Commit 80bd1357 authored by Florian de Boissieu's avatar Florian de Boissieu
Browse files

change package name

parent 2d9415f8
Package: DiversityMappR
Title: DiversityMappR: an R package for α- and β-diversity mapping using remotely-sensed images
Package: biodivMapR
Title: biodivMapR: an R package for α- and β-diversity mapping using remotely-sensed images
Version: 0.0.0.9000
Authors@R: c( person("Jean-Baptiste", "Feret", email = "jb.feret@teledetection.fr", role = c("aut", "cre")),
person("Florian", "de Boissieu", email = "florian.deboissieu@irstea.fr", role = c("ctb"), comment = "clean code, format as package"))
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_CheckConvertData.R
# ==============================================================================
# PROGRAMMERS:
......@@ -113,7 +113,7 @@ Convert.Raster2BIL <- function(Raster.Path, Sensor = "unknown", Output.Directory
if (!Sensor == "unknown") {
HDR.Temp.Path <- system.file("extdata", "HDR", paste0(Sensor, ".hdr"), package = "DiversityMappR")
HDR.Temp.Path <- system.file("extdata", "HDR", paste0(Sensor, ".hdr"), package = "biodivMapR")
if (file.exists(HDR.Temp.Path)) {
message("reading header template corresponding to the sensor located here:")
print(HDR.Temp.Path)
......
# ===============================================================================
# DiversityMappR
# biodivMapR
# Lib_ContinuumRemoval.R
# ===============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_FilterData.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_ImageProcess.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_MapAlphaDiversity.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_MapBetaDiversity.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_MapSpectralSpecies.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# biodivMapR
# Lib_PerformPCA.R
# ==============================================================================
# PROGRAMMERS:
......
# ==============================================================================
# DiversityMappR
# Lib_ValidationDiversityMappR.R
# biodivMapR
# Lib_ValidationbiodivMapR.R
# ==============================================================================
# PROGRAMMERS:
# Jean-Baptiste FERET <jb.feret@irstea.fr>
......
......@@ -6,7 +6,7 @@ knitr::opts_chunk$set(
)
## ----Input / Output files------------------------------------------------
# Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'DiversityMappR')
# Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
# Check.Data.Format(Input.Image.File)
#
# Input.Image.File = Convert.Raster2BIL(Raster.Path = Input.Image.File,
......@@ -67,7 +67,7 @@ knitr::opts_chunk$set(
# Path.Raster = file.path(Dir.Raster,Name.Raster)
#
# # location of the directory where shapefiles used for validation are saved
# vect = system.file('extdata', 'VECTOR', package = 'DiversityMappR')
# vect = system.file('extdata', 'VECTOR', package = 'biodivMapR')
# Shannon.All = list() # ??
#
# # list vector data
......
---
title: "Tutorial for DiversityMappR"
title: "Tutorial for biodivMapR"
author: "Jean-Baptiste Féret, Florian de Boissieu"
date: "`r Sys.Date()`"
output:
......@@ -48,7 +48,7 @@ The output directory defined with `Output.Dir` will contain all the results. For
```{r Input / Output files}
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'DiversityMappR')
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
Check.Data.Format(Input.Image.File)
Input.Image.File = Convert.Raster2BIL(Raster.Path = Input.Image.File,
......@@ -155,7 +155,7 @@ Name.Raster = 'SpectralSpecies'
Path.Raster = file.path(Dir.Raster,Name.Raster)
# location of the directory where shapefiles used for validation are saved
vect = system.file('extdata', 'VECTOR', package = 'DiversityMappR')
vect = system.file('extdata', 'VECTOR', package = 'biodivMapR')
Shannon.All = list() # ??
# list vector data
......
