inst/extdata/micem1.for.R

micem1.for <-
list(`Rows in stage` = list(NULL, NULL, NULL, NULL, c(1L, 12L, 
7L, 2L, 13L), c(2L, 3L, 7L, 8L, 12L, 13L), c(1L, 2L, 3L, 7L, 
8L, 12L, 13L), c(1L, 2L, 3L, 6L, 7L, 8L, 12L, 13L), c(1L, 2L, 
3L, 5L, 6L, 7L, 8L, 12L, 13L), c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 
8L, 12L, 13L), c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 12L, 13L
), c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 11L, 12L, 13L), 1:13), 
    Family = structure(list(family = "binomial", link = "logit", 
        linkfun = function (mu) 
        .Call(C_logit_link, mu), linkinv = function (eta) 
        .Call(C_logit_linkinv, eta), variance = function (mu) 
        mu * (1 - mu), dev.resids = function (y, mu, wt) 
        .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y, 
            n, mu, wt, dev) 
        {
            m <- if (any(n > 1)) 
                n
            else wt
            -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m * 
                y), round(m), mu, log = TRUE))
        }, mu.eta = function (eta) 
        .Call(C_logit_mu_eta, eta), initialize = quote({
            if (NCOL(y) == 1) {
                if (is.factor(y)) 
                  y <- y != levels(y)[1L]
                n <- rep.int(1, nobs)
                y[weights == 0] <- 0
                if (any(y < 0 | y > 1)) 
                  stop("y values must be 0 <= y <= 1")
                mustart <- (weights * y + 0.5)/(weights + 1)
                m <- weights * y
                if ("binomial" == "binomial" && any(abs(m - round(m)) > 
                  0.001)) 
                  warning(gettextf("non-integer #successes in a %s glm!", 
                    "binomial"), domain = NA)
            }
            else if (NCOL(y) == 2) {
                if ("binomial" == "binomial" && any(abs(y - round(y)) > 
                  0.001)) 
                  warning(gettextf("non-integer counts in a %s glm!", 
                    "binomial"), domain = NA)
                n <- (y1 <- y[, 1L]) + y[, 2L]
                y <- y1/n
                if (any(n0 <- n == 0)) 
                  y[n0] <- 0
                weights <- weights * n
                mustart <- (n * y + 0.5)/(n + 1)
            }
            else stop(gettextf("for the '%s' family, y must be a vector of 0 and 1's\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures", 
                "binomial"), domain = NA)
        }), validmu = function (mu) 
        all(is.finite(mu)) && all(mu > 0 & mu < 1), valideta = function (eta) 
        TRUE, simulate = function (object, nsim) 
        {
            ftd <- fitted(object)
            n <- length(ftd)
            ntot <- n * nsim
            wts <- object$prior.weights
            if (any(wts%%1 != 0)) 
                stop("cannot simulate from non-integer prior.weights")
            if (!is.null(m <- object$model)) {
                y <- model.response(m)
                if (is.factor(y)) {
                  yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd), 
                    labels = levels(y))
                  split(yy, rep(seq_len(nsim), each = n))
                }
                else if (is.matrix(y) && ncol(y) == 2) {
                  yy <- vector("list", nsim)
                  for (i in seq_len(nsim)) {
                    Y <- rbinom(n, size = wts, prob = ftd)
                    YY <- cbind(Y, wts - Y)
                    colnames(YY) <- colnames(y)
                    yy[[i]] <- YY
                  }
                  yy
                }
                else rbinom(ntot, size = wts, prob = ftd)/wts
            }
            else rbinom(ntot, size = wts, prob = ftd)/wts
        }), class = "family"), `Number of model parameters` = 3L, 
    `Fixed parameter estimates` = structure(list(m = 1:13, `(Intercept)` = c(0, 
    0, 0, 0, -5.2170560238124279, -5.1543128082172132, -5.2633607247872733, 
    -5.2188440239571374, -5.2137569221022115, -5.2537897902650101, 
    -5.5629000834780111, -5.4020575127524477, -5.1994786508089019
    ), logdose = c(0, 0, 0, 0, 2.1931788281792155, 2.1822518551479178, 
    2.2211900899285091, 2.1956838399497705, 2.1818029621545185, 
