Merge pull request #55 from IDEMSInternational/main

Update from MC

R/total_temperature_summaries.R

@@ -52,12 +52,15 @@ total_temperature_summaries <- function(country,
       }
     }
   }
-  if (length(summary_data) == 2) summary_data <- dplyr::full_join(summary_data[[1]], summary_data[[2]])
+  if (length(summary_data) == 2){
+    summary_data <- dplyr::full_join(summary_data[[1]], summary_data[[2]])
+  } else {
+    summary_data <- summary_data[[1]]
+  }
   summary_data$year <- as.integer(summary_data$year)
   if ("month" %in% names(summary_data)){
     summary_data$month <- as.integer(forcats::as_factor(summary_data$month))
   }
-
   list_return <- list(definitions, summary_data)
   return(list_return) # return a list with the metadata and the data itself
 }

README.Rmd

@@ -13,19 +13,51 @@ knitr::opts_chunk$set(
 )
 ```
 
-# epicsawrap
+# epicsawrap: R Package for Integrating rpicsa and epicsadata Functions for API Apps
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/IDEMSInternational/epicsawrap/workflows/R-CMD-check/badge.svg)](https://github.com/IDEMSInternational/epicsawrap/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/IDEMSInternational/epicsawrap/branch/main/graph/badge.svg)](https://app.codecov.io/gh/IDEMSInternational/epicsawrap?branch=main)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 
-The goal of epicsawrap is to ...
+## Overview
+
+**epicsawrap** is an R package that brings together the functionality of **rpicsa** and **epicsadata** packages to be used in creating API applications for crop and climate analysis. It provides a convenient interface for accessing and utilizing the functions from both packages, enabling the development of web-based tools and services for agricultural decision support.
+
+The package combines the capabilities of **rpicsa** for PICSA and climatic analysis for crops with **epicsadata** for retrieving climate and weather data, creating a powerful tool for addressing the needs of farmers, agronomists, and researchers.
 
 ## Installation
 
-You can install the development version of epicsawrap from [GitHub](https://github.com/) with:
+You can install **epicsawrap** from CRAN using the following command:
 
 ``` r
-# install.packages("devtools")
+# Install the 'devtools' package if you haven't already
+if (!require(devtools)) {
+  install.packages("devtools")
+}
+
+# Install 'epicsawrap' from GitHub
 devtools::install_github("IDEMSInternational/epicsawrap")
-```
+```
+
+
+## Documentation
+For detailed information on each function, including arguments, usage, and examples, please refer to the package documentation. You can access it using the following command:
+
+```{r, message = FALSE, warning = FALSE, eval=FALSE, include=TRUE}
+?epicsawrap
+```
+
+The GitHub page for the `rpicsa` package can be found [here](https://github.com/IDEMSInternational/rpicsa).
+The GitHub page for the `epicsadata` package can be found [here](https://github.com/IDEMSInternational/epicsadata).
+
+## Contributing
+We welcome contributions from the community. If you have any bug reports, feature requests, or would like to contribute code to rpicsa, please visit our GitHub repository.
+
+## License
+This package is open-source and distributed under the GNU Lesser General Public License v3.0 License. Feel free to use, modify, and distribute it as needed.
+
+## Contact
+If you have any questions, suggestions, or feedback, please feel free to reach out to us.

README.md

@@ -1,22 +1,73 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# epicsawrap
+# epicsawrap: R Package for Integrating rpicsa and epicsadata Functions for API Apps
 
 <!-- badges: start -->
 
+[![R-CMD-check](https://github.com/IDEMSInternational/epicsawrap/workflows/R-CMD-check/badge.svg)](https://github.com/IDEMSInternational/epicsawrap/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/IDEMSInternational/epicsawrap/branch/main/graph/badge.svg)](https://app.codecov.io/gh/IDEMSInternational/epicsawrap?branch=main)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 
-The goal of epicsawrap is to …
+## Overview
+
+**epicsawrap** is an R package that brings together the functionality of
+**rpicsa** and **epicsadata** packages to be used in creating API
+applications for crop and climate analysis. It provides a convenient
+interface for accessing and utilizing the functions from both packages,
+enabling the development of web-based tools and services for
+agricultural decision support.
+
+The package combines the capabilities of **rpicsa** for PICSA and
+climatic analysis for crops with **epicsadata** for retrieving climate
+and weather data, creating a powerful tool for addressing the needs of
+farmers, agronomists, and researchers.
 
