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# install.packages(c("bcdata", "dplyr", "remotes"))
# remotes::install_github("bcgov/rems")
library(rems)
library(bcdata)
library(dplyr)

# Get the watershed boundary - I don't know if this is exactly the boundary you 
# want but you could read in any spatial file you have instead using the sf package. Eg: 
# columbia <- sf::read_sf("path-to-my-columbia-boundary.shp")
columbia <- bcdc_query_geodata("eaubc-freshwater-ecoregions") %>% 

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library(sf)
#> Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0

system("ogr2ogr --version", intern = TRUE)
#> [1] "GDAL 2.4.2, released 2019/06/28"
system("proj", intern = TRUE)
#> character(0)

file <- system.file("gpkg/tl.gpkg", package = "sf")

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locations <- data.frame(id = "E309447")

library(rems)
library(dplyr)

hist_db <- attach_historic_data()
filtered_historic <- hist_db %>% 
  filter(EMS_ID %in% locations$id) %>% 
  collect()

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# If you haven't installed homebrew, see some instructions here: 
# https://github.com/bcgov/envreportutils/wiki/Macbook-Pro-Setup-for-Data-Science-at-EnvReportBC#homebrew
# These have not been tested on macOS Catalina, but the Mojave instructions _should_ work.
# If you run into issues, this looks like it might be helpful: 
# https://medium.com/faun/macos-catalina-xcode-homebrew-gems-developer-headaches-cf7b1edf10b7

# The osgeo homebrew tap is in a bit of a mess, so `brew install saga-gis` doesn't work (as of 2019-10-30). 
# This is because SAGA dependencies have been updated, but they haven't updated the brew formula for SAGA itself.
# Same goes for QGIS; and now that there is a fully self-contained signed installer, I recommend that over heomebrew for QGIS 
# (https://qgis.org/en/site/forusers/download.html)

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## First make up some mock data
my_data <- data.frame(date = seq(as.Date("2010-01-01"), as.Date("2015-12-31"), 
                                by = "1 month"), 
                     value = rnorm(72))

## Remove some observations so we have an incomplete data set
my_incomplete_data <- my_data[sort(sample(nrow(my_data), 60)), ]

## Make a data frame with a full series of dates from the min date to the max date
## in the incomplete data frame

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##
# osgeo/gdal:ubuntu-full

# This file is available at the option of the licensee under:
# Public domain
# or licensed under X/MIT (LICENSE.TXT) Copyright 2019 Even Rouault <even.rouault@spatialys.com>
# ACT: Copied from https://raw.githubusercontent.com/OSGeo/gdal/master/gdal/docker/ubuntu-full/Dockerfile

ARG PROJ_INSTALL_PREFIX=/usr/local

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values <- runif(100)

# get runs where values > 0.75 (these are TRUE/FALSE)
runs <- rle(values > 0.75)

# Mask out the runs with lengths < 3
runs$values[runs$lengths < 3] <- FALSE

# Get a vector of positions that meet the run criteria

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values <- runif(100)

# get runs where values > 0.75 (these are TRUE/FALSE)
runs <- rle(values > 0.75)

# Mask out the runs with lengths < 3
runs$values[runs$lengths < 3] <- FALSE

# Get a vector of positions that meet the run criteria
masked <- inverse.rle(runs)