---
title: "Introduction to the climate package"
author: "Bartosz Czernecki, Arkadiusz Głogowski, Jakub Nowosad"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to the climate package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
  
```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
old <- options(scipen = 999)
```

The goal of the  **climate** R package is to automatize downloading of meteorological
and hydrological data from publicly available repositories:

- OGIMET [(ogimet.com)](http://ogimet.com/index.phtml.en) 
- University of Wyoming - atmospheric vertical profiling data (http://weather.uwyo.edu/upperair/).
- Polish Institute of Meteorology and Water Management - National Research Institute [(IMGW-PIB)](https://dane.imgw.pl/)
- National Oceanic & Atmospheric Administration - Earth System Research Laboratory - Global
  Monitoring Division [(NOAA)](https://gml.noaa.gov/ccgg/trends/)
- National Oceanic & Atmospheric Administration - National Climatic Data Center - Integrated Surface Hourly (ISH) [(NOAA)](https://www1.ncdc.noaa.gov/pub/data/noaa/)

## Functions 

The **climate** package consists of ten main functions - three for meteorological data, one for hydrological data and six auxiliary functions and datasets:
  
### Meteorological data
  
- **meteo_ogimet()** - Downloading hourly and daily meteorological data from the SYNOP stations available in the ogimet.com collection.
Any meteorological (aka SYNOP) station working under the World Meteorological Organizaton  (WMO) framework after year 2000 should be accessible.

- **meteo_imgw()** - Downloading hourly, daily, and monthly meteorological data from the SYNOP/CLIMATE/PRECIP stations available in the dane.imgw.pl collection. 
It is a wrapper for `meteo_monthly()`, `meteo_daily()`, and `meteo_hourly()`

- **meteo_noaa_hourly()** - Downloading hourly NOAA Integrated Surface Hourly (ISH) meteorological data - Some stations have > 100 years long history of observations

- **sounding_wyoming()** - Downloading measurements of the vertical profile of atmosphere (aka rawinsonde data)

### Hydrological data

- **hydro_imgw()** - Downloading hourly, daily, and monthly hydrological data from the SYNOP / CLIMATE / PRECIP stations available in the
danepubliczne.imgw.pl collection.
It is a wrapper for `hydro_annual()`, `hydro_monthly()`, and `hydro_daily()`

### Auxiliary functions and datasets

- **stations_ogimet()** - Downloading information about all stations available in the selected
country in the Ogimet repository
- **nearest_stations_ogimet()** - Downloading information about nearest stations to the selected point
available for the selected country in the Ogimet repository
- **imgw_meteo_stations** - Built-in metadata from the IMGW-PIB repository for meteorological   stations, their geographical coordinates, and ID numbers
- **imgw_hydro_stations** - Built-in metadata from the IMGW-PIB repository for hydrological   stations, their geographical coordinates, and ID numbers
- **imgw_meteo_abbrev** - Dictionary explaining variables available for meteorological stations (from the IMGW-PIB repository)
- **imgw_hydro_abbrev** - Dictionary explaining variables available for hydrological stations (from the IMGW-PIB repository)

## Examples

Examples shows application of climate package with additional use of tools that help with processing the data to increase legible of downloaded data.  

- [dplyr](https://CRAN.R-project.org/package=dplyr)
- [tidyr](https://CRAN.R-project.org/package=tidyr)

### Example 1

Finding a 50 nearest meteorological stations for a given coordinates in a given country(ies):

``` {r stations , eval=T, fig.width=7,fig.height=7, fig.fullwidth=TRUE}
library(climate)
ns = nearest_stations_ogimet(country = c("United Kingdom", "France"),
                             point = c(-3, 50),
                             no_of_stations = 50, 
                             add_map = TRUE)
```

``` {r stations-2, eval=T}
if (is.data.frame(ns)) {
 knitr::kable(head(ns, 15))
}
```


### Example 2

Summary of stations available in Ogimet repository for a selected country:

``` {r stations-3, eval=T, fig.width=7, fig.height=7, fig.fullwidth=T}
library(climate)
PL = stations_ogimet(country = "Poland", add_map = TRUE)

if (is.data.frame(PL)) {
    knitr::kable(head(PL))
}
```

### Example 3
Downlading hourly meteorological data from Svalbard (Norway) for year 2016 using NOAA service
  
```{r noaa_svalbard, include=FALSE}
df = readRDS(system.file("extdata/vignettes/svalbard_noaa.rds", package = "climate"))
```

``` {r windrose,eval=F}
# downloading data with NOAA service:
df = meteo_noaa_hourly(station = "010080-99999", year = 2016)

# You can also download the same (but more granular) data with Ogimet.com (example for year 2016):
# df = meteo_ogimet(interval = "hourly", 
#                   date = c("2016-01-01", "2016-12-31"),
#                   station = c("01008"))
```

``` {r noaa-kable,eval=T}
knitr::kable(head(df))
```