 ## Installation
 
-You can install the development version of epicsawrap from
-[GitHub](https://github.com/) with:
+You can install **epicsawrap** from CRAN using the following command:
 
 ``` r
-# install.packages("devtools")
+# Install the 'devtools' package if you haven't already
+if (!require(devtools)) {
+  install.packages("devtools")
+}
+
+# Install 'epicsawrap' from GitHub
 devtools::install_github("IDEMSInternational/epicsawrap")
 ```
+
+## Documentation
+
+For detailed information on each function, including arguments, usage,
+and examples, please refer to the package documentation. You can access
+it using the following command:
+
+``` r
+?epicsawrap
+```
+
+The GitHub page for the `rpicsa` package can be found
+[here](https://github.com/IDEMSInternational/rpicsa). The GitHub page
+for the `epicsadata` package can be found
+[here](https://github.com/IDEMSInternational/epicsadata).
+
+## Contributing
+
+We welcome contributions from the community. If you have any bug
+reports, feature requests, or would like to contribute code to rpicsa,
+please visit our GitHub repository.
+
+## License
+
+This package is open-source and distributed under the GNU Lesser General
+Public License v3.0 License. Feel free to use, modify, and distribute it
+as needed.
+
+## Contact
+
+If you have any questions, suggestions, or feedback, please feel free to
+reach out to us.

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(epicsawrap)
+
+test_check("epicsawrap")

tests/testthat/test-annual_rainfall_summaries.R

@@ -1,21 +1,17 @@
-# library(testthat)
-# library(rpicsa)
-# 
-# # Test case 1
-# country <- "zm"
-# station_id <- "01122"
-# summaries <- c("annual_rain")
-# result <- epicsawrap::annual_rainfall_summaries(country, station_id, summaries)
-# 
-# definitions <- definitions(country = "zm", station_id = "16", 
-#                            summaries = summaries)
-# epicsadata::get_daily_data(country = country, station_id = station_id)
-# 
-# country <- "zm"
-# station_id_2 <- "16"
-# summaries_2 <- c("start_rains", "end_rains", "annual_rain", "seasonal_rain")
-# result_2 <- epicsawrap::annual_rainfall_summaries(country, station_id_2, summaries_2)
-# 
+library(testthat)
+library(epicsawrap)
+
+# Test case 1
+epicsadata::gcs_auth_file(file = "testdata/e-picsa-e630400792e7.json")
+test_1_results <- readRDS("testdata/test_1_annual_summaries.rds")
+country <- "zm"
+station_id <- "test_1"
+
+test_that("Correct summaries are calculated", {
+  result <- annual_rainfall_summaries(country, station_id)
+  expect_true(identical(result[[2]], test_1_results))
+})
+
 # test_that("Correct summaries are calculated", {
 #   # Test case 2
 #   expect_no_error(result)
@@ -28,7 +24,7 @@
 #   expect_error(epicsawrap::annual_rainfall_summaries(country, station_id, "end_season"))
 # 
 #   # Test case 2: Error is thrown if start_ is not calculated but needed
-#   expect_error(epicsawrap::annual_rainfall_summaries(country, station_id_2, c("end_rains", "seasonal_rain")))
+#   expect_error(epicsawrap::annual_rainfall_summaries(country, station_id, c("seasonal_rain")))
 # 
 #   # Test case 3: Warning if both end are given and seasonal wanted
 #   expect_warning(epicsawrap::annual_rainfall_summaries(country, station_id_2, c("start_rains", "end_rains", "end_season", "seasonal_rain")))

