CRAN Package Check Results for Package epigrowthfit

Last updated on 2025-01-12 04:48:18 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.15.3 147.40 93.77 241.17 OK --no-tests
r-devel-linux-x86_64-debian-gcc 0.15.3 132.09 69.68 201.77 OK --no-tests
r-devel-linux-x86_64-fedora-clang 0.15.3 858.06 ERROR
r-devel-linux-x86_64-fedora-gcc 0.15.3 996.22 ERROR
r-devel-windows-x86_64 0.15.3 140.00 489.00 629.00 ERROR
r-patched-linux-x86_64 0.15.3 188.64 94.56 283.20 OK --no-tests
r-release-macos-arm64 0.15.3 208.00 NOTE
r-release-macos-x86_64 0.15.3 685.00 NOTE
r-release-windows-x86_64 0.15.3 137.00 411.00 548.00 ERROR
r-oldrel-macos-arm64 0.15.3 253.00 NOTE
r-oldrel-macos-x86_64 0.15.3 533.00 NOTE
r-oldrel-windows-x86_64 0.15.3 188.00 577.00 765.00 ERROR

Check Details

Version: 0.15.3
Check: tests
Result: ERROR Running ‘coef.R’ [8s/18s] Running ‘confint.R’ [50s/129s] Running ‘datetime.R’ Running ‘egf.R’ [7s/24s] Running ‘egf_enum.R’ Running ‘egf_eval.R’ Running ‘egf_examples_day_of_week.R’ Running ‘egf_examples_excess.R’ Running ‘egf_examples_fixed.R’ [4s/12s] Running ‘egf_examples_random.R’ [115s/178s] Running ‘egf_link.R’ Running ‘egf_misc.R’ [8s/21s] Running ‘egf_options.R’ Running ‘egf_utils.R’ [8s/20s] Running ‘epidemic.R’ Running ‘extract.R’ [8s/20s] Running ‘fitted.R’ [7s/21s] Running ‘gi.R’ [4s/12s] Running ‘include.R’ [159s/421s] Running ‘language.R’ Running ‘prior.R’ Running ‘profile.R’ [30s/117s] Running ‘summary.R’ [8s/21s] Running ‘utils.R’ Running ‘validity.R’ Running ‘zzz.R’ Running the tests in ‘tests/egf_utils.R’ failed. Complete output: > attach(asNamespace("epigrowthfit")) > library(methods) > library(tools) > options(warn = 2L, error = if (interactive()) recover) > example("egf", package = "epigrowthfit"); o.1 <- m1; o.2 <- m2 egf> ## Simulate 'N' incidence time series exhibiting exponential growth egf> set.seed(180149L) egf> N <- 10L egf> f <- function(time, r, c0) { egf+ lambda <- diff(exp(log(c0) + r * time)) egf+ c(NA, rpois(lambda, lambda)) egf+ } egf> time <- seq.int(0, 40, 1) egf> r <- rlnorm(N, -3.2, 0.2) egf> c0 <- rlnorm(N, 6, 0.2) egf> data_ts <- egf+ data.frame(country = gl(N, length(time), labels = LETTERS[1:N]), egf+ time = rep.int(time, N), egf+ x = unlist(Map(f, time = list(time), r = r, c0 = c0))) egf> rm(f, time) egf> ## Define fitting windows (here, two per time series) egf> data_windows <- egf+ data.frame(country = gl(N, 1L, 2L * N, labels = LETTERS[1:N]), egf+ wave = gl(2L, 10L), egf+ start = c(sample(seq.int(0, 5, 1), N, TRUE), egf+ sample(seq.int(20, 25, 1), N, TRUE)), egf+ end = c(sample(seq.int(15, 20, 1), N, TRUE), egf+ sample(seq.int(35, 40, 1), N, TRUE))) egf> ## Estimate the generative model egf> m1 <- egf+ egf(model = egf_model(curve = "exponential", family = "pois"), egf+ formula_ts = cbind(time, x) ~ country, egf+ formula_windows = cbind(start, end) ~ country, egf+ formula_parameters = ~(1 | country:wave), egf+ data_ts = data_ts, egf+ data_windows = data_windows, egf+ se = TRUE) computing a Hessian matrix ... egf> ## Re-estimate the generative model with: egf> ## * Gaussian prior on beta[1L] egf> ## * LKJ prior on all random effect covariance matrices egf> ## (here there happens to be just one) egf> ## * initial value of 'theta' set explicitly egf> ## * theta[3L] fixed at initial value egf> m2 <- egf+ update(m1, egf+ formula_priors = list(beta[1L] ~ Normal(mu = -3, sigma = 1), egf+ Sigma ~ LKJ(eta = 2)), egf+ init = list(theta = c(log(0.5), log(0.5), 0)), egf+ map = list(theta = 3L)) computing a Hessian matrix ... > > > ## egf_sanitize_formula_ts ######################################## > ## egf_sanitize_formula_windows ######################################## > > l1 <- list(cbind(x, y) ~ 1, + cbind(x, y) ~ g, + cbind(x, y) ~ 1 + g, + cbind(x, y) ~ (g), + cbind(x, y) ~ g:h, + cbind(x, y) ~ I(g + h), + cbind(x, y) ~ I(g * h), + cbind(x - 1, cumsum(y)) ~ g) > l2 <- list(~g, + cbind(x, y) ~ g + h, + cbind(x, y) ~ g * h, + cbind(x, y) ~ 0 + g, + cbind(x, y) ~ g - 1, + cbind(x, y) ~ offset(h) + g, + (cbind(x, y)) ~ g, + cbind(x) ~ g, + cbind(x, y, z) ~ g, + rbind(x, y) ~ g) # i.e., anything other than 'cbind' > > stopifnot(identical(lapply(l1, egf_sanitize_formula_ts), + l1[c(1L, 2L, 2L, 2L, 5:8)])) > for (formula in l2) + assertError(egf_sanitize_formula_ts(formula)) > > > ## egf_sanitize_formula_parameters ##################################### > > model <- egf_model(curve = "exponential", family = "pois") > top <- egf_top(model) > > s <- + function(formula) + egf_sanitize_formula_parameters(formula, top, check = TRUE) > > fp1 <- ~x * y + (z | g) + (zz | g/h) > l1 <- rep.int(expr(simplify_terms(fp1)), 2L) > names(l1) <- c("log(r)", "log(c0)") > > fp2 <- expr(replace(fp1, 2:3, expr(quote(log(r)), fp1[[2L]]))) > l2 <- replace(l1, "log(c0)", expr(~1)) > > fp3 <- c(fp2, expr(log(c0) ~ x)) > l3 <- replace(l2, "log(c0)", expr(~x)) > > stopifnot(exprs = { + identical(s(fp1), l1) + identical(s(fp2), l2) + identical(s(fp3), l3) + }) > assertWarning(s(~0 + x)) > > > ## egf_sanitize_formula_priors ######################################### > > p1 <- Normal(mu = 0, sigma = 1) > p2 <- Normal(mu = 1, sigma = c(0.5, 1)) > p3 <- Normal(mu = -1, sigma = 2) > p4 <- LKJ(eta = 1) > > fp. <- list(foo(bar) ~ p1, + baz ~ p1, + beta ~ p1, + theta[[1L]] ~ p1, + theta[2:3] ~ p2, + theta[-(1:5)] ~ p3, + theta[replace(logical(6L), 4L, TRUE)] ~ p1, + Sigma ~ p4) > > ip. <- list( + top = list(names = c("foo(bar)", "baz"), family = "norm"), + bottom = list( + beta = list(length = 4L, family = "norm"), + theta = list(length = 6L, family = "norm"), + Sigma = list(length = 1L, family = c("lkj", "wishart", "invwishart"), + rows = 4L))) > > priors <- egf_sanitize_formula_priors(formula = fp., info = ip.) > > p2.elt <- + function(i) { + p2[["parameters"]][["sigma"]] <- p2[["parameters"]][["sigma"]][[i]] + p2 + } > > stopifnot(exprs = { + is.list(priors) + length(priors) == 2L + identical(names(priors), c("top", "bottom")) + + identical(priors[["top"]], + `names<-`(list(p1, p1), ip.[["top"]][["names"]])) + identical(priors[["bottom"]], + list(beta = list(p1, p1, p1, p1), + theta = list(p1, p2.elt(1L), p2.elt(2L), p1, NULL, p3), + Sigma = list(p4))) + }) > > > ## egf_make_frame ###################################################### > > model <- egf_model(curve = "exponential", family = "pois") > > formula_ts <- cbind(day, count) ~ country > formula_windows <- cbind(left, right) ~ country > formula_parameters <- list(`log(r)` = ~x1 + (1 | g1) + (1 | g1:g2), + `log(c0)` = ~(1 | g3)) > > data_ts <- data.frame(country = gl(6L, 11L), + day = seq.int(0, 10, by = 1), + count = rpois(11L, 100 * exp(0.04 * 0:10))) > data_windows <- data.frame(country = gl(3L, 2L), + left = rep.int(c(0, 5), 3L), + right = rep.int(c(5, 10), 3L), + x1 = c(5.00, 8.34, -0.57, -7.19, -9.71, 1.25), + x2 = rnorm(6L), + x3 = rnorm(6L), + g1 = c("a", "b", "b", "b", "b", "a"), + g2 = c("c", "d", "d", "d", "c", "c"), + g3 = c("f", "f", "e", "e", "e", "f")) > > subset_ts <- quote(day > 0) > subset_windows <- quote(x1 < 0) > select_windows <- quote(.) > > na_action_ts <- "pass" > na_action_windows <- "omit" > > frame <- egf_make_frame(model = model, + formula_ts = formula_ts, + formula_windows = formula_windows, + formula_parameters = formula_parameters, + data_ts = data_ts, + data_windows = data_windows, + subset_ts = subset_ts, + subset_windows = subset_windows, + select_windows = select_windows, + na_action_ts = na_action_ts, + na_action_windows = na_action_windows) > > stopifnot(exprs = { + is.list(frame) + length(frame) == 4L + identical(names(frame), c("ts", "windows", "parameters", "extra")) + }) > > l1 <- frame[["ts"]] > l1.e <- data.frame(ts = gl(2L, 10L, labels = 2:3), + window = factor(rep.int(c(NA, 1, 2, NA, 3, NA), + c(1L, 4L, 5L, 1L, 4L, 5L)), + labels = sprintf("window_%d", 1:3)), + time = rep.int(seq.int(1, 10, by = 1), 2L), + x = data_ts[["count"]][c(NA, 14:22, NA, 25:33)]) > attr(l1.e, "first") <- c(1L, 5L, 11L) > attr(l1.e, "last") <- c(5L, 10L, 15L) > stopifnot(identical(l1, l1.e)) > > l2 <- frame[["windows"]] > l2.e <- data.frame(ts = factor(c(2, 2, 3)), + window = gl(3L, 1L, labels = sprintf("window_%d", 1:3)), + start = c(1, 5, 1), + end = c(5, 10, 5)) > stopifnot(identical(l2, l2.e)) Error: identical(l2, l2.e) is not TRUE Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.15.3
Check: tests
Result: ERROR Running ‘coef.R’ Running ‘confint.R’ [53s/69s] Running ‘datetime.R’ Running ‘egf.R’ Running ‘egf_enum.R’ Running ‘egf_eval.R’ Running ‘egf_examples_day_of_week.R’ Running ‘egf_examples_excess.R’ Running ‘egf_examples_fixed.R’ Running ‘egf_examples_random.R’ [41s/34s] Running ‘egf_link.R’ Running ‘egf_misc.R’ Running ‘egf_options.R’ Running ‘egf_utils.R’ Running ‘epidemic.R’ Running ‘extract.R’ Running ‘fitted.R’ Running ‘gi.R’ Running ‘include.R’ [274s/277s] Running ‘language.R’ Running ‘prior.R’ Running ‘profile.R’ [33s/50s] Running ‘summary.R’ Running ‘utils.R’ Running ‘validity.R’ Running ‘zzz.R’ Running the tests in ‘tests/egf_examples_random.R’ failed. Complete output: > library(epigrowthfit) > options(warn = 2L, error = if (interactive()) recover, egf.cores = 2L) > > > ## exponential ######################################################### > > r <- log(2) / 20 > c0 <- 100 > s <- 0.2 > > mu <- log(c(r, c0)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "exponential", family = "pois"), + nsim = 20L, + seed = 775494L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-05 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 5e-02) + }) > > > ## subexponential ###################################################### > > alpha <- log(2) / 20 > c0 <- 100 > p <- 0.95 > s <- 0.2 > > mu <- c(log(alpha), log(c0), qlogis(p)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "subexponential", family = "pois"), + nsim = 20L, + seed = 