From 8225f719738c84fe896354c0e180d89f621c8d0a Mon Sep 17 00:00:00 2001 From: Roy Mendelssohn Date: Thu, 9 Jan 2020 16:58:51 -0800 Subject: [PATCH] v0.4.6 --- DESCRIPTION | 7 +++--- NEWS.md | 4 ++++ R/plotBBox.R | 8 +++---- R/plotTrack.R | 4 ++-- cran-comments.md | 4 ++-- data/cmocean.RData | Bin 10604 -> 0 bytes man/cmocean.Rd | 38 ------------------------------ man/plotBBox.Rd | 19 +++++++++++---- man/plotTrack.Rd | 22 +++++++++++++---- man/rerddapXtracto.Rd | 1 - man/rxtracto.Rd | 20 ++++++++++++---- man/rxtracto_3D.Rd | 18 ++++++++++---- man/rxtractogon.Rd | 18 ++++++++++---- vignettes/UsingrerddapXtracto.Rmd | 22 ++++++++--------- 14 files changed, 102 insertions(+), 83 deletions(-) mode change 100644 => 100755 R/plotTrack.R delete mode 100644 data/cmocean.RData delete mode 100644 man/cmocean.Rd mode change 100644 => 100755 man/plotBBox.Rd mode change 100644 => 100755 man/plotTrack.Rd mode change 100644 => 100755 man/rerddapXtracto.Rd mode change 100644 => 100755 man/rxtracto.Rd mode change 100644 => 100755 man/rxtracto_3D.Rd mode change 100644 => 100755 man/rxtractogon.Rd diff --git a/DESCRIPTION b/DESCRIPTION index c5109e8..0588e2c 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,8 @@ Package: rerddapXtracto Type: Package Title: Extracts Environmental Data from 'ERDDAP' Web Services -Version: 0.4.5 +Version: 0.4.6 +Date: 2020-01-08 Authors@R: person("Roy", "Mendelssohn", email = "roy.mendelssohn@noaa.gov", role = c("aut","cre")) Description: Contains three functions that access environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts @@ -25,7 +26,7 @@ Imports: methods, ncdf4, parsedate, - plotdap, + plotdap (>= 0.0.5), readr, rerddap (>= 0.6.0), sf, @@ -38,7 +39,7 @@ Suggests: maptools, rgdal, rmarkdown -RoxygenNote: 6.1.1 +RoxygenNote: 7.0.2 Encoding: UTF-8 LazyData: TRUE VignetteBuilder: knitr diff --git a/NEWS.md b/NEWS.md index b0b5ad4..dfaecb9 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# rerddapXtracto 0.4.6 + +Changed vignette to work with latest version of 'plotdap' that now uses the colors from the 'cmocean' package + # rerddapXtracto 0.4.5 Added maptools and rgdal to Suggests to be consistent with of plotdap v0.0.4 diff --git a/R/plotBBox.R b/R/plotBBox.R index e2a57ee..1cfdb82 100644 --- a/R/plotBBox.R +++ b/R/plotBBox.R @@ -5,7 +5,7 @@ #' #' @export #' @param resp data frame returned from 'rxtracto()' -#' @param plotColor the color to use in plot from 'rerddap' +#' @param plotColor the color to use in plot from 'cmocean' #' @param time a function to map multi-time to one, or else identity #' for animation #' @param myFunc function of one argument to transform the data @@ -30,7 +30,7 @@ #' tcoord = tcoord, zcoord = zcoord) #' } #' # low resolution selected to keep time to render down -#' p <- plotBBox(MBsst, plotColor = 'temperature', maxpixels = 300) +#' p <- plotBBox(MBsst, plotColor = 'thermal', maxpixels = 300) plotBBox <- function(resp, plotColor = 'viridis', time = NA, myFunc = NA, mapData = NULL, crs = NULL, @@ -106,8 +106,8 @@ plotBBox <- function(resp, plotColor = 'viridis', time = NA, myFunc = NA, ggplot2::guides(fill = ggplot2::guide_colourbar(title = name))) } if (animate) { - xlim <- c(min(myStruct$longitude), max(myStruct$longitude)) - ylim <- c(min(myStruct$latitude), max(myStruct$latitude)) + xlim <- c(min(myStruct$data$lon), max(myStruct$data$lon)) + ylim <- c(min(myStruct$data$lat), max(myStruct$data$lat)) suppressMessages(myplot <- plotdap::add_ggplot( myplot, ggplot2::coord_sf( crs = myplot$crs, datum = myplot$datum, diff --git a/R/plotTrack.R b/R/plotTrack.R old mode 100644 new mode 100755 index f65dba8..2427d44 --- a/R/plotTrack.R +++ b/R/plotTrack.R @@ -7,7 +7,7 @@ #' @param ycoord passed to 'rxtracto()' #' @param tcoord passed to 'rxtracto()' #' @param resp data frame returned from 'rxtracto()' -#' @param plotColor the color to use in plot from 'rerddap' +#' @param plotColor the color to use in plot from 'cmocean' #' @param myFunc function of one argument to transform the data #' @param mapData map data from 'maps' or 'mapdata', must be of class 'map' #' @param crs valid crs string @@ -30,7 +30,7 @@ #' swchl <- rxtracto(swchlInfo, parameter = 'chlorophyll', xcoord = xpos, #' ycoord = ypos, tcoord = tpos, zcoord = zpos, xlen = .2, ylen = .2) #' } -#' p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'chlorophyll') +#' p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'algae') plotTrack <- function(resp, xcoord, ycoord, tcoord, plotColor = 'viridis', myFunc = NA, mapData = NULL, crs = NULL, diff --git a/cran-comments.md b/cran-comments.md index f975350..7e46b5b 100755 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,6 @@ -## update Version 0.4.5 +## update Version 0.4.6 -Minor update, added maptools and rgdal to Suggests to be consistent with plotdap v0.0.4. +Minor update so that the vignette is consistent with 'plotdap' version 0.0.5 ## Test environments diff --git a/data/cmocean.RData b/data/cmocean.RData deleted file mode 100644 index 0de1594f5bc458f581cd295d0319af88dda8877c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10604 zcmV-yDU;UyH+ooF0004LBHlIv03iV!0000G&sfaiY9}c$T>vQ&2UKVgRpoBy< zK89b za3Wr)*|YOjn1qWT07_EgaWRIpsqpEj>!CDqHiQ#8J%+MbRgn5`2`BoC!T*Kj7>I_o zKF#M06ZyXX9!VS+QrsO|=|x6MB-*X`tc?ISM-Wbm=G6fE=U1!L6hAy*NOari`42&0 z*P+pdtD{#{L^zqJ(4DhI=^GaY2tghBH@9QSaEzTllo5HG3n!V75dE%JBTEcDbaJ z7gU@dxO8}yyewh&rI_tug-9b7OIH|TqUd}->7~rpLef!hi-2=#Y0+I#;a##qIPZIn zy{a~~{xs)>M`PXox2J&rGUHL39}y2RLa%`ro<$`j0Em&BaZ_OKJ8j~jT9baa5-#r; zJY;In9~`*fBZ-Hb_M`Az?Sv!s)Qk?116qXd+ppKAg?knk-PV5_DsR4;TE+?JG!pnS zG@hD1ap%1ueK!KRHs5w~^i(VC#V2B!GgFg3QBMjdA@(#?M5>2lV-}2pUS0ct=_B6? z`y4y_ut~sSi?rhb+jHhBldxkeol)E4!kDda90y!goUUz+7w^b=4#G<)Yz?56*s~08 z1kgsI-C>1V?w?myCNg_fiRrVK6c6=au)t0L;QzS?