tests/testthat/test-AdamByHand.R

In nickbrazeau/discent: Estimation of Deme Inbreeding Spatial Coefficients with Gradient Descent

test_that("Fi adam by hand", {
  # sim data
  data("IBD_simulation_data", package = "discent")
  dat <- IBD_simulation_data

  # start params
  our_start_params <- rep(0.2, 3)
  names(our_start_params) <- 1:3
  our_start_params <- c(our_start_params, "m" = 1e3)

  # tidy date and calculate gradient for F1
  input <- dat %>%
    dplyr::filter(deme1 != deme2) %>%
    dplyr::filter(deme1 == 1 | deme2 == 1)


  input <- input %>%
    dplyr::mutate(gendist = ifelse(gendist > 0.999, 0.999,
                                   ifelse(gendist < 0.001, 0.001,
                                          gendist))) %>% # reasonable bounds on logit
    dplyr::mutate(gendist = logit(gendist))


  # now run model
  inputdisc <- dat %>%
    dplyr::filter(deme1 != deme2)
  ret <- deme_inbreeding_spcoef_vanilla(discdat = inputdisc,
                                        start_params = our_start_params,
                                        learningrate = 1e-3,
                                        b1 = 0.9,
                                        b2 = 0.999,
                                        e = 1e-8,
                                        steps = 1e3,
                                        normalize_geodist = F,
                                        report_progress = T,
                                        return_verbose = T)
  # back out for Fi adam
  b1 <- 0.9
  b2 <- 0.999
  e <- 1e-8
  learningrate <- 1e-3
  mt_f1 <- b1 * 0 + (1-b1) * ret$fi_gradtraj[2,1]
  vt_f1 <- b2 * 0 + (1-b2) * (ret$fi_gradtraj[2,1]^2)
  mt_f1hat <- mt_f1 / (1 - b1^1)
  vt_f1hat <- vt_f1 / (1 - b2^1)
  fnew1 = logit(ret$fi_run[1,1]) - learningrate * (mt_f1hat/(sqrt(vt_f1hat) + e))
  fnew1 <- expit(fnew1)
  ret$fi_run[2,1]

  # test out
  testthat::expect_equal(fnew1, ret$fi_run[2,1])

})


test_that("M adam by hand", {
  # sim data
  data("IBD_simulation_data", package = "discent")
  dat <- IBD_simulation_data

  # start params
  our_start_params <- rep(0.2, 3)
  names(our_start_params) <- 1:3
  our_start_params <- c(our_start_params, "m" = 1e3)

  # tidy date and calculate gradient for F1
  input <- dat %>%
    dplyr::filter(deme1 != deme2) %>%
    dplyr::filter(deme1 == 1 | deme2 == 1)


  input <- input %>%
    dplyr::mutate(gendist = ifelse(gendist > 0.999, 0.999,
                                   ifelse(gendist < 0.001, 0.001,
                                          gendist))) %>% # reasonable bounds on logit
    dplyr::mutate(gendist = logit(gendist))

  # now run model
  inputdisc <- dat %>%
    dplyr::filter(deme1 != deme2)
  ret <- deme_inbreeding_spcoef_vanilla(discdat = inputdisc,
                                        start_params = our_start_params,
                                        learningrate = 1e-3,
                                        b1 = 0.9,
                                        b2 = 0.999,
                                        e = 1e-8,
                                        steps = 1e3,
                                        normalize_geodist = F,
                                        report_progress = T,
                                        return_verbose = T)
  # back out for m adam
  b1 <- 0.9
  b2 <- 0.999
  e <- 1e-8
  learningrate <- 1e-5
  mt_m <- b1 * 0 + (1-b1) * ret$fi_gradtraj[2,1]
  vt_m <- b2 * 0 + (1-b2) * (ret$fi_gradtraj[2,1]^2)
  mt_mhat <- mt_m / (1 - b1^1)
  vt_mhat <- vt_m / (1 - b2^1)
  mnew1 <- ret$m_run[1] - learningrate * (mt_mhat/(sqrt(vt_mhat) + e))
  ret$m_run[1]

  # test out
  testthat::expect_equal(mnew1, ret$m_run[1])

})