change package name

DESCRIPTION

-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"))

R/Lib_CheckConvertData.R

 # ==============================================================================
-# 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)

R/Lib_ContinuumRemoval.R

 # ===============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_ContinuumRemoval.R
 # ===============================================================================
 # PROGRAMMERS:

R/Lib_FilterData.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_FilterData.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_ImageProcess.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_ImageProcess.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_MapAlphaDiversity.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_MapAlphaDiversity.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_MapBetaDiversity.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_MapBetaDiversity.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_MapSpectralSpecies.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_MapSpectralSpecies.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_PerformPCA.R

 # ==============================================================================
-# DiversityMappR
+# biodivMapR
 # Lib_PerformPCA.R
 # ==============================================================================
 # PROGRAMMERS:

R/Lib_Validation_DiversityMappR.R

 # ==============================================================================
-# DiversityMappR
-# Lib_ValidationDiversityMappR.R
+# biodivMapR
+# Lib_ValidationbiodivMapR.R
 # ==============================================================================
 # PROGRAMMERS:
 # Jean-Baptiste FERET <jb.feret@irstea.fr>

doc/tutorial.R

@@ -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

doc/tutorial.Rmd

 ---
-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

doc/tutorial.html

@@ -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>

examples/example_script.R

 # ===============================================================================
-# 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

man/Get.Diversity.From.Plots.Rd

 % 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}

man/Get.List.Shp.Rd

 % 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}

man/Get.Projection.Rd

 % 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}

vignettes/tutorial.Rmd

 ---
-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