#A)#0w5oVPufcaDY6z6?*1V(F zHTYi^`o=v;63uldMSF=D*KeT$Dj}NR%F|+754Z$x$u>KOj&dV}fxy|Og3wp-KP|sa z(&#|KaX>vHjF%p>ZST4Xb$o{0ZoMgtB{vEo+kFgbCIKcpm`oRMa?B~b= z7<@&A&qf$VAy;>#vnG;&meHAk+SI$}`Q|2IQEt2rFu>%jpuuN=Is1ULr}#CP;vxTp zknT!Mvv0i{XPhk$?0_X_f;xyVI)DeeWv8+8{*~{eKI)&eb!amT53g31C(rdVW%IfP zrv`kXg}$}i1DNTf{GP}+0C5K1lXdyF;sCCZYhHW4tvABiSdcjZ_1&Qv*TnZ@1fvU0 zIdPyp(Hz%Gp%<3k#Q$mI5$3v=0*IG(hzZ0NsmJk$DBH9kRKGv^3jms$ynYDjKlN`? z9KKg)oRi#ig4N{^M-YmVIjLY!o^9dpE8P8a9FTp!0tQaHway;|oP-jCVJNR{bYC)@WcK5m< zd&;M`p>DVs+=&&?0$|r3N7zj(0K>bApC(1H!5CgV$%J{;Bt-Z}zs*$DojJpY zxeSgfD?0*gveL`hLrf*>W4z4Zon*g2*L~c$w^Ng!DwB6z5=sE|(y!FiZNAFBLNaM| zxLw9m&Jf(C6~s`Sa>^hKbA27*ZYFl zXG6=GjC$4_gF`~fWn_gMYuDPZhjq8D64X-bp!%GddR11SwF@lE+Ufh~#i(#*ohLyC z;XvUcb+dGnzEWnbO<`q+^RPxydc$U3axs${r}_!4z*KT#o34pSF{gz61ZjqRT^SN^xDeQ*qcsy{QdNZh z9R#kJ+CdsUDS<9ra$bxm{(;-wtRL~XBD{s^;pL!V=IPlBc1KoM%lR~ME$Ny-mUa}VWt|n`I#e% z8$-9wR7oNB#)B5IiQ>XHs5HC0*V+*{3efZ! z;(v7+?A$XW3yfZ^H3D7x$9zvIw9$&Du=!4p0Mkaw#6Ua|0fU=J4^F zMstM$n9QW1W!-`*mrMnj*Jd3t!P)D)f+9hu1j2s5XSXerJoP{j#bN zoRNrwKRJ#=yZwOtLbRMPxJ*OI7HGB|45q##%f{2)>JTkBU!O{mpLz|*g7^*B_9&{F zwj!b3i?GEmO7|S}e{EPRYFF0Jz0;-xJ#$l8V7&ro|M)h|DA!i)cX)_GN& zEfLSI>N+7(yGOZWYbmMKCR18en|CD?o65%7);0AN@9TnxL*_KKaf+6Q6%pd`%EaLub_WyrWzRt7{J`e3 z@#Cs`G9}PhCNbjlCJ=MIwe_7sjEa~-23fCXrx3g08K@uM48He7Pm5A-n8CUCeJ#u& zcWO8*;)4U-2UtyhbVP0k{+4mUx3H&`y=Bw>GC$h0^iSj8YE3y4xS-5f9<=(5aFqZDmljQEU^HW}(D4t&owj?v!fw1!plRM{1WQco)BX@s_9zB$^sCZ$5ta zM^-|i{>K%)poJJf%2dym$+nM3L=xopIb)bS0iJE=7pk>*NOJDBYBLgQ6+G#ulO%UM z^}6mIGwuBSo(N(j^F+JF;LJ$ zLC4@(tm)sea>eXcI_5^!v^7>m;8W402v+ITUm+}M1NfFu7^oDEf*F!PWuHZe#^L%y zJ}c#FE$IPS^oHub+i(sx9+tvttvR{y%RZEXi=y+E@ZkA3eE&d`jeu&V+?D%oCP%*f zaGVE+Ka)m{)>xFnF;UYaYgNbDIySS;OQB1NPyH^3 zBp9Aqp~d~%NjW!zID}m2s=&rY3C?E`17!oR*BfmpFdbX_Z=H}Irt}(^jl?Yc>;_(` z5`BJ(;;^zr7@<%5U=~f+t4X^bF7*yS9uiF!E(p2*F0wXGXQan9k=;XrX-o#`%Os19 z!wd*;?hl;pc%2-^{kqFebU&68rokC-pw2g2soDfwPeYVXD@pnHb=Upwl1g3L#90gw}yic*8v7L?w$v%0*2j`hpPv2xV7aQ8)_tJ0;X)DGA7FyYXpNGt_!tbfoZ5zHGVcJLp{ih znzScr)yE?e>53t7EqE{WRQRNp86aOugvkkXq)R-!g0!iq|2^e1ws?OZ{po(=hWrp{U@a&W5(YygfBzZ_ z&wXc0$Qa2BoE1fJ>|4Sjn~;ZSD8#myF;P`RXkNMaWYq_I`k-8VZjpJdWaXuF zJMiSvbu`#0_|=M@_?)6;)fAzTj_i;Ieu-3WC{*q}c>J6j>5TZZ{?XMzdhdVU_#_9Q zFta*bkqpZ^a~Y}{V!XgjOt+VtC0#U1e`Ghmtc2_%e+)O5 z@;7!h%#6@PTh^;qgI==-)woz=_r}=Ty^RPRRf&c9sr=@D1Mo@t=*e|#}N6Quj|bT^QoQYXc^_my{nc7Y0Uj zvpR-M3S3xw=%#=8meo}DpZ1mJ>l>=y)*cUgN}*V}h z0AP71g*N9Bp{ET^m-Tf)`0_ZMJRsJ;OReh_d>8y|CJGu@*{K2%iUyAn!A9{HD2U9(5Cyd z5_c%(J%8ciJ499i8qcDS*0J587pXsJ8P(0=^dRp@=kg^OefhG}_+PVMlXKjWutEKV zF9DdKNR8);B!!O-xnS;#4!6hN_Ps09DElyYHgsNsI8t8E1g#Dfeu6I5oWY^oejZ40 zWs3qNy|6G#KODfCeJk?%xQelk(Q|;>op74kA&DGiPY5`+tdL&)asJrl=Q=7)UMZn| zy9m6mxI%$1%wpmCF+A0jq27^#Iv`>2UB|u|c}~R&0pCZ$8Moun(X5Mp_8ea(^E`kj z5o=ExT?Zz!WcAlh_s~dOuslQ~Mt>C!y*Ng9j5UM|DiGKusQ{**&MUG|vLG98jH5|5 zKqzw#e;n7Y8*! z*`#MmX9}4o@QKHAh=M`bDRF<%Z@WfHD;b)2*O3E^Ad7i~qtH`>Dlx&G<~N_V^D>m$ zu^;Ip6Q-h-@=k=EV#iB-uSh&urIPb~`|Vg zRwSa1G~C&W{C{Nx&5tj;zCUSwr&ZHJv&vpuQ73ja)p$HhUZ=Ne#`V;ZHAxajzPgvS zJH9ejUMPbuZ^3P!B!RQ(xlbv40(qC6 zmHA9)o*+m#uRwLwc9m|N<}T+k0=Zqs0L5^{>OeiB;|L!?)