653927L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(beta[3L] ~ Normal(mu = qlogis(p), sigma = 0.05), + theta[3L] ~ Normal(mu = log(s), sigma = 0.25), + Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-04 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 2e-02) + }) > > > ## gompertz ############################################################ > > alpha <- log(2) / 20 > tinfl <- 100 > K <- 25000 > s <- 0.2 > > mu <- log(c(alpha, tinfl, K)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "gompertz", family = "pois"), + nsim = 20L, + seed = 685399L, + mu = mu, + Sigma = Sigma, + cstart = 10) > oo <- options(warn = 1L) # FIXME: diagnose NA/NaN function evaluation > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) Warning in nlminb(start = par, objective = fn, gradient = gr, control = control, : NA/NaN function evaluation Warning in he(par) : restarting interrupted promise evaluation *** caught segfault *** address (nil), cause 'memory not mapped' Traceback: 1: MakeADHessObject(obj$env$data, obj$env$parameters, obj$env$reportenv, gf = obj$env$ADGrad$ptr, skip = skip, DLL = obj$env$DLL) 2: sparseHessianFun(env, skipFixedEffects = skipFixedEffects) 3: he(par) 4: newton(par = c(b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0), fn = function (par.random, order = 0, ...) { par[random] <- par.random par[-random] <- par.fixed res <- f(par, order = order, set_tail = random[1], ...) switch(order + 1, res, res[random], res[random, random])}, gr = function (x) f0(x, order = 1), he = function (par.random) { par[random] <- par.random par[-random] <- par.fixed spHess(par, random = TRUE, set_tail = random[1])}, env = <environment>, trace = FALSE) 5: do.call("newton", c(list(par = eval(random.start), fn = f0, gr = function(x) f0(x, order = 1), he = H0, env = env), inner.control)) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 10: try(do.call("newton", c(list(par = eval(random.start), fn = f0, gr = function(x) f0(x, order = 1), he = H0, env = env), inner.control)), silent = silent) 11: ff(x, order = 1) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 16: try({ if (MCcontrol$doMC) { ff(x, order = 0) MC(last.par, n = MCcontrol$n, seed = MCcontrol$seed, order = 1) } else ff(x, order = 1)}, silent = silent) 17: gradient(.par, ...) 18: nlminb(start = par, objective = fn, gradient = gr, control = control, ...) 19: (function (par, fn, gr, control, ...) { ans <- nlminb(start = par, objective = fn, gradient = gr, control = control, ...) m <- match("objective", names(ans), 0L) names(ans)[m] <- "value" ans})(par = c(beta = -4.33717960326274, beta = 4.56212107455623, beta = 9.8686999898085, theta = 0, theta = 0, theta = 0, theta = 0, theta = 0, theta = 0), fn = function (x = last.par[lfixed()], ...) { if (tracepar) { cat("par:\n") print(x) } if (!validpar(x)) return(NaN) if (is.null(random)) { ans <- f(x, order = 0) if (!ADreport) { if (is.finite(ans) && ans < value.best) { last.par.best <<- x value.best <<- ans } } } else { ans <- try({ if (MCcontrol$doMC) { ff(x, order = 0) MC(last.par, n = MCcontrol$n, seed = MCcontrol$seed, order = 0) } else ff(x, order = 0) }, silent = silent) if (is.character(ans)) ans <- NaN } ans}, gr = function (x = last.par[lfixed()], ...) { if (is.null(random)) { ans <- f(x, order = 1) } else { ans <- try({ if (MCcontrol$doMC) { ff(x, order = 0) MC(last.par, n = MCcontrol$n, seed = MCcontrol$seed, order = 1) } else ff(x, order = 1) }, silent = silent) if (is.character(ans)) ans <- rep(NaN, length(x)) } if (tracemgc) cat("outer mgc: ", max(abs(ans)), "\n") ans}, control = list()) 20: do.call(optimizer, optimizer_args) 21: egf.egf_model(model = list(curve = "gompertz", excess = FALSE, family = "pois", day_of_week = 0L), formula_ts = cbind(time, x) ~ ts, formula_windows = cbind(start, end) ~ ts, formula_parameters = ~(1 | ts), data_ts = list(ts = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 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18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L), time = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 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94, 103, 112, 145, 130, 160, 162, 167, 175, 201, 209, 208, 219, 263, 247, 248, 256, 226, 282, 278, 284, 254, 248, 291, 284, 302, 284, 310, 347, 336, 323, 321, 307, 308, 309, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 4, 1, 4, 5, 2, 3, 10, 5, 8, 10, 10, 19, 17, 23, 27, 31, 46, 36, 57, 50, 72, 64, 85, 103, 90, 96, 95, 100, 135, 146, 142, 183, 178, 170, 189, 187, 198, 224, 226, 238, 240, 251, 211, 241, 234, 254, 281, 224, 273, 250, 289, 251, 299, 254, 308, 289, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 2, 2, 3, 2, 4, 4, 11, 11, 7, 11, 6, 18, 13, 19, 26, 25, 33, 42, 50, 40, 53, 47, 69, 64, 84, 86, 90, 99, 92, 107, 95, 117, 134, 131, 145, 135, 151, 164, 189, 177, 200, 193, 217, 208, 200, 223, 247, 248, 278, 243, 246, 272, 296, 298, 291, 310, 291, 292, 305, 324, 