# helper functions for working with ABAP data

#modified version to include covariates
abapToUnmarked_single2 <- function (abap_data, pentads = NULL, cap_visits = NULL, siteCovs = NULL, siteCovs_clean = TRUE)
{
  if (!requireNamespace("unmarked", quietly = TRUE)) {
    stop("Package unmarked doesn't seem to be installed. Please install before using this function.",
         call. = FALSE)
  }
  pentad_id <- unique(abap_data$Pentad)
  max_visits <- abap_data %>% dplyr::count(Pentad) %>% dplyr::pull(n) %>%
    max()
  if (!is.null(pentads)) {
    sf::st_agr(pentads) = "constant"
    pentad_xy <- pentads %>% dplyr::filter(pentad %in% pentad_id) %>%
      dplyr::arrange(pentad) %>% sf::st_centroid() %>%
      sf::st_coordinates() %>% as.data.frame() %>% dplyr::rename_all(tolower)
  }
  vpad <- rep(NA, max_visits)
  format_df <- abap_data %>% dplyr::select(Pentad, Spp, TotalHours,
                                           StartDate) %>% dplyr::mutate(Spp = ifelse(Spp == "-",
                                                                                     0L, 1L), julian_day = lubridate::yday(StartDate)) %>%
    dplyr::nest_by(Pentad) %>% dplyr::arrange(Pentad) %>%
    dplyr::mutate(hourpad = list(head(c(data$TotalHours,
                                        vpad), max_visits)), jdaypad = list(head(c(data$julian_day,
                                                                                   vpad), max_visits)))
  det_hist <- format_df %>% dplyr::mutate(dets = list(head(c(data$Spp,
                                                             vpad), max_visits)))
  Y <- do.call("rbind", det_hist$dets)
  rownames(Y) <- format_df$Pentad
  obs_hours <- do.call("rbind", format_df$hourpad)
  rownames(obs_hours) <- format_df$Pentad
  obs_jday <- do.call("rbind", format_df$jdaypad)
  rownames(obs_jday) <- format_df$Pentad

  n_sites <- nrow(Y)

  #reduce the data to a max number of visits (cap_visits)
  Y_red        <- matrix(NA_integer_, n_sites, cap_visits)
  hours_red    <- matrix(NA_real_,    n_sites, cap_visits)
  jday_red     <- matrix(NA_real_,    n_sites, cap_visits)

  for (i in seq_len(n_sites)) {

    valid_cols <- which(!is.na(Y[i, ]))

    if (length(valid_cols) == 0L) next

    if (length(valid_cols) > cap_visits) {
      valid_cols <- valid_cols[seq_len(cap_visits)]
      # or sample(valid_cols, cap_visits)
    }

    n_keep <- length(valid_cols)

    Y_red[i, seq_len(n_keep)]     <- Y[i, valid_cols]
    hours_red[i, seq_len(n_keep)] <- obs_hours[i, valid_cols]
    jday_red[i, seq_len(n_keep)]  <- obs_jday[i, valid_cols]
  }

  #add totalspp as another covariate
  #TotalSpp_mat is a pentad by occasion matrix showing the total spp for each visit
  format_totalspp <- abap_data %>%
    select(Pentad, TotalSpp) %>%
    nest_by(Pentad) %>%
    arrange(Pentad) %>%
    mutate(totalspp_pad = list(head(c(data$TotalSpp, vpad), cap_visits)))

  TotalSpp_mat <- do.call("rbind", format_totalspp$totalspp_pad)
  rownames(TotalSpp_mat) <- format_totalspp$Pentad

  #drop sites with NAs for any siteCovs
  #also need to drop the correct row in other objs
  if (siteCovs_clean && !is.null(siteCovs)){
    keep <- complete.cases(siteCovs)
    siteCovs <- siteCovs[keep, ]
    pentad_xy <- pentad_xy[keep,]
    Y_red <- Y_red[keep, ]
    hours_red <- hours_red[keep,]
    jday_red <- jday_red[keep,]
    TotalSpp_mat <- TotalSpp_mat[keep,]
    n_sites <- dim(Y_red)[1]
  }

  obs_covs <- list(hours = as.data.frame(hours_red), jday = as.data.frame(jday_red), totalspp = as.data.frame(TotalSpp_mat))

  if (is.null(siteCovs)) { #no extra sitecovs (argument = F)
    if (!is.null(pentads)) {
      umf_abap <- unmarked::unmarkedFrameOccu(y = Y_red, siteCovs = pentad_xy,
                                              obsCovs = obs_covs)
    }
    else {
      umf_abap <- unmarked::unmarkedFrameOccu(y = Y_red, obsCovs = obs_covs)
    }
  }
  else { #extra sitecovs provided
    if (!is.null(pentads)) { #pentads provided
      site_covs <- cbind(pentad_xy, siteCovs)
      umf_abap <- unmarked::unmarkedFrameOccu(y = Y_red, siteCovs = site_covs,
                                              obsCovs = obs_covs)
    }
    else {
      umf_abap <- unmarked::unmarkedFrameOccu(y = Y_red, siteCovs = siteCovs,
                                              obsCovs = obs_covs)
    }
  }
  return(umf_abap)
}