Revert "Merge branch 'v0.3' into master"

This reverts commit 011a292427eef689a4770ce10b964a4442d9e7ea, reversing
changes made to 5d453c1d05d356e08b5dee19dcce89cd57b53f4a.

.travis.yml

@@ -1,18 +1,11 @@
-matrix:
-  include:
-    - language: python
-      python:
-        - "2.7"
-        - "3.6"
-      
-      install:
-        - pip install --upgrade pip
-        - pip install -U -r python/requirements.txt
-      
-      script:
-        - cd python && python setup.py develop test
-    - language: R
-      sudo: false
-      cache: packages
-      before_install:
-        - cd R
+language: python
+python:
+  - "2.7"
+  - "3.6"
+
+install:
+  - pip install --upgrade pip
+  - pip install -U -r python/requirements.txt
+
+script:
+  - cd python && python setup.py develop test

R/DESCRIPTION

@@ -16,16 +16,13 @@ Depends:
     Rcpp (>= 0.12.0)
 Imports:
     dplyr (>= 0.5.0),
-    dygraphs,
     extraDistr,
     ggplot2,
     grid,
     rstan (>= 2.14.0),
     scales,
     stats,
-    tidyr (>= 0.6.1),
-    utils,
-    xts
+    tidyr (>= 0.6.1)
 Suggests:
     knitr,
     testthat,

R/NAMESPACE

@@ -5,9 +5,7 @@ S3method(predict,prophet)
 export(add_regressor)
 export(add_seasonality)
 export(cross_validation)
-export(dyplot.prophet)
 export(fit.prophet)
-export(layer_changepoints)
 export(make_future_dataframe)
 export(plot_forecast_component)
 export(predictive_samples)

R/R/diagnostics.R

@@ -26,7 +26,7 @@ generate_cutoffs <- function(df, horizon, k, period) {
     stop('Less data than horizon.')
   }
   tzone <- attr(cutoff, "tzone")  # Timezone is wiped by putting in array
-  result <- cutoff
+  result <- c(cutoff)
   if (k > 1) {
     for (i in 2:k) {
       cutoff <- cutoff - period
@@ -74,7 +74,7 @@ simulated_historical_forecasts <- function(model, horizon, units, k,
   }
   cutoffs <- generate_cutoffs(df, horizon, k, period)
   predicts <- data.frame()
-  for (i in seq_along(cutoffs)) {
+  for (i in 1:length(cutoffs)) {
     cutoff <- cutoffs[i]
     # Copy the model
     m <- prophet_copy(model, cutoff)
@@ -84,7 +84,7 @@ simulated_historical_forecasts <- function(model, horizon, units, k,
     # Calculate yhat
     df.predict <- dplyr::filter(df, ds > cutoff, ds <= cutoff + horizon)
     # Get the columns for the future dataframe
-    columns <- 'ds'
+    columns <- c('ds')
     if (m$growth == 'logistic') {
       columns <- c(columns, 'cap')
       if (m$logistic.floor) {