$e?wZ!GoH+quS@-;{?a z$^3eWY38R_sx@AltHiMYhKZGw_U2~iOt&d(Av4F7_RY;P>=j#5oB!c?z$IXG>X6#2p`HLnd&pLJ~2fY_40ITJEE9XuCCTG%vEfOs#9U)99!PMZc-5wvTU^aK^K#34 zcc(Cu25KEJn*M-WF->ZQWDZO4O^c8{0xn#oj+g+D#Awn===v^GZAWd&nXSqim&$3x z)Gf)GCs4(#+fwf7hDNl|5x(;q*+lM1G#9q9NLQ09EzmM~cfFG3>@R|#027yE?hZS; z-yIHA+Wna6Wvcf&xzP_d>kPvU6fIv$V+?CAY3x0oa;gdS2-iN*_C6Ihz_tttf4CV6 zJ@moI;4!ad91ozrb1RgRA5>n<+Rg7$wIF`?_yC5dxxd)wlfjLX0SXA?VF59a?{C~HOKhz&OrnI51}r=t;Z%wA&!+aU{bBQid^ z+PnSw>JI=|kb4M~tQj@3P#?2}IlSr{s?;Yk$RDsDhFvMK?53R+ClAG6`D=@8M8{{h zdROem!RX>>TnS=Y6pb|Y>5E&G>O}6=C$1G6e$v4Iu{MW4|eBH(->Bhdf#>{Ql?-+=}nl&v88VaL;Q1 z%p$&tZ$&)@x!m0n%{W4CF;@1XF6UMYi~+sg8wj^Vy1u>*xV@!p0FCSl?ldpT!=ika zhfomYT_4ZXoY|&8yvPDw{tP8kZknD4N?@tJovCa_WVU9e?`uKvb@#KHGi`uhg_7Io zIRnKBpQ)O`;}so(KRJ`H__+L7)y@p6ZzmqPtiK}f>>|7{a^w94N$b^Gn;=4?%mOR; zfGdTY?x_~ebeF261I3CBlQ8Xtn!w^id$188gtEbn|Hm(=vP&^9diMaSoQGMcZcejV`-!3H&x+fasjM`Mpg z>SapXbvdIp8jgocu6v}@N9});`23{8UC}2%#LLNG!zo0cfmnf_woUvV#v845MRRA5 zeN#_Es5QTD?BNQYj_lc$U<0%t)Z6X!t;nMX3NJ4MSw`F?#a&@XVtF2ghC`Gh+b~gO zL^u4!`8S5~EpxU=icKih+O|#Ak>x*d<1yfhgHHVh`tlVyl9{E59S(dw}^j$66Z52J4~!^xCFdo8CH z&dKzyb_~(ip)+k4=*iAoH#D0A6qNX8ur@oZK#)R=u(uRQNZDOT20$vkq~?vqb`1;N zVKaxQ9R&eb2R#O_1Zk!@A<#B`DDwreHuF$x+{86x8D~B;t8(@DW0cqgV#!0Z?0H7e zPcGup?lblPzGB!U6>iK5$|Eeh1;^j5vPnWomY0bnHS?zlc}vBag$K@p*(~y}zG|!}Z)=#&AGiiMcm^Qr1se$sP@r zh60~X%A@V-;GB0Q+xg@Qd}$+WaD!~-BY3aB5{d!Cx4_mOt0!+%H{8_(_mbInw>%f> zL^#I-Qs=fGfytlFs+?&^IHe6<2Qk>9M#vU?_>y9?T6hSupmD!!jNVKnm$885vxihZ zIM&TL_cdy)M>>x!TAe~2JLY3ujORe=@m9}7Giu9U5zKo84vz5ID^a8)kk1Iu*pVBY z2G;poWv_6TOFlaDFuQ#r zEi6z}OZH=^ZTT;AYB6!t7?2vecFe>{(8-vR?A;!oe#-}oM%wBqpghlB+&g-dmH{vc zT()w>)?T<_F#Bq2cv``*I>&9z;gCXQcLptO9ya2K@GbyUk&VGftG4f=;~ZPDwU%GB zV`$Y_105K|mTO=6=PhY9Z)2|P!4h+Om}vrL3R~_DlgeHMBw&wi;(OW7Ej<*%zOLMb z2;TXPWgWd}lpF-?w+_dywNSi^syopvj2r?UZJC1sT@vd+1XvP&NwnVL{mu$!nG83Sz&WV{*0>fg2LPkZn<&LefczcKkvA7 zbS9AUzMFoLzVG;O25#=2chXx=1v-P^mn7)^G7ZDn$bxdnB5epSinYveP-CS6bI_7K zbkS9$5^D>bYan})Vv{CVvS3Wp<_-;gac#NHLolgsL>dP{5@OdbbO`BCd7K#eT{6t* zWISeJ;HN-?Q4Q$yysOaG*5#Y$SAU1crl;<3*D4n1iY*(2Qj@Qlsu|?v`e9#gduSS} zB*b}iI)oHwSPt#>@51z3!;rsC7x`3TCe0+rP# z?hALBQdX8H-)3F<@V0DqFjoM;CVl36Dmqs`s*UM%y`< zWmB}e@AGI-?V@_q^<`v-prKt~m*N8GZy663o8Bw4O(_Ch1w#&Z&^62zJwAANPOH$Z z#>oi4$YZyY0Cl~HqO3xvrOj)L@|H~S)#?W|!G_v<3u&OHvn-Aw-DlIz|Co2;f-1sO zR&L43TByKs!J^H@ z{bl&j>H{b?r_g}D>; z0>e#_lNq{ALr8E+1sf7&4RM;tLCjF7WWvz1^{rTlcTB0J&lG=1)p_!2ztH} z)gCeR&Sw9)tCdf@&blVqcT%N^Q6KgBJmN=kR>;N}TC3`KJNuq|xy#gbh1!ip5`>y? zO_11wcjs!ZD>do*h@Ej_6mkQ%+XpgHF`w-C!)CyvHh2Qd9wCH{j4$Y~)cU(O_Y$wq zyFAwWbuLbE4esTT(-g&Pm_=Vyj^eX36d6!7 z`9Ry*egPIqOE=3`6JQ>;oKUxC;7hRmr|~v#dt74uA(bO_kw*eoq-R5602a&BEA}XM zm?@GMvI8Ha!