291, 335, 312, 317, 304, 354, 335, 312, 336, 314, 308, NA, 21, 21, 25, 24, 27, 22, 34, 34, 31, 32, 36, 46, 63, 57, 52, 64, 56, 70, 77, 77, 83, 81, 92, 100, 106, 108, 120, 107, 117, 115, 114, 139, 141, 155, 144, 141, 129, 154, 151, 163, 173, 178, 190, 177, 194, 180, 194, 236, 179, 210, 218, 245, 207, 211, 220, 222, 220, 216, 236, 241, 251, 239, 251, 239, 255, 226, 251, 254, 246, 236, 214, 241, 244, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 1, 0, 2, 0, 0, 2, 2, 3, 6, 7, 6, 10, 14, 19, 16, 25, 38, 36, 38, 35, 57, 62, 83, 105, 90, 117, 140, 141, 157, 179, 193, 210, 253, 286, 284, 296, 294, 303, 339, 336, 361, 383, 413, 437, 398, 433, 429, 493, 427, 453, 461, 479, 489, 479, 495, 455, 480, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 3, 1, 2, 3, 3, 1, 14, 12, 7, 19, 22, 26, 48, 45, 49, 51, 78, 67, 95, 91, 118, 119, 115, 139, 162, 193, 191, 222, 233, 252, 215, 260, 268, 273, 296, 284, 283, 304, 324, 302, 288, 341, 324, 329, 303, 349, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 1, 1, 2, 3, 3, 6, 8, 7, 7, 10, 7, 14, 21, 17, 26, 21, 34, 38, 39, 54, 44, 47, 58, 75, 68, 87, 83, 94, 133, 111, 141, 150, 128, 156, 175, 157, 180, 190, 210, 176, 227, 228, 260, 230, 240, 248, 262, 244, 251, 258, 266, 286, 278, 295, 312, 314, 329, 317, 303, 304, 302, 297, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 2, 0, 1, 1, 5, 5, 4, 8, 9, 11, 21, 22, 23, 17, 33, 54, 47, 43, 56, 80, 78, 85, 95, 127, 128, 134, 141, 156, 192, 199, 214, 227, 229, 263, 274, 291, 300, 281, 274, 303, 380, 327, 366, 353, 396, 415, 425, 415, 395, 406, 413, 436, 442, 428, 454, 444, 429)), data_windows = list( ts = 1:20, start = c(48L, 6L, 34L, 59L, 23L, 36L, 47L, 10L, 43L, 64L, 43L, 60L, 38L, 33L, 23L, 1L, 42L, 89L, 41L, 52L ), end = c(100, 66, 99, 121, 77, 104, 93, 74, 95, 139, 97, 116, 96, 85, 90, 73, 91, 130, 99, 104)), formula_priors = list( Sigma ~ LKJ(eta = 2))) 22: (function (model, ...) UseMethod("egf", model))(model = list(curve = "gompertz", excess = FALSE, family = "pois", day_of_week = 0L), formula_ts = cbind(time, x) ~ ts, formula_windows = cbind(start, end) ~ ts, formula_parameters = ~(1 | ts), data_ts = list(ts = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 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23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L), x = c(NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 4, 5, 3, 7, 5, 6, 13, 18, 15, 11, 21, 23, 27, 41, 40, 57, 62, 61, 90, 73, 95, 114, 117, 114, 145, 161, 166, 177, 221, 197, 209, 225, 261, 239, 260, 300, 300, 291, 333, 316, 328, 331, 328, 342, 387, 375, 378, 381, 401, 382, 370, 420, 379, 381, NA, 1, 0, 0, 2, 1, 10, 2, 4, 7, 7, 11, 8, 16, 13, 26, 29, 28, 31, 40, 34, 47, 58, 70, 62, 70, 68, 102, 84, 97, 121, 113, 143, 156, 167, 164, 190, 197, 187, 206, 229, 238, 249, 260, 259, 253, 252, 290, 290, 323, 315, 317, 335, 302, 346, 331, 382, 317, 347, 344, 379, 395, 400, 384, 389, 367, 351, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 2, 2, 2, 1, 0, 3, 3, 5, 3, 10, 5, 6, 3, 7, 13, 17, 15, 26, 26, 26, 27, 35, 44, 44, 40, 50, 67, 77, 90, 81, 82, 84, 92, 110, 103, 129, 135, 140, 158, 146, 176, 188, 169, 202, 202, 227, 219, 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177, 194, 180, 194, 236, 179, 210, 218, 245, 207, 211, 220, 222, 220, 216, 236, 241, 251, 239, 251, 239, 255, 226, 251, 254, 246, 236, 214, 241, 244, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 1, 0, 2, 0, 0, 2, 2, 3, 6, 7, 6, 10, 14, 19, 16, 25, 38, 36, 38, 35, 57, 62, 83, 105, 90, 117, 140, 141, 157, 179, 193, 210, 253, 286, 284, 296, 294, 303, 339, 336, 361, 383, 413, 437, 398, 433, 429, 493, 427, 453, 461, 479, 489, 479, 495, 455, 480, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 3, 1, 2, 3, 3, 1, 14, 12, 7, 19, 22, 26, 48, 45, 49, 51, 78, 67, 95, 91, 118, 119, 115, 139, 162, 193, 191, 222, 233, 252, 215, 260, 268, 273, 296, 284, 283, 304, 324, 302, 288, 341, 324, 329, 303, 349, NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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formula_priors = list( Sigma ~ LKJ(eta = 2))) 23: do.call(egf, args) 24: egf.simulate.egf_model(zz, formula_priors = list(Sigma ~ LKJ(eta = 2))) 25: egf(zz, formula_priors = list(Sigma ~ LKJ(eta = 2))) An irrecoverable exception occurred. R is aborting now ... Running the tests in ‘tests/egf_utils.R’ failed. Complete output: > attach(asNamespace("epigrowthfit")) > library(methods) > library(tools) > options(warn = 2L, error = if (interactive()) recover) > example("egf", package = "epigrowthfit"); o.1 <- m1; o.2 <- m2 egf> ## Simulate 'N' incidence time series exhibiting exponential growth egf> set.seed(180149L) egf> N <- 10L egf> f <- function(time, r, c0) { egf+ lambda <- diff(exp(log(c0) + r * time)) egf+ c(NA, rpois(lambda, lambda)) egf+ } egf> time <- seq.int(0, 40, 1) egf> r <- rlnorm(N, -3.2, 0.2) egf> c0 <- rlnorm(N, 6, 0.2) egf> data_ts <- egf+ data.frame(country = gl(N, length(time), labels = LETTERS[1:N]), egf+ time = rep.int(time, N), egf+ x = unlist(Map(f, time = list(time), r = r, c0 = c0))) egf> rm(f, time) egf> ## Define fitting windows (here, two per time series) egf> data_windows <- egf+ data.frame(country = gl(N, 1L, 2L * N, labels = LETTERS[1:N]), egf+ wave = gl(2L, 10L), egf+ start = c(sample(seq.int(0, 5, 1), N, TRUE), egf+ sample(seq.int(20, 25, 1), N, TRUE)), egf+ end = c(sample(seq.int(15, 20, 1), N, TRUE), egf+ sample(seq.int(35, 40, 1), N, TRUE))) egf> ## Estimate the generative model egf> m1 <- egf+ egf(model = egf_model(curve = "exponential", family = "pois"), egf+ formula_ts = cbind(time, x) ~ country, egf+ formula_windows = cbind(start, end) ~ country, egf+ formula_parameters = ~(1 | country:wave), egf+ data_ts = data_ts, egf+ data_windows = data_windows, egf+ se = TRUE) computing a Hessian matrix ... egf> ## Re-estimate the generative model with: egf> ## * Gaussian prior on beta[1L] egf> ## * LKJ prior on all random effect covariance matrices egf> ## (here there happens to be just one) egf> ## * initial value of 'theta' set explicitly egf> ## * theta[3L] fixed at initial value egf> m2 <- egf+ update(m1, egf+ formula_priors = list(beta[1L] ~ Normal(mu = -3, sigma = 1), egf+ Sigma ~ LKJ(eta = 2)), egf+ init = list(theta = c(log(0.5), log(0.5), 0)), egf+ map = list(theta = 3L)) computing a Hessian matrix ... > > > ## egf_sanitize_formula_ts ######################################## > ## egf_sanitize_formula_windows ######################################## > > l1 <- list(cbind(x, y) ~ 1, + cbind(x, y) ~ g, + cbind(x, y) ~ 1 + g, + cbind(x, y) ~ (g), + cbind(x, y) ~ g:h, + cbind(x, y) ~ I(g + h), + cbind(x, y) ~ I(g * h), + cbind(x - 1, cumsum(y)) ~ g) > l2 <- list(~g, + cbind(x, y) ~ g + h, + cbind(x, y) ~ g * h, + cbind(x, y) ~ 0 + g, + cbind(x, y) ~ g - 1, + cbind(x, y) ~ offset(h) + g, + (cbind(x, y)) ~ g, + cbind(x) ~ g, + cbind(x, y, z) ~ g, + rbind(x, y) ~ g) # i.e., anything other than 'cbind' > > stopifnot(identical(lapply(l1, egf_sanitize_formula_ts), + l1[c(1L, 2L, 2L, 2L, 5:8)])) > for (formula in l2) + assertError(egf_sanitize_formula_ts(formula)) > > > ## egf_sanitize_formula_parameters ##################################### > > model <- egf_model(curve = "exponential", family = "pois") > top <- egf_top(model) > > s <- + function(formula) + egf_sanitize_formula_parameters(formula, top, check = TRUE) > > fp1 <- ~x * y + (z | g) + (zz | g/h) > l1 <- rep.int(expr(simplify_terms(fp1)), 2L) > names(l1) <- c("log(r)", "log(c0)") > > fp2 <- expr(replace(fp1, 2:3, expr(quote(log(r)), fp1[[2L]]))) > l2 <- replace(l1, "log(c0)", expr(~1)) > > fp3 <- c(fp2, expr(log(c0) ~ x)) > l3 <- replace(l2, "log(c0)", expr(~x)) > > stopifnot(exprs = { + identical(s(fp1), l1) + identical(s(fp2), l2) + identical(s(fp3), l3) + }) > assertWarning(s(~0 + x)) > > > ## egf_sanitize_formula_priors ######################################### > > p1 <- Normal(mu = 0, sigma = 1) > p2 <- Normal(mu = 1, sigma = c(0.5, 1)) > p3 <- Normal(mu = -1, sigma = 2) > p4 <- LKJ(eta = 1) > > fp. <- list(foo(bar) ~ p1, + baz ~ p1, + beta ~ p1, + theta[[1L]] ~ p1, + theta[2:3] ~ p2, + theta[-(1:5)] ~ p3, + theta[replace(logical(6L), 4L, TRUE)] ~ p1, + Sigma ~ p4) > > ip. <- list( + top = list(names = c("foo(bar)", "baz"), family = "norm"), + bottom = list( + beta = list(length = 4L, family = "norm"), + theta = list(length = 6L, family = "norm"), + Sigma = list(length = 1L, family = c("lkj", "wishart", "invwishart"), + rows = 4L))) > > priors <- egf_sanitize_formula_priors(formula = fp., info = ip.) > > p2.elt <- + function(i) { + p2[["parameters"]][["sigma"]] <- p2[["parameters"]][["sigma"]][[i]] + p2 + } > > stopifnot(exprs = { + is.list(priors) + length(priors) == 2L + identical(names(priors), c("top", "bottom")) + + identical(priors[["top"]], + `names<-`(list(p1, p1), ip.[["top"]][["names"]])) + identical(priors[["bottom"]], + list(beta = list(p1, p1, p1, p1), + theta = list(p1, p2.elt(1L), p2.elt(2L), p1, NULL, p3), + Sigma = list(p4))) + }) > > > ## egf_make_frame ###################################################### > > model <- egf_model(curve = "exponential", family = "pois") > > formula_ts <- cbind(day, count) ~ country > formula_windows <- cbind(left, right) ~ country > formula_parameters <- list(`log(r)` = ~x1 + (1 | g1) + (1 | g1:g2), + `log(c0)` = ~(1 | g3)) > > data_ts <- data.frame(country = gl(6L, 11L), + day = seq.int(0, 10, by = 1), + count = rpois(11L, 100 * exp(0.04 * 0:10))) > data_windows <- data.frame(country = gl(3L, 2L), + left = rep.int(c(0, 5), 3L), + right = rep.int(c(5, 10), 3L), + x1 = c(5.00, 8.34, -0.57, -7.19, -9.71, 1.25), + x2 = rnorm(6L), + x3 = rnorm(6L), + g1 = c("a", "b", "b", "b", "b", "a"), + g2 = c("c", "d", "d", "d", "c", "c"), + g3 = c("f", "f", "e", "e", "e", "f")) > > subset_ts <- quote(day > 0) > subset_windows <- quote(x1 < 0) > select_windows <- quote(.) > > na_action_ts <- "pass" > na_action_windows <- "omit" > > frame <- egf_make_frame(model = model, + formula_ts = formula_ts, + formula_windows = formula_windows, + formula_parameters = formula_parameters, + data_ts = data_ts, + data_windows = data_windows, + subset_ts = subset_ts, + subset_windows = subset_windows, + select_windows = select_windows, + na_action_ts = na_action_ts, + na_action_windows = na_action_windows) > > stopifnot(exprs = { + is.list(frame) + length(frame) == 4L + identical(names(frame), c("ts", "windows", "parameters", "extra")) + }) > > l1 <- frame[["ts"]] > l1.e <- data.frame(ts = gl(2L, 10L, labels = 2:3), + window = factor(rep.int(c(NA, 1, 2, NA, 3, NA), + c(1L, 4L, 5L, 1L, 4L, 5L)), + labels = sprintf("window_%d", 1:3)), + time = rep.int(seq.int(1, 10, by = 1), 2L), + x = data_ts[["count"]][c(NA, 14:22, NA, 25:33)]) > attr(l1.e, "first") <- c(1L, 5L, 11L) > attr(l1.e, "last") <- c(5L, 10L, 15L) > stopifnot(identical(l1, l1.e)) > > l2 <- frame[["windows"]] > l2.e <- data.frame(ts = factor(c(2, 2, 3)), + window = gl(3L, 1L, labels = sprintf("window_%d", 1:3)), + start = c(1, 5, 1), + end = c(5, 10, 5)) > stopifnot(identical(l2, l2.e)) Error: identical(l2, l2.e) is not TRUE Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.15.3
Check: tests
Result: ERROR Running 'coef.R' [5s] Running 'confint.R' [54s] Running 'datetime.R' [2s] Running 'egf.R' [5s] Running 'egf_enum.R' [2s] Running 'egf_eval.R' [2s] Running 'egf_examples_day_of_week.R' [2s] Running 'egf_examples_excess.R' [2s] Running 'egf_examples_fixed.R' [2s] Running 'egf_examples_random.R' [61s] Running 'egf_link.R' [2s] Running 'egf_misc.R' [6s] Running 'egf_options.R' [2s] Running 'egf_utils.R' [6s] Running 'epidemic.R' [2s] Running 'extract.R' [6s] Running 'fitted.R' [5s] Running 'gi.R' [2s] Running 'include.R' [93s] Running 'language.R' [2s] Running 'prior.R' [2s] Running 'profile.R' [37s] Running 'summary.R' [6s] Running 'utils.R' [2s] Running 'validity.R' [2s] Running 'zzz.R' [2s] Running the tests in 'tests/egf_utils.R' failed. Complete output: > attach(asNamespace("epigrowthfit")) > library(methods) > library(tools) > options(warn = 2L, error = if (interactive()) recover) > example("egf", package = "epigrowthfit"); o.1 <- m1; o.2 <- m2 egf> ## Simulate 'N' incidence time series exhibiting exponential growth egf> set.seed(180149L) egf> N <- 10L egf> f <- function(time, r, c0) { egf+ lambda <- diff(exp(log(c0) + r * time)) egf+ c(NA, rpois(lambda, lambda)) egf+ } egf> time <- seq.int(0, 40, 1) egf> r <- rlnorm(N, -3.2, 0.2) egf> c0 <- rlnorm(N, 6, 0.2) egf> data_ts <- egf+ data.frame(country = gl(N, length(time), labels = LETTERS[1:N]), egf+ time = rep.int(time, N), egf+ x = unlist(Map(f, time = list(time), r = r, c0 = c0))) egf> rm(f, time) egf> ## Define fitting windows (here, two per time series) egf> data_windows <- egf+ data.frame(country = gl(N, 1L, 2L * N, labels = LETTERS[1:N]), egf+ wave = gl(2L, 10L), egf+ start = c(sample(seq.int(0, 5, 1), N, TRUE), egf+ sample(seq.int(20, 25, 1), N, TRUE)), egf+ end = c(sample(seq.int(15, 20, 1), N, TRUE), egf+ sample(seq.int(35, 40, 1), N, TRUE))) egf> ## Estimate the generative model egf> m1 <- egf+ egf(model = egf_model(curve = "exponential", family = "pois"), egf+ formula_ts = cbind(time, x) ~ country, egf+ formula_windows = cbind(start, end) ~ country, egf+ formula_parameters = ~(1 | country:wave), egf+ data_ts = data_ts, egf+ data_windows = data_windows, egf+ se = TRUE) computing a Hessian matrix ... egf> ## Re-estimate the generative model with: egf> ## * Gaussian prior on beta[1L] egf> ## * LKJ prior on all random effect covariance matrices egf> ## (here there happens to be just one) egf> ## * initial value of 'theta' set explicitly egf> ## * theta[3L] fixed at initial value egf> m2 <- egf+ update(m1, egf+ formula_priors = list(beta[1L] ~ Normal(mu = -3, sigma = 1), egf+ Sigma ~ LKJ(eta = 2)), egf+ init = list(theta = c(log(0.5), log(0.5), 0)), egf+ map = list(theta = 3L)) computing a Hessian matrix ... > > > ## egf_sanitize_formula_ts ######################################## > ## egf_sanitize_formula_windows ######################################## > > l1 <- list(cbind(x, y) ~ 1, + cbind(x, y) ~ g, + cbind(x, y) ~ 1 + g, + cbind(x, y) ~ (g), + cbind(x, y) ~ g:h, + cbind(x, y) ~ I(g + h), + cbind(x, y) ~ I(g * h), + cbind(x - 1, cumsum(y)) ~ g) > l2 <- list(~g, + cbind(x, y) ~ g + h, + cbind(x, y) ~ g * h, + cbind(x, y) ~ 0 + g, + cbind(x, y) ~ g - 1, + cbind(x, y) ~ offset(h) + g, + (cbind(x, y)) ~ g, + cbind(x) ~ g, + cbind(x, y, z) ~ g, + rbind(x, y) ~ g) # i.e., anything other than 'cbind' > > stopifnot(identical(lapply(l1, egf_sanitize_formula_ts), + l1[c(1L, 2L, 2L, 2L, 5:8)])) > for (formula in l2) + assertError(egf_sanitize_formula_ts(formula)) > > > ## egf_sanitize_formula_parameters ##################################### > > model <- egf_model(curve = "exponential", family = "pois") > top <- egf_top(model) > > s <- + function(formula) + egf_sanitize_formula_parameters(formula, top, check = TRUE) > > fp1 <- ~x * y + (z | g) + (zz | g/h) > l1 <- rep.int(expr(simplify_terms(fp1)), 2L) > names(l1) <- c("log(r)", "log(c0)") > > fp2 <- expr(replace(fp1, 2:3, expr(quote(log(r)), fp1[[2L]]))) > l2 <- replace(l1, "log(c0)", expr(~1)) > > fp3 <- c(fp2, expr(log(c0) ~ x)) > l3 <- replace(l2, "log(c0)", expr(~x)) > > stopifnot(exprs = { + identical(s(fp1), l1) + identical(s(fp2), l2) + identical(s(fp3), l3) + }) > assertWarning(s(~0 + x)) > > > ## egf_sanitize_formula_priors ######################################### > > p1 <- Normal(mu = 0, sigma = 1) > p2 <- Normal(mu = 1, sigma = c(0.5, 1)) > p3 <- Normal(mu = -1, sigma = 2) > p4 <- LKJ(eta = 1) > > fp. <- list(foo(bar) ~ p1, + baz ~ p1, + beta ~ p1, + theta[[1L]] ~ p1, + theta[2:3] ~ p2, + theta[-(1:5)] ~ p3, + theta[replace(logical(6L), 4L, TRUE)] ~ p1, + Sigma ~ p4) > > ip. <- list( + top = list(names = c("foo(bar)", "baz"), family = "norm"), + bottom = list( + beta = list(length = 4L, family = "norm"), + theta = list(length = 6L, family = "norm"), + Sigma = list(length = 1L, family = c("lkj", "wishart", "invwishart"), + rows = 4L))) > > priors <- egf_sanitize_formula_priors(formula = fp., info = ip.) > > p2.elt <- + function(i) { + p2[["parameters"]][["sigma"]] <- p2[["parameters"]][["sigma"]][[i]] + p2 + } > > stopifnot(exprs = { + is.list(priors) + length(priors) == 2L + identical(names(priors), c("top", "bottom")) + + identical(priors[["top"]], + `names<-`(list(p1, p1), ip.[["top"]][["names"]])) + identical(priors[["bottom"]], + list(beta = list(p1, p1, p1, p1), + theta = list(p1, p2.elt(1L), p2.elt(2L), p1, NULL, p3), + Sigma = list(p4))) + }) > > > ## egf_make_frame ###################################################### > > model <- egf_model(curve = "exponential", family = "pois") > > formula_ts <- cbind(day, count) ~ country > formula_windows <- cbind(left, right) ~ country > formula_parameters <- list(`log(r)` = ~x1 + (1 | g1) + (1 | g1:g2), + `log(c0)` = ~(1 | g3)) > > data_ts <- data.frame(country = gl(6L, 11L), + day = seq.int(0, 10, by = 1), + count = rpois(11L, 100 * exp(0.04 * 0:10))) > data_windows <- data.frame(country = gl(3L, 2L), + left = rep.int(c(0, 5), 3L), + right = rep.int(c(5, 10), 3L), + x1 = c(5.00, 8.34, -0.57, -7.19, -9.71, 1.25), + x2 = rnorm(6L), + x3 = rnorm(6L), + g1 = c("a", "b", "b", "b", "b", "a"), + g2 = c("c", "d", "d", "d", "c", "c"), + g3 = c("f", "f", "e", "e", "e", "f")) > > subset_ts <- quote(day > 0) > subset_windows <- quote(x1 < 0) > select_windows <- quote(.) > > na_action_ts <- "pass" > na_action_windows <- "omit" > > frame <- egf_make_frame(model = model, + formula_ts = formula_ts, + formula_windows = formula_windows, + formula_parameters = formula_parameters, + data_ts = data_ts, + data_windows = data_windows, + subset_ts = subset_ts, + subset_windows = subset_windows, + select_windows = select_windows, + na_action_ts = na_action_ts, + na_action_windows = na_action_windows) > > stopifnot(exprs = { + is.list(frame) + length(frame) == 4L + identical(names(frame), c("ts", "windows", "parameters", "extra")) + }) > > l1 <- frame[["ts"]] > l1.e <- data.frame(ts = gl(2L, 10L, labels = 2:3), + window = factor(rep.int(c(NA, 1, 2, NA, 3, NA), + c(1L, 4L, 5L, 1L, 4L, 5L)), + labels = sprintf("window_%d", 1:3)), + time = rep.int(seq.int(1, 10, by = 1), 2L), + x = data_ts[["count"]][c(NA, 14:22, NA, 25:33)]) > attr(l1.e, "first") <- c(1L, 5L, 11L) > attr(l1.e, "last") <- c(5L, 10L, 15L) > stopifnot(identical(l1, l1.e)) > > l2 <- frame[["windows"]] > l2.e <- data.frame(ts = factor(c(2, 2, 3)), + window = gl(3L, 1L, labels = sprintf("window_%d", 1:3)), + start = c(1, 5, 1), + end = c(5, 10, 5)) > stopifnot(identical(l2, l2.e)) Error: identical(l2, l2.e) is not TRUE Execution halted Flavor: r-devel-windows-x86_64

Version: 0.15.3
Check: installed package size
Result: NOTE installed size is 94.3Mb sub-directories of 1Mb or more: libs 93.7Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.15.3
Check: tests
Result: ERROR Running 'coef.R' [5s] Running 'confint.R' [54s] Running 'datetime.R' [2s] Running 'egf.R' [5s] Running 'egf_enum.R' [2s] Running 'egf_eval.R' [2s] Running 'egf_examples_day_of_week.R' [1s] Running 'egf_examples_excess.R' [2s] Running 'egf_examples_fixed.R' [2s] Running 'egf_examples_random.R' [7s] Running 'egf_link.R' [1s] Running 'egf_misc.R' [6s] Running 'egf_options.R' [1s] Running 'egf_utils.R' [6s] Running 'epidemic.R' [2s] Running 'extract.R' [5s] Running 'fitted.R' [5s] Running 'gi.R' [2s] Running 'include.R' [95s] Running 'language.R' [1s] Running 'prior.R' [2s] Running 'profile.R' [38s] Running 'summary.R' [5s] Running 'utils.R' [1s] Running 'validity.R' [2s] Running 'zzz.R' [2s] Running the tests in 'tests/egf_examples_random.R' failed. Complete output: > library(epigrowthfit) > options(warn = 2L, error = if (interactive()) recover, egf.cores = 2L) > > > ## exponential ######################################################### > > r <- log(2) / 20 > c0 <- 100 > s <- 0.2 > > mu <- log(c(r, c0)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "exponential", family = "pois"), + nsim = 20L, + seed = 775494L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-05 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 5e-02) + }) > > > ## subexponential ###################################################### > > alpha <- log(2) / 20 > c0 <- 100 > p <- 0.95 > s <- 0.2 > > mu <- c(log(alpha), log(c0), qlogis(p)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "subexponential", family = "pois"), + nsim = 20L, + seed = 653927L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(beta[3L] ~ Normal(mu = qlogis(p), sigma = 0.05), + theta[3L] ~ Normal(mu = log(s), sigma = 0.25), + Sigma ~ LKJ(eta = 2))) Flavor: r-release-windows-x86_64

Version: 0.15.3
Check: tests
Result: ERROR Running 'coef.R' [7s] Running 'confint.R' [67s] Running 'datetime.R' [2s] Running 'egf.R' [6s] Running 'egf_enum.R' [2s] Running 'egf_eval.R' [2s] Running 'egf_examples_day_of_week.R' [2s] Running 'egf_examples_excess.R' [2s] Running 'egf_examples_fixed.R' [3s] Running 'egf_examples_random.R' [53s] Running 'egf_link.R' [2s] Running 'egf_misc.R' [8s] Running 'egf_options.R' [2s] Running 'egf_utils.R' [8s] Running 'epidemic.R' [2s] Running 'extract.R' [7s] Running 'fitted.R' [6s] Running 'gi.R' [2s] Running 'include.R' [130s] Running 'language.R' [2s] Running 'prior.R' [2s] Running 'profile.R' [50s] Running 'summary.R' [7s] Running 'utils.R' [2s] Running 'validity.R' [2s] Running 'zzz.R' [3s] Running the tests in 'tests/egf_examples_random.R' failed. Complete output: > library(epigrowthfit) > options(warn = 2L, error = if (interactive()) recover, egf.cores = 2L) > > > ## exponential ######################################################### > > r <- log(2) / 20 > c0 <- 100 > s <- 0.2 > > mu <- log(c(r, c0)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "exponential", family = "pois"), + nsim = 20L, + seed = 775494L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-05 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 5e-02) + }) > > > ## subexponential ###################################################### > > alpha <- log(2) / 20 > c0 <- 100 > p <- 0.95 > s <- 0.2 > > mu <- c(log(alpha), log(c0), qlogis(p)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "subexponential", family = "pois"), + nsim = 20L, + seed = 653927L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(beta[3L] ~ Normal(mu = qlogis(p), sigma = 0.05), + theta[3L] ~ Normal(mu = log(s), sigma = 0.25), + Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-04 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 2e-02) + }) > > > ## gompertz ############################################################ > > alpha <- log(2) / 20 > tinfl <- 100 > K <- 25000 > s <- 0.2 > > mu <- log(c(alpha, tinfl, K)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "gompertz", family = "pois"), + nsim = 20L, + seed = 685399L, + mu = mu, + Sigma = Sigma, + cstart = 10) > oo <- options(warn = 1L) # FIXME: diagnose NA/NaN function evaluation > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) > options(oo) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 5e-04 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 5e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 2e-02) + }) > > > ## logistic ############################################################ > > r <- log(2) / 20 > tinfl <- 100 > K <- 25000 > s <- 0.2 > > mu <- log(c(r, tinfl, K)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "logistic", family = "pois"), + nsim = 20L, + seed = 397981L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(Sigma ~ LKJ(eta = 2))) > > p1 <- as.list(coef(zz)) > p2 <- as.list(coef(mm)) > > stopifnot(exprs = { + max(abs(mm[["gradient"]])) < 1e-02 + all.equal(p1[["beta"]], p2[["beta"]], tolerance = 1e-02) + all.equal(theta2cov(p1[["theta"]]), theta2cov(p2[["theta"]]), tolerance = 2e-02) + }) > > > ## richards ############################################################ > > r <- log(2) / 20 > tinfl <- 100 > K <- 25000 > a <- 1.005 > s <- 0.2 > > mu <- log(c(r, tinfl, K, a)) > Sigma <- diag(rep.int(s^2, length(mu))) > > zz <- simulate(egf_model(curve = "richards", family = "pois"), + nsim = 20L, + seed = 949642L, + mu = mu, + Sigma = Sigma, + cstart = 10) > mm <- egf(zz, + formula_priors = list(beta[4L] ~ Normal(mu = log(a), sigma = 0.005), + theta[4L] ~ Normal(mu = log(s), sigma = 0.25), + Sigma ~ LKJ(eta = 2))) Error in nlminb(start = par, objective = fn, gradient = gr, control = control, : (converted from warning) NA/NaN function evaluation Calls: egf ... <Anonymous> -> egf.egf_model -> do.call -> <Anonymous> -> nlminb Execution halted Flavor: r-oldrel-windows-x86_64