R/R/plot.R

@@ -1,374 +0,0 @@
-#' Merge history and forecast for plotting.
-#'
-#' @param m Prophet object.
-#' @param fcst Data frame returned by prophet predict.
-#'
-#' @importFrom dplyr "%>%"
-#' @keywords internal
-df_for_plotting <- function(m, fcst) {
-  # Make sure there is no y in fcst
-  fcst$y <- NULL
-  df <- m$history %>%
-    dplyr::select(ds, y) %>%
-    dplyr::full_join(fcst, by = "ds") %>%
-    dplyr::arrange(ds)
-  return(df)
-}
-
-#' Plot the prophet forecast.
-#'
-#' @param x Prophet object.
-#' @param fcst Data frame returned by predict(m, df).
-#' @param uncertainty Boolean indicating if the uncertainty interval for yhat
-#'  should be plotted. Must be present in fcst as yhat_lower and yhat_upper.
-#' @param plot_cap Boolean indicating if the capacity should be shown in the
-#'  figure, if available.
-#' @param xlabel Optional label for x-axis
-#' @param ylabel Optional label for y-axis
-#' @param ... additional arguments
-#'
-#' @return A ggplot2 plot.
-#'
-#' @examples
-#' \dontrun{
-#' history <- data.frame(ds = seq(as.Date('2015-01-01'), as.Date('2016-01-01'), by = 'd'),
-#'                       y = sin(1:366/200) + rnorm(366)/10)
-#' m <- prophet(history)
-#' future <- make_future_dataframe(m, periods = 365)
-#' forecast <- predict(m, future)
-#' plot(m, forecast)
-#' }
-#'
-#' @export
-plot.prophet <- function(x, fcst, uncertainty = TRUE, plot_cap = TRUE,
-                         xlabel = 'ds', ylabel = 'y', ...) {
-  df <- df_for_plotting(x, fcst)
-  gg <- ggplot2::ggplot(df, ggplot2::aes(x = ds, y = y)) +
-    ggplot2::labs(x = xlabel, y = ylabel)
-  if (exists('cap', where = df) && plot_cap) {
-    gg <- gg + ggplot2::geom_line(
-      ggplot2::aes(y = cap), linetype = 'dashed', na.rm = TRUE)
-  }
-  if (x$logistic.floor && exists('floor', where = df) && plot_cap) {
-    gg <- gg + ggplot2::geom_line(
-      ggplot2::aes(y = floor), linetype = 'dashed', na.rm = TRUE)
-  }
-  if (uncertainty && exists('yhat_lower', where = df)) {
-    gg <- gg +
-      ggplot2::geom_ribbon(ggplot2::aes(ymin = yhat_lower, ymax = yhat_upper),
-                           alpha = 0.2,
-                           fill = "#0072B2",
-                           na.rm = TRUE)
-  }
-  gg <- gg +
-    ggplot2::geom_point(na.rm=TRUE) +
-    ggplot2::geom_line(ggplot2::aes(y = yhat), color = "#0072B2",
-                       na.rm = TRUE) +
-    ggplot2::theme(aspect.ratio = 3 / 5)
-  return(gg)
-}
-
-#' Plot the components of a prophet forecast.
-#' Prints a ggplot2 with panels for trend, weekly and yearly seasonalities if
-#' present, and holidays if present.
-#'
-#' @param m Prophet object.
-#' @param fcst Data frame returned by predict(m, df).
-#' @param uncertainty Boolean indicating if the uncertainty interval should be
-#'  plotted for the trend, from fcst columns trend_lower and trend_upper.
-#' @param plot_cap Boolean indicating if the capacity should be shown in the
-#'  figure, if available.
-#' @param weekly_start Integer specifying the start day of the weekly
-#'  seasonality plot. 0 (default) starts the week on Sunday. 1 shifts by 1 day
-#'  to Monday, and so on.
-#' @param yearly_start Integer specifying the start day of the yearly
-#'  seasonality plot. 0 (default) starts the year on Jan 1. 1 shifts by 1 day
-#'  to Jan 2, and so on.
-#'
-#' @return Invisibly return a list containing the plotted ggplot objects
-#'
-#' @export
-#' @importFrom dplyr "%>%"
-prophet_plot_components <- function(
-  m, fcst, uncertainty = TRUE, plot_cap = TRUE, weekly_start = 0,
-  yearly_start = 0
-) {
-  # Plot the trend
-  panels <- list(plot_forecast_component(fcst, 'trend', uncertainty, plot_cap))
-  # Plot holiday components, if present.
-  if (!is.null(m$holidays) && ('holidays' %in% colnames(fcst))) {
-    panels[[length(panels) + 1]] <- plot_forecast_component(
-      fcst, 'holidays', uncertainty, FALSE)
-  }
-  # Plot weekly seasonality, if present
-  if ("weekly" %in% colnames(fcst)) {
-    panels[[length(panels) + 1]] <- plot_weekly(m, uncertainty, weekly_start)
-  }
-  # Plot yearly seasonality, if present
-  if ("yearly" %in% colnames(fcst)) {
-    panels[[length(panels) + 1]] <- plot_yearly(m, uncertainty, yearly_start)
-  }
-  # Plot other seasonalities
-  for (name in names(m$seasonalities)) {
-    if (!(name %in% c('weekly', 'yearly')) &&
-        (name %in% colnames(fcst))) {
-      panels[[length(panels) + 1]] <- plot_seasonality(m, name, uncertainty)
-    }
-  }
-  # Plot extra regressors
-  if ((length(m$extra_regressors) > 0)
-      & ('extra_regressors' %in% colnames(fcst))) {
-    panels[[length(panels) + 1]] <- plot_forecast_component(
-      fcst, 'extra_regressors', uncertainty, FALSE)
-  }
-
-  # Make the plot.
-  grid::grid.newpage()
-  grid::pushViewport(grid::viewport(layout = grid::grid.layout(length(panels),
-                                                               1)))
-  for (i in seq_along(panels)) {
-    print(panels[[i]], vp = grid::viewport(layout.pos.row = i,
-                                           layout.pos.col = 1))
-  }
-  return(invisible(panels))
-}
-
-#' Plot a particular component of the forecast.
-#'
-#' @param fcst Dataframe output of `predict`.
-#' @param name String name of the component to plot (column of fcst).
-#' @param uncertainty Boolean to plot uncertainty intervals.
-#' @param plot_cap Boolean indicating if the capacity should be shown in the
-#'  figure, if available.
-#'
-#' @return A ggplot2 plot.
-#'
-#' @export
-plot_forecast_component <- function(
-  fcst, name, uncertainty = TRUE, plot_cap = FALSE
-) {
-  gg.comp <- ggplot2::ggplot(
-      fcst, ggplot2::aes_string(x = 'ds', y = name, group = 1)) +
-    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE)
-  if (exists('cap', where = fcst) && plot_cap) {
-    gg.comp <- gg.comp + ggplot2::geom_line(
-      ggplot2::aes(y = cap), linetype = 'dashed', na.rm = TRUE)
-  }
-  if (exists('floor', where = fcst) && plot_cap) {
-    gg.comp <- gg.comp + ggplot2::geom_line(
-      ggplot2::aes(y = floor), linetype = 'dashed', na.rm = TRUE)
-  }
-  if (uncertainty) {
-    gg.comp <- gg.comp +
-      ggplot2::geom_ribbon(
-        ggplot2::aes_string(
-          ymin = paste0(name, '_lower'), ymax = paste0(name, '_upper')
-        ),
-        alpha = 0.2,
-        fill = "#0072B2",
-        na.rm = TRUE)
-  }
-  return(gg.comp)
-}
-
-#' Prepare dataframe for plotting seasonal components.
-#'
-#' @param m Prophet object.
-#' @param ds Array of dates for column ds.
-#'
-#' @return A dataframe with seasonal components on ds.
-#'
-#' @keywords internal
-seasonality_plot_df <- function(m, ds) {