(6qhQ9|wbf=F5d6dtq{#-Y<8?8~&7yA`IUN5y1*~IGhB8BsL@tq|fujDOF+%_x)wN1$x znVKOov8*_ZCa`2KDt{%}>$~IO`ENo@tJ!O78&n77G#Q-lJ1Yerxor3m)gpF&_miYU zzU%R#;JkLhavpTX-M%&f1Q#^eM(miPeyMs~FqVH;1Na|C+==eR1;|uPSpN2Z2 z{Nh2TdpOI&hC`^@%q4OZ0H? ze26Zs0sRL|(RyJW(#lPz@(pgwFm6uA+!w!AR9dZw3@F4^i-$bj$rkh8R^<&WZ`;sQT(H_0;5pu&@q65T;Pm z0LUP%5EHgcmOK4^{I2;}419GFwlqL_{f#6Lp>uv=^Igz&N)fEeAB=7$!%;9KJPKZ(BKoU`i##+1jn2*5RgGS;X`gys5AjSfNanm+rCdX|a! zuLa5oQHh8Yv6+KO8cF#ql)2Vk?vip4d$L=uTNcr+TB$y3 zcG-%byJfGzqID`zp_0&QrEhzI0|yAHynq*BAIpU^9{?bAeo3Qcpy24{`Nwe6eBICk zIR|kvG*!Yb?b1KpX2^PW@|+(bQPp=~sP$<9^yC_!TyVM%4XPkF^xhILAYKXbS`5vb zE~6893S28Y#^vuTCmGMXNw7CQOlrtk5d*_xXSjnid@VFF(NhIosLYvE>NY5t4bS5K zT>87X(Kqc+Q7qDF{?uR)o3p?v%(4#&7K&_Oc^*~-LwB*s6U4qd!MHIltY>$9w8~~J zz2a)+Fsb*$^}4SwgM!|+mP|n>ylstSY}!wuH8VY#x=Gu2($h}E69-jz6cWkA4xYOm z?CV$)Lf5AbI=Naqe1Iwps_KD&bg)HitxSl&XnzBo0=Uj&z~5M%Bmh4^w?N;@Un$~*LN(Kp!34s=Zpf1hP?y&n&oXw8x}Y2I zi&vO!!6czlh$x_8lc{G%bEp3sX?#2N$Wt5$30q5Re5iwvBFw`h8+`~GfRX0P|1)de zPg6Lh6&5tj+ha2)0pkMqCyRNcyrbd046+R)`oV=fkfw)Pcza_zhLU1r1=w-1uRQg( z;@*__spgGcN?&KucAwP`YJX~xcVAR}Ix#k2!TzjKg5Mbv`l$d=>7L;*+*4U&!Z=P@ zlD+|73TWd(Yx!n^qBHb%gC0#qPBef5b97UBn)*6{uX-wks-w&@p4YR5FmbyzgpVw- zRHFIxXpw}EDURMwcV3s7?d+KRD^?syzR4D3EvK^|YBGQ5pM9Z7{HZvMS5IV+MF^BJ zOS5f80nFjOvwsth6Q(qZ#WjG24aJ-Q9}#oNrYT{?gh3HS=Gz^tkD)eBE@1~z+W|j; z7hLj~MA80VhbmW|?>-@WKgscd7mHEHFN7lCZWl7X*$Uo zGoqM%Qz|K{h)(TxaxET~?Dr`xqI!O?`FupI@7YK|Tb`p6S@x$-mk6Ls=^LGG&iT6Q zcGmz{HpW_UXOpvDC$75rnk(x72U1J=#zQIIBVJ8Z4#{2DyxG`ZS_l4O!0Db zr_h=LUUQpvFxQ3~TNW)#^UM(75I*RI6|(^&0f!t7j2X}rQvkW(S4fPKY~L&DqHdMO zbx!ht6hl|gGY4Q^h~XOKqNklZvKX-K1LIR%SW*T;DHzsUT|hGsT)2nFzcjn4A%A_~ zjJ;V=_70h<#NkQW9bempW}~kyoRXBkRQ>>DD5Kv10mxFQ)CBbuFb#_W00000 G0a;oYVV~Uq diff --git a/man/cmocean.Rd b/man/cmocean.Rd deleted file mode 100644 index 61df79f..0000000 --- a/man/cmocean.Rd +++ /dev/null @@ -1,38 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/cmocean.R -\docType{data} -\name{cmocean} -\alias{cmocean} -\title{cmocean colors -The cmocean color palette by Kristen Thyng} -\format{An object of class \code{list} of length 22.} -\usage{ -cmocean -} -\description{ -str(cmocean) -List of 22 -$ algae -$ amp -$ balance -$ curl -$ deep -$ delta -$ dense -$ diff -$ gray -$ haline -$ ice -$ matter -$ oxy -$ phase -$ rain -$ solar -$ speed -$ tarn -$ tempo -$ topo -$ thermal -$ turbid -} -\keyword{datasets} diff --git a/man/plotBBox.Rd b/man/plotBBox.Rd old mode 100644 new mode 100755 index dcad881..2e5249b --- a/man/plotBBox.Rd +++ b/man/plotBBox.Rd @@ -4,14 +4,23 @@ \alias{plotBBox} \title{plot result of 'rxtracto_3D'} \usage{ -plotBBox(resp, plotColor = "viridis", time = NA, myFunc = NA, - mapData = NULL, crs = NULL, animate = FALSE, cumulative = FALSE, - name = NA, maxpixels = 10000) +plotBBox( + resp, + plotColor = "viridis", + time = NA, + myFunc = NA, + mapData = NULL, + crs = NULL, + animate = FALSE, + cumulative = FALSE, + name = NA, + maxpixels = 10000 +) } \arguments{ \item{resp}{data