tests/testthat/test-crop_success_probabilities.R

@@ -1,40 +1,18 @@
-# library(testthat)
-# 
-# # External functions call
-# # Test case 1: Test with all parameter
-# result <- epicsawrap::crop_success_probabilities(
-#   country = "zm",
-#   station_id = "16",
-#   planting_dates = c(92, 122, 153),
-#   water_requirements = c(300, 500, 700),
-#   planting_length = c(120, 180),
-#   start_before_season = TRUE
-# )
-# 
-# # Test case 2: Test with missing planting_length parameter
-# result_2 <- epicsawrap::crop_success_probabilities(
-#   country = "zm",
-#   station_id = "16",
-#   planting_dates = c(1, 2, 3),
-#   water_requirements = c(100, 200, 300),
-#   start_before_season = TRUE
-# )
-# 
-# # Test case 2: Test with all missing parameters
-# result_3 <- epicsawrap::crop_success_probabilities(
-#   country = "zm",
-#   station_id = "16"
-# )
-# 
-# # Define test cases
-# test_that("crop_success_probabilities returns correct results", {
-#   expect_no_error(result)
-#   expect_no_error(result_2)
-#   expect_no_error(result_3)
-# })
-# 
-# # Define test cases
-# test_that("crop_success_probabilities returns same results whether parameters are defined or not", {
-#   expect_identical(result[[2]], result_3[[2]])
-# })
-# 
+library(testthat)
+library(epicsawrap)
+
+# Test case 1
+epicsadata::gcs_auth_file(file = "testdata/e-picsa-e630400792e7.json")
+test_1_results <- readRDS("testdata/test_1_crop_success_probabilities.rds")
+country <- "zm"
+station_id <- "test_1"
+test_that("Correct summaries are calculated", {
+  result <- crop_success_probabilities(country, station_id, water_requirements = c(0, 100, 300))
+  expect_true(identical(result[[2]], test_1_results))
+})
+
+
+crop_success_probabilities(country, "01122", water_requirements = c(0, 100, 300))
+
+
+daily <- epicsadata::get_daily_data(country = country, station_id = station_id)

tests/testthat/test-season_start_probabilities.R

@@ -1,20 +1,15 @@
-# library(testthat)
-# 
-# # External functions call
-# # Test case 1: Test with all parameters
-# result <-
-#   season_start_probabilities(
-#     country = "zm",
-#     station_id = "16",
-#     start_dates = c(10, 20, 100)
-#   )
-# 
-# # Test case 2: Test with missing parameters
-# result_2 <-
-#   season_start_probabilities(country = "zm", station_id = "16")
-# 
-# # Define test cases
-# test_that("season_start_probabilities returns correct results", {
-#   expect_no_error(result)
-#   expect_no_error(result_2)
-# })
+library(testthat)
+library(epicsawrap)
+
+# Test case 1
+epicsadata::gcs_auth_file(file = "testdata/e-picsa-e630400792e7.json")
+test_1_results <- readRDS("testdata/test_1_season_start_probabilities.rds")
+country <- "zm"
+station_id <- "test_1"
+test_that("Correct summaries are calculated", {
+  result <- season_start_probabilities(country, station_id, c(0, 150, 300))
+  expect_true(identical(result[[2]], test_1_results))
+})
+
+
+

tests/testthat/test-total_temperature_summaries.R

@@ -1,27 +1,17 @@
-# library(testthat)
-# 
-# # Test case 1: Test with to = "annual"
-# result <- epicsawrap:::total_temperature_summaries(
-#   country = "zm",
-#   station_id = "23",
-#   summaries = c("mean_tmin", "mean_tmax"),
-#   to = "annual"
-# )
-# 
-# # Test case 2: Test with to = "monthly"
-# result_2 <- epicsawrap:::total_temperature_summaries(
-#   country = "zm",
-#   station_id = "1",
-#   summaries = c("mean_tmin", "mean_tmax"),
-#   to = "monthly"
-# )
-# 
-# # Define test cases
-# test_that("total_temperature_summaries returns correct results", {
-#   # Mock the necessary external functions or datasets if needed
-#   expect_length(result, 2)
-#   expect_length(result_2, 2)
-# 
-#   expect_no_error(result)
-#   expect_no_error(result_2)
-# })
+library(testthat)
+library(epicsawrap)
+
+# Test case 1
+epicsadata::gcs_auth_file(file = "testdata/e-picsa-e630400792e7.json")
+test_1_annual <- readRDS("testdata/test_1_annual.rds")
+test_1_monthly <- readRDS("testdata/test_1_monthly.rds")
+country <- "zm"
+station_id <- "test_1"
+
+test_that("Correct summaries are calculated", {
+  result_annual <- annual_temperature_summaries(country, station_id)
+  result_monthly <- monthly_temperature_summaries(country, station_id)
+
+  expect_true(identical(result_annual[[2]], test_1_annual))
+  expect_true(identical(result_monthly[[2]], test_1_monthly))
+})

tests/.gitignore → tests/testthat/testdata/.gitignore

@@ -1,2 +1,2 @@
 e-picsa-e630400792e7.json
-test.R
+epicsae630400792e7.json