-  df_list <- list(ds = ds, cap = 1, floor = 0)
-  for (name in names(m$extra_regressors)) {
-    df_list[[name]] <- 0
-  }
-  df <- as.data.frame(df_list)
-  df <- setup_dataframe(m, df)$df
-  return(df)
-}
-
-#' Plot the weekly component of the forecast.
-#'
-#' @param m Prophet model object
-#' @param uncertainty Boolean to plot uncertainty intervals.
-#' @param weekly_start Integer specifying the start day of the weekly
-#'  seasonality plot. 0 (default) starts the week on Sunday. 1 shifts by 1 day
-#'  to Monday, and so on.
-#'
-#' @return A ggplot2 plot.
-#'
-#' @keywords internal
-plot_weekly <- function(m, uncertainty = TRUE, weekly_start = 0) {
-  # Compute weekly seasonality for a Sun-Sat sequence of dates.
-  days <- seq(set_date('2017-01-01'), by='d', length.out=7) + as.difftime(
-    weekly_start, units = "days")
-  df.w <- seasonality_plot_df(m, days)
-  seas <- predict_seasonal_components(m, df.w)
-  seas$dow <- factor(weekdays(df.w$ds), levels=weekdays(df.w$ds))
-
-  gg.weekly <- ggplot2::ggplot(seas, ggplot2::aes(x = dow, y = weekly,
-                                                  group = 1)) +
-    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE) +
-    ggplot2::labs(x = "Day of week")
-  if (uncertainty) {
-    gg.weekly <- gg.weekly +
-      ggplot2::geom_ribbon(ggplot2::aes(ymin = weekly_lower,
-                                        ymax = weekly_upper),
-                           alpha = 0.2,
-                           fill = "#0072B2",
-                           na.rm = TRUE)
-  }
-  return(gg.weekly)
-}
-
-#' Plot the yearly component of the forecast.
-#'
-#' @param m Prophet model object.
-#' @param uncertainty Boolean to plot uncertainty intervals.
-#' @param yearly_start Integer specifying the start day of the yearly
-#'  seasonality plot. 0 (default) starts the year on Jan 1. 1 shifts by 1 day
-#'  to Jan 2, and so on.
-#'
-#' @return A ggplot2 plot.
-#'
-#' @keywords internal
-plot_yearly <- function(m, uncertainty = TRUE, yearly_start = 0) {
-  # Compute yearly seasonality for a Jan 1 - Dec 31 sequence of dates.
-  days <- seq(set_date('2017-01-01'), by='d', length.out=365) + as.difftime(
-    yearly_start, units = "days")
-  df.y <- seasonality_plot_df(m, days)
-  seas <- predict_seasonal_components(m, df.y)
-  seas$ds <- df.y$ds
-
-  gg.yearly <- ggplot2::ggplot(seas, ggplot2::aes(x = ds, y = yearly,
-                                                  group = 1)) +
-    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE) +
-    ggplot2::labs(x = "Day of year") +
-    ggplot2::scale_x_datetime(labels = scales::date_format('%B %d'))
-  if (uncertainty) {
-    gg.yearly <- gg.yearly +
-      ggplot2::geom_ribbon(ggplot2::aes(ymin = yearly_lower,
-                                        ymax = yearly_upper),
-                           alpha = 0.2,
-                           fill = "#0072B2",
-                           na.rm = TRUE)
-  }
-  return(gg.yearly)
-}
-
-#' Plot a custom seasonal component.
-#'
-#' @param m Prophet model object.
-#' @param name String name of the seasonality.
-#' @param uncertainty Boolean to plot uncertainty intervals.
-#'
-#' @return A ggplot2 plot.
-#'
-#' @keywords internal
-plot_seasonality <- function(m, name, uncertainty = TRUE) {
-  # Compute seasonality from Jan 1 through a single period.
-  start <- set_date('2017-01-01')
-  period <- m$seasonalities[[name]]$period
-  end <- start + period * 24 * 3600
-  plot.points <- 200
-  days <- seq(from=start, to=end, length.out=plot.points)
-  df.y <- seasonality_plot_df(m, days)
-  seas <- predict_seasonal_components(m, df.y)
-  seas$ds <- df.y$ds
-  gg.s <- ggplot2::ggplot(
-      seas, ggplot2::aes_string(x = 'ds', y = name, group = 1)) +
-    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE)
-  if (period <= 2) {
-    fmt.str <- '%T'
-  } else if (period < 14) {
-    fmt.str <- '%m/%d %R'
-  } else {
-    fmt.str <- '%m/%d'
-  }
-  gg.s <- gg.s +
-    ggplot2::scale_x_datetime(labels = scales::date_format(fmt.str))
-  if (uncertainty) {
-    gg.s <- gg.s +
-    ggplot2::geom_ribbon(
-      ggplot2::aes_string(
-        ymin = paste0(name, '_lower'), ymax = paste0(name, '_upper')
-      ),
-      alpha = 0.2,
-      fill = "#0072B2",
-      na.rm = TRUE)
-  }
-  return(gg.s)
-}
-
-#' Plot the prophet forecast.
-#'
-#' @param x Prophet object.
-#' @param fcst Data frame returned by predict(m, df).
-#' @param uncertainty Boolean indicating if the uncertainty interval for yhat
-#'  should be plotted. Must be present in fcst as yhat_lower and yhat_upper.
-#' @param ... additional arguments
-#' @importFrom dplyr "%>%"
-#' @return A dygraph plot.
-#'
-#' @examples
-#' \dontrun{
-#' history <- data.frame(ds = seq(as.Date('2015-01-01'), as.Date('2016-01-01'), by = 'd'),
-#'                       y = sin(1:366/200) + rnorm(366)/10)
-#' m <- prophet(history)
-#' future <- make_future_dataframe(m, periods = 365)
-#' forecast <- predict(m, future)
-#' dyplot.prophet(m, forecast)
-#' }
-#'
-#' @export
-dyplot.prophet <- function(x, fcst, uncertainty=TRUE, 
-                           ...) 
-{
-  forecast.label='Predicted'
-  actual.label='Actual'
-  # create data.frame for plotting
-  df <- df_for_plotting(x, fcst)
-  
-  # build variables to include, or not, the uncertainty data
-  if(uncertainty && exists("yhat_lower", where = df))
-  {
-    colsToKeep <- c('y', 'yhat', 'yhat_lower', 'yhat_upper')
-    forecastCols <- c('yhat_lower', 'yhat', 'yhat_upper')
-  } else
-  {
-    colsToKeep <- c('y', 'yhat')
-    forecastCols <- c('yhat')
-  }
-  # convert to xts for easier date handling by dygraph
-  dfTS <- xts::xts(df %>% dplyr::select_(.dots=colsToKeep), order.by = df$ds)
-
-  # base plot
-  dyBase <- dygraphs::dygraph(dfTS)
-  
-  presAnnotation <- function(dygraph, x, text) {
-    dygraph %>%
-      dygraphs::dyAnnotation(x, text, text, attachAtBottom = TRUE)
-  }
-  
-  dyBase <- dyBase %>% 
-    dygraphs::dyOptions(colors = RColorBrewer::brewer.pal(3, "Set1")) %>%
-    # plot actual values
-    dygraphs::dySeries('y', label=actual.label) %>% 
-    # plot forecast and ribbon
-    dygraphs::dySeries(forecastCols, label=forecast.label) %>% 
-    # allow zooming
-    dygraphs::dyRangeSelector() %>% 
-    # make unzoom button
-    dygraphs::dyUnzoom()
-  if (!is.null(x$holidays)) {
-    for (i in 1:nrow(x$holidays)) {
-      # make a gray line
-      dyBase <- dyBase %>% dygraphs::dyEvent(x$holidays$ds[i],color = "rgb(200,200,200)", strokePattern = "solid")
-      dyBase <- dyBase %>% dygraphs::dyAnnotation(x$holidays$ds[i], x$holidays$holiday[i], x$holidays$holiday[i], attachAtBottom = TRUE)
-    }
-  }
-  return(dyBase)
-}
-