......@@ -14,7 +14,7 @@
<meta name="date" content="2019-07-03" />
<title>Tutorial for DiversityMappR</title>
<title>Tutorial for biodivMapR</title>
......@@ -93,7 +93,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<h1 class="title toc-ignore">Tutorial for DiversityMappR</h1>
<h1 class="title toc-ignore">Tutorial for biodivMapR</h1>
<h4 class="author">Jean-Baptiste Féret, Florian de Boissieu</h4>
<h4 class="date">2019-07-03</h4>
......@@ -121,7 +121,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<p>The input images are expected to be in ENVI HDR format, BIL interleaved. To check if the flormat is good use fucntion <code>Check.Data.Format</code>. If not they should be converted with function <code>Convert.Raster2BIL</code>.</p>
<p>A mask can also be set to work on a selected part of the input image. The mask is expected to be a raster in the same format as the image (ENVI HDR), with values 0 = masked or 1 = selected. If no mask is to be used set <code>Input.Mask.File = FALSE</code>.</p>
<p>The output directory defined with <code>Output.Dir</code> will contain all the results. For each image processed, a subdirectory will be automatically created after its name.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Input.Image.File =<span class="st"> </span><span class="kw">system.file</span>(<span class="st">'extdata'</span>, <span class="st">'RASTER'</span>, <span class="st">'S2A_T33NUD_20180104_Subset'</span>, <span class="dt">package =</span> <span class="st">'DiversityMappR'</span>)
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Input.Image.File =<span class="st"> </span><span class="kw">system.file</span>(<span class="st">'extdata'</span>, <span class="st">'RASTER'</span>, <span class="st">'S2A_T33NUD_20180104_Subset'</span>, <span class="dt">package =</span> <span class="st">'biodivMapR'</span>)
<span class="kw">Check.Data.Format</span>(Input.Image.File)
Input.Image.File =<span class="st"> </span><span class="kw">Convert.Raster2BIL</span>(<span class="dt">Raster.Path =</span> Input.Image.File,
......@@ -210,7 +210,7 @@ Name.Raster =<span class="st"> 'SpectralSpecies'</span>
Path.Raster =<span class="st"> </span><span class="kw">file.path</span>(Dir.Raster,Name.Raster)
<span class="co"># location of the directory where shapefiles used for validation are saved</span>
vect =<span class="st"> </span><span class="kw">system.file</span>(<span class="st">'extdata'</span>, <span class="st">'VECTOR'</span>, <span class="dt">package =</span> <span class="st">'DiversityMappR'</span>)
vect =<span class="st"> </span><span class="kw">system.file</span>(<span class="st">'extdata'</span>, <span class="st">'VECTOR'</span>, <span class="dt">package =</span> <span class="st">'biodivMapR'</span>)
Shannon.All =<span class="st"> </span><span class="kw">list</span>() <span class="co"># ??</span>
<span class="co"># list vector data</span>
......
# ===============================================================================
# DiversityMappR
# biodivMapR
# ===============================================================================
# PROGRAMMERS:
#
......@@ -7,7 +7,7 @@
#
# Copyright 2019/06 Jean-Baptiste FERET
#
# DiversityMappR is free software: you can redistribute it and/or modify
# biodivMapR is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
......@@ -27,7 +27,7 @@
################################################################################
# path (absolute or relative) for the image to process
# expected to be in ENVI HDR format, BIL interleaved
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'DiversityMappR')
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
Check.Data.Format(Input.Image.File)
# convert the image using Convert.Raster2BIL if not in the proper format
......@@ -114,7 +114,7 @@ Name.Raster = 'SpectralSpecies'
Path.Raster = file.path(Dir.Raster,Name.Raster)
# location of the directory where shapefiles used for validation are saved
vect = system.file('extdata', 'VECTOR', package = 'DiversityMappR')
vect = system.file('extdata', 'VECTOR', package = 'biodivMapR')
Shannon.All = list()
# list vector data
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Lib_Validation_DiversityMappR.R
% Please edit documentation in R/Lib_Validation_biodivMapR.R
\name{Get.Diversity.From.Plots}
\alias{Get.Diversity.From.Plots}
\title{gets alpha diversity indicators from plot}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Lib_Validation_DiversityMappR.R
% Please edit documentation in R/Lib_Validation_biodivMapR.R
\name{Get.List.Shp}
\alias{Get.List.Shp}
\title{Get list of shapefiles in a directory}
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Lib_Validation_DiversityMappR.R
% Please edit documentation in R/Lib_Validation_biodivMapR.R
\name{Get.Projection}
\alias{Get.Projection}
\title{get projection of a raster or a vector}
......
---
title: "Tutorial for DiversityMappR"
title: "Tutorial for biodivMapR"
author: "Jean-Baptiste Féret, Florian de Boissieu"
date: "`r Sys.Date()`"
output:
......@@ -48,7 +48,7 @@ The output directory defined with `Output.Dir` will contain all the results. For
```{r Input / Output files}
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'DiversityMappR')
Input.Image.File = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
Check.Data.Format(Input.Image.File)
Input.Image.File = Convert.Raster2BIL(Raster.Path = Input.Image.File,
......@@ -155,7 +155,7 @@ Name.Raster = 'SpectralSpecies'
Path.Raster = file.path(Dir.Raster,Name.Raster)
# location of the directory where shapefiles used for validation are saved
vect = system.file('extdata', 'VECTOR', package = 'DiversityMappR')
vect = system.file('extdata', 'VECTOR', package = 'biodivMapR')
Shannon.All = list() # ??
# list vector data
......
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