    2.189420205844463, 2.3167232511312115, 2.2504654161378723, 
    2.1670668900941292), prep = c(0, 0, 0, 0, -1.1379165290656961, 
    -1.1656336277601194, -1.1813970334165849, -1.1441581488728725, 
    -1.1047505801442437, -1.0891347024272062, -1.2567297771557207, 
    -1.055757452657704, -0.92580231352391595)), class = "data.frame", row.names = c(NA, 
    -13L)), `Studentized deviance residuals` = structure(list(
        c(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, 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, 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, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
        12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 
        13L, 13L, 13L, 13L, 13L, 13L), c(1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 
        6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L), c(-0.011556587243762295, 
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        0.0036886128043492894, -0.027045609878369542, 0.14868666212425735, 
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        0.00071181997853358991, 0.025001839115046331, 0.020805141545657713, 
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        0.11508897119712225, 0.076845536985569785, -0.0098619715938985664, 
        -0.024290119079168337), c(0, 0, 0, 0, 0.17019028542189174, 
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        0, 0, 0, 0, 0.17019028542189174, 0.10861046172355526, 
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        0.20703977429406278, 0.31415267082938964, 0.45971985136818999, 
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        0.17019028542189174, 0.10861046172355526, 0.13248317294766421, 
        0.14663364744554477, 0.18168784274295152, 0.20703977429406278, 
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        0, 0, 0, 0, 0.17019028542189174, 0.10861046172355526, 
        0.13248317294766421, 0.14663364744554477, 0.18168784274295152, 
        0.20703977429406278, 0.31415267082938964, 0.45971985136818999, 
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        0.18168784274295152, 0.20703977429406278, 0.31415267082938964, 
        0.45971985136818999, 0.53359537356161657, 0, 0, 0, 0, 
        0.17019028542189174, 0.10861046172355526, 0.13248317294766421, 
        0.14663364744554477, 0.18168784274295152, 0.20703977429406278, 
        0.31415267082938964, 0.45971985136818999, 0.53359537356161657
        ), c(-Inf, Inf, Inf, -Inf, -0.19461388559398021, -0.11446935753446984, 
        -0.0055943274078398024, 0.067981372627813286, -0.24970750996386787, 
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        Inf, -Inf, -0.2305188972688913, -0.17307618167108671, 
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        Inf, -Inf, -0.15804686608834559, -0.063622603483285606, 
        0.030931608371126285, 0.091395031113260111, -0.25695606930625864, 
        0.57128370194089562, 0.27563787935760165, 0.015752619682596475, 
        -0.012838086879070334, -Inf, Inf, Inf, -Inf, -0.12896016304217126, 
        -0.032285104730682967, 0.050856396316705799, 0.10149752173891274, 
        -0.25209258159066145, 0.57688027514605578, 0.27881331633922446, 
        0.016302384804952851, -0.013286135047951255, Inf, Inf, 
        Inf, -Inf, -0.15368352432760413, -0.13359960473785662, 
        -0.040230530737237709, 0.025155295995205513, -0.14885756509659898, 
        0.71815506286765307, 0.38020507692292077, 0.061873910434689351, 
        0.0043691940133545387, Inf, Inf, Inf, -Inf, -0.14076719449644429, 
        -0.081170714903316746, 0.0066722437489523841, 0.064059498939255569, 
        -0.25179423676354601, 0.55587855806710385, 0.2446120759778711, 
        -0.021452133434194699, -0.045521607350224619)), .Names = c("m", 
    "obs", "devresid", NA, NA), row.names = c("2", "3", "4", 
    "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "21", 
    "31", "41", "51", "61", "71", "81", "91", "101", "111", "121", 
    "131", "141", "22", "32", "42", "52", "62", "72", "82", "92", 
    "102", "112", "122", "132", "142", "23", "33", "43", "53", 