R/R/prophet.R

@@ -6,7 +6,7 @@
 ## of patent rights can be found in the PATENTS file in the same directory.
 
 ## Makes R CMD CHECK happy due to dplyr syntax below
-utils::globalVariables(c(
+globalVariables(c(
   "ds", "y", "cap", ".",
   "component", "dow", "doy", "holiday", "holidays", "holidays_lower", "holidays_upper", "ix",
   "lower", "n", "stat", "trend", "row_number", "extra_regressors", "col",
@@ -190,21 +190,21 @@ validate_column_name <- function(
     'trend', 'seasonal', 'seasonalities', 'daily', 'weekly', 'yearly',
     'holidays', 'zeros', 'extra_regressors', 'yhat'
   )
-  rn_l = paste0(reserved_names,"_lower")
-  rn_u = paste0(reserved_names,"_upper")
+  rn_l = paste(reserved_names,"_lower",sep="")
+  rn_u = paste(reserved_names,"_upper",sep="")
   reserved_names = c(reserved_names, rn_l, rn_u,
     c("ds", "y", "cap", "floor", "y_scaled", "cap_scaled"))
   if(name %in% reserved_names){
     stop("Name ", name, " is reserved.")
   }
-  if(check_holidays && !is.null(m$holidays) &&
+  if(check_holidays & !is.null(m$holidays) &
      (name %in% unique(m$holidays$holiday))){
     stop("Name ", name, " already used for a holiday.")
   }
-  if(check_seasonalities && (!is.null(m$seasonalities[[name]]))){
+  if(check_seasonalities & (!is.null(m$seasonalities[[name]]))){
     stop("Name ", name, " already used for a seasonality.")
   }
-  if(check_regressors && (!is.null(m$seasonalities[[name]]))){
+  if(check_regressors & (!is.null(m$seasonalities[[name]]))){
     stop("Name ", name, " already used for an added regressor.")
   }
 }
@@ -274,8 +274,11 @@ set_date <- function(ds = NULL, tz = "GMT") {
     ds <- as.character(ds)
   }
 
-  fmt <- if (min(nchar(ds)) < 12) "%Y-%m-%d" else "%Y-%m-%d %H:%M:%S"
-  ds <- as.POSIXct(ds, format = fmt, tz = tz)
+  if (min(nchar(ds)) < 12) {
+    ds <- as.POSIXct(ds, format = "%Y-%m-%d", tz = tz)
+  } else {
+    ds <- as.POSIXct(ds, format = "%Y-%m-%d %H:%M:%S", tz = tz)
+  }
   attr(ds, "tzone") <- tz
   return(ds)
 }
@@ -459,7 +462,7 @@ set_changepoints <- function(m) {
     m$changepoints.t <- sort(
       time_diff(m$changepoints, m$start, "secs")) / m$t.scale
   } else {
-    m$changepoints.t <- 0  # dummy changepoint
+    m$changepoints.t <- c(0)  # dummy changepoint
   }
   return(m)
 }
@@ -473,7 +476,7 @@ set_changepoints <- function(m) {
 #' @keywords internal
 get_changepoint_matrix <- function(m) {
   A <- matrix(0, nrow(m$history), length(m$changepoints.t))
-  for (i in seq_along(m$changepoints.t)) {
+  for (i in 1:length(m$changepoints.t)) {
     A[m$history$t >= m$changepoints.t[i], i] <- 1
   }
   return(A)
@@ -491,7 +494,7 @@ get_changepoint_matrix <- function(m) {
 fourier_series <- function(dates, period, series.order) {
   t <- time_diff(dates, set_date('1970-01-01 00:00:00'))
   features <- matrix(0, length(t), 2 * series.order)
-  for (i in seq_len(series.order)) {
+  for (i in 1:series.order) {
     x <- as.numeric(2 * i * pi * t / period)
     features[, i * 2 - 1] <- sin(x)
     features[, i * 2] <- cos(x)
@@ -511,7 +514,7 @@ fourier_series <- function(dates, period, series.order) {
 #' @keywords internal
 make_seasonality_features <- function(dates, period, series.order, prefix) {
   features <- fourier_series(dates, period, series.order)
-  colnames(features) <- paste(prefix, seq_len(ncol(features)), sep = '_delim_')
+  colnames(features) <- paste(prefix, 1:ncol(features), sep = '_delim_')
   return(data.frame(features))
 }
 