frame returned from 'rxtracto()'} -\item{plotColor}{the color to use in plot from 'rerddap'} +\item{plotColor}{the color to use in plot from 'cmocean'} \item{time}{a function to map multi-time to one, or else identity for animation} @@ -50,5 +59,5 @@ MBsst <- rxtracto_3D(dataInfo, parameter, xcoord = xcoord, ycoord = ycoord, tcoord = tcoord, zcoord = zcoord) } # low resolution selected to keep time to render down -p <- plotBBox(MBsst, plotColor = 'temperature', maxpixels = 300) +p <- plotBBox(MBsst, plotColor = 'thermal', maxpixels = 300) } diff --git a/man/plotTrack.Rd b/man/plotTrack.Rd old mode 100644 new mode 100755 index 82ead8d..254318e --- a/man/plotTrack.Rd +++ b/man/plotTrack.Rd @@ -4,9 +4,21 @@ \alias{plotTrack} \title{plot result of 'rxtracto'} \usage{ -plotTrack(resp, xcoord, ycoord, tcoord, plotColor = "viridis", - myFunc = NA, mapData = NULL, crs = NULL, animate = FALSE, - cumulative = FALSE, name = NA, shape = 20, size = 0.5) +plotTrack( + resp, + xcoord, + ycoord, + tcoord, + plotColor = "viridis", + myFunc = NA, + mapData = NULL, + crs = NULL, + animate = FALSE, + cumulative = FALSE, + name = NA, + shape = 20, + size = 0.5 +) } \arguments{ \item{resp}{data frame returned from 'rxtracto()'} @@ -17,7 +29,7 @@ plotTrack(resp, xcoord, ycoord, tcoord, plotColor = "viridis", \item{tcoord}{passed to 'rxtracto()'} -\item{plotColor}{the color to use in plot from 'rerddap'} +\item{plotColor}{the color to use in plot from 'cmocean'} \item{myFunc}{function of one argument to transform the data} @@ -54,5 +66,5 @@ swchlInfo <- rerddap::info('erdSWchla8day') swchl <- rxtracto(swchlInfo, parameter = 'chlorophyll', xcoord = xpos, ycoord = ypos, tcoord = tpos, zcoord = zpos, xlen = .2, ylen = .2) } -p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'chlorophyll') +p <- plotTrack(swchl, xpos, ypos, tpos, plotColor = 'algae') } diff --git a/man/rerddapXtracto.Rd b/man/rerddapXtracto.Rd old mode 100644 new mode 100755 index 2872608..5b3638e --- a/man/rerddapXtracto.Rd +++ b/man/rerddapXtracto.Rd @@ -3,7 +3,6 @@ \docType{package} \name{rerddapXtracto} \alias{rerddapXtracto} -\alias{rerddapXtracto-package} \title{rerddapXtracto: Routines to simplify data extraction using ERD's ERDDAP web service.} \description{ The rerddapXtracto package subsets and extracts satellite and other oceanographic related data diff --git a/man/rxtracto.Rd b/man/rxtracto.Rd old mode 100644 new mode 100755 index 7453850..4080fc9 --- a/man/rxtracto.Rd +++ b/man/rxtracto.Rd @@ -4,10 +4,22 @@ \alias{rxtracto} \title{Extract environmental data along a trajectory from an 'ERDDAP' server using 'rerddap'.