *README.md
+b943a1546a1e17be4eea235ec7b4616b *build/partial.rdb
 5315b36e8817a0b7bd5c8e6924641a1e *data/HDiscdata.rda
 2eebe5bdd610e465cb1ff1d06edd02fa *data/OCdata.rda
-cded81821e1f74350089f0037741d609 *inst/CITATION
+118c14e19a9bbe15410daf9974b3b4a0 *inst/CITATION
 444a38c2d05ba69ccf0521416b769ea4 *man/HDiscdata.Rd
 7db69e8b57eb9577441f8947716557e7 *man/OCdata.Rd
 389c4364d9e596481045e699b63e619e *man/figures/Figure-1.png
@@ -26,5 +26,5 @@ e4f9e2247801e87e5dc9c22c9e835411 *man/interactionR_boot.Rd
 d27a5c4bb701982313d7db1259afbf87 *man/interactionR_mover.Rd
 14cfaa120fe33edd8a385894331ad6ad *man/interactionR_table.Rd
 344b1fa06218a3f98f31a1d1d7be838e *tests/testthat.R
-d8e2f5742232c1d568d5552b9131a0f5 *tests/testthat/test-interactionR.R
+b244d5a80a5632d208f7299f1f649c51 *tests/testthat/test-interactionR.R
 bc5bf0cd4544a8579895039e359b34ef *tests/testthat/test-interactionR_table.R

NEWS.md

@@ -1,3 +1,8 @@
+interactionR 0.1.7
+==================
+
+*Patch to correct pvalue estimation for SI and relax argument checkings
+
 interactionR 0.1.6
 ==================
 

R/global.R

@@ -1,5 +1,5 @@
 utils::globalVariables(c(
   "stats", "binomial", "coef", "confint.default", "glm",
   "pnorm", "qnorm", "quantile", "update", "vcov", "askYesNo", "grep",
-  "str2lang", "model.frame", "is"
+  "str2lang", "model.frame", "is", "plnorm"
 ))

R/helpers.R

@@ -8,15 +8,19 @@ invalid <- function(model) {
 }
 
 check_arguments <- function(model, exposure_names) {
+  original_names <- exposure_names
+  modified_names <- grep(paste0("^", original_names[1], "|^", original_names[2]), names(coef(model)), value = TRUE)
+
   if (!invalid(model)) {
     stop("The 'model' argument must be a regression model object fit with glm(), coxph() or clogit()")
-  } else if (!is(exposure_names, "character")  || length(exposure_names) != 2) {
+  } else if (!is(exposure_names, "character") || length(exposure_names) != 2) {
     stop("Argument 'exposure_names' requires a character vector of the names of the two exposure variables")
-  } else if (anyNA(match(exposure_names, names(coef(model))))) {
+  } else if (length(modified_names) < 2) {
     stop("At least one of the exposure names you have identified cannot be found in your model")
   }
 }
 
+
 extract_pvals <- function(model) {
   if ("glm" %in% class(model)) {
    return(summary(model)$coefficients[,4])

R/interactionR.R

@@ -389,7 +389,7 @@ interactionR <- function(model, exposure_names = c(), ci.type = "delta", ci.leve
 
     SIL <- exp(lnSI - z * se_SI)
     SIU <- exp(lnSI + z * se_SI)
-    p.SI <- 1 - pnorm(exp(lnSI/se_SI))
+    p.SI <- 1 - plnorm(exp(lnSI/se_SI))
 
   } else {
     stop("Argument 'ci.type' must be 'delta' or 'mover' ")
@@ -457,6 +457,8 @@ interactionR <- function(model, exposure_names = c(), ci.type = "delta", ci.leve
     raw_data <- dat.ir
   }
 
+  d$p = round(d$p, 5)
+
   ir <- list(dframe = d, exp_names = c(beta1, beta2), analysis = em, call = model$call, dat = raw_data)
   attr(ir, "class") <- "interactionR"
 

R/interactionR_delta.R

@@ -197,7 +197,7 @@ interactionR_delta <- function(model, exposure_names = c(), ci.level = 0.95, em
 
   CI.ll_SI <- exp(lnSI - z * se_SI)
   CI.ul_SI <- exp(lnSI + z * se_SI)
-  p.SI <- NA
+  p.SI <- 1 - plnorm(exp(lnSI/se_SI))
 
   d <- data.frame(Measures = c(
     "OR00", "OR01", "OR10", "OR11", paste("OR(",
@@ -266,8 +266,8 @@ interactionR_delta <- function(model, exposure_names = c(), ci.level = 0.95, em
   if (exists("dat.ir")) {
     raw_data <- dat.ir
   }
-  #d$p = ifelse(d$p < 0.001, "<0.001", round(d$p, 8))
-  d$p = round(d$p, 6)
+
+  d$p = round(d$p, 5)
 
   ir <- list(dframe = d, exp_names = c(beta1, beta2), analysis = em, call = model$call, dat = raw_data)
   attr(ir, "class") <- "interactionR"