@@ -538,13 +541,13 @@ make_holiday_features <- function(m, dates) {
           && !is.na(.$upper_window)) {
         offsets <- seq(.$lower_window, .$upper_window)
       } else {
-        offsets <- 0
+        offsets <- c(0)
       }
       names <- paste(.$holiday, '_delim_', ifelse(offsets < 0, '-', '+'),
                      abs(offsets), sep = '')
       dplyr::data_frame(ds = .$ds + offsets * 24 * 3600, holiday = names)
     }) %>%
-    dplyr::mutate(x = 1) %>%
+    dplyr::mutate(x = 1.) %>%
     tidyr::spread(holiday, x, fill = 0)
 
   holiday.features <- data.frame(ds = set_date(dates)) %>%
@@ -682,7 +685,7 @@ add_seasonality <- function(m, name, period, fourier.order, prior.scale = NULL)
 #'
 #' @keywords internal
 make_all_seasonality_features <- function(m, df) {
-  seasonal.features <- data.frame(row.names = seq_len(nrow(df)))
+  seasonal.features <- data.frame(row.names = 1:nrow(df))
   prior.scales <- c()
 
   # Seasonality features
@@ -710,7 +713,7 @@ make_all_seasonality_features <- function(m, df) {
 
   if (ncol(seasonal.features) == 0) {
     seasonal.features <- data.frame(zeros = rep(0, nrow(df)))
-    prior.scales <- 1
+    prior.scales <- c(1.)
   }
   return(list(seasonal.features = seasonal.features,
               prior.scales = prior.scales))
@@ -1034,7 +1037,9 @@ predict.prophet <- function(object, df = NULL, ...) {
     cols <- c(cols, 'floor')
   }
   df <- df[cols]
-  df <- dplyr::bind_cols(df, seasonal.components, intervals)
+  df <- df %>%
+    dplyr::bind_cols(seasonal.components) %>%
+    dplyr::bind_cols(intervals)
   df$yhat <- df$trend + df$seasonal
   return(df)
 }
@@ -1056,7 +1061,7 @@ piecewise_linear <- function(t, deltas, k, m, changepoint.ts) {
   # Get cumulative slope and intercept at each t
   k_t <- rep(k, length(t))
   m_t <- rep(m, length(t))
-  for (s in seq_along(changepoint.ts)) {
+  for (s in 1:length(changepoint.ts)) {
     indx <- t >= changepoint.ts[s]
     k_t[indx] <- k_t[indx] + deltas[s]
     m_t[indx] <- m_t[indx] + gammas[s]
@@ -1081,14 +1086,14 @@ piecewise_logistic <- function(t, cap, deltas, k, m, changepoint.ts) {
   # Compute offset changes
   k.cum <- c(k, cumsum(deltas) + k)
   gammas <- rep(0, length(changepoint.ts))
-  for (i in seq_along(changepoint.ts)) {
+  for (i in 1:length(changepoint.ts)) {
     gammas[i] <- ((changepoint.ts[i] - m - sum(gammas))
                   * (1 - k.cum[i] / k.cum[i + 1]))
   }
   # Get cumulative rate and offset at each t
   k_t <- rep(k, length(t))
   m_t <- rep(m, length(t))
-  for (s in seq_along(changepoint.ts)) {
+  for (s in 1:length(changepoint.ts)) {
     indx <- t >= changepoint.ts[s]
     k_t[indx] <- k_t[indx] + deltas[s]
     m_t[indx] <- m_t[indx] + gammas[s]
@@ -1135,14 +1140,14 @@ predict_seasonal_components <- function(m, df) {
   upper.p <- (1 + m$interval.width)/2
 
   components <- dplyr::data_frame(component = colnames(seasonal.features)) %>%
-    dplyr::mutate(col = seq_len(n())) %>%
+    dplyr::mutate(col = 1:n()) %>%
     tidyr::separate(component, c('component', 'part'), sep = "_delim_",
                     extra = "merge", fill = "right") %>%
     dplyr::select(col, component)
   # Add total for all regression components
   components <- rbind(
     components,
-    data.frame(col = seq_len(ncol(seasonal.features)), component = 'seasonal'))
+    data.frame(col = 1:ncol(seasonal.features), component = 'seasonal'))
   # Add totals for seasonality, holiday, and extra regressors
   components <- add_group_component(
     components, 'seasonalities', names(m$seasonalities))
@@ -1159,7 +1164,7 @@ predict_seasonal_components <- function(m, df) {
     dplyr::group_by(component) %>% dplyr::do({
       comp <- (as.matrix(seasonal.features[, .$col])
                %*% t(m$params$beta[, .$col, drop = FALSE])) * m$y.scale
-      dplyr::data_frame(ix = seq_len(nrow(seasonal.features)),
+      dplyr::data_frame(ix = 1:nrow(seasonal.features),
                         mean = rowMeans(comp, na.rm = TRUE),
                         lower = apply(comp, 1, stats::quantile, lower.p,
                                       na.rm = TRUE),
@@ -1213,9 +1218,9 @@ sample_posterior_predictive <- function(m, df) {
                      "seasonal" = matrix(, nrow = nrow(df), ncol = nsamp),
                      "yhat" = matrix(, nrow = nrow(df), ncol = nsamp))
 
-  for (i in seq_len(n.iterations)) {
+  for (i in 1:n.iterations) {
     # For each set of parameters from MCMC (or just 1 set for MAP),
-    for (j in seq_len(samp.per.iter)) {
+    for (j in 1:samp.per.iter) {
       # Do a simulation with this set of parameters,
       sim <- sample_model(m, df, seasonal.features, i)
       # Store the results
@@ -1383,6 +1388,310 @@ make_future_dataframe <- function(m, periods, freq = 'day',
   return(data.frame(ds = dates))
 }
 