### Example 4
Downloading atmospheric vertical profile (sounding) for Łeba, PL station:

```{r sonda-read, eval=T, include=F, echo=F}
library(climate)
data("profile_demo")
df2 = profile_demo[[1]] 
colnames(df2)[c(1, 3:4)] = c("PRESS", "TEMP", "DEWPT") # changing column names
```

```{r sonda, eval=F, include=T}
profile_demo <- sounding_wyoming(wmo_id = 12120,
                                 yy = 2000,
                                 mm = 3,
                                 dd = 23,
                                 hh = 0)
df2 = profile_demo[[1]] 
colnames(df2)[c(1, 3:4)] = c("PRESS", "TEMP", "DEWPT") # changing column names
```


```{r sonda2, echo=FALSE}
knitr::kable(head(df2, 10), caption = "Exemplary data frame of sounding preprocessing")
```

### Example 5
Preparing an annual summary of air temperature and precipitation using **dplyr** syntax for 10-years period (1991-2000)

```{r imgw_meteo, include=FALSE}
df = readRDS(system.file("extdata/vignettes/leba_monthly.rds", package = "climate"))
```

```{r imgw_meteo-2, eval=FALSE, include=TRUE}
library(climate)
df = meteo_imgw(interval = "monthly", rank = "synop", year = 1991:2000, station = "ŁEBA") 
# please note that sometimes 2 names are used for the same station in different years
```

```{r imgw_meteo-3, fig.width=7, fig.height=7, fig.fullwidth=TRUE, error=TRUE, eval=TRUE, include=TRUE}
suppressMessages(library(dplyr))
df2 = dplyr::select(df, station:t2m_mean_mon, rr_monthly)

monthly_summary = df2 %>% 
  dplyr::group_by(mm) %>% 
  dplyr::summarise(tmax = mean(tmax_abs, na.rm = TRUE), 
                   tmin = mean(tmin_abs, na.rm = TRUE),
                   tavg = mean(t2m_mean_mon, na.rm = TRUE), 
                   precip = sum(rr_monthly) / n_distinct(yy))            

monthly_summary = as.data.frame(t(monthly_summary[, c(5, 2, 3, 4)])) 
monthly_summary = round(monthly_summary, 1)
colnames(monthly_summary) = month.abb
```

```{r imgw_meteo2, echo=FALSE, error=TRUE}
knitr::kable(head(monthly_summary), 
             caption = "Exemplary data frame of meteorological preprocessing.")
```

### Example 6
Calculate the mean maximum value of the flow on the stations in each year with **dplyr**'s `summarise()`, and spread data by year using **tidyr**'s `spread()` to get the annual means of maximum flow in the consecutive columns.

```{r data, eval=TRUE, include=FALSE, echo=FALSE}
h = readRDS(system.file("extdata/vignettes/hydro_monthly.rds", package = "climate"))
```

```{r data-2, eval=FALSE, include=TRUE}
library(climate)
library(dplyr)
library(tidyr)
h = hydro_imgw(interval = "monthly", year = 2001:2002, coords = TRUE)
```
```{r data-3, eval=TRUE, include=TRUE, echo=TRUE}
knitr::kable(head(h))
```



```{r filtering, eval=TRUE, include=TRUE}
h2 = h %>%
  dplyr::filter(idex == 3) %>%
  dplyr::select(id, station, X, Y, hyy, Q) %>%
  dplyr::group_by(hyy, id, station, X, Y) %>%
  dplyr::summarise(annual_mean_Q = round(mean(Q, na.rm = TRUE), 1)) %>% 
  tidyr::pivot_wider(names_from = hyy, values_from = annual_mean_Q)

knitr::kable(head(h2))
```

```{r filtering2, echo=FALSE, eval=FALSE}

knitr::kable(head(h2),
             caption = "Exemplary data frame of hydrological preprocesssing.")
```

## Acknowledgment

Ogimet.com, University of Wyoming, and Institute of Meteorology and Water Management - National Research Institute (IMGW-PIB), National Oceanic & Atmospheric Administration (NOAA) - Earth System Research Laboratories - Global Monitoring Laboratory, Global Monitoring Division and Integrated Surface Hourly (NOAA ISH) are the sources of the data.

## Contribution

Contributions to this package are welcome. 
The preferred method of contribution is through a GitHub pull request. 
Feel also free to contact us by creating [an issue](https://github.com/bczernecki/climate/issues).

## Citation

To cite the `climate` package in publications, please use [this paper](https://www.mdpi.com/2071-1050/12/1/394):
  
  Czernecki, B.; Głogowski, A.; Nowosad, J. Climate: An R Package to Access Free In-Situ Meteorological and Hydrological Datasets for Environmental Assessment. Sustainability 2020, 12, 394. https://doi.org/10.3390/su12010394"

LaTeX version can be obtained with:
```
library(climate)
citation("climate")
```
<!-- ![Mean maximum annual flow](../../docs/articles/articles/pl_files/figure-html/unnamed-chunk-1-1.png) -->


```{r setup_restore, include = FALSE}
options(old)
```
