Merge branch 'feature/combine_mlnmr_data' into develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: multinma
 Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
-Version: 0.7.2.9002
+Version: 0.7.2.9003
 Authors@R: 
     person(given = c("David", "M."),
            family = "Phillippo",

NEWS.md

@@ -1,5 +1,10 @@
 # multinma 0.7.2.9000
 
+* Feature: Networks with integration points can now be combined with 
+`combine_network()`, where previously these were discarded. One potential use 
+case is to specify different types of marginal distributions or correlation 
+structures for different AgD studies in the network, by setting these up 
+separately with `add_integration()` before combining with `combine_network()`.
 * Fix: Resolved a bug where trying to fit meta-regression models with discrete 
 covariates would sometimes result in a misspecified and inestimable model, due 
 to the inclusion of additional columns in the design matrix for the reference 

R/nma_data.R

@@ -1202,6 +1202,38 @@ combine_network <- function(..., trt_ref) {
   if (o_ipd %in% c("ordered", "competing") && o_agd_arm %in% c("ordered", "competing"))
     check_multi_combine(purrr::map(c(ipd, agd_arm), ".r"))
 
+  # Check integration points
+  if (any(purrr::map_lgl(s, inherits, what = "mlnmr_data")) &&
+      all(purrr::map_lgl(s, inherits, what = "mlnmr_data") |
+        (purrr::map_lgl(s, has_ipd) & !purrr::map_lgl(s, has_agd_arm) & !purrr::map_lgl(s, has_agd_contrast)))) {
+
+    has_int <- TRUE
+
+    s_int <- s[purrr::map_lgl(s, inherits, what = "mlnmr_data")]
+
+    # Check int_names
+    l_int_names <- purrr::map(s_int, "int_names")
+    if (!all(purrr::map_lgl(l_int_names, ~identical(., l_int_names[[1]])))) {
+      abort("Cannot combine AgD sources with different sets of covariates with integration points.")
+    } else {
+      int_names <- l_int_names[[1]]
+    }
+
+    # Check n_int
+    l_n_int <- purrr::map_dbl(s_int, "n_int")
+    if (!all(l_n_int == l_n_int[1])) {
+      abort("Cannot combine AgD sources with different numbers of integration points.")
+    } else {
+      n_int <- l_n_int[[1]]
+    }
+
+  } else if (any(purrr::map_lgl(s, inherits, what = "mlnmr_data"))) {
+    message("Dropping integration points from combined network, some AgD sources do not have integration points.")
+    has_int <- FALSE
+  } else {
+    has_int <- FALSE
+  }
+
   # Produce nma_data object
   ipd <- dplyr::bind_rows(ipd)
   agd_arm <- dplyr::bind_rows(agd_arm)
@@ -1217,6 +1249,14 @@ combine_network <- function(..., trt_ref) {
          outcome = outcome),
     class = "nma_data")
 
+  # Integration data setup
+  if (has_int) {
+    out$n_int <- n_int
+    out$int_names <- int_names
+
+    class(out) <- c("mlnmr_data", class(out))
+  }
+
   # If trt_ref not specified, mark treatments factor as default, calculate
   # current reference trt
   if (missing(trt_ref)) {

tests/testthat/test-data_combine.R

@@ -379,3 +379,71 @@ test_that("combine_network works combining survival outcomes from same type of i
                     set_ipd(ndmm_agd, studyf, trtf,
                                  Surv = Surv(eventtime, status))$ipd)
 })
+
+test_that("combine_network respects mlnma_data objects with integration points", {
+
+  ipd_net <- set_ipd(plaque_psoriasis_ipd, study = studyc, trt = trtc, r = pasi75)
+
+  agd_net1 <- set_agd_arm(
+    filter(plaque_psoriasis_agd, studyc %in% c("FEATURE", "FIXTURE", "JUNCTURE")),
+    study = studyc, trt = trtc, r = pasi75_r, n = pasi75_n
+  ) %>%
+    add_integration(durnpso = distr(qgamma, mean = durnpso_mean, sd = durnpso_sd),
+                    weight = distr(qgamma, mean = weight_mean, sd = weight_sd), cor = diag(2))
+
+  agd_net2 <- set_agd_arm(
+    filter(plaque_psoriasis_agd, !studyc %in% c("FEATURE", "FIXTURE", "JUNCTURE")),
+    study = studyc, trt = trtc, r = pasi75_r, n = pasi75_n
+  )
+
+  agd_net3 <- set_agd_arm(
+    filter(plaque_psoriasis_agd, !studyc %in% c("FEATURE", "FIXTURE", "JUNCTURE")),
+    study = studyc, trt = trtc, r = pasi75_r, n = pasi75_n
+  ) %>%
+    add_integration(durnpso = distr(qgamma, mean = durnpso_mean, sd = durnpso_sd),
+                    weight = distr(qgamma, mean = weight_mean, sd = weight_sd), cor = diag(2))
+
+  expect_s3_class(combine_network(agd_net1),
+                  c("mlnmr_data", "nma_data"), exact = TRUE)
+
+  expect_s3_class(combine_network(ipd_net, agd_net1),
+                  c("mlnmr_data", "nma_data"), exact = TRUE)
+
+  expect_s3_class(combine_network(ipd_net, agd_net1, agd_net3),
+                  c("mlnmr_data", "nma_data"), exact = TRUE)
+
+  expect_s3_class(combine_network(agd_net1, agd_net3),
+                  c("mlnmr_data", "nma_data"), exact = TRUE)
+
+  expect_s3_class(
+    expect_message(combine_network(agd_net1, agd_net2),
+                   "Dropping integration points"),
+      "nma_data", exact = TRUE)
+
+  expect_s3_class(
+    expect_message(combine_network(ipd_net, agd_net1, agd_net2),
+                   "Dropping integration points"),
+    "nma_data", exact = TRUE)
+
+  expect_s3_class(combine_network(ipd_net, agd_net2), "nma_data")
+
+  agd_net4 <- set_agd_arm(
+    filter(plaque_psoriasis_agd, !studyc %in% c("FEATURE", "FIXTURE", "JUNCTURE")),
+    study = studyc, trt = trtc, r = pasi75_r, n = pasi75_n
+  ) %>%
+    add_integration(durnpso = distr(qgamma, mean = durnpso_mean, sd = durnpso_sd))
+
+  expect_error(combine_network(agd_net1, agd_net4), "different sets of covariates")
+  expect_error(combine_network(ipd_net, agd_net1, agd_net4), "different sets of covariates")
+
+  agd_net5 <- set_agd_arm(
+    filter(plaque_psoriasis_agd, !studyc %in% c("FEATURE", "FIXTURE", "JUNCTURE")),
+    study = studyc, trt = trtc, r = pasi75_r, n = pasi75_n
+  ) %>%
+    add_integration(durnpso = distr(qgamma, mean = durnpso_mean, sd = durnpso_sd),
+                    weight = distr(qgamma, mean = weight_mean, sd = weight_sd), cor = diag(2),
+                    n_int = 8)
+
+  expect_error(combine_network(agd_net1, agd_net5), "different numbers of integration points")
+  expect_error(combine_network(ipd_net, agd_net1, agd_net5), "different numbers of integration points")
+})