+#' Merge history and forecast for plotting.
+#'
+#' @param m Prophet object.
+#' @param fcst Data frame returned by prophet predict.
+#'
+#' @importFrom dplyr "%>%"
+#' @keywords internal
+df_for_plotting <- function(m, fcst) {
+  # Make sure there is no y in fcst
+  fcst$y <- NULL
+  df <- m$history %>%
+    dplyr::select(ds, y) %>%
+    dplyr::full_join(fcst, by = "ds") %>%
+    dplyr::arrange(ds)
+  return(df)
+}
+
+#' Plot the prophet forecast.
+#'
+#' @param x Prophet object.
+#' @param fcst Data frame returned by predict(m, df).
+#' @param uncertainty Boolean indicating if the uncertainty interval for yhat
+#'  should be plotted. Must be present in fcst as yhat_lower and yhat_upper.
+#' @param plot_cap Boolean indicating if the capacity should be shown in the
+#'  figure, if available.
+#' @param xlabel Optional label for x-axis
+#' @param ylabel Optional label for y-axis
+#' @param ... additional arguments
+#'
+#' @return A ggplot2 plot.
+#'
+#' @examples
+#' \dontrun{
+#' history <- data.frame(ds = seq(as.Date('2015-01-01'), as.Date('2016-01-01'), by = 'd'),
+#'                       y = sin(1:366/200) + rnorm(366)/10)
+#' m <- prophet(history)
+#' future <- make_future_dataframe(m, periods = 365)
+#' forecast <- predict(m, future)
+#' plot(m, forecast)
+#' }
+#'
+#' @export
+plot.prophet <- function(x, fcst, uncertainty = TRUE, plot_cap = TRUE,
+                         xlabel = 'ds', ylabel = 'y', ...) {
+  df <- df_for_plotting(x, fcst)
+  gg <- ggplot2::ggplot(df, ggplot2::aes(x = ds, y = y)) +
+    ggplot2::labs(x = xlabel, y = ylabel)
+  if (exists('cap', where = df) && plot_cap) {
+    gg <- gg + ggplot2::geom_line(
+      ggplot2::aes(y = cap), linetype = 'dashed', na.rm = TRUE)
+  }
+  if (x$logistic.floor && exists('floor', where = df) && plot_cap) {
+    gg <- gg + ggplot2::geom_line(
+      ggplot2::aes(y = floor), linetype = 'dashed', na.rm = TRUE)
+  }
+  if (uncertainty && exists('yhat_lower', where = df)) {
+    gg <- gg +
+      ggplot2::geom_ribbon(ggplot2::aes(ymin = yhat_lower, ymax = yhat_upper),
+                           alpha = 0.2,
+                           fill = "#0072B2",
+                           na.rm = TRUE)
+  }
+  gg <- gg +
+    ggplot2::geom_point(na.rm=TRUE) +
+    ggplot2::geom_line(ggplot2::aes(y = yhat), color = "#0072B2",
+                       na.rm = TRUE) +
+    ggplot2::theme(aspect.ratio = 3 / 5)
+  return(gg)
+}
+
+#' Plot the components of a prophet forecast.
+#' Prints a ggplot2 with panels for trend, weekly and yearly seasonalities if
+#' present, and holidays if present.
+#'
+#' @param m Prophet object.
+#' @param fcst Data frame returned by predict(m, df).
+#' @param uncertainty Boolean indicating if the uncertainty interval should be
+#'  plotted for the trend, from fcst columns trend_lower and trend_upper.
+#' @param plot_cap Boolean indicating if the capacity should be shown in the
+#'  figure, if available.
+#' @param weekly_start Integer specifying the start day of the weekly
+#'  seasonality plot. 0 (default) starts the week on Sunday. 1 shifts by 1 day
+#'  to Monday, and so on.
+#' @param yearly_start Integer specifying the start day of the yearly
+#'  seasonality plot. 0 (default) starts the year on Jan 1. 1 shifts by 1 day
+#'  to Jan 2, and so on.
+#'
+#' @return Invisibly return a list containing the plotted ggplot objects
+#'
+#' @export
+#' @importFrom dplyr "%>%"
+prophet_plot_components <- function(
+  m, fcst, uncertainty = TRUE, plot_cap = TRUE, weekly_start = 0,
+  yearly_start = 0
+) {
+  # Plot the trend
+  panels <- list(plot_forecast_component(fcst, 'trend', uncertainty, plot_cap))
+  # Plot holiday components, if present.
+  if (!is.null(m$holidays) & ('holidays' %in% colnames(fcst))) {
+    panels[[length(panels) + 1]] <- plot_forecast_component(
+      fcst, 'holidays', uncertainty, FALSE)
+  }
+  # Plot weekly seasonality, if present
+  if ("weekly" %in% colnames(fcst)) {
+    panels[[length(panels) + 1]] <- plot_weekly(m, uncertainty, weekly_start)
+  }
+  # Plot yearly seasonality, if present
+  if ("yearly" %in% colnames(fcst)) {
+    panels[[length(panels) + 1]] <- plot_yearly(m, uncertainty, yearly_start)
+  }
+  # Plot other seasonalities
+  for (name in names(m$seasonalities)) {
+    if (!(name %in% c('weekly', 'yearly')) &&
+        (name %in% colnames(fcst))) {
+      panels[[length(panels) + 1]] <- plot_seasonality(m, name, uncertainty)
+    }
+  }
+  # Plot extra regressors
+  if ((length(m$extra_regressors) > 0)
+      & ('extra_regressors' %in% colnames(fcst))) {
+    panels[[length(panels) + 1]] <- plot_forecast_component(
+      fcst, 'extra_regressors', uncertainty, FALSE)
+  }
+
+  # Make the plot.
+  grid::grid.newpage()
+  grid::pushViewport(grid::viewport(layout = grid::grid.layout(length(panels),
+                                                               1)))
+  for (i in 1:length(panels)) {
+    print(panels[[i]], vp = grid::viewport(layout.pos.row = i,
+                                           layout.pos.col = 1))
+  }
+  return(invisible(panels))
+}
+
+#' Plot a particular component of the forecast.
+#'
+#' @param fcst Dataframe output of `predict`.
+#' @param name String name of the component to plot (column of fcst).
+#' @param uncertainty Boolean to plot uncertainty intervals.
+#' @param plot_cap Boolean indicating if the capacity should be shown in the
+#'  figure, if available.
+#'
+#' @return A ggplot2 plot.
+#'
+#' @export
+plot_forecast_component <- function(