} \usage{ -rxtracto(dataInfo, parameter = NULL, xcoord = NULL, ycoord = NULL, - zcoord = NULL, tcoord = NULL, xlen = 0, ylen = 0, zlen = 0, - xName = "longitude", yName = "latitude", zName = "altitude", - tName = "time", verbose = FALSE) +rxtracto( + dataInfo, + parameter = NULL, + xcoord = NULL, + ycoord = NULL, + zcoord = NULL, + tcoord = NULL, + xlen = 0, + ylen = 0, + zlen = 0, + xName = "longitude", + yName = "latitude", + zName = "altitude", + tName = "time", + verbose = FALSE +) } \arguments{ \item{dataInfo}{- the return from an 'rerddap::info' call to an 'ERDDAP' server} diff --git a/man/rxtracto_3D.Rd b/man/rxtracto_3D.Rd old mode 100644 new mode 100755 index 0e81815..eb3d09f --- a/man/rxtracto_3D.Rd +++ b/man/rxtracto_3D.Rd @@ -4,10 +4,20 @@ \alias{rxtracto_3D} \title{Extract environmental data in a 3-dimensional box from an 'ERDDAP' server using 'rerddap'.} \usage{ -rxtracto_3D(dataInfo, parameter = NULL, xcoord = NULL, ycoord = NULL, - zcoord = NULL, tcoord = NULL, xName = "longitude", - yName = "latitude", zName = "altitude", tName = "time", - verbose = FALSE, cache_remove = TRUE) +rxtracto_3D( + dataInfo, + parameter = NULL, + xcoord = NULL, + ycoord = NULL, + zcoord = NULL, + tcoord = NULL, + xName = "longitude", + yName = "latitude", + zName = "altitude", + tName = "time", + verbose = FALSE, + cache_remove = TRUE +) } \arguments{ \item{dataInfo}{- the return from an 'rerddap:info' call to an 'ERDDAP' server} diff --git a/man/rxtractogon.Rd b/man/rxtractogon.Rd old mode 100644 new mode 100755 index 12dfcbd..b5d4f0d --- a/man/rxtractogon.Rd +++ b/man/rxtractogon.Rd @@ -4,10 +4,20 @@ \alias{rxtractogon} \title{Extract environmental data in a polygon using 'ERDDAP' and 'rerddap'.} \usage{ -rxtractogon(dataInfo, parameter, xcoord = NULL, ycoord = NULL, - zcoord = NULL, tcoord = NULL, xName = "longitude", - yName = "latitude", zName = "altitude", tName = "time", - verbose = FALSE, cache_remove = TRUE) +rxtractogon( + dataInfo, + parameter, + xcoord = NULL, + ycoord = NULL, + zcoord = NULL, + tcoord = NULL, + xName = "longitude", + yName = "latitude", + zName = "altitude", + tName = "time", + verbose = FALSE, + cache_remove = TRUE +) } \arguments{ \item{dataInfo}{- the return from an 'rerddap:info' call to an 'ERDDAP' server} diff --git a/vignettes/UsingrerddapXtracto.Rmd b/vignettes/UsingrerddapXtracto.Rmd index 3f6c9c3..0cc3f2d 100755 --- a/vignettes/UsingrerddapXtracto.Rmd +++ b/vignettes/UsingrerddapXtracto.Rmd @@ -197,7 +197,7 @@ We plot the track line with the locations colored according to the mean of the s require("ggplot2") require("plotdap") -myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'chlorophyll') +myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'algae') myPlot ``` @@ -209,7 +209,7 @@ To make a cumulative animation of the track: ```{r animateTrack, echo = TRUE, eval = FALSE} -myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'chlorophyll', +myPlot <- plotTrack(swchl1, xpos, ypos, tpos, plotColor = 'algae', animate = TRUE, cumulative = TRUE) ``` @@ -232,7 +232,7 @@ xlim <- c(-160, -105) topoInfo <- rerddap::info('etopo360') topo <- rxtracto(topoInfo, parameter = 'altitude', xcoord = xpos, ycoord = ypos, xlen = .1, ylen = .1) myFunc = function(x) -x -topoPlot <- plotTrack(topo, xpos, ypos, NA, plotColor = 'density', name = 'Depth', myFunc = myFunc) +topoPlot <- plotTrack(topo, xpos, ypos, NA, plotColor = 'dense', name = 'Depth', myFunc = myFunc) topoPlot ``` @@ -325,7 +325,7 @@ We can map the data using `plotBBox()`: require("ggplot2") require("plotdap") myFunc <- function(x) log(x) -chlalogPlot <- plotBBox(VIIRS, plotColor = 'chlorophyll', myFunc = myFunc) +chlalogPlot <- plotBBox(VIIRS, plotColor = 'algae', myFunc = myFunc) chlalogPlot ``` @@ -408,7 +408,7 @@ myFunc <- function(x) log(x) sanctchl1 <- sanctchl sanctchl1$chla <- sanctchl1$chla[, , 2] sanctchl1$time <- sanctchl1$time[2] -sanctchlPlot <- plotBBox(sanctchl1, plotColor = 'chlorophyll', myFunc = myFunc) +sanctchlPlot <- plotBBox(sanctchl1, plotColor = 'algae', myFunc = myFunc) sanctchlPlot ``` @@ -421,7 +421,7 @@ require("gganimate") require("ggplot2") require("plotdap") myFunc <- function(x) log(x) -sanctchlPlot <- plotBBox(sanctchl, plotColor = 'chlorophyll', myFunc = myFunc, time = identity, animate = TRUE) +sanctchlPlot <- plotBBox(sanctchl, plotColor = 'algae', myFunc = myFunc, time = identity, animate = TRUE) ``` ![Sanctuary Animation](sanctuary.gif) @@ -444,7 +444,7 @@ Mapping the data to show the canyon: require("ggplot2") require("mapdata") myFunc = function(x) -x -bathyPlot <- suppressMessages((plotBBox(bathy, plotColor = 'density', myFunc = myFunc, name = 'Depth'))) +bathyPlot <- suppressMessages((plotBBox(bathy, plotColor = 'dense', myFunc = myFunc, name = 'Depth'))) bathyPlot ``` @@ -470,7 +470,7 @@ str(soda70) ```{r soda70Plot, fig.width = 6, fig.height = 3, fig.align = 'center', warning = FALSE} require("ggplot2") require("plotdap") -sodaPlot <- plotBBox(soda70, plotColor = 'temperature', name = 'temp_at_70m', maxpixels = 30000) +sodaPlot <- plotBBox(soda70, plotColor = 'thermal', name = 'temp_at_70m', maxpixels = 30000) sodaPlot ``` @@ -497,7 +497,7 @@ NAtlSSS <- rxtracto_3D(dataInfo, parameter = parameter, xcoord = sssLons, ycoord ```{r NAtlSSSplot, eval = FALSE, echo = TRUE} require("ggplot2") require("plotdap") -NAtlSSSPlot <- plotBBox(NAtlSSS, plotColor = 'salinity', name = "salinity", maxpixels = 30000) +NAtlSSSPlot <- plotBBox(NAtlSSS, plotColor = 'haline', name = "salinity", maxpixels = 30000) NAtlSSSPlot ``` @@ -537,8 +537,8 @@ Plotting the results using `plotBBox()`: ```{r ifrPSALplot, fig.width = 6, fig.height = 3, fig.align='center', warning = FALSE} require("ggplot2") require("plotdap") -ifrPSALPlot <- plotBBox(ifrPSAL, plotColor = 'salinity', name = "salinity", maxpixels = 30000) -print(ifrPSALPlot) +ifrPSALPlot <- plotBBox(ifrPSAL, plotColor = 'haline', name = "salinity", maxpixels = 30000) +ifrPSALPlot ```