Merge branch 'master' of https://github.com/reichlab/kcde

reichlab · Apr 5, 2017 · 6f8c8e5c82ec63e2e8f8bc2a143ec75460d86ab4 · 6f8c8e5
2 parents cbc9e5b + a0cb272
commit 6f8c8e5c82ec63e2e8f8bc2a143ec75460d86ab4
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,5 +2,5 @@ method-description
 ^.*\.Rproj$
 ^\.Rproj\.user$
 .gitignore
-*.org
-^\.travis\.yml$
+^\.travis\.yml$
+^codecov\.yml$
diff --git a/.gitignore b/.gitignore
@@ -2,17 +2,11 @@
 .Rhistory
 .RData

-*.Rproj
-
 data
 data-raw
-
 *.bbl
 *.log
 *.synctex.gz
 *concordance.tex
-
 *.so
 *.o
-
-*.org
diff --git a/.travis.yml b/.travis.yml
@@ -3,3 +3,6 @@
 language: R
 sudo: false
 cache: packages
+
+after_success:
+  - Rscript -e 'covr::codecov()'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: kcde
 Title: Kernel conditional density estimation with flexible kernel
-    specifications.
+    specifications
 Version: 0.0.0.9000
 Authors@R: person("Evan", "Ray", , "elray@umass.edu", c("aut", "cre"))
 Description: A flexible implementation of kernel conditional density estimation.
@@ -19,11 +19,20 @@ Imports:
    robust,
    pdtmvn,
    plyr
-License: What license is it under?
+License: GPL-3
 LazyData: true
 Suggests:
    knitr,
-    testthat
+    testthat,
+    covr,
+    reshape,
+    cdcfluview,
+    dplyr,
+    lubridate,
+    ggplot2,
+    grid
+URL: https://github.com/reichlab/kcde
+BugReports: https://github.com/reichlab/kcde/issues
 VignetteBuilder: knitr
 Remotes: reichlab/pdtmvn
-RoxygenNote: 5.0.1
+RoxygenNote: 5.0.1
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-[![Travis-CI Build Status](https://travis-ci.org/reichlab/kcde.svg?branch=master)](https://travis-ci.org/reichlab/kcde)
-
 # kcde