+  fcst, name, uncertainty = TRUE, plot_cap = FALSE
+) {
+  gg.comp <- ggplot2::ggplot(
+      fcst, ggplot2::aes_string(x = 'ds', y = name, group = 1)) +
+    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE)
+  if (exists('cap', where = fcst) && plot_cap) {
+    gg.comp <- gg.comp + ggplot2::geom_line(
+      ggplot2::aes(y = cap), linetype = 'dashed', na.rm = TRUE)
+  }
+  if (exists('floor', where = fcst) && plot_cap) {
+    gg.comp <- gg.comp + ggplot2::geom_line(
+      ggplot2::aes(y = floor), linetype = 'dashed', na.rm = TRUE)
+  }
+  if (uncertainty) {
+    gg.comp <- gg.comp +
+      ggplot2::geom_ribbon(
+        ggplot2::aes_string(
+          ymin = paste0(name, '_lower'), ymax = paste0(name, '_upper')
+        ),
+        alpha = 0.2,
+        fill = "#0072B2",
+        na.rm = TRUE)
+  }
+  return(gg.comp)
+}
+
+#' Prepare dataframe for plotting seasonal components.
+#'
+#' @param m Prophet object.
+#' @param ds Array of dates for column ds.
+#'
+#' @return A dataframe with seasonal components on ds.
+#'
+#' @keywords internal
+seasonality_plot_df <- function(m, ds) {
+  df_list <- list(ds = ds, cap = 1, floor = 0)
+  for (name in names(m$extra_regressors)) {
+    df_list[[name]] <- 0
+  }
+  df <- as.data.frame(df_list)
+  df <- setup_dataframe(m, df)$df
+  return(df)
+}
+
+#' Plot the weekly component of the forecast.
+#'
+#' @param m Prophet model object
+#' @param uncertainty Boolean to plot uncertainty intervals.
+#' @param weekly_start Integer specifying the start day of the weekly
+#'  seasonality plot. 0 (default) starts the week on Sunday. 1 shifts by 1 day
+#'  to Monday, and so on.
+#'
+#' @return A ggplot2 plot.
+#'
+#' @keywords internal
+plot_weekly <- function(m, uncertainty = TRUE, weekly_start = 0) {
+  # Compute weekly seasonality for a Sun-Sat sequence of dates.
+  days <- seq(set_date('2017-01-01'), by='d', length.out=7) + as.difftime(
+    weekly_start, units = "days")
+  df.w <- seasonality_plot_df(m, days)
+  seas <- predict_seasonal_components(m, df.w)
+  seas$dow <- factor(weekdays(df.w$ds), levels=weekdays(df.w$ds))
+
+  gg.weekly <- ggplot2::ggplot(seas, ggplot2::aes(x = dow, y = weekly,
+                                                  group = 1)) +
+    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE) +
+    ggplot2::labs(x = "Day of week")
+  if (uncertainty) {
+    gg.weekly <- gg.weekly +
+      ggplot2::geom_ribbon(ggplot2::aes(ymin = weekly_lower,
+                                        ymax = weekly_upper),
+                           alpha = 0.2,
+                           fill = "#0072B2",
+                           na.rm = TRUE)
+  }
+  return(gg.weekly)
+}
+
+#' Plot the yearly component of the forecast.
+#'
+#' @param m Prophet model object.
+#' @param uncertainty Boolean to plot uncertainty intervals.
+#' @param yearly_start Integer specifying the start day of the yearly
+#'  seasonality plot. 0 (default) starts the year on Jan 1. 1 shifts by 1 day
+#'  to Jan 2, and so on.
+#'
+#' @return A ggplot2 plot.
+#'
+#' @keywords internal
+plot_yearly <- function(m, uncertainty = TRUE, yearly_start = 0) {
+  # Compute yearly seasonality for a Jan 1 - Dec 31 sequence of dates.
+  days <- seq(set_date('2017-01-01'), by='d', length.out=365) + as.difftime(
+    yearly_start, units = "days")
+  df.y <- seasonality_plot_df(m, days)
+  seas <- predict_seasonal_components(m, df.y)
+  seas$ds <- df.y$ds
+
+  gg.yearly <- ggplot2::ggplot(seas, ggplot2::aes(x = ds, y = yearly,
+                                                  group = 1)) +
+    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE) +
+    ggplot2::labs(x = "Day of year") +
+    ggplot2::scale_x_datetime(labels = scales::date_format('%B %d'))
+  if (uncertainty) {
+    gg.yearly <- gg.yearly +
+      ggplot2::geom_ribbon(ggplot2::aes(ymin = yearly_lower,
+                                        ymax = yearly_upper),
+                           alpha = 0.2,
+                           fill = "#0072B2",
+                           na.rm = TRUE)
+  }
+  return(gg.yearly)
+}
+
+#' Plot a custom seasonal component.
+#'
+#' @param m Prophet model object.
+#' @param name String name of the seasonality.
+#' @param uncertainty Boolean to plot uncertainty intervals.
+#'
+#' @return A ggplot2 plot.
+#'
+#' @keywords internal
+plot_seasonality <- function(m, name, uncertainty = TRUE) {
+  # Compute seasonality from Jan 1 through a single period.
+  start <- set_date('2017-01-01')
+  period <- m$seasonalities[[name]]$period
+  end <- start + period * 24 * 3600
+  plot.points <- 200
+  days <- seq(from=start, to=end, length.out=plot.points)
+  df.y <- seasonality_plot_df(m, days)
+  seas <- predict_seasonal_components(m, df.y)
+  seas$ds <- df.y$ds
+  gg.s <- ggplot2::ggplot(
+      seas, ggplot2::aes_string(x = 'ds', y = name, group = 1)) +
+    ggplot2::geom_line(color = "#0072B2", na.rm = TRUE)
+  if (period <= 2) {
+    fmt.str <- '%T'
+  } else if (period < 14) {
+    fmt.str <- '%m/%d %R'
+  } else {
+    fmt.str <- '%m/%d'
+  }
+  gg.s <- gg.s +
+    ggplot2::scale_x_datetime(labels = scales::date_format(fmt.str))
+  if (uncertainty) {
+    gg.s <- gg.s +
+    ggplot2::geom_ribbon(
+      ggplot2::aes_string(
+        ymin = paste0(name, '_lower'), ymax = paste0(name, '_upper')
+      ),
+      alpha = 0.2,
+      fill = "#0072B2",
+      na.rm = TRUE)
+  }
+  return(gg.s)
+}
+
 #' Copy Prophet object.
 #'
 #' @param m Prophet model object.