README.md

@@ -1,6 +1,6 @@
 # About interactionR
 
-[![R-CMD-check](https://github.com/epi-zen/interactionR/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/epi-zen/interactionR/actions/workflows/check-standard.yaml)
+[![R-CMD-check](https://github.com/tunsmart/interactionR/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/tunsmart/interactionR/actions/workflows/check-standard.yaml)
 [![](https://www.r-pkg.org/badges/version/interactionR)](https://cran.r-project.org/package=interactionR)
 ![Downloads](https://cranlogs.r-pkg.org/badges/interactionR)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/interactionR)](https://cran.r-project.org/package=interactionR)
@@ -23,11 +23,11 @@ interactionR is on
 `install.packages("interactionR")`.
 
 You can also install the development version from
-[GitHub](https://github.com/epi-zen/interactionR) with:
+[GitHub](https://github.com/tunsmart/interactionR) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("epi-zen/interactionR")
+devtools::install_github("tunsmart/interactionR")
 ```
 
 # Implementation
@@ -197,7 +197,7 @@ both development and releases.
 ### To report problems, bugs or issues
 
 Please use [interactionR
-issues](https://github.com/epi-zen/interactionR/issues) here on Github.
+issues](https://github.com/tunsmart/interactionR/issues) here on Github.
 
 ### To get support
 

inst/CITATION

@@ -1,16 +1,15 @@
 citHeader("To cite interactionR in publications use:")
 
-citEntry(
-  entry    = "Article",
-  title    = "InteractionR: An R package for full reporting of
-  effect modification and interaction",
-  author   = as.person("Babatunde Yusuf Alli"),
+bibentry(
+  "Article",
+  title    = "InteractionR: An R package for full reporting of effect modification and interaction",
+  author   = "Babatunde Yusuf Alli",
   journal  = "Software Impacts",
   year     = "2021",
   volume   = "10",
   number   = "00147",
   pages    = "0-0",
-  url      = "https://doi.org/10.1016/j.simpa.2021.100147",
+  doi      = "10.1016/j.simpa.2021.100147",
   textVersion = paste("Babatunde Y. Alli (2021).",
   "InteractionR: An R package for full reporting of effect modification and interaction.", "Software Impacts, 10, 100147.", "doi:10.1016/j.simpa.2021.100147")
 )

tests/testthat/test-interactionR.R

@@ -74,6 +74,46 @@ test_that("generates error when exposure name cannot be found in model", {
   )
 })
 
+
+test_that("works correctly with numeric exposure variables", {
+  model <- glm(exp3 ~ exp1 * exp2, data=d)
+  expect_no_error(
+    interactionR(model,
+                 exposure_names = c("exp1", "exp2"),
+                 ci.type = "delta", ci.level = 0.95,
+                 em = FALSE, recode = FALSE
+    )
+  )
+})
+
+test_that("works correctly with character/factor exposure variables", {
+  d$exp1 <- as.factor(exp1)
+  d$exp2 <- as.factor(exp2)
+  model <- glm(outcome ~ exp1 * exp2, data=d, family = binomial(link = "logit"))
+  expect_no_error(
+    interactionR(model,
+                 exposure_names = c("exp1", "exp2"),
+                 ci.type = "delta", ci.level = 0.95,
+                 em = FALSE, recode = FALSE
+    )
+  )
+})
+
+test_that("works correctly with unknown postfix in exposure variables (using factor levels)", {
+  d$exp1 <- factor(exp1, levels = c(0, 1), labels = c("No", "Yes"))
+  d$exp2 <- factor(exp2, levels = c(0, 1), labels = c("No", "Yes"))
+
+  model <- glm(outcome ~ exp1 * exp2, data=d, family = binomial(link = "logit"))
+  expect_no_error(
+    interactionR(model,
+                 exposure_names = c("exp1", "exp2"),
+                 ci.type = "delta", ci.level = 0.95,
+                 em = FALSE, recode = FALSE
+    )
+  )
+})
+
+
 test_that("generates error when exposures interaction cannot be found in the model", {
   model <- glm(outcome ~ exp2*exp3 + exp1, data=d)
   expect_error(