    "63", "73", "83", "93", "103", "113", "123", "133", "143", 
    "24", "34", "44", "54", "64", "74", "84", "94", "104", "114", 
    "124", "134", "144", "25", "35", "45", "55", "65", "75", 
    "85", "95", "105", "115", "125", "135", "145", "26", "36", 
    "46", "56", "66", "76", "86", "96", "106", "116", "126", 
    "136", "146", "27", "37", "47", "57", "67", "77", "87", "97", 
    "107", "117", "127", "137", "147"), class = "data.frame"), 
    `Residual deviance` = c(0, 0, 0, 0, 0.070094554936652786, 
    0.042878808629687827, 0.090565696053336794, 0.1326363083101868, 
    0.27326811475926771, 0.3838321728132022, 1.1086845415844579, 
    2.6666248039042637, 4.277235090456224), `Null deviance` = c(0, 
    0, 0, 0, 48.04360640548586, 46.202138803250769, 70.446276616427113, 
    74.853924359677933, 74.854990170358946, 76.912161088831127, 
    120.97154757114782, 121.41282675353065, 124.59527356116526
    ), PhiHat = c(0, 0, 0, 0, 0.035047277468326393, 0.014292936209895942, 
    0.022641424013334199, 0.026527261662037359, 0.045544685793211283, 
    0.054833167544743169, 0.13858556769805724, 0.29629164487825155, 
    0.4277235090456224), `Deviance residuals and augments` = structure(list(
        m = c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 
        6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 
        7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 
        9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 
        10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 
        11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 
        12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 
        13, 13, 13, 13, 13, 13), AorD = c("D", "D", "A", "A", 
        "A", "A", "D", "A", "A", "A", "A", "D", "D", "A", "D", 
        "D", "A", "A", "A", "D", "D", "A", "A", "A", "D", "D", 
        "D", "D", "D", "A", "A", "A", "D", "D", "A", "A", "A", 
        "D", "D", "D", "D", "D", "A", "A", "D", "D", "D", "A", 
        "A", "A", "D", "D", "D", "D", "D", "A", "D", "D", "D", 
        "D", "A", "A", "A", "D", "D", "D", "D", "D", "D", "D", 
        "D", "D", "D", "A", "A", "A", "D", "D", "D", "D", "D", 
        "D", "D", "D", "D", "D", "D", "A", "A", "D", "D", "D", 
        "D", "D", "D", "D", "D", "D", "D", "D", "A", "D", "D", 
        "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", "D", 
        "D", "D", "D"), obs = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
        9L, 10L, 11L, 12L, 13L), deviance = c(-0.17659526947778575, 
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        -0.40963443515157588, -0.15991674922364227, -0.011522249279278494, 
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        -1.0026519182509945, 1.5782122861924055, 1.1915641791303915, 
        0.1029909020038367, -0.11146488634309797, -0.18150079150828363, 
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        1.1470610459143704, 0.092821698024644045, -0.10037200456323514, 
        -0.14428541383838081, 0.19534103305031869, 0.14166505714204269, 
        -0.36922396492569221, -0.33215122512065298, -0.088448580426521053, 
        0.063296592001903698, 0.23569232618007974, -1.0917795796899268, 
        1.4940044307056108, 1.1228146091720055, 0.087282383878490952, 
        -0.094337654524409467, -0.087129020507979923, 0.26498458611238257, 
        0.21131964427050923, -0.29942136148226101, -0.27070560585084047, 
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    1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 1, 2, 3, 4, 5, 6, 
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        "Observation", "leverage"))), `t statistics` = structure(list(
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        -7.2435226703460431, -8.7645012776914299, -8.924588655438626, 
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        -4.0237101835736748)), class = "data.frame", row.names = c(NA, 
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        response.cols = c(4, 8), indep.cols = c(9, 3), family = binomial("logit"), 
        data = micem1)))

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forsearch documentation built on April 4, 2025, 5:52 a.m.