+[![Travis-CI Build Status](https://travis-ci.org/reichlab/kcde.svg?branch=master)](https://travis-ci.org/reichlab/kcde) [![Coverage Status](https://img.shields.io/codecov/c/github/reichlab/kcde/master.svg)](https://codecov.io/github/reichlab/kcde?branch=master)
+
 Kernel conditional density estimation with flexible kernel specifications.
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1 @@
+comment: false
diff --git a/inst/doc/kcde.R b/inst/doc/kcde.R
@@ -0,0 +1,169 @@
+## ----InitialBlock, echo = FALSE------------------------------------------
+library(knitr)
+opts_knit$set(concordance=TRUE)
+
+## ----FluDataLoadData, echo = TRUE----------------------------------------
+library(cdcfluview)
+library(dplyr)
+library(lubridate)
+library(ggplot2)
+library(grid)
+library(kcde)
+
+usflu<-get_flu_data("national", "ilinet", years=1997:2015)
+ili_national <- transmute(usflu,
+    region.type = REGION.TYPE,
+    region = REGION,
+    year = YEAR,
+    week = WEEK,
+    total_cases = as.numeric(X..WEIGHTED.ILI))
+ili_national$time <- ymd(paste(ili_national$year, "01", "01", sep = "-"))
+week(ili_national$time) <- ili_national$week
+ili_national$time_index <- seq_len(nrow(ili_national))
+
+str(ili_national)
+
+## ----FluDataInitialPlotTotalCases, echo = TRUE---------------------------
+ggplot() +
+    geom_line(aes(x = as.Date(time), y = total_cases), data =
+ili_national) +
+    geom_vline(aes(xintercept = as.numeric(as.Date(time))),
+        colour = "grey",
+        data = ili_national[is.na(ili_national$total_cases), ]) +
+    scale_x_date() +
+    xlab("Time") +
+    ylab("Total Cases") +
+    theme_bw()
+
+## ----FluDataHistogramPlotTotalCases, echo = TRUE-------------------------
+hist_df <- rbind(
+	data.frame(value = ili_national$total_cases,
+    	variable = "Total Cases"),
+    data.frame(value = log(ili_national$total_cases),
+    	variable = "log(Total Cases)")
+)
+
+ggplot(aes(x = value), data = hist_df) +
+    geom_histogram() +
+    facet_wrap( ~ variable, ncol = 2) +
+    xlab("Total Cases") +
+    theme_bw()
+
+## ----FluDataACFPlotTotalCases, echo = TRUE-------------------------------
+last_na_ind <- max(which(is.na(ili_national$total_cases)))
+non_na_inds <- seq(from = last_na_ind + 1, to=nrow(ili_national))
+acf(ili_national$total_cases[non_na_inds],
+  lag.max = 52 * 4)
+
+## ----FluDataKernelComponentsSetup, echo = TRUE---------------------------
+## Definitions of kernel components.  A couple of notes:
+##   1) In the current implementation, it is required that separate kernel
+##      components be used for lagged (predictive) variables and for leading
+##      (prediction target) variables.
+##   2) The current syntax is verbose; in a future version of the package,
+##      convenience functions may be provided.
+
+## Define kernel components -- 3 pieces:
+##   1) Periodic kernel acting on time index
+##   2) pdtmvn kernel acting on lagged total cases (predictive) -- all continuous
+##   3) pdtmvn kernel acting on lead total cases (prediction target) -- all continuous
+kernel_components <- list(
+    list(
+        vars_and_offsets = data.frame(var_name = "time_index",
+            offset_value = 0L,
+            offset_type = "lag",
+            combined_name = "time_index_lag0",
+            stringsAsFactors = FALSE),
+        kernel_fn = periodic_kernel,
+        theta_fixed = list(period=pi / 52.2),
+        theta_est = list("bw"),
+        initialize_kernel_params_fn = initialize_params_periodic_kernel,
+        initialize_kernel_params_args = NULL,
+        vectorize_kernel_params_fn = vectorize_params_periodic_kernel,
+        vectorize_kernel_params_args = NULL,
+        update_theta_from_vectorized_theta_est_fn = update_theta_from_vectorized_theta_est_periodic_kernel,
+        update_theta_from_vectorized_theta_est_args = NULL
+    ),
+    list(
+        vars_and_offsets = data.frame(var_name = "total_cases",
+            offset_value = 1L,
+            offset_type = "horizon",
+            combined_name = "total_cases_horizon1",
+            stringsAsFactors = FALSE),
+        kernel_fn = pdtmvn_kernel,
+        rkernel_fn = rpdtmvn_kernel,
+        theta_fixed = list(
+            parameterization = "bw-diagonalized-est-eigenvalues",
+            continuous_vars = "total_cases_horizon1",
+            discrete_vars = NULL,
+            discrete_var_range_fns = NULL,
+            lower = -Inf,
+            upper = Inf
+        ),
+        theta_est = list("bw"),
+        initialize_kernel_params_fn = initialize_params_pdtmvn_kernel,
+        initialize_kernel_params_args = NULL,
+        vectorize_kernel_params_fn = vectorize_params_pdtmvn_kernel,
+        vectorize_kernel_params_args = NULL,
+        update_theta_from_vectorized_theta_est_fn = update_theta_from_vectorized_theta_est_pdtmvn_kernel,
+        update_theta_from_vectorized_theta_est_args = NULL
+    ))
+#,
+#    list(
+#        vars_and_lags = vars_and_lags[3:5, ],
+#        kernel_fn = pdtmvn_kernel,
+#        rkernel_fn = rpdtmvn_kernel,
+#        theta_fixed = NULL,
+#        theta_est = list("bw"),
+#        initialize_kernel_params_fn = initialize_params_pdtmvn_kernel,
+#        initialize_kernel_params_args = list(
+#            continuous_vars = vars_and_lags$combined_name[3:4],
+#            discrete_vars = vars_and_lags$combined_name[5],
+#            discrete_var_range_fns = list(
+#                c_lag2 = list(a = pdtmvn::floor_x_minus_1, b = floor, in_range = pdtmvn::equals_integer, discretizer = round_up_.5))
+#        ),
+#        vectorize_theta_est_fn = vectorize_params_pdtmvn_kernel,
+#        vectorize_theta_est_args = NULL,
+#        update_theta_from_vectorized_theta_est_fn = update_theta_from_vectorized_theta_est_pdtmvn_kernel,
+#        update_theta_from_vectorized_theta_est_args = list(
+#            parameterization = "bw-diagonalized-est-eigenvalues"
+#        )
+#    ))
+
+## ----FluDataKCDESetup, echo=TRUE-----------------------------------------
+kcde_control <- create_kcde_control(X_names = "time_index",
+    y_names = "total_cases",
+    time_name = "time",
+    prediction_horizons = 1L,
+    kernel_components = kernel_components,
+    crossval_buffer = ymd("2010-01-01") - ymd("2009-01-01"),
+    loss_fn = neg_log_score_loss,
+    loss_fn_prediction_args = list(
+        prediction_type = "distribution",
+        log = TRUE),
+    filter_control <- NULL,
+    loss_args = NULL,
+    prediction_inds_not_included = c())
+
+## ----FluDataKCDEEstimation, echo=TRUE------------------------------------
+# flu_kcde_fit_orig_scale <- kcde(data = ili_national[ili_national$year <= 2014, ],
+#    kcde_control = kcde_control)
+
+## ----FluDataKCDEPredictiveSampleAndPlot, echo=TRUE-----------------------
+# predictive_sample <- kcde_predict(kcde_fit = flu_kcde_fit_orig_scale,
+#         prediction_data = ili_national[ili_national$year == 2014 & ili_national$week == 53, , drop = FALSE],
+#         leading_rows_to_drop = 0,
+#         trailing_rows_to_drop = 1L,
+#         additional_training_rows_to_drop = NULL,
+#         prediction_type = "sample",
+#         n = 10000L)
+
+# ggplot() +
+# 	geom_density(aes(x = predictive_sample)) +
+# 	geom_vline(aes(xintercept = ili_national$total_cases[ili_national$year == 2015 & ili_national$week == 1]),
+# 		colour = "red") +
+# 	xlab("Total Cases") +
+# 	ylab("Predictive Density") +
+# 	ggtitle("Realized total cases vs. one week ahead predictive density\nWeek 1 of 2015") +
+# 	theme_bw()
+