R/R/utils.R

@@ -1,33 +0,0 @@
-#' Get layers to overlay significant changepoints on prophet forecast plot.
-#'
-#' @param m Prophet model object.
-#' @param threshold Numeric, changepoints where abs(delta) >= threshold are
-#'  significant. (Default 0.01)
-#' @param cp_color Character, line color. (Default "red")
-#' @param cp_linetype Character or integer, line type. (Default "dashed")
-#' @param trend Logical, if FALSE, do not draw trend line. (Default TRUE)
-#' @param ... Other arguments passed on to layers.
-#'
-#' @return A list of ggplot2 layers.
-#'
-#' @examples
-#' \dontrun{
-#' plot(m, fcst) + layer_changepoints(m)
-#' }
-#'
-#' @export
-layer_changepoints <- function(m, threshold = 0.01, cp_color = "red",
-                               cp_linetype = "dashed", trend = TRUE, ...) {
-  layers <- list()
-  if (trend) {
-    trend_layer <- ggplot2::geom_line(
-      ggplot2::aes_string("ds", "trend"), color = cp_color, ...)
-    layers <- append(layers, trend_layer)
-  }
-  signif_changepoints <- m$changepoints[abs(m$params$delta) >= threshold]
-  cp_layer <- ggplot2::geom_vline(
-    xintercept = as.integer(signif_changepoints), color = cp_color,
-    linetype = cp_linetype, ...)
-  layers <- append(layers, cp_layer)
-  return(layers)
-}

R/man/df_for_plotting.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{df_for_plotting}
 \alias{df_for_plotting}
 \title{Merge history and forecast for plotting.}

R/man/dyplot.prophet.Rd

@@ -1,35 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
-\name{dyplot.prophet}
-\alias{dyplot.prophet}
-\title{Plot the prophet forecast.}
-\usage{
-dyplot.prophet(x, fcst, uncertainty = TRUE, ...)
-}
-\arguments{
-\item{x}{Prophet object.}
-
-\item{fcst}{Data frame returned by predict(m, df).}
-
-\item{uncertainty}{Boolean indicating if the uncertainty interval for yhat
-should be plotted. Must be present in fcst as yhat_lower and yhat_upper.}
-
-\item{...}{additional arguments}
-}
-\value{
-A dygraph plot.
-}
-\description{
-Plot the prophet forecast.
-}
-\examples{
-\dontrun{
-history <- data.frame(ds = seq(as.Date('2015-01-01'), as.Date('2016-01-01'), by = 'd'),
-                      y = sin(1:366/200) + rnorm(366)/10)
-m <- prophet(history)
-future <- make_future_dataframe(m, periods = 365)
-forecast <- predict(m, future)
-dyplot.prophet(m, forecast)
-}
-
-}

R/man/layer_changepoints.Rd

@@ -1,35 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{layer_changepoints}
-\alias{layer_changepoints}
-\title{Get layers to overlay significant changepoints on prophet forecast plot.}
-\usage{
-layer_changepoints(m, threshold = 0.01, cp_color = "red",
-  cp_linetype = "dashed", trend = TRUE, ...)
-}
-\arguments{
-\item{m}{Prophet model object.}
-
-\item{threshold}{Numeric, changepoints where abs(delta) >= threshold are
-significant. (Default 0.01)}
-
-\item{cp_color}{Character, line color. (Default "red")}
-
-\item{cp_linetype}{Character or integer, line type. (Default "dashed")}
-
-\item{trend}{Logical, if FALSE, do not draw trend line. (Default TRUE)}
-
-\item{...}{Other arguments passed on to layers.}
-}
-\value{
-A list of ggplot2 layers.
-}
-\description{
-Get layers to overlay significant changepoints on prophet forecast plot.
-}
-\examples{
-\dontrun{
-plot(m, fcst) + layer_changepoints(m)
-}
-
-}

R/man/plot.prophet.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{plot.prophet}
 \alias{plot.prophet}
 \title{Plot the prophet forecast.}

R/man/plot_forecast_component.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{plot_forecast_component}
 \alias{plot_forecast_component}
 \title{Plot a particular component of the forecast.}

R/man/plot_seasonality.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{plot_seasonality}
 \alias{plot_seasonality}
 \title{Plot a custom seasonal component.}

R/man/plot_weekly.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{plot_weekly}
 \alias{plot_weekly}
 \title{Plot the weekly component of the forecast.}

R/man/plot_yearly.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{plot_yearly}
 \alias{plot_yearly}
 \title{Plot the yearly component of the forecast.}

R/man/prophet_plot_components.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{prophet_plot_components}
 \alias{prophet_plot_components}
 \title{Plot the components of a prophet forecast.

R/man/seasonality_plot_df.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/prophet.R
 \name{seasonality_plot_df}
 \alias{seasonality_plot_df}
 \title{Prepare dataframe for plotting seasonal components.}

README.md

@@ -1,7 +1,5 @@
 # Prophet: Automatic Forecasting Procedure
 
-[![Build Status](https://travis-ci.org/facebook/prophet.svg?branch=master)](https://travis-ci.org/facebook/prophet)
-
 Prophet is a procedure for forecasting time series data.  It is based on an additive model where non-linear trends are fit with yearly and weekly seasonality, plus holidays. It works best with daily periodicity data with at least one year of historical data. Prophet is robust to missing data, shifts in the trend, and large outliers.
 
 Prophet is [open source software](https://code.facebook.com/projects/) released by Facebook's [Core Data Science team](https://research.fb.com/category/data-science/).  It is available for download on [CRAN](https://cran.r-project.org/package=prophet) and [PyPI](https://pypi.python.org/